bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrode and Langmuir probe tools used for flow damping studies in the Helically Symmetric Experiment
Authors: Gerhardt S. P. , Anderson D. T. , Anderson F. S. B. , Talmadge J. N.
Published: October 2004

A system of electrodes and Langmuir probes has been developed for the measurement of plasma flow damping in the Helically Symmetric Experiment (HSX) stellarator. A biased electrode is used to apply a J×B torque to the plasma. The fast switching electrode power supply allows the electrode voltage to be applied in ∼1 μs, which is much faster than any of the plasma time scales; the electrode current is terminated on a similar time scale at the end of the electrode pulse. A pair of multitipped Mach probes have been designed to measure the plasma flows in a magnetic surface with good spatial and time resolution (Δt>20 μs). The unmagnetized model by Hutchinson is used to analyze the Mach probe data, and radial force balance is found to be well satisfied during electrode bias. These probes allow for measurements of the transient response of the plasma flows and floating potential when the electrode is energized. An example of using the system for the estimation of viscous damping times in HSX is provided.
Two new sealed sample cells for small angle x-ray scattering from macromolecules in solution and complex fluids using synchrotron radiation
Authors: Cavalcanti L. P. , Torriani I. L. , Plivelic T. S. , Oliveira C. L. P. , Kellermann G. , Neuenschwander R.
Published: October 2004

Two different vacuum tight sample cells for in situ temperature dependent small angle scattering from liquids are presented in this article. In the first one, the sample fills a 1 mm thickness gap sealed on both sides by two thin parallel mica windows (volume 300 μl). In the second one, the liquid is injected into a 1 mm cylindrical capillary tube (volume 130 μl). The cells are lodged into temperature controlled chambers directly connected to the beamline vacuum path. Several important improvements with respect to similar instrumentation previously reported are: (1) versatile application of the mica cell, that can be used for all types of samples (gels, liquid crystals, and dispersions in organic solvents) and (2) the design of the chamber for the capillary cell allows registration of wider angle data and a convenient replacement of the capillary tube after each experiment. Signal to background ratio and data reproducibility were tested using protein solutions. We give a brief report of scattering experiments performed with different protein samples and two-dimensional data collection.
A sensitive, handheld vapor sensor based on microcantilevers
Authors: Pinnaduwage L. A. , Hedden D. L. , Gehl A. , Boiadjiev V. I. , Hawk J. E. , Farahi R. H. , Thundat T. , Houser E. J. , Stepnowski S. , McGill R. A. , Deel L. , Lareau R. T.
Published: October 2004

We report the development of a handheld sensor based on piezoresistive microcantilevers that does not depend on optical detection, yet has high detection sensitivity. The sensor is able to detect vapors from the plastic explosives pentaerythritol tetranitrate and hexahydro-1,3,5-triazine at levels below 10 parts per trillion within few seconds of exposure under ambient conditions. A differential measurement technique has yielded a rugged sensor that is unaffected by vibration and is able to function as a “sniffer.” The microelectromechanical system sensor design allows for the incorporation of hundreds of microcantilevers with suitable coatings in order to achieve sufficient selectivity in the future, and thus could provide an inexpensive, unique platform for the detection of chemical, biological, and explosive materials.
Improvements in two-dimensional magnet pole design
Authors: Martí Z. , Traveria M. , Campmany J.
Published: October 2004

We present here an improved methodology to design magnet poles in two dimensions using two models for the pole profile. To this end, we have developed a group of codes that run on MS-DOS and UNIX and use both POISSON and OPERA-2D codes. This procedure includes the evaluation of the sensitivity of the final pole profile to geometrical and current intensity errors in order to estimate mechanical and operational tolerances. In order to test the feasibility of this method, we have applied it to the case of the 1.2 T combined magnet of the new synchrotron to be built nearby Barcelona.
Amorphous-to-crystal transition of nitrogen- and oxygen-doped Ge2Sb2Te5 films studied by in situ resistance measurements
Authors: Privitera S. , Rimini E. , Zonca R.
Published: October 2004

The amorphous-to-crystal transition has been studied through in situ resistance measurements in Ge2Sb2Te5 thin films doped by ion implantation with nitrogen or oxygen. The dependence of the electrical resistivity and structure on the annealing temperature and time has been investigated in samples with different dopant concentrations. Enhancement of the thermal stability and increase of the mobility gap for conduction have been observed in O- and N-doped amorphous Ge2Sb2Te5. Larger effects have been found in the case of nitrogen doping.
Virtual instrument automation of ion channeling setup for 1.7 MV tandetron accelerator
Authors: Suresh K. , Sundaravel B. , Panigrahi B. K. , Nair K. G. M. , Viswanathan B.
Published: October 2004

A virtual instrument based automated ion channeling experimental setup has been developed and implemented in a 1.7 MV tandetron accelerator. Automation of the PC based setup is done using a windows based virtual instrument software allowing the setup to be easily ported between different computer operating systems. The virtual instrument software has been chosen to achieve quick and easy development of versatile, multi-purpose user friendly graphical interface for carrying out channeling experiments. The software has been modular designed to provide independent control of the stepper motors for fixing the sample at any user defined orientation, running and on-line display of azimuthal and tilt angular scans, auto storage of the angular scan data. Using this automated setup, the crystallographic axis of the sample can be aligned with the incident ion beam rapidly minimizing the beam damages to the sample. A standard single crystalline GaAs(100) has been characterized with this set up using 2 MeV  He++ ion beam. The crystalline quality (χmin) and channeling half angle (ψ1/2) are measured to be 3.7% and 0.48°, respectively, which are close to the theoretical values. Salient features, working principles and design details of the automated setup are discussed in this paper.
Vertical dispersion Johann x-ray spectrometer with asymmetrically cut crystal
Authors: Renner O. , Podorov S. G. , Wehrhan O. , Förster E.
Published: October 2004

Theoretical design of a new type of the bent crystal spectrometer based on a combination of the vertical dispersion principle with diffraction of x rays from the asymmetrically cut crystal is reported. The novel instrument produces simultaneously two sets of mirror-symmetric spectra, and provides large dispersion, high spectral and 1D spatial resolution with a variable magnification. The analytic formulas describing the function of the spectrometer are complemented by its detailed quantitative analysis based on the ray tracing procedure. The method for reconstruction of the recorded spectra is described, the parameters influencing the precision of the wavelength determination are discussed. The comparison of the main predicted and experimentally observed characteristics verifies the developed theory and demonstrates the spectrometer performance. The novel instrument is particularly suitable for precise measurements of profiles and positions of the narrow-band spectral features observed in the emission of laser-generated plasmas.
A polymer gate dielectric for high-mobility polymer thin-film transistors and solvent effects
Authors: Park Joonhyung , Park S. Young , Shim Sang-Oak , Kang Hyewon , Lee Hong H.
Published: October 2004

A polymer gate dielectric of poly(2-hydroxyethyl methacrylate) is introduced to the polymer thin-film transistor (TFT) with poly(3-hexylthiophene) as its active layer. With this polymer dielectric, the field-effect mobility is 0.1cm2V−1s−1. The solvent used in forming the active layer on the polymer dielectric film has pronounced effects on the device performance. These solvent effects are related to the roughness of the dielectric surface a solvent can induce. The solvent that induces the least roughness is found to be the most desirable for better device performance. The roughness can in turn be related to solubility parameter.
Back-side-illuminated high-speed Ge photodetector fabricated on Si substrate using thin SiGe buffer layers
Authors: Huang Zhihong , Oh Jungwoo , Campbell Joe C.
Published: October 2004

We report photodiodes fabricated on Ge grown on Si substrate. The Ge growth was preceded by two SixGe1−x buffer layers. Dark current as low as 1.07μA was achieved at 10V reverse bias for 24μm-diam mesa devices. At 1.3μm wavelength, the responsivity was 0.37A∕W at 0V and 0.57A∕W when above 2V reverse bias. The 3dB bandwidth was 8.1GHz at a reverse bias of 10V.
Teflon™-coated silicon apertures for supported lipid bilayer membranes
Authors: Wilk S. J. , Goryll M. , Laws G. M. , Goodnick S. M. , Thornton T. J. , Saraniti M. , Tang J. , Eisenberg R. S.
Published: October 2004

We present a method for microfabricating apertures in a silicon substrate using well-known cleanroom technologies resulting in highly reproducible giga-seal resistance bilayer formations. Using a plasma etcher, 150μm apertures have been etched through a silicon wafer. Teflon™ has been chemically vapor deposited so that the surface resembles bulk Teflon and is hydrophobic. After fabrication, reproducible high resistance bilayers were formed and characteristic measurements of a self-inserted single OmpF porin ion channel protein were made.
Fine adjustment of conductivity in polymer-dispersed liquid crystals
Authors: Cupelli D. , Nicoletta F. P. , Filpo G. De , Chidichimo G. , Fazio A. , Gabriele B. , Salerno G.
Published: October 2004

The electrical properties of polymer-dispersed liquid crystals (PDLCs) are an important characteristic in their electro-optical performance. Conductivity effects can set up depolarization fields in the films reducing the effective field across the liquid crystal droplets. Both theoretical and experimental investigations have confirmed that the electric field across nematic droplets depends on the liquid crystal and polymer conductivities. In this letter, we have found that the doping of a PDLC with low percentages of a conductive polymer allows a fine adjustment of polymer matrix conductivity. In addition, we have found a large reduction in the re-orientation fields and relaxation times as a function of conductive polymer loading. Results are in rather good agreement with a simple phenomenological model.
High-quality CdS nanoribbons with lasing cavity
Authors: Liu Y. K. , Zapien J. A. , Geng C. Y. , Shan Y. Y. , Lee C. S. , Lifshitz Y. , Lee S. T.
Published: October 2004

High-density and high-quality CdS nanoribbons were synthesized by a thermal evaporation process. The nanoribbons were characterized by scanning electron microscopy, transmission electron microscopy, x-ray diffraction, and photoluminescence spectroscopy. CdS nanoribbons were found to be single crystals of high phase purity and low defect density. Lasing was observed in the CdS nanoribbons upon optical pumping. The growth of CdS nanoribbons was explained by the vapor–liquid–solid mechanism.
7
W
average power, high-beam-quality green generation in MgO-doped stoichiometric periodically poled lithium tantalate
Authors: Getman A. G. , Popov S. V. , Taylor J. R.
Published: October 2004

A periodically-poled MgO-doped stoichiometric lithium tantalate crystal is applied for single-pass, 67% peak-power efficient, 7.05W average power second-harmonic generation of a single-mode Yb-doped all-fiber fundamental source. Reduced photorefraction and green-induced infrared absorption of the material allowed to maintain a low M2 value of the high-average-power 532nm beam.
Controlling dissociative adsorption for effective growth of carbon nanotubes
Authors: Kayastha Vijaya , Yap Yoke Khin , Dimovski Svetlana , Gogotsi Yury
Published: October 2004

Dissociative adsorption has been widely simplified as part of the vapor–liquid–solid (VLS) growth model. We found that the addition of specific carrier gases can critically modify the growth rate and growth density of multiwall carbon nanotubes (MWNTs). These results were explained by dissociative adsorption of C2H2 molecules and a solid-core VLS growth model. Based on these integrated mechanisms, vertically aligned MWNTs were grown with an initial growth rate as high as ∼800μm∕h. This efficient growth process results at temperature and C2H2 partial pressures at which the decomposition and segregation rates of carbon are balanced. Appropriate use of carrier gas is one of the factors that could facilitate efficient and continuous growth of carbon nanotubes in the future.
A coherent positron beam for reflection high-energy positron diffraction
Authors: Kawasuso A. , Ishimoto T. , Maekawa M. , Fukaya Y. , Hayashi K. , Ichimiya A.
Published: October 2004

A 10 keV positron beam has been developed using coaxially symmetric electromagnetic lenses for reflection high-energy positron diffraction (RHEPD) experiments. The beam brightness is ∼107 e+/s/cm2/rad2/V which is comparable to that obtained using brightness enhancement technique. The beam parallel and normal coherence lengths are over 100 and 40 Å, respectively, which are long enough to observe diffraction patterns associated with large surface super-structures. RHEPD patterns from a Si(111)-(7×7) reconstructed surface have been successfully observed with a much better quality than previously reported.
International consortium on phase contrast imaging and radiology beamline at the Pohang Light Source
Authors: Baik S. , Kim H. S. , Jeong M. H. , Lee C. S. , Je J. H. , Hwu Y. , Margaritondo G.
Published: October 2004

We describe the general characteristics and the first result of a new synchrotron beamline at the Pohang Light Source in Korea. The beamline, operated by a Korean–Taiwanese–Swiss consortium, is dedicated to microimaging experiment in real time with coherent x rays. The performances of the first tests already reach excellent levels when compared to other similar facilities worldwide. The key feature is the use of unmonochromatized x rays to achieve very high lateral and time resolution.
Sliding mode control for active vibration isolation of a long range scanning tunneling microscope
Authors: Lan Kuo-Jung , Yen Jia-Yush , Kramar John A.
Published: October 2004

An active vibration isolation (AVI) system has been designed and implemented for the Molecular Measuring Machine (M3) at the National Institute of Standards and Technology (NIST). NIST is investigating active vibration isolation as an approach to improving the M3 image resolution and measurement speed. This article presents the full dynamic model of the AVI system with the Mallock suspension used for the M3 system suspension. A decoupling process is employed to decompose the complicate dynamics into separate axis. This article then applied a sliding mode controller (SMC) to overcome the system nonlinearities. Experimental results show that the controller is effective, achieving a vibration attenuation of 10 dB at some frequencies, depending on the axis.
Effects of plasma density on relativistic self-injection for electron laser wake-field acceleration
Authors: Zhidkov A. , Koga J. , Hosokai T. , Kinoshita K. , Uesaka M.
Published: October 2004

Density effects on the dynamics of a cavity produced in the wake of an ultraintense (a0=eE/mcω≫1) and short (ωplτ/π<1) laser pulse and on the duration of accelerated electrons are studied via two-dimensional particle-in-cell simulation. Formation of a nonbreaking cavity is a crucial part of relativistic self-injection of plasma electrons from the front of a laser pulse and their further acceleration leading to a beam-quality femtosecond bunch. This self-injection appears in a uniform plasma when the group velocity of the pulse becomes smaller than the maximal electron velocity accelerated in the ponderomotive bias, Φ=mc2a02/2. However with increasing density, this mechanism starts to contend with relativistic wave breaking. Though additional injection due to the relativistic wave breaking increases the total charge of energetic electrons, the duration of the bunch increases to the picosecond range and its energy distribution becomes a Maxwellian.
Resolution scaling in noncontact scanning impedance imaging
Authors: Green Benjamin C. , Shang Tao , Morine Jacey C. , Liu Hongze , Schultz Stephen M. , Oliphant Travis E. , Hawkins Aaron R.
Published: October 2004

Noncontact scanning impedance imaging has been presented as a method to provide high resolution, high contrast images for a variety of material systems. This technique combines electrical impedance measurements with very high resolution scanning. This article reports on efforts to scale this technique down to the very important single micron range and reveals measurements for both thick and thin samples with a measured minimum resolution below 30 μm. A design for a shielded impedance probe applicable to this process is outlined and probes of several different sizes were made and tested. Fabrication of these impedance probes is explained and a testing methodology to characterize the probes’ imaging capability is outlined. Measured results are reported and compared to a predictive model based on image blurring. Two-dimensional impedance images of objects have also been made indicating good image contrast and high resolution. Based on measured data and the model, scaling down to submicron resolution dimensions should be possible given small diameter probes and thin test samples.
Characterization of a radio-frequency line-plasma source in longitudinal line cusps created by permanent magnets
Authors: Sakawa Youichi , Yano Kentaro , Shoji Tatsuo
Published: October 2004

Characterization of a compact, high density, and uniform rf line-plasma source has been investigated. Plasma production is conducted in a rectangular discharge chamber (200×100×20 mm3) with a pair of permanent magnets placed on top and bottom of the chamber. A rf current is applied to an internal antenna covered with a quartz tube, and the plasma is produced by an inductive rf discharge. A magnetic field B0 structure of longitudinal line cusps is produced around the edge of the magnets. Ion-saturation current-density Jis profile is controlled by varying the width of the magnets and/or the distance between the antenna and the magnets, because the electrons created in the low-B0 region are reflected in the high-B0 region. The measured Jis profiles are explained by solving the equation of motion for electrons under the cusped magnetic field. A 140 mm wide plasma [plasma density ≃(1.8–2.5)×1012 cm−3 for electron temperature=4–8 eV] of a uniformity variation within 90% is produced using a 140 mm long antenna for an Ar pressure of 20 mTorr and a rf power of 3 kW.
On the stabilization of fast magnetoacoustic waves by toroidally trapped energetic ions
Authors: Belikov V. S. , Kolesnichenko Ya. I. , White R. B.
Published: October 2004

A theory of the trapped-particle-driven fast magnetoacoustic instability with the frequency below the ion gyrofrequency in toroidal plasmas is developed. It is shown that the l=0 resonance (where l is the number of the cyclotron harmonic), which was ignored in previous theories, typically has a strong stabilizing influence on the instability. It is concluded that the fast magnetoacoustic instability observed in the National Spherical Torus Experiment [E. Fredrickson, N. N. Gorelenkev, C. Z. Cheng et al., Phys. Rev. Lett. 87, 145001 (2001)] is caused by the circulating energetic ions only.
Ultrathin (∼10 nm) carbon foils in space instrumentation
Authors: McComas D. J. , Allegrini F. , Pollock C. J. , Funsten H. O. , Ritzau S. , Gloeckler G.
Published: October 2004

Over the past several decades, a number of groups have successfully developed and flown space instruments based on ultrathin (0.5–3.5 μg cm−2 or ∼2–17 nm nominal thickness) carbon foils suspended on fine metallic grids. These foils have proven to be remarkably robust in surviving the rigors of the launch and space environments and have functioned as required over long mission lifetimes. This study examines the scientific basis of possible failure mechanisms and the actual flight histories of ultrathin carbon foils. In all, we were able to document 138 separate foils used in 17 independent space instruments on 16 different spacecraft with a cumulative functioning flight history of 93 foil-years in space. All of these foils clearly survived their launches, and there is no evidence for any significant degradation over their various flight histories. This successful flight heritage, combined with laboratory data on foil survivability, shows that properly implemented ultrathin carbon foils are a mature and reliable technology for space flight applications.
Fast nondeterministic random bit generator based on weakly correlated physical events
Authors: Stipčević Mario
Published: October 2004

Nondeterministic random bits are needed in many scientific fields. Unfortunately today’s computers are very limited in ability to produce them. We present here a method for extraction of nondeterministic random bits from random physics processes and one practical realization of a physical generator based on it. Even if processes are weakly correlateed the method is shown to deliver increasingly good randomness in the limit of slow sampling. A sample of approximately 109 bits produced by the physical generator prototype is subjected to a series of well-known statistical tests showing no weaknesses.
Significance of floral colour and scent in three Solanum sect. Cyphomandropsis species (Solanaceae) with different floral rewards
Authors: Passarelli Lilian , Bruzzone Liliana
Published: October 2004

The role of scent and floral colour in three Solanum sect. Cyphomandropsis species with different floral rewards was studied. In the two studied species with pollen rewards, S. glaucophyllum Desf. and S. stuckertii Bitter, the principal advertisement to pollinators is the colour of the perianth and anthers, including areas that absorb UV light. In the last species, the scent emitted by the osmophores of the connective also plays a significant role in flower attraction. The floral perfume would be the only advertisement in species such as S. adelphum Morton, with perfume reward in which the cryptical anther colour does not contrast with that of the perianth. The internal face of the petals remains hidden. In this case no differences in the patterns of areas that absorb visible light and UV light were found. The main visitors to Solanum are species of Bombus and Augochloropsis. These pollinators visit S. glaucophyllum and S. stuckertii, species with pollen reward, but they do not visit flowers with perfume reward, for example S. adelphum.
Seed mass, seed production, germination and seedling traits in two phenological types of Bidens pilosa (Asteraceae)
Authors: Gurvich Diego E. , Enrico Lucas , Funes Guillermo , Zak Marcelo R.
Published: October 2004

Bidens pilosa L. is a summer annual that shows a particular phenological pattern in the Córdoba mountains, Argentina. Some individuals start flowering 1 month after germination (early type), but most of the population starts flowering 4 months after germination (normal type). The aims of this study were to (1) analyse whether differences in flowering phenology affect seed mass and seed production, and (2) assess whether possible differences in seed traits of the two parental phenological types would affect germinability, germination rate, seedling growth and flowering phenology of offspring under laboratory conditions. The study showed that the numbers of seeds per capitulum and per plant were greater in the normal type than in the early type plants. This can be related to plant height, since in the field, normal-type plants are larger than early type plants. However, early type plants produced heavier seeds than normal-type plants. Germination rate was faster in the early type seeds, but total germination was higher in the normal ones. Seedling growth, in terms of height and the date of first flowering, did not differ between the phenological types of parental seed sources. Our results showed that differences in flowering phenology were associated with seed mass and seed production differences. Seed mass appears to be related to germination characteristics but not to seedling growth nor to flowering phenology of offspring.
The freshwater diatom genus Kobayasiella (Bacillariophyta) in Tasmania, Australia
Authors: Vanhoutte K. , Verleyen E. , Vyverman W. , Chepurnov V. , Sabbe K.
Published: October 2004

Representatives of the diatom genus Kobayasiella Lange-Bertalot (Bacillariophyta) are common in benthic diatom communities of oligotrophic and dystrophic highland lakes in Tasmania Australia. A taxonomic revision of this genus revealed the presence of four unknown taxa, which are here formally described. Kobayasiella acidophila sp. nov., K.�australis sp. nov., K.�hodgsonii sp. nov. and K.�tasmanica sp. nov. differ from all described Kobayasiella species in dimensions and stria density (K.�acidophila, K.�hodgsonii), the presence of elongated areolae at the valve apex (K.�australis) or the presence of multiple longitudinal ridges on the valve face (K.�tasmanica). Kobayasiella�hodgsonii was the most widespread and abundant species. It closely resembles Kobayasiella saxicola (Manguin) Lange-Bertalot, which was originally described from New Caledonia. However, specimens belonging to the former species were consistently narrower in comparison with the type specimens of K.�saxicola. Given the small size and inconspicuous features of most representatives of the genus Kobayasiella, its global species diversity has almost certainly been underestimated.
Shields of offence: signalling competitive ability in the dusky moorhen, Gallinula tenebrosa
Authors: Crowley Camille E. , Magrath Robert D.
Published: October 2004

The 'status-signalling' hypothesis states that individuals might avoid unprofitable fights by signalling their competitive ability and assessing the signals of others. The frontal shields of rails (Aves : Rallidae) are fleshy structures that are displayed prominently during agonistic interactions. Shield maintenance probably requires elevated levels of testosterone and deposition of carotenoid pigments, which implies that shield size and colour could be honest signals of the ability or willingness to fight. We used field observations and a model experiment to study the signalling function of the red shield of the dusky moorhen, Gallinula tenebrosa. Birds with relatively larger shields were more likely to win aggressive encounters, and the outcome was apparently unaffected, or less strongly affected, by body size, weight, condition and sex. Shield size increased with body size and weight, but neither explained more than 26% of the variation in shield size, even after controlling for age and date. Shield size was not affected by body condition, as estimated from residuals of a regression of weight on body size. Moorhens confronted with a model fitted with a large shield retreated more quickly than they did when presented with the same model bearing a small shield, supporting the results from natural interactions. We conclude that the frontal shield functions as a signal during agonistic interactions, and possibly signals the ability or willingness to fight.
Curbing the U.S. carbon deficit
Authors: Jackson Robert B. , Schlesinger William H.
Published: October 2004

The U.S. emitted ≈1.58 petagrams (Pg) of fossil fuel carbon in 2001, approximately one-quarter of global CO
2
production. With climate change increasingly likely, strategies to reduce carbon emissions and stabilize climate are needed, including greater energy efficiency, renewable energy sources, geoengineering, decarbonization, and geological and biological sequestration. Two of the most commonly proposed biological strategies are restoring organic carbon in agricultural soils and using plantations to sequester carbon in soils and wood. Here, we compare scenarios of land-based sequestration to emissions reductions arising from increased fuel efficiency in transportation, targeting ways to reduce net U.S. emissions by 10% (≈0.16 Pg of carbon per year). Based on mean sequestration rates, converting all U.S. croplands to no-till agriculture or retiring them completely could sequester ≈0.059 Pg of carbon per year for several decades. Summary data across a range of plantations reveal an average rate of carbon storage an order of magnitude larger than in agricultural soils; in consequence, one-third of U.S. croplands or 44 million hectares would be needed for plantations to reach the target of ≈0.16 Pg of carbon per year. For fossil fuel reductions, cars and light trucks generated ≈0.31 Pg of carbon in U.S. emissions in 2001. To reduce net emissions by 0.16 Pg of carbon per year, a doubling of fuel efficiency for cars and light trucks is needed, a change feasible with current technology. Issues of permanence, leakage, and economic potentials are discussed briefly, as is the recognition that such scenarios are only a first step in addressing total U.S. emissions.
Centromere-encoded RNAs are integral components of the maize kinetochore
Authors: Topp Christopher N. , Zhong Cathy X. , Dawe R. Kelly
Published: October 2004

RNA is involved in a variety of chromatin modification events, ranging from large-scale structural rearrangements to subtle local affects. Here, we extend the evidence for RNA–chromatin interactions to the centromere core. The data indicate that maize centromeric retrotransposons (CRMs) and satellite repeats (CentC) are not only transcribed, but that nearly half of the CRM and CentC RNA is tightly bound to centromeric histone H3 (CENH3), a key inner kinetochore protein. RNAs from another tandem repeat (180-bp knob sequence) or an abundant euchromatic retroelement (Opie) are undetectable within the same anti-CENH3 immune complexes. Both sense and antisense strands of CRM and CentC, but not small interfering RNAs homologous to either repeat, were found to coimmunoprecipitate with CENH3. The bulk of the immunoprecipitated RNA ranged in size from 40 to 200 nt. These data provide evidence for a pool of protected, single-stranded centromeric RNA within the centromere/kinetochore complex.
Palatability: response to nutritional need or need-free stimulation of appetite?
Authors: Yeomans Martin R. , Blundell John E. , Leshem Micah
Published: October 2004

The traditional view of palatability was that it reflected some underlying nutritional deficit and was part of a homeostatically driven motivational system. However, this idea does not fit with the common observation that palatability can lead to short-term overconsumption. Here, we attempt to re-evaluate the basis of palatability, first by reviewing the role of salt-need both in the expression of liking for salty tastes, and paradoxically, in dissociating need from palatability, and second by examining the role of palatability in short-term control of appetite. Despite the clarity of this system in animals, however, most salt (NaCl) intake in man occurs in a need-free state. Similar conclusions can be drawn in relation to the palatability of food in general. Importantly, the neural systems underlying the hedonic system relating to palatability and homeostatic controls of eating are separate, involving distinct brain structures and neurochemicals. If palatability was a component of homeostatic control, reducing need-state should reduce palatability. However, this is not so, and if anything palatability exerts a stronger stimulatory effect on eating when sated, and over-consumption induced by palatability may contribute to obesity. Differential responsivity to palatability may be a component of the obese phenotype, perhaps through sensitisation of the neural structures related to hedonic aspects of eating. Together, these disparate data clearly indicate that palatability is not a simple reflection of need state, but acts to promote intake through a distinct hedonic system, which has inputs from a variety of other systems, including those regulating need. This conclusion leads to the possibility of novel therapies for obesity based on modulation of hedonic rather than homeostatic controls. Potential developments are discussed.
Modulatory factors in the effect of energy density on energy intake
Authors: Westerterp-Plantenga M. S.
Published: October 2004

The effect of energy density (ED) on energy intake (EI) has been assessed in short-term and long-term experiments. In the short term, it was found that ED affects EI directly in situations when the subjects cannot estimate the ED of the food; then subjects mainly monitor the weight of the food ingested. In the long term, the effects of ED on EI are modulated. Average daily EI appears to be related to ED of the food and drinks when ED is determined by specific macronutrients, but not when ED is only determined by the weight of water. Thus, the short-term effect ED has on EI cannot be extrapolated to the long term, because a possible dominating effect of the weight of water determining ED undoes the relationship of ED with EI. Moreover, in the long-term portion sizes are used to compensate for correctly estimated ED, resulting in less variation in EI than ED alone would imply. Finally, dietary restraint compensates for the effect of a relatively high ED on daily EI, whereas dietary unrestraint compensates for the effect of relatively low ED on daily EI. We conclude that the short-term effect of ED on EI is modulated by the effect of water on ED, and compensated for by the effect of dietary restraint and adapted portion sizes.
Cross sections and transport coefficients for electrons in Zn vapour
Authors: R D White  , R P McEachran  , R E Robson  , M T Elford  , K Bartschat
Published: October 2004

In this paper we present details of the following:

ab initiocalculations of a set of electron impact cross sections for atomic Zn; and

transport coefficients and distribution functions for an electron swarm in Zn vapour, obtained from a multiterm solution of Boltzmann's equation using these cross sections, over a range of reduced fields,E/N, and gas temperatures of practical interest.

Our work has been motivated, in part, by recent suggestions that zinc could be an attractive replacement for mercury in making high-pressure gas discharge lamps more environment-friendly (Born M2001J. Phys. D: Appl. Phys.34909; Born M2002Plasma Sources Sci. Technol.11A55). Current models of such lamps require a knowledge of the plasma electrical conductivity, which can be calculated from the (e, Zn) cross sections and mobility coefficients presented in this paper.
Phylogenetic Analysis of the Formin Homology 2 Domain
Authors: Higgs Henry N. , Peterson Kevin J.
Published: October 2004

Formin proteins are key regulators of eukaryotic actin filament assembly and elongation, and many species possess multiple formin isoforms. A nomenclature system based on fundamental features would be desirable, to aid the rapid identification and characterization of novel formins. In this article, we attempt to systematize the formin family by performing phylogenetic analyses of the formin homology 2 (FH2) domain, an independently folding region common to all formins, which alone can influence actin dynamics. Through database searches, we identify 101 FH2 domains from 26 eukaryotic species, including 15 in mice. Sequence alignments reveal a highly conserved yeast-specific insert in the “knob loop” region of the FH2 domain, with unknown functional consequences. Phylogenetic analysis using minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML) algorithms strongly supports the existence of seven metazoan groups. Yeast FH2 domains segregate from all other eukaryotes, including metazoans, other fungi, plants, and protists. Sequence comparisons of non-FH2 regions support relationships between three metazoan groups (Dia, DAAM, and FRL) and examine previously identified coiled-coil and Diaphanous auto-regulatory domain sequences. This analysis allows for a formin nomenclature system based on sequence relationships, as well as suggesting strategies for the determination of biochemical and cellular activities of these proteins.
ColorHOR—novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome
Authors: Paar Vladimir , Pavin Nenad , Rosandić Marija , Glunčić Matko , Basar Ivan , Pezer Robert , Žinić Sonja Durajlija
Published: October 2004

Motivation: GenBank data are at present lacking alpha satellite higher-order repeat (HOR) annotation. Furthermore, exact HOR consensus lengths have not been reported so far. Given the fast growth of sequence databases in the centromeric region, it is of increasing interest to have efficient tools for computational identification and analysis of HORs from known sequences.

Results: We develop a graphical user interface method, ColorHOR, for fast computational identification of HORs in a given genomic sequence, without requiring a priori information on the composition of the genomic sequence. ColorHOR is based on an extension of the key-string algorithm and provides a color representation of the order and orientation of HORs. For the key string, we use a robust 6 bp string from a consensus alpha satellite and its representative nature is tested. ColorHOR algorithm provides a direct visual identification of HORs (direct and/or reverse complement). In more detail, we first illustrate the ColorHOR results for human chromosome 1. Using ColorHOR we determine for the first time the HOR annotation of the GenBank sequence of the whole human genome. In addition to some HORs, corresponding to those determined previously biochemically, we find new HORs in chromosomes 4, 8, 9, 10, 11 and 19. For the first time, we determine exact consensus lengths of HORs in 10 chromosomes. We propose that the HOR assignment obtained by using ColorHOR be included into the GenBank database.

Availability: The program with graphical user interface application for ColorHOR is freely available at http://www.hazu.hr/KSA/colorHOR.html. It can be run on any platform on which wxPython is supported.

Contact:  paar@hazu.hr

Supplementary information:  http://www.hazu.hr/KSA/colorHOR.html.
Local correlation of expression profiles with gene annotations—proof of concept for a general conciliatory method
Authors: Pinto F. R. , Cowart L. Ashley , Hannun Yusuf A. , Rohrer B. , Almeida J. S.
Published: October 2004

Motivation: Integrated analysis of expression data and gene ontology annotations is a prime example of biological data that need co-explanatory interpretation. This particular application is used to validate a new method for integrated analysis of varied biological information.

Results: The proposed method consists of determining local correlation coefficients and the corresponding P-values calculated per biological entity. This measure considers the combined intensity and significance of the agreement or disagreement, between two data sources about the same biological entity. The method is applied to the integrated analysis of gene expression and annotation of two gene sets, one from yeast and other from mouse. The potential of the method to generate accurate mechanistic hypothesis is also demonstrated. Specially, negative correlation results pose a new kind of biological hypothesis. Method performance was compared with annotation enrichment methods, and optimal conditions for the superiority of local correlation results are discussed.

Availability: The matlab functions described in this article are available at http://bioinformatics.musc.edu/~frpinto/

Contact:  almeidaj@musc.edu

Supplementary information: Further information, tables and figures are available at http://bioinformatics.musc.edu/~frpinto/
Fast and accurate database homology search using upper bounds of local alignment scores
Authors: Itoh Masumi , Goto Susumu , Akutsu Tatsuya , Kanehisa Minoru
Published: October 2004

Motivation: It is widely recognized that homology search and ortholog clustering are very useful for analyzing biological sequences. However, recent growth of sequence database size makes homolog detection difficult, and rapid and accurate methods are required.

Results: We present a novel method for fast and accurate homology detection, assuming that the Smith–Waterman (SW) scores between all similar sequence pairs in a target database are computed and stored. In this method, SW alignment is computed only if the upper bound, which is derived from our novel inequality, is higher than the given threshold. In contrast to other methods such as FASTA and BLAST, this method is guaranteed to find all sequences whose scores against the query are higher than the specified threshold. Results of computational experiments suggest that the method is dozens of times faster than SSEARCH if genome sequence data of closely related species are available.

Availability: The programs for fast homolog detection can be downloaded from ftp://ftp.kuicr.kyoto-u.ac.jp/itoh/

Contact:  itoh@kuicr.kyoto-u.ac.jp
HyPhy: hypothesis testing using phylogenies
Authors: Pond Sergei L. Kosakovsky , Frost Simon D. W. , Muse Spencer V.
Published: October 2004

Summary: The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution.

Availability:  http://www.hyphy.org

Contact:  muse@stat.ncsu.edu

Supplementary information:  HyPhydocumentation and tutorials are available at http://www.hyphy.org
A new approach to prediction of short-range conformational propensities in proteins
Authors: Gront Dominik , Kolinski Andrzej
Published: October 2004

Motivation: Knowledge-based potentials are valuable tools for protein structure modeling and evaluation of the quality of the structure prediction obtained by a variety of methods. Potentials of such type could be significantly enhanced by a proper exploitation of the evolutionary information encoded in related protein sequences. The new potentials could be valuable components of threading algorithms, ab-initio protein structure prediction, comparative modeling and structure modeling based on fragmentary experimental data.

Results: A new potential for scoring local protein geometry is designed and evaluated. The approach is based on the similarity of short protein fragments measured by an alignment of their sequence profiles. Sequence specificity of the resulting energy function has been compared with the specificity of simpler potentials using gapless threading and the ability to predict specific geometry of protein fragments. Significant improvement in threading sensitivity and in the ability to generate sequence-specific protein-like conformations has been achieved.

Availability: see: http://www.biocomp.chem.uw.edu.pl

Contact:  dgront@chem.uw.edu.pl
PDBML: the representation of archival macromolecular structure data in XML
Authors: Westbrook John , Ito Nobutoshi , Nakamura Haruki , Henrick Kim , Berman Helen M.
Published: October 2004

Summary: The Protein Data Bank (PDB) has recently released versions of the PDB Exchange dictionary and the PDB archival data files in XML format collectively named PDBML. The automated generation of these XML files is driven by the data dictionary infrastructure in use at the PDB. The correspondences between the PDB dictionary and the XML schema metadata are described as well as the XML representations of PDB dictionaries and data files.

Availability: The current software translated XML schema file is located at http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd, and on the PDB mmCIF resource page at http://deposit.pdb.org/mmcif/. PDBML files are stored on the PDB beta ftp site at ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML

Contact:  jwest@rcsb.rutgers.edu
Automatic extraction of gene/protein biological functions from biomedical text
Authors: Koike Asako , Niwa Yoshiki , Takagi Toshihisa
Published: October 2004

Motivation: With the rapid advancement of biomedical science and the development of high-throughput analysis methods, the extraction of various types of information from biomedical text has become critical. Since automatic functional annotations of genes are quite useful for interpreting large amounts of high-throughput data efficiently, the demand for automatic extraction of information related to gene functions from text has been increasing.

Results: We have developed a method for automatically extracting the biological process functions of genes/protein/families based on Gene Ontology (GO) from text using a shallow parser and sentence structure analysis techniques. When the gene/protein/family names and their functions are described in ACTOR (doer of action) and OBJECT (receiver of action) relationships, the corresponding GO-IDs are assigned to the genes/proteins/families. The gene/protein/family names are recognized using the gene/protein/family name dictionaries developed by our group. To achieve wide recognition of the gene/protein/family functions, we semi-automatically gather functional terms based on GO using co-occurrence, collocation similarities and rule-based techniques. A preliminary experiment demonstrated that our method has an estimated recall of 54–64% with a precision of 91–94% for actually described functions in abstracts. When applied to the PUBMED, it extracted over 190 000 gene–GO relationships and 150 000 family–GO relationships for major eukaryotes.

Availability: The extracted gene functions are available at http://prime.ontology.ims.u-tokyo.ac.jp

Contact:  akoike@hgc.jp
Comparison of computational methods for the identification of cell cycle-regulated genes
Authors: de Lichtenberg Ulrik , Jensen Lars Juhl , Fausbøll Anders , Jensen Thomas S. , Bork Peer , Brunak Søren
Published: October 2004

Motivation: DNA microarrays have been used extensively to study the cell cycle transcription programme in a number of model organisms. The Saccharomyces cerevisiae data in particular have been subjected to a wide range of bioinformatics analysis methods, aimed at identifying the correct and complete set of periodically expressed genes.

Results: Here, we provide the first thorough benchmark of such methods, surprisingly revealing that most new and more mathematically advanced methods actually perform worse than the analysis published with the original microarray data sets. We show that this loss of accuracy specifically affects methods that only model the shape of the expression profile without taking into account the magnitude of regulation. We present a simple permutation-based method that performs better than most existing methods.

Supplementary information: Results and benchmark sets are available at http://www.cbs.dtu.dk/cellcycle

Contact:  brunak@cbs.dtu.dk
PDZBase: a protein–protein interaction database for PDZ-domains
Authors: Beuming Thijs , Skrabanek Lucy , Niv Masha Y. , Mukherjee Piali , Weinstein Harel
Published: October 2004

Summary: PDZBase is a database that aims to contain all known PDZ-domain-mediated protein–protein interactions. Currently, PDZBase contains approximately 300 such interactions, which have been manually extracted from >200 articles. The database can be queried through both sequence motif and keyword-based searches, and the sequences of interacting proteins can be visually inspected through alignments (for the comparison of several interactions), or as residue-based diagrams including schematic secondary structure information (for individual complexes).

Availability:  http://icb.med.cornell.edu/services/pdz/start.

Contact:  pdzbase@med.cornell.edu.