bluuebunny/crossref_metadata_2025 huggingface dataset:
Space charge limited flow of a thin electron beam confined by a strong magnetic field
Authors: Rokhlenko A. , Lebowitz J. L.
Published: September 2004

An approximate analytic theory is developed and implemented numerically for calculating the space charge limited current and electric field of a thin cylindrical beam or current sheet between two wide parallel electrodes. The flow is confined by a sufficiently strong magnetic field. Assuming that the potential and current density are almost homogeneous in the direction transversal to the flow, the beam current and its profile are computed by a variational method. The average current density scales as the reciprocal of the beam width when the latter becomes very small. The total cylindrical beam current thus decreases proportionly to its diameter while the total current of a sheet becomes almost independent of the width in this regime.
Statistical investigation of transport barrier effects produced by biasing in a nonfusion magnetoplasma
Authors: Magni S. , Riccardi C. , Roman H. E.
Published: September 2004

The effects of a biasing potential on the statistical properties of the fluctuating flux, particle density and radial velocity time series in the nonfusion magnetoplasma Thorello [C. Riccardi, D. Xuantong, M. Salierno, L. Gamberale, and M. Fontanesi, Phys. Plasmas 4, 3749 (1997)] are studied. The shape evolution of the probability distribution function (PDF) of the temporal coarse-grained fluctuating flux is investigated as a function of the radial position in the plasma equatorial plane, for different values of the bias potential applied to a limiter. A reduction of cross correlations between density and radial velocity, concomitant with an increase in the shearing rate of the radial electric field, is found near the center of the plane as a function of the bias potential. The partial density-velocity cross correlations, evaluated at different time scales, reach their asymptotic values for times of the order of those describing the change in shape of the fluctuating flux PDF. The magnitude of the shearing rate of the radial electric field, calculated at different radial positions in the plane, is consistent with the expected decorrelation mechanism of turbulent transport.
Effect of current rate on energy deposition into exploding metal wires in vacuum
Authors: Sarkisov G. S. , Struve K. W. , McDaniel D. H.
Published: September 2004

This paper presents direct experimental proof of a significant increase of energy deposition into a metal core before voltage breakdown with the current rate for nanosecond exploding wires in a vacuum. This effect is demonstrated for nine different refractory and nonrefractory metals. The strongest influence of current rate was demonstrated for tungsten wires. Increasing the current rate from 20 to 150 A/ns changes the wire core from a solid to a cluster-like state. For nonrefractory metals such as Ag, Al, Cu, and Au, fast explosion allows deposition inside a metal core 1.5–2.9 times the atomization enthalpy before voltage breakdown. The slow explosion, with 20 A/ns, gives 2–3 times less energy deposition before voltage breakdown than the fast-explosion mode. The current-rate effect is important for optimization of wire ablation, reduction of the mass left behind in the wire-array load, and final x-ray yield in modern multi-MA wire-array Z-pinch facilities.
Electron Bernstein wave generation in a linear plasma system
Authors: Yadav Vipin K. , Bora D.
Published: September 2004

Electron Bernstein wave (EBW) generation via mode conversion is observed in a short cylindrical electron cyclotron resonance (ECR) plasma system. ECR plasma with input microwave power varying from 160 to 800 W is produced at an operating pressure of 10−3 mbar with hydrogen gas with a maximum plasma density of 3.1×1010 cm−3 at the center and plasma temperature of 10 eV. The axial magnetic field required for ECR in the system is produced by two identical magnetic coils arranged in the Helmholtz configuration. The fundamental ECR surface (B=875 G) is located at the geometrical center of the plasma system. Microwaves of 2.45±0.02 GHz from a magnetron in TE10 mode are launched radially to have extraordinary (X) wave in plasma. The EBW is observed to be generated at the upper hybrid resonance layer at a distance of 2 cm from the center towards the microwave source. The EBW is assumed to be generated through X-B mode conversion which is inferred by the observation of the parametric decay of the incident wave. The experimental results pertaining to the EBW detection and characterization are discussed in this paper.
Magnetosonic modes with a beam of dust or secondary ions
Authors: Cramer N. F. , Verheest F. , Cattaert T. , Hellberg M. A. , Matthews A. P. , Krumm P.
Published: September 2004

Charged dust particles on near-Keplerian orbits in planetary rings drift relative to the corotating background plasma, and this relative streaming may drive dust-modified magnetosonic waves unstable. Using a magnetofluid model, this situation is revisited, and it is shown that a correct description can be obtained at frequencies and Doppler shifts that are small compared to the electron gyrofrequency. An excellent agreement is reached between the analytical approximation and the numerical solution of the full or reduced dispersion law. A very low-frequency, small wave number beam instability may occur at supermagnetosonic beam velocities of the dust component, but, based on the existing data, is unlikely to play a role in planetary rings. Instability is also found for submagnetosonic speeds, which might be relevant to Saturn’s E ring.
Spatially limited ion acoustic wave activity in low-pressure helicon discharges
Authors: Corr C. S. , Plihon N. , Chabert P. , Sutherland O. , Boswell R. W.
Published: September 2004

Ion acoustic wave phenomena are studied and compared in two low-pressure argon discharges created by helicon sources. The wave amplitudes are spatially localized near the edge of a plasma column as the amplitudes of the “mirror waves” that are separated from the helicon source frequency by the ion wave frequency. Dependencies of the ion wave on radial position, pressure, input power, and magnetic field are investigated. Measurements of the wavelength show that the wave is traveling azimuthally at approximately the ion sound speed in the direction of electron gyration. Although the wave spectra are indicative of a parametric decay phenomenon, it seems more likely that the radial plasma pressure gradient drives an ion acoustic instability which then modulates the helicon source.
Suppression of vortex-shedding noise via derivative-free shape optimization
Authors: Marsden Alison L. , Wang Meng , Dennis J. E. , Moin Parviz
Published: September 2004

In this Letter we describe the application of a derivative-free optimization technique, the surrogate management framework (SMF), for designing the shape of an airfoil trailing edge which minimizes the noise of vortex shedding. Constraints on lift and drag are enforced within SMF using a filter. Several optimal shapes have been identified for the case of laminar vortex shedding with reasonable computational cost using several shape parameters, and results show a significant reduction in acoustic power. Physical mechanisms for noise reduction are discussed.
Improved two-point model for limiter scrape-off layer
Authors: Tokar M. Z. , Kobayashi M. , Feng Y.
Published: September 2004

An analytical model for a limiter scrape-off layer (SOL) is proposed, which takes self-consistently into account both conductive and convective contributions to the heat transport in SOL. The particle flows in the SOL main part are determined by considering the recycling of neutrals. The model allows us to interpret the results of numerical simulation by the code EMC3-EIRENE [Y. Feng, F. Sardei, P. Grigull, K. McCormick, J. Kisslinger, D. Reiter, and Y. Igitkhanov, Plasma Phys. Controlled Fusion 44, 611 (2002)] for the edge region of Tokamak Experiment for Technology Oriented Research (TEXTOR) [Proceedings of the 16th IEEE Symposium on Fusion Engineering, 1995 (Institute for Electrical and Electronics Engineers, Piscataway, NJ, 1995), p. 470].
The Effect of a Radome on Submillimeter Site-Testing Measurements
Authors: G. Calisse Paolo
Published: September 2004

We evaluate the effect that radome transparency has on atmospheric opacity measurements performed by the skydip technique. We show that, except at rather high opacities, it is not sufficient to ignore losses in the radome (or ‘window’) during the data analysis and then subtract them from the derived atmospheric opacity. Perhaps surprisingly, unless radome transparency is correctly modelled, the atmosphere will appear to have a minimum opacity that is many times greater that the radome losses. Our conclusion is that some previous site studies may have significantly underestimated the quality of the best submilli-metre sites, and that the difference between these sites and poorer sites may be much greater than currently believed. We also show that part of the residual 857-GHz opacity at the best sites, currently ascribed to ‘dry-air opacity’, can in fact be just an artefact caused by not properly modelling the radome during the data analysis.
An Historical Light Curve of CF Octantis from Digitised Images of the Bamberg Plate Archive
Authors: Innis J. L. , Heil P. , Thompson K. , Coates D. W.
Published: September 2004

Digital images were made of Bamberg Observatory Sky Patrol plates of the field surrounding the active-chromosphere star CF Octantis (HD 196818). These images, taken with an inexpensive camera, were analysed using standard aperture photometry techniques. Good agreement was found with catalogued photographic magnitudes for stars in the range mpg ∼8.5 to ∼10.5. The root-mean-square deviations in the measured differences for non-variable field stars was found to be of order 0.10 mag, although a small number of larger differences occurred. For CF Oct, a period search of data from 1966 recovered the known 20 d variation due to starspot rotational modulation, with a range of variation of order 0.5 mag photographic. For active-chromosphere stars with moderately large photometric variations (>∼0.3 mag), and moderate to long rotation periods (>∼1 week), careful analysis of similarly obtained digital copies of archive plates may provide valuable insights into historical actvity.
The HI Content of Compact Groups of Galaxies
Authors: Stevens J. B. , Webster R. L. , Barnes D. G. , Pisano D. J. , Drinkwater M. J.
Published: September 2004

The HI content of Hickson Compact Groups in the southern hemisphere is measured using data from the HI Parkes All-Sky Survey (HIPASS), and dedicated observations using the narrow band filter on the Multibeam instrument on the Parkes telescope. The expected HI mass of these groups was estimated using the luminosity, diameter, and morphological types of the member galaxies, calibrated from published data. Taking careful account of non-detection limits, the results show that the compact group population that has been detected by these observations has an HI content similar to that of galaxies in the reference field sample. The upper limits for the undetected groups lie within the normal range; improvement of these limits will require a large increase in sensitivity.
Comprehensive Analysis of RGU Photometry in the Direction to M5
Authors: Karaali S. , Bilir S. , Buser R.
Published: September 2004

The RGU-photographic investigation of an intermediate latitude field in the direction to the Galactic centre is presented. 164 extra-galactic objects, identified by comparison of Minnesota and Basel charts, are excluded from the program. Also, a region with size 0.104 square-degrees, contaminated by cluster (M5) stars and affected by background light of the bright star HD 136202 is omitted. Contrary to previous investigations, a reddening of E(B – V) = 0.046, corresponding to E(G – R) = 0.07 mag is adopted. The separation of dwarfs and evolved stars is carried out by an empirical method, already applied in some of our works. A new calibration for the metallicity determination is used for dwarfs, while the absolute magnitude determination for stars of all categories is performed using the procedures given in the literature. There is good agreement between the observed logarithmic space density histograms and the galactic model gradients. Also, the local luminosity function agrees with Gliese's (1969) and Hipparcos (Jahreiss & Wielen 1997) luminosity functions, for stars with 2 < M(G) ≤ 8 mag. For giants, we obtained two different local space densities from comparison with two Galactic models, i.e. D*(0) = 6.63, close to that of Gliese (1969), and D*(0) = 6.79. A metallicity gradient, d[Fe/H]/dz = –0.20 dex kpc–1, is detected for dwarfs (only) with absolute magnitudes 4 < M(G) ≤ 6, corresponding to a spectral type interval F5–K0.
psrchive and psrfits: An Open Approach to Radio Pulsar Data Storage and Analysis
Authors: Hotan A. W. , van Straten W. , Manchester R. N.
Published: September 2004

A new set of software applications and libraries for use in the archival and analysis of pulsar astronomical data is introduced. Known collectively as the psrchive scheme, the code was developed in parallel with a new data storage format called psrfits, which is based on the Flexible Image Transport System (FITS). Both of these projects utilise a modular, object-oriented design philosophy. psrchive is an open source development environment that incorporates an extensive range of c++ object classes and pre-built command line and graphical utilities. These deal transparently and simultaneously with multiple data storage formats, thereby enhancing data portability and facilitating the adoption of the psrfits file format. Here, data are stored in a series of modular header–data units that provide flexibility and scope for future expansion. As it is based on FITS, various standard libraries and applications may be used for data input, output, and visualisation. Both psrchive and psrfits are made publicly available to the academic community in the hope that this will promote their widespread use and acceptance.
PFP 1: A Large Planetary Nebula Caught in the First Stages of ISM Interaction
Authors: Pierce Mark J. , Frew David J. , Parker Quentin A. , Köppen Joachim
Published: September 2004

This paper presents (Hα + [Nii]) imaging and spectroscopy of a previously unknown, highly evolved planetary nebula of low excitation which is in the first stages of an interaction with the interstellar medium (ISM). It was discovered serendipitously from AAO/UKST Hα Survey images as part of a project to exploit the survey data and has evaded detection by previous surveys due to its very low surface brightness. It is a remarkable hollow-sphere planetary nebula, some 19´ across, making it one of the largest examples of its type. We estimate a radius of 1.5 pc and a distance of 550 pc as derived from a new Hα surface brightness–radius relation. PFP 1 has near-perfect circular symmetry, broken only at the north-western edge which is coupled with significantly increased (Hα + [Nii]) intensity, both of which provide evidence for an interaction with the ISM. We find a near solar composition for this object with possibly enhanced He and N abundances. A blue central star candidate has been identified from the SuperCosmos Sky Survey data.
Synthesis and Spectroscopic Characterization of β-Di-, β-Tri-, and β-Hexapeptides Built with (S)-2-Methylene-3-aminoalkanoic Acids Derived from Alanine, Valine, and Leucine
Authors: Bierbaum Daniel J. , Seebach Dieter
Published: September 2004

Methylthiomethylation and subsequent sulfoxidation and pyrolysis of the N-Boc-protected β3-amino acid methyl esters derived from Ala, Val, and Leu provided the α-methylene esters; these were then used to synthesize the β-peptides specified in the title (step-by-step and fragment coupling in solution). The novel β-peptides were fully characterized, but neither solid-state nor solution structures were found.
Resolution of the insect ouabain paradox
Authors: Torrie Leah S. , Radford Jonathan C. , Southall Tony D. , Kean Laura , Dinsmore Andrew J. , Davies Shireen A. , Dow Julian A. T.
Published: September 2004

Many insects are highly resistant to plant toxins, such as the cardiac glycoside ouabain. How can the epithelia that must handle such toxins, also be refractory to them? In
Drosophila
, the Malpighian (renal) tubule contains large amounts of Na
+
,K
+
ATPase that is known biochemically to be exquisitely sensitive to ouabain, yet the intact tissue is almost unaffected by even extraordinary concentrations. The explanation is that the tubules are protected by an active ouabain transport system, colocated with the Na
+
,K
+
ATPase, thus preventing ouabain from reaching inhibitory concentrations within the basolateral infoldings of principal cells. These data show that the Na
+
,K
+
ATPase, previously thought to be unimportant, may be as vital in insect tissues as in vertebrates, but can be cryptic to conventional pharmacology.
Phylogenetic discovery bias in
Bacillus anthracis
using single-nucleotide polymorphisms from whole-genome sequencing
Authors: Pearson Talima , Busch Joseph D. , Ravel Jacques , Read Timothy D. , Rhoton Shane D. , U'Ren Jana M. , Simonson Tatum S. , Kachur Sergey M. , Leadem Rebecca R. , Cardon Michelle L. , Van Ert Matthew N. , Huynh Lynn Y. , Fraser Claire M. , Keim Paul
Published: September 2004

Phylogenetic reconstruction using molecular data is often subject to homoplasy, leading to inaccurate conclusions about phylogenetic relationships among operational taxonomic units. Compared with other molecular markers, single-nucleotide polymorphisms (SNPs) exhibit extremely low mutation rates, making them rare in recently emerged pathogens, but they are less prone to homoplasy and thus extremely valuable for phylogenetic analyses. Despite their phylogenetic potential, ascertainment bias occurs when SNP characters are discovered through biased taxonomic sampling; by using whole-genome comparisons of five diverse strains of
Bacillus anthracis
to facilitate SNP discovery, we show that only polymorphisms lying along the evolutionary pathway between reference strains will be observed. We illustrate this in theoretical and simulated data sets in which complex phylogenetic topologies are reduced to linear evolutionary models. Using a set of 990 SNP markers, we also show how divergent branches in our topologies collapse to single points but provide accurate information on internodal distances and points of origin for ancestral clades. These data allowed us to determine the ancestral root of
B
.
anthracis
, showing that it lies closer to a newly described “C” branch than to either of two previously described “A” or “B” branches. In addition, subclade rooting of the C branch revealed unequal evolutionary rates that seem to be correlated with ecological parameters and strain attributes. Our use of nonhomoplastic whole-genome SNP characters allows branch points and clade membership to be estimated with great precision, providing greater insight into epidemiological, ecological, and forensic questions.
Distinct roles of transcription factors TFIIIB and TFIIIC in RNA polymerase III transcription reinitiation
Authors: Ferrari Roberto , Rivetti Claudio , Acker Joël , Dieci Giorgio
Published: September 2004

Eukaryotic RNA polymerase (Pol) III is recruited to target promoters by a stable preinitiation complex containing transcription factors TFIIIC and TFIIIB. After the first transcription cycle, reinitiation proceeds through facilitated recycling, a process by which the terminating Pol III rapidly reloads onto the same transcription unit. Here, we show that Pol III is repeatedly recaptured
in vitro
by the first transcribed gene, even in the presence of a juxtaposed competitor promoter complex, thus suggesting that facilitated recycling is not merely due to a stochastic reassociation process favored by the small size of class III genes. The transcription factor requirements for facilitated reinitiation were investigated by taking advantage of Pol III templates that support both TFIIIC-dependent and TFIIIC-independent transcription. A TFIIIC-less transcription system, in which TFIIIB was reconstituted from recombinant TATA box-binding protein and Brf1 proteins and a crude fraction containing the Bdp1 component, was sufficient to direct efficient Pol III recycling on short (≈100 bp) class III genes. Unexpectedly, however, on longer (>300 bp) transcription units, reinitiation in the presence of TFIIIB alone was compromised, and TFIIIC was further required to reestablish a high reinitiation rate. Transcription reinitiation was also severely impaired when recombinant Bdp1 protein replaced the corresponding crude fraction in reconstituted TFIIIB. The data reveal an unexpected complexity in the Pol III reinitiation mechanism and suggest the existence of a handing-back network between Pol III, TFIIIC, and TFIIIB on actively transcribed class III genes.
Ten- to 50-nm-long quasi-ballistic carbon nanotube devices obtained without complex lithography
Authors: Javey Ali , Qi Pengfei , Wang Qian , Dai Hongjie
Published: September 2004

A simple method combining photolithography and shadow (or angle) evaporation is developed to fabricate single-walled carbon nanotube (SWCNT) devices with tube lengths of ≈10–50 nm between metal contacts. Large numbers of such short devices are obtained without the need of complex tools such as electron beam lithography. Metallic SWCNTs with lengths of ≈10 nm, near the mean free path of
l
op
≈ 15 nm for optical phonon scattering, exhibit nearly ballistic transport at high biases and can carry unprecedented 100-μA currents per tube. Semiconducting SWCNT fieldeffect transistors with ≈50-nm channel lengths are routinely produced to achieve quasi-ballistic operations for molecular transistors. The results demonstrate highly length-scaled and high-performance interconnects and transistors realized with SWCNTs.
Identification of key phosphorylation sites in the circadian clock protein KaiC by crystallographic and mutagenetic analyses
Authors: Xu Yao , Mori Tetsuya , Pattanayek Rekha , Pattanayek Sabuj , Egli Martin , Johnson Carl Hirschie
Published: September 2004

In cyanobacteria, KaiC is an essential hexameric clock protein that forms the core of a circadian protein complex. KaiC can be phosphorylated, and the ratio of phospho-KaiC to non-phospho-KaiC is correlated with circadian period. Structural analyses of KaiC crystals identify three potential phosphorylation sites within a 10-Å radius of the ATP binding regions that are at the T432, S431, and T426 residues in the KaiCII domains. When these residues are mutated by alanine substitution singly or in combination, KaiC phosphorylation is altered, and circadian rhythmicity is abolished. These alanine substitutions do not prevent KaiC from hexamerizing. Intriguingly, the ability of KaiC overexpression to repress its own promoter is also not prevented by alanine substitutions at these sites, implying that the capability of KaiC to repress its promoter is not sufficient to allow the clockwork to oscillate. The KaiC structure and the mutational analysis suggest that S431 and T426 may share a phosphate that can shuttle between these two residues. Because the phosphorylation status of KaiC oscillates over the daily cycle, and KaiC phosphorylation is essential for clock function as shown here, daily modulations of KaiC activity by phosphorylation at T432 and S431/T426 seem to be key components of the circadian clockwork in cyanobacteria.
A family of variably expressed outer-membrane proteins (Vomp) mediates adhesion and autoaggregation in
Bartonella quintana
Authors: Zhang Peng , Chomel Bruno B. , Schau Maureen K. , Goo Jeanna S. , Droz Sara , Kelminson Karen L. , George Smitha S. , Lerche Nicholas W. , Koehler Jane E.
Published: September 2004

Bartonella
species are fastidious, Gram-negative human pathogens that can persist in the host bloodstream for years and bind to and invade several types of host cells. For many pathogens, adhesion to host cells and extracellular matrix (ECM) components is a critical virulence determinant. Bacteria often vary expression of surface adhesins by phase or antigenic variation to subvert the host immune response and permit adaptive interaction with different host structures. We developed a macaque animal model for
Bartonella quintana
infection to detect changes in bacterial outer-membrane proteins (OMP) during prolonged bloodstream infection. We identified a gene family encoding four highly conserved, 100-kDa, variably expressed OMP (Vomp), two of which function as adhesins. The variable expression of Vomp family members appears to be mediated by deletion of one or more
vomp
genes during chronic bloodstream infection.
vomp
deletion was observed also in isolates from humans with chronic
B. quintana
infection. The Vomp are closely related to the afimbrial adhesin, YadA, a virulence factor of
Yersinia enterocolitica
. The surface-expressed Vomp contain conserved structural features of YadA, including collagen-binding motifs. We demonstrate that the
B. quintana
Vomp are multifunctional OMP involved in binding to collagen and autoaggregation: VompC confers the ability to bind collagen IV, and VompA is necessary and sufficient for autoaggregation. The
B. quintana
Vomp are members of the newly recognized family of YadA-like trimeric autotransporters; the Vomp constitute a multigene family, they are variably expressed, and different virulence properties are attributable to individual Vomp family members.
Behavioral and regulatory abnormalities in mice deficient in the NPAS1 and NPAS3 transcription factors
Authors: Erbel-Sieler Claudia , Dudley Carol , Zhou Yudong , Wu Xinle , Estill Sandi Jo , Han Tina , Diaz-Arrastia Ramon , Brunskill Eric W. , Potter S. Steven , McKnight Steven L.
Published: September 2004

Laboratory mice bearing inactivating mutations in the genes encoding the NPAS1 and NPAS3 transcription factors have been shown to exhibit a spectrum of behavioral and neurochemical abnormalities. Behavioral abnormalities included diminished startle response, as measured by prepulse inhibition, and impaired social recognition. NPAS1/NPAS3-deficient mice also exhibited stereotypic darting behavior at weaning and increased locomotor activity. Immunohistochemical staining assays showed that the NPAS1 and NPAS3 proteins are expressed in inhibitory interneurons and that the viability and anatomical distribution of these neurons are unaffected by the absence of either transcription factor. Adult brain tissues from NPAS3- and NPAS1/NPAS3-deficient mice exhibited a distinct reduction in reelin, a large, secreted protein whose expression has been reported to be attenuated in the postmortem brain tissue of patients with schizophrenia. These observations raise the possibility that a regulatory program controlled in inhibitory interneurons by the NPAS1 and NPAS3 transcription factors may be either substantively or tangentially relevant to psychosis.
Hyperleptinemia prevents lipotoxic cardiomyopathy in acyl CoA synthase transgenic mice
Authors: Lee Young , Naseem R. Haris , Duplomb Laurence , Park Byung-Hyun , Garry Daniel J. , Richardson James A. , Schaffer Jean E. , Unger Roger H.
Published: September 2004

The physiologic function of the progressive hyperleptinemia of diet-induced obesity is unknown. However, that lipotoxicity in nonadipose tissues of congenitally unleptinized obese rodents is far greater than in hyperleptinemic diet-induced obesity rodents has suggested an antilipotoxic role. To test this hypothesis, mice with severe lipotoxic cardiomyopathy, induced transgenically by cardiomyocyte-specific overexpression of the acyl CoA synthase (ACS) gene, were made hyperleptinemic by treatment with recombinant adenovirus containing the leptin cDNA. Normoleptinemic control ACS-transgenic mice developed severe dilated cardiomyopathy with thickened left ventricular walls and profound impairment of systolic function on echocardiogram; histologically, there was severe myofiber disorganization and interstitial fibrosis, with intracytoplasmic lipid vacuoles identifiable by electron microscope. By contrast, the hearts of hyperleptinemic ACS-transgenic mice appeared normal, with normal echocardiograms and cardiac triglyceride (TG) contents. Their lower myocardial TG content was ascribed primarily to profound lowering of plasma TG and free fatty acids; free fatty acids were 17% of normal at 8 weeks. Additionally, enhanced myocardial AMP-activated protein kinase phosphorylation may have increased fatty acid oxidation, thereby contributing to the lowering of lipid stores. We conclude that obesity-level hyperleptinemia protects the heart from lipotoxicity.
Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation
Authors: Olsen Jesper V. , Mann Matthias
Published: September 2004

MS-based proteomics usually involves the fragmentation of tryptic peptides (tandem MS or MS
2
) and their identification by searching protein sequence databases. In ion trap instruments fragments can be further fragmented and analyzed, a process termed MS/MS/MS or MS
3
. Here, we report that efficient ion capture in a linear ion trap leads to MS
3
acquisition times and spectra quality similar to those for MS
2
experiments with conventional 3D ion traps. Fragmentation of N- or C-terminal ions resulted in informative and low-background spectra, even at subfemtomol levels of peptide. Typically C-terminal ions are chosen for further fragmentation, and the MS
3
spectrum greatly constrains the C-terminal amino acids of the peptide sequence. MS
3
spectra allow resolution of ambiguities in identification, a crucial problem in proteomics. Because of the sensitivity and rapid scan rates of the linear ion trap, several MS
3
spectra per peptide can be obtained even when sequencing very complex mixtures. We calculate the probability that an experimental MS
3
spectrum originates from fragmentation of a given N- or C-terminal ion of a peptide under consideration. This MS
3
identification score can be combined with the MS
2
scores of the precursor peptide from existing search engines. When MS
3
is performed on the linear ion trap–Fourier transform mass spectrometer combination, accurate peptide masses further increase confidence in peptide identification.
Molecular dimension explored in evolution to promote proteomic complexity
Authors: Fernández Ariel , Berry R. Stephen
Published: September 2004

The architecture of present-day protein interaction networks depends on how protein associations evolved. Here, we explore how and why evolution-related mutations influence protein structure to promote protein associations, and thereby network development. We specifically address two questions: (
i
) How can protein folds remain conserved while proteins accommodate new binding partnerships as genes duplicate? (
ii
) What is the structural/molecular basis for hub proteins being the most likely to acquire new connections? The answers stem from the examination of the structure wrapping, or protection from water attack. Wrapping is shown to be a crucial consideration in the exploration and evolution of proteomic interactivity.
Learned and professional society libraries and copyright
Authors: Lees Nigel
Published: September 2004

An account is given of the effects of the EU Copyright Directive on the working of the library of a learned society and the changes in practices required to conform with it.
The open access scientific journal: an empirical study
Authors: Hedlund Turid , Gustafsson Tomas , Björk Bo‐Christer
Published: September 2004

The open access (OA) model for journals is compared to the open source principle for computer software. Since the early 1990s nearly 1,000 OA scientific journals have emerged – mostly as voluntary community efforts, although recently some professionally operating publishers have used author charges or institutional membership. This study of OA journals without author charges shows that their impact is still relatively small, but awareness of it is increasing. The average number of research articles per year is lower than for major scientific journals but the publication times are shorter.
The demand side of STM publishing: understanding value creation in new market units
Authors: Akie Ronald , Baron Joel , Berkooz Gahl
Published: September 2004

Five factors are shaping the STM publishing industry: the shift from a supply‐driven to a user‐driven industry; conversion of paper‐based products to an all electronic environment; commoditization of online publishing technology; consolidation; and saturation of the traditional buyer market. Opportunities exist for publishers who can leverage their traditional content assets into new products that help specifically defined user‐groups accelerate and enhance the value creation process in vertical industry sectors. Research conducted with one group of researchers within one group of functions in one given industry describes the results of such an approach.
CrossRef and the research experience
Authors: Brand Amy
Published: September 2004

CrossRef is an independent membership association for building collaborative publishing technologies. Its mission is to provide services that enable the scholar to reach source material easily; it focuses on methods that are best achieved through collective agreement among publishers. The CrossRef network now covers millions of journal articles and other content items from hundreds of publishers. This article looks at CrossRef's significance for the online research experience, four years after the launch of the CrossRef initiative.
Research practices and scholarly communication in the digital environment
Authors: Houghton John W. , Steele Colin , Henty Margaret
Published: September 2004

This paper examines changing research practices in the digital environment. A review of the literature and our own field research in Australia suggest that there is a new mode of knowledge production emerging, changing research practices and bringing new information access and dissemination needs. Adjustments will be required to accommodate these changes, but new opportunities are emerging for more cost‐effective and sustainable information access and dissemination. It will be necessary, however, to take an holistic approach and treat the creation, production and distribution of scholarly information, the management of information rights and access, systems of review and evaluation and the underlying infrastructure as parts of a single research information and scholarly communication system.
Book Reviews
Authors: Toledano Kathryn , Watkinson Anthony
Published: September 2004

Online Usage Statistics: A Publisher's Guide edited by Bernard Rous The Professional/Scholarly Publishing (PSP) Division of the Association of American Publishers, 2003. US$25 (members) or US$50 (non‐members)
ProViz: protein interaction visualization and exploration
Authors: Iragne Florian , Nikolski Macha , Mathieu Bertrand , Auber David , Sherman David
Published: September 2004

Summary: ProViz is a tool for the visualization of protein–protein interaction networks, developed by the IntAct European project. It provides facilities for navigating in large graphs and exploring biologically relevant features, and adopts emerging standards such as GO and PSI-MI.

Availability: ProViz is available under the GPL and may be freely downloaded. Source code and binaries are available at http://cbi.labri.fr/eng/proviz.htm

Contact:  david.sherman@labri.fr
SNPbox: a modular software package for large-scale primer design
Authors: Weckx Stefan , De Rijk Peter , Van Broeckhoven Christine , Del-Favero Jurgen
Published: September 2004

Summary: We developed a modular software package SNPbox that automates and standardizes the generation of PCR primers and is used in the strategy for constructing single nucleotide polymorphisms (SNPs) maps. In this strategy, the focus of primer design can be either on the validation of annotated public SNPs or on the SNP discovery in exon regions or extended genomic regions, both by resequencing. SNPbox relies on Primer3 for the primer design and combines this program with other publicly available software tools such as BLAST, Spidey and RepeatMasker, and newly developed algorithms. Primer conditions were chosen such that PCR amplifications are uniform for each PCR amplicon facilitating the use of high-throughput genetic platforms. SNPbox can also be used for the design of primer sets for mutation analysis, STR marker genotyping and microarray oligo design. Of the 2500 primer sets designed by SNPbox, 95% successfully amplified genomic DNA under uniform PCR conditions.

Availability: The software is available from the authors upon request.

Contact:  jurgen.delfavero@ua.ac.be

Supplementary information: SNPbox_supplement.
Detecting overlapping coding sequences with pairwise alignments
Authors: Firth Andrew E. , Brown Chris M.
Published: September 2004

Motivation: Overlapping gene coding sequences (CDSs) are particularly common in viruses but also occur in more complex genomes. Detecting such genes with conventional gene-finding algorithms can be difficult for several reasons. If an overlapping CDS is on the same read-strand as a known CDS, then there may not be a distinct promoter or mRNA. Furthermore, the constraints imposed by double-coding can result in atypical codon biases. However, these same constraints lead to particular mutation patterns that may be detectable in sequence alignments.

Results: In this paper, we investigate several statistics for detecting double-coding sequences with pairwise alignments—including a new maximum-likelihood method. We also develop a model for double-coding sequence evolution. Using simulated sequences generated with the model, we characterize the distribution of each statistic as a function of sequence composition, length, divergence time and double-coding frame. Using these results, we develop several algorithms for detecting overlapping CDSs.

The algorithms were tested on known overlapping CDSs and other overlapping open reading frames (ORFs) in the hepatitis B virus (HBV), Escherichia coli and Salmonella typhimurium genomes. The algorithms should prove useful for detecting novel overlapping genes—especially short coding ORFs in viruses.

Availability: Programs may be obtained from the authors.

Contact:  chris.brown@otago.ac.nz

Supplementary information:  http://biochem.otago.ac.nz/double.html
Evaluating putative chimeric sequences from PCR-amplified products
Authors: Gonzalez Juan M. , Zimmermann Johannes , Saiz-Jimenez Cesareo
Published: September 2004

Motivation: PCR amplification of highly homologous genes from complex DNA mixtures is known to generate a significant proportion of chimeric sequences. Ribosomal RNA genes are used for microbial species detection and identification in natural environments, and current assessments of microbial diversity are based on these sequences. Thus, chimeric sequences could lead to the discovery of non-existent microbial species and false diversity estimates.

Methods: In essence, our only source of information to decide if a sequence is chimeric or not is to compare it with known, non-chimeric sequences. Putative chimeric sequences were analyzed from sequence fragments of selected length (referred to as words) by comparing nucleotides at corresponding positions. Distances for each word between reference sequences (closely related to the tested sequence) were compared to the differences introduced by the tested sequence. The proposed strategy considers the actual variability existing in different regions throughout the analyzed sequences. The result is an efficient strategy for the evaluation of putative chimeric sequences.

Availability: A program computing the above procedure, Chimera and Cross-Over Detection and Evaluation (Ccode), is available at http://www.irnase.csic.es/users/jmgrau/index.html and http://www.rtphc.csic.es/download.html

Contact:  jmgrau@irnase.csic.es
The SSEA server for protein secondary structure alignment
Authors: Fontana Paolo , Bindewald Eckart , Toppo Stefano , Velasco Riccardo , Valle Giorgio , Tosatto Silvio C. E.
Published: September 2004

Summary: We present a web server that computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a library of domain folds. It can calculate global and local secondary structure element alignments. A combination of local and global alignment steps can be used to search for domains inside the query sequence or help in the discrimination of novel folds. Both the SCOP and PDB fold libraries, clustered at 95 and 40% sequence identity, are available for alignment.

Availability: The web server interface is freely accessible to academic users at http://protein.cribi.unipd.it/ssea/. The executable version and benchmarking data are available from the same web page.

Contact:  silvio@cribi.unipd.it
Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
Authors: Haft Daniel H. , Selengut Jeremy D. , Brinkac Lauren M. , Zafar Nikhat , White Owen
Published: September 2004

Motivation: The presence or absence of metabolic pathways and structures provide a context that makes protein annotation far more reliable. Compiling such information across microbial genomes improves the functional classification of proteins and provides a valuable resource for comparative genomics.

Results: We have created a Genome Properties system to present key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties.

Availability: Genome Properties can be found at http://www.tigr.org/Genome_Properties

Contact:  selengut@tigr.org

Supplementary information:  http://www.tigr.org/tigr-scripts/CMR2/genome_properties_references.spl
Layered Lithospheric Mantle Beneath the Ontong Java Plateau: Implications from Xenoliths in Alnöite, Malaita, Solomon Islands
Authors: ISHIKAWA AKIRA , MARUYAMA SHIGENORI , KOMIYA TSUYOSHI
Published: September 2004

A varied suite of mantle xenoliths from Malaita, Solomon Islands, was investigated to constrain the evolution of the mantle beneath the Ontong Java Plateau. Comprehensive petrological and thermobarometric studies make it possible to identify the dominant processes that produced the compositional diversity and to reconstruct the lithospheric stratigraphy in the context of a paleogeotherm. P–T estimates show that both peridotites and pyroxenites can be assigned to a shallower or deeper origin, separated by a garnet-poor zone of 10 km between 90 and 100 km. This zone is dominated by refractory spinel harzburgites (Fo91–92), indicating the occurrence of an intra-lithospheric depleted zone. Shallower mantle (∼Moho to 95 km) is composed of variably metasomatized peridotite with subordinate pyroxenite derived from metacumulates. Deeper mantle (∼95–120 km) is represented by pyroxenite and variably depleted peridotites that are unevenly distributed; the least-depleted garnet lherzolite (Fo90–91) lies just below the garnet-poor depleted zone (∼100–110 km), whereas the presence of pyroxenite is restricted to the deepest region (∼110–120 km), together with relatively Fe-enriched garnet lherzolite (Fo87–88). This depth-related variation (including the depleted zone) can be explained by assuming that the degree of melting for a basalt–peridotite hybrid source was systematically different at each level of arrival depth within a single adiabatically ascending mantle plume: (1) the depleted zone at the top of the mantle plume, where garnet was totally consumed in the residual solid; (2) an intermediate part of the plume dominated by the least-depleted garnet lherzolite just above the depth of the peridotite solidus; (3) the deepest pyroxenite-rich zone, whose petrochemical variation is best explained by the interaction between peridotite and normative quartz-rich basaltic melt, below the solidus of peridotite and liquidus of basalt. We explain the obvious lack of pyroxenites at shallower depths as the effective extraction of hybrid melt from completely molten basalt through the partially molten ambient peridotite, which caused the voluminous eruption of the Ontong Java Plateau basalts. From these interpretations, we conclude that the lithosphere forms a genetically unrelated two-layered structure, comprising shallower oceanic lithosphere and deeper impinged plume material, which involved a recycled basaltic component, now present as a pyroxenitic heterogeneity. This interpretation for the present lithospheric structure may explain the seismically anomalous root beneath the Ontong Java Plateau.
Management of Severe Burn Injuries in Neonates
Authors: Sun Bing-Wei , Zhou Xiao-Qin , Xia Chen-Lin , Chen Yu-Lin
Published: September 2004

Although rare, burns suffered by neonates can be fatal. Many complex difficulties are faced during the management of burns in neonates because of the neonate's complex physiological and pathological changes. We compiled a retrospective review from the treatment of four burned neonates (including a premature neonate). All four neonates suffered bath-related burns in the hospital as a result of careless nursing when being bathed. The total body surface area burned ranged from 1 to 60% in these patients, and all survived the burn injury. All the patients were treated in the Burn Intensive Care Unit with close co-operation of burn surgeons and neonatologists. Based on our experience as well as a review of literature, management recommendations are proposed as the following: 1) prompt and aggressive fluid resuscitation, 2) early administration of oxygen and keeping the patient warm, 3) application of specific biological dressing and recombinant human growth hormone if necessary, 4) establishment of a multidisciplinary team, and 5) removal of necrosis tissue early and aggressively. Furthermore, a very important issue is also discussed, which is about the prevention of newborn burns in the neonate unit in developing countries.