bluuebunny/crossref_metadata_2025 huggingface dataset:
Shock waves in a liquid containing small gas bubbles
Authors: Kameda Masaharu , Matsumoto Yoichiro
Published: July 2002

Numerical and experimental studies of the transient shock wave phenomena in a liquid containing non-condensable gas bubbles are presented. In the numerical analysis, individual bubbles are tracked to estimate the effect of volume oscillations on the wave phenomena. Thermal processes inside each bubble, which have significant influence on the volume oscillation, are calculated directly using full equations for mass, momentum and energy conservation, and those results are combined with the averaged conservation equations of the bubbly mixture to simulate the propagation of the shock wave. A silicone oil/nitrogen bubble mixture, in which the initial bubble radius is about 0.6 mm and the gas volume fraction is 0.15% – 0.4%, is used in the shock tube experiments. The inner diameter of the shock tube is chosen to be 18 mm and 52 mm in order to investigate the multidimensional effects on the wave phenomena. In a fairly uniform bubbly mixture, the experimental results agree well with the numerical ones computed using a uniform spatial distribution of bubbles. On the other hand, in all the other experiments, the bubbles in the shock tubes are not distributed uniformly, being relatively concentrated along the axis of the tube. This non-uniformity substantially alters the profile of the shock waves. The numerical predictions where such a distribution is taken into account agree well with those experimental data.
On the role of viscosity in shear instabilities
Authors: Villermaux Emmanuel
Published: July 2002

This paper aims at investigating the viscous corrections to mode selection and associated growth rate in the inflectional instability of shear layers. While, in the inviscid limit, the most unstable mode and its growth rate are fully determined by the initial thickness of the layer 2L and the velocity jump 2u it experiences, we show here that these quantities are modified by a factor {1+[(a/0.2)/Re]2}−1/2 in the small Reynolds number Re=uL/ν limit, with a a constant depending on the detailed shape of the initial velocity profile. This result agrees well with early numerical computations of Betchov and Szewczyk [Phys. Fluids 6, 1391 (1963)] and its interest is discussed in several different contexts.
Proper orthogonal decomposition and low-dimensional models for driven cavity flows
Authors: Cazemier W. , Verstappen R. W. C. P. , Veldman A. E. P.
Published: July 2002

A proper orthogonal decomposition (POD) of the flow in a square lid-driven cavity at Re=22,000 is computed to educe the coherent structures in this flow and to construct a low-dimensional model for driven cavity flows. Among all linear decompositions, the POD is the most efficient in the sense that it captures the largest possible amount of kinetic energy (for any given number of modes). The first 80 POD modes of the driven cavity flow are computed from 700 snapshots that are taken from a direct numerical simulation (DNS). The first 80 spatial POD modes capture (on average) 95% of the fluctuating kinetic energy. From the snapshots a motion picture of the coherent structures is made by projecting the Navier–Stokes equation on a space spanned by the first 80 spatial POD modes. We have evaluated how well the dynamics of this 80-dimensional model mimics the dynamics given by the Navier–Stokes equations. The results can be summarized as follows. A closure model is needed to integrate the 80-dimensional system at Re=22,000 over long times. With a simple closure the energy spectrum of the DNS is recovered. A linear stability analysis shows that the first (Hopf) bifurcation of the 80-dimensional dynamical system takes place at Re=7,819. This number lies about 0.7% above the critical Reynolds number given in Poliashenko and Aidun [J. Comput. Phys. 121, 246 (1995)] and differs by about 2% from the first instability found with DNS. In addition to that, the unstable eigenvector displays the correct mechanism: a centrifugal instability of the primary eddy, however, the frequency of the periodic solution after the first bifurcation differs from that of the DNS. The stability of periodic solutions of the 80-dimensional system is analyzed by means of Floquet multipliers. For Re=11,188−11,500 the ratio of the two periods of the stable 2-periodic solution of the 80-dimensional system is approximately the same as the ratio of the two periods of the 2-periodic solution of the DNS at Re=11,000. For slightly higher Reynolds numbers both solutions lose one period. The periodic solutions of the dynamical system at Re=11,800 and the DNS at Re=12,000 have approximately the same period and have qualitatively the same behavior.
Spectral estimation of plasma fluctuations. I. Comparison of methods
Authors: Riedel Kurt S. , Sidorenko Alexander , Thomson David J.
Published: July 2002

The relative root mean squared errors (RMSE) of nonparametric methods for spectral estimation is compared for microwave scattering data of plasma fluctuations. These methods reduce the variance of the periodogram estimate by averaging the spectrum over a frequency bandwidth. As the bandwidth increases, the variance decreases, but the bias error increases. The plasma spectra vary by over four orders of magnitude, and therefore, using a spectral window is necessary. The smoothed tapered periodogram is compared with the adaptive multiple taper methods and hybrid methods. It is found that a hybrid method, which uses four orthogonal tapers and then applies a kernel smoother, performs best. For 300 point data segments, even an optimized smoothed tapered periodogram has a 24% larger relative RMSE than the hybrid method. Two new adaptive multitaper weightings which outperform Thomson’s original adaptive weighting are presented.
Spectral estimation of plasma fluctuations. II. Nonstationary analysis of edge localized mode spectra
Authors: Riedel Kurt S. , Sidorenko Alexander , Bretz Norton , Thomson David J.
Published: July 2002

Several analysis methods for nonstationary fluctuations are described and applied to the edge localized mode (ELM) instabilities of limiter H-mode plasmas. The microwave scattering diagnostic observes poloidal kθ values of 3.3 cm−1, averaged over a 20 cm region at the plasma edge. A short autoregressive filter enhances the nonstationary component of the plasma fluctuations by removing much of the background level of stationary fluctuations. Between ELM’s, the spectrum predominantly consists of broadband 300–700 kHz fluctuations propagating in the electron diamagnetic drift direction, indicating the presence of a negative electric field near the plasma edge. The time-frequency spectrogram is computed with the multiple taper technique. By using the singular value decomposition of the spectrogram, it is shown that the spectrum during the ELM is broader and more symmetric than that of the stationary spectrum. The ELM period and the evolution of the spectrum between ELM’s varies from discharge to discharge. For the discharge under consideration which has distinct ELM’s with a 1 ms period, the spectrum has a maximum in the electron drift direction which relaxes to a near constant value in the first half millisecond after the end of the ELM and then grows slowly. In contrast, the level of the fluctuations in the ion drift direction increases exponentially by a factor of 8 in the 5 ms after the ELM. High frequency precursors are found which occur 1 ms before the ELM’s and propagate in the ion drift direction. These precursors are very short (∼10 μs), coherent bursts, and they predict the occurrence of an ELM with a high success rate. A second detector, measuring fluctuations 20 cm from the plasma edge with kθ values of 8.5 cm−1, shows no precursor activity. The spectra in the ion drift direction are very similar on both detectors, while the ‘‘electron’’ spectrum level is significantly larger on this second detector.
Diffusion across a layered medium and relation to transport in thermonuclear plasmas
Authors: Lopes Cardozo N. J. , Peters M.
Published: July 2002

The generic characteristics of diffusion in a medium exhibiting strong variations of the diffusivity are considered. The varying diffusivity is parametrized by alternating layers of high and low diffusivity. The limiting case is considered that the insulating layers determine the net transport. Some salient features of tokamak transport, such as the fact that perturbative experiments yield a higher diffusivity than a steady-state power balance, are shown to be a natural result of the inhomogeneity. The importance of a possible inhomogeneous diffusivity for the comparison of measurements with theoretical expressions for the diffusivity is discussed.
Acceleration of electrons in the vicinity of a lower hybrid waveguide array
Authors: Fuchs V. , Goniche M. , Demers Y. , Jacquet P. , Mailloux J.
Published: July 2002

The interaction of tokamak plasma edge electrons with the electric near field generated by a lower hybrid slow wave antenna is studied. Antenna field spectra of interest for current drive and/or plasma heating have lobes at high-n∥ values (n∥≳30) intense enough for resonant acceleration of the relatively cold (∼25 eV) edge electrons. For waveguide electric fields, typically around 3 kV/cm, the higher-order modes overlap in the phase-space [B. V. Chirikov, Phys. Rep. 52, 263 (1979)], so that electron global stochasticity is induced. For Tokamak de Varennes (TdeV) [Décoste et al., Phys. Plasmas 1, 1497 (1994)] conditions and for 90° waveguide phasing, the stochastic limit in the current drive direction is about 2 keV, determined by the last overlapping mode. The progress of electrons through accessible phase space is very efficient: the TdeV 32 waveguide array can accelerate the electrons to the possible limit. An area-preserving map is derived to study the electron dynamics. Surface-of-section plots fully confirm the resonant wave-particle nature of the interaction.
Thomas–Fermi-like and average atom models for dense and hot matter
Authors: Fromy P. , Deutsch C. , Maynard G.
Published: July 2002

All the Thomas–Fermi approaches to the thermodynamics and atomic physics properties of dense and ionized matter consisting of a single element are systematically derived and compared within a density-functional theoretical framework. The corresponding results are contrasted to those of the average atom model by using similar approximations for exchange, correlation, and gradient corrections. Emphasis is led on equations of state, ionization, level shifts, and radial moments. The same numerical algorithms are used to unravel similar trends or identify specific ones, in terms of density and temperature variations. The most sophisticated Thomas–Fermi–Dirac–Weizäcker method yields the closest results to the hybrid average atom model using quantized bound states. Parameters ranges of potential interest for inertially confined thermonuclear fusion stress out density in the 0.1–10 times the solid, and temperature up to 10 keV.
Nonlinear dynamics of a beam-driven magnetic plasma: Streaming or mass motion
Authors: Mohanty J. N. , Naik Antaryami
Published: July 2002

Explicit results pertaining to nonlinear oscillations in a magnetoactive beam–plasma system that shows transient or streaming phenomena are analytically presented. The nonlinear differential equation is formulated and solved in terms of a modified elliptic integral of motion. The phase-space mappings, and their striking features both in strong streaming and nonstreaming situations, are shown. The new features concerning streaming plasma analysis are illustrated in the form of frequency modulation, especially at the onset of chaos. The diminishing trend of modulated frequency in the strong streaming regions is concluded. The findings may have important implications for magnetospheric and cosmic plasma settings where beam plasma interactions exist.
One-dimensional full-wave description of plasma emission and absorption in the ion cyclotron range of frequency in tokamaks
Authors: Fraboulet David , Bécoulet Alain , Nguyen Frédéric
Published: July 2002

To maintain the ignition state in a tokamak fusion reactor, a control must be performed on the population of alpha-products, and this implies the ability to diagnose those α-particles. It is studied here whether the detection of emission radiated in the ion cyclotron range of frequency by a reactor plasma can provide useful information concerning fusion products, especially concerning their density profile. It is shown that the detection of the radiation emitted by the fast alpha particules along their cyclotron motion can give access to moments of their distribution function. This requires one to compute the phase of the emitted field, using a full-wave approach. Such a technique allows one to set in a convenient way the inverse problem of the determination of the emitting α-particles distribution through the radiation detection. A brief analysis of the expected situation in a reactor-relevant plasma is given. In parallel, the one-dimensional full-wave code developed in this frame is also useful for studying the physics of fast wave plasma heating. It enables one to take into account the mode conversion of the fast wave into the ion Bernstein wave that appears near each ion cyclotron resonance. Results show that higher order terms may significantly alter the energy partitioning, in hot plasma cases involving mode conversion heating and/or ion cyclotron high harmonics heating.
Correlated stopping of relativistic electrons in superdense plasmas
Authors: Deutsch C. , Fromy P.
Published: July 2002

The electromagnetic stopping of intense and relativistic electron beams (REB) arising from femtosecond lasers interacting with a precompressed deuterium+tritium (DT) fuel is investigated within the Bohr–Fermi formalism with a large impact parameter. Dynamical intrabeam correlations through long-range collision with target electrons are shown to be quantitatively significant for various arrangements of projectile electrons and the overall REB penetration in the DT fuel. One thus expects much shorter stopping ranges yielding an easier access to fuel ignition through hot spots production.
The distribution of flares, statistics of magnetohydrodynamic turbulence and coronal heating
Authors: Einaudi G. , Velli M.
Published: July 2002

In this paper theoretical evidence in favor of the hypothesis that coronal dissipation occurs in bursts at very small spatial scales is presented. Each individual burst, though unobservable and energetically insignificant, is thought to represent the building block of coronal activity. In this framework, a large number of coherently triggered bursts is what appears as one of the many observed solar atmospheric events (i.e., blinkers, heating events, explosive events, flashes, microflares, flares,…). Histograms of such events, when computed, in terms of total energy, duration and peak luminosity appear to display power-law behavior. Simulations of the energy dissipation in the simplest possible forced magnetohydrodynamic (MHD) system, admitting reconnection events, indeed displays such kind of behavior: dissipative events of varying intensity, size and duration may be defined, whose distributions follow power laws. The meaning of cellular automaton models, introduced to describe the power-law statistics of observed energetic events on the Sun, i.e., solar flares, is then discussed. Finally, a minimal set of constraints necessary to render such automaton models more relevant for the description of dynamic phenomena described by magnetohydrodynamic equations is introduced.
Quasilocalized charge approximation in strongly coupled plasma physics
Authors: Golden Kenneth I. , Kalman Gabor J.
Published: July 2002

The quasilocalized charge approximation (QLCA) was proposed in 1990 [G. Kalman and K. I. Golden, Phys. Rev. A 41, 5516 (1990)] as a formalism for the analysis of the dielectric response tensor and collective mode dispersion in strongly coupled Coulomb liquids. The approach is based on a microscopic model in which the charges are quasilocalized on a short-time scale in local potential fluctuations. The authors review the application of the QLC approach to a variety of systems which can exhibit strongly coupled plasma behavior: (i) the one-component plasma (OCP) model in three dimensions (e.g., laser-cooled trapped ions) and (ii) in two dimensions (e.g., classical 2D electron liquid trapped above the free surface of liquid helium), (iii) binary ionic mixture in a neutralizing uniform background (e.g., carbon–oxygen white dwarf interiors), (iv) charged particle bilayers (e.g., semiconductor electronic bilayers), and (v) charged particles in polarizable background (e.g., laboratory dusty plasmas).
Second-order radio frequency kinetic theory with applications to flow drive and heating in tokamak plasmas
Authors: Jaeger E. F. , Berry L. A. , Batchelor D. B.
Published: July 2002

A comprehensive kinetic theory is developed to treat radio frequency (rf) driven plasma flow in one-dimensional geometry. The kinetic equation is expanded to second order in the perturbing rf electric field. No assumption is made regarding the smallness of the ion Larmor radius relative to wavelength. Moments of the second-order distribution function give time-averaged expressions for the rf-driven particle transport, forces, and heating, including the wave kinetic flux. On the transport time scale, the rf force in the poloidal direction is balanced by neoclassical viscosity, and the force in the radial direction is balanced by ambipolar electric fields. Comparison is made with previous theories which have relied on incompressible fluid approximations and a Reynolds stress model for the rf pressure. Substantial differences are seen in situations involving the ion Bernstein wave, which is compressional in nature. Linear electron Landau damping and magnetic pumping, by themselves, do not lead to significant poloidal flow. But ion cyclotron damping of either fast magnetosonic waves or ion Bernstein waves can drive significant flow at power levels typical of plasma heating experiments.
A hydrocarbon reaction model for low temperature hydrogen plasmas and an application to the Joint European Torus
Authors: Alman D. A. , Ruzic D. N. , Brooks J. N.
Published: July 2002

A model of collisional processes of hydrocarbons in hydrogen plasmas has been developed to aid in computer modeling efforts relevant to plasma–surface interactions. It includes 16 molecules (CH up to CH4, C2H to C2H6, and C3H to C3H6) and four reaction types (electron impact ionization/dissociative ionization, electron impact dissociation, proton impact charge exchange, and dissociative recombination). Experimental reaction rates or cross sections have been compiled, and estimates have been made for cases where these are not available. The proton impact charge exchange reaction rates are calculated from a theoretical model using molecular polarizabilities. Dissociative recombination rates are described by the equation A/TB where parameter A is fit using polarizabilities and B is estimated from known reaction rates. The electron impact ionization and dissociation cross sections are fit to known graphs using four parameters: threshold energy, maximum value of the cross section, energy at the maximum, and a constant for the exponential decay as energy increases. The model has recently been used in an analysis of the Joint European Torus [P. H. Rebut, R. J. Bickerton, and B. E. Keen, Nucl. Fusion 25, 1011 (1985)] MARK II carbon inner divertor using the WBC Monte Carlo impurity transport code. The updated version of WBC, which includes the full set of hydrocarbon reactions, helps to explain an observed asymmetry in carbon deposition near the divertor.
Review of electrical resistivity measurements of dense aluminum and comparison to theory
Authors: Benage John F.
Published: July 2002

Four recent experiments that measured the electrical resistivity of aluminum at conditions where the aluminum is in a dense, strongly coupled, plasma state have been analyzed. The properties of dense, strongly coupled plasmas cannot be treated using standard plasma theory, which treats the correlations among particles as a small effect. Many theories have been developed which predict the properties of such plasmas, but there is little experimental data with which to compare. These recent experiments provide data for a comprehensive comparison of electrical resistivity with dense plasma theories. The experiments were carried out under a wide range of conditions, from temperatures <1 eV up to 25 eV and densities from nearly solid to <1% solid. The data from these experiments are compared with various theoretical models, the best of which give predictions consistent with the data for most of the experimental conditions, but not all. A discussion of yet unresolved issues is also presented.
Spectral stability of Alfvén filament configurations
Authors: Bergmans J. , Kuvshinov B. N. , Lakhin V. P. , Schep T. J.
Published: July 2002

The two-fluid plasma equations that describe nonlinear Alfvén perturbations have singular solutions in the form of current–vortex filaments. These filaments are analogous to point vortices in ideal hydrodynamics and geostrophic fluids. In this work the spectral (linear) stability of current–vortex filament configurations is analyzed and compared with the results obtained for point vortices in ideal hydrodynamics and the Charney-Hasegawa-Mima equation. We consider single rows, double rows—von Kármán streets—and single and double rings of vortices. In all cases the stability picture for the current–vortex filaments is remarkably different from that of the other two models, which can be recovered as limiting cases of the two-fluid Alfvén model. New regions of perturbations against which the system is stable are identified and the dependence on physical parameters is described.
Far UV pulsed laser melting of silicon
Authors: Gorodetsky G. , Kanicki Jerzy , Kazyaka T. , Melcher R. L.
Published: July 2002

Calorimetric, acoustic, and morphological studies of silicon irradiated with intense 14-ns, 193-nm excimer laser pulses are reported. To within the experimental uncertainty, the entire radiation absorbed is converted to heat at all fluences. The volume changes on melting leads to enhanced acoustic wave generation. The morphology of the surface damage is consistent with the existence of both standing surface acoustic waves and of capillary waves.
External field enhanced optical bistability in nematic liquid crystals
Authors: Ong Hiap Liew
Published: July 2002

The exact solution is obtained for describing the external field effects in the optically induced molecular reorientation and bistability in a homeotropic nematic liquid crystal. With a low external field applied transverse or parallel to the laser propagation direction, optical bistability can always be suppressed or enhanced and hence can be seen in all existing nematics at a low laser power (typically < 1 kW/cm2). The fields corresponding to the tricritical point are obtained.
Experimental observation of polarization instability in a birefringent optical fiber
Authors: Trillo S. , Wabnitz S. , Stolen R. H. , Assanto G. , Seaton C. T. , Stegeman G. I.
Published: July 2002

We present the first experimental demonstration of spatial instability in the nonlinear evolution of the state of polarization of an intense light beam in a birefringent Kerr-like medium. As the peak power crosses the threshold for the instability, we observed strong intensity-dependent power transfer between the two counter-rotating circularly polarized waves propagating along a birefringent optical fiber. The experimental results agree well with the theory.
Heteroepitaxial growth of InP directly on Si by low pressure metalorganic chemical vapor deposition
Authors: Lee M. K. , Wuu D. S. , Tung H. H.
Published: July 2002

Heteroepitaxial growth of InP on Si by low pressure metalorganic chemical vapor deposition is reported. The trimethylindium-trimethylphosphine adduct was used as the In source in this study and PH3 as the source of P. From x-ray and scanning electron microscopy examinations, good crystallinity InP epilayers with mirrorlike surfaces can be grown directly on (100) and (111) Si substrates. The carrier concentration profile shows that the carrier distribution in the InP epilayer is very uniform. The efficient photoluminescence compared with that of InP homoepitaxy shows that the InP/Si epilayers are of good quality.
Improved flatness in GaAs/AlGaAs heterointerfaces grown by flow-rate modulation epitaxy
Authors: Kobayashi Naoki , Horikoshi Yoshiji
Published: July 2002

This letter deals with the atomically flat interfaces at GaAs/AlGaAs heterojunctions grown by a modified metalorganic chemical vapor deposition, flow-rate modulation epitaxy. Single quantum wells show low-temperature photoluminescence with narrower linewidths than those grown by conventional metalorganic chemical vapor deposition. An x-ray diffraction spectrum of (GaAs)2 (AlAs)2 superlattices exhibits no forbidden (003) and (001) diffractions, suggesting that the interfaces are fairly flat.
Ion milled tips for scanning tunneling microscopy
Authors: Biegelsen D. K. , Ponce F. A. , Tramontana J. C. , Koch S. M.
Published: July 2002

Ion milling of electrochemically etched tungsten tips is shown to improve the characteristics for scanning tunneling microscopy. The primary mechanism for the enhancement of tip reliability is identified to be the removal of a residual oxide. A greatly decreased radius of curvature is also achieved without significantly changing the macrostructural geometry of the tip.
Relaxation of strained-layer semiconductor structures via plastic flow
Authors: Dodson Brian W. , Tsao Jeffrey Y.
Published: July 2002

An outstanding puzzle concerning strained-layer semiconductors is that metastable structures can be grown in which exact coherence with the lattice is apparently conserved in layers much thicker than the equilibrium critical thickness. Using standard descriptions of dislocation dynamics and relaxation via plastic flow, a model for the relaxation of an initially coherent metastable strained layer is developed. This model is applied to relief of mismatch strain in the SiGe/Si(100) system, and good agreement with experimental data is found. Furthermore, the combined effect of relaxation kinetics and finite instrumental resolution on the observed critical thickness was calculated. The results successfully reproduce experimental data on metastable critical thickness in the SiGe/Si(100) system.
First GaInAsP-InP double-heterostructure laser emitting at 1.27 μm on a silicon substrate
Authors: Razeghi M. , Defour M. , Omnes F. , Maurel Ph. , Chazelas J. , Brillouet F.
Published: July 2002

We report the first successful room-temperature GaInAsP-InP double-heterostructure laser emitting at 1.27 μm, grown by low-pressure metalorganic chemical vapor deposition on a Si substrate. A pulsed threshold current density of 10 kA/cm2 at room temperature with an external quantum efficiency of 10% per facet and an output power of 20 mW (for an oxide-defined stripe geometry with 12 μm stripe width and 250 μm cavity length) has been measured. The first aging test in pulse operation shows an increase of threshold current of only 7% for a cumulative time of 80 s at room temperature.
The NK1 receptor mediates both the hyperalgesia and the resistance to morphine in mice lacking noradrenaline
Authors: Jasmin Luc , Tien Duc , Weinshenker David , Palmiter Richard D. , Green Paul G. , Janni Gabriella , Ohara Peter T.
Published: July 2002

Noradrenaline (NA), a key neurotransmitter of the endogenous pain inhibitory system, acutely inhibits nociceptive transmission (including that mediated by substance P), potentiates opioid analgesia, and underlies part of the antinociceptive effects of the widely prescribed tricyclic antidepressants. Lesions of noradrenergic neurons, however, result in either normal or reduced pain behavior and variable changes in morphine antinociception, undermining the proposed association between noradrenaline (NA) deficiency and chronic pain (hyperalgesia). We used mice lacking the gene coding for dopamine β-hydroxylase, the enzyme responsible for synthesis of NA from dopamine, to reexamine the consequences of a lack of NA on pain behavior. Here, we show that absence of NA in the central nervous system results in a substance P-mediated chronic hyperalgesia (decreased nociceptive threshold) to thermal, but not mechanical, stimuli and decreased efficacy of morphine. Contrary to studies that show substance P-mediated hyperalgesia requires intense stimuli, we found that even a mild stimulus is sufficient to evoke substance P-dependent hyperalgesia in the NA-deficient mice. Restoring central NA normalized both the nociceptive threshold and morphine efficacy, which is consistent with a tonic inhibitory effect of NA on nociceptive transmission. Unexpectedly, however, antagonists to the substance P receptor (the NK1 receptor) could achieve the same effect as NA replacement. We conclude that when unopposed by NA, substance P acting at the NK1 receptor causes chronic thermal hyperalgesia, and that the reduced opioid efficacy associated with a lack of NA is due to increased NK1-receptor stimulation.
Atmospheric carbon dioxide levels for the last 500 million years
Authors: Rothman Daniel H.
Published: July 2002

The last 500 million years of the strontium-isotope record are shown to correlate significantly with the concurrent record of isotopic fractionation between inorganic and organic carbon after the effects of recycled sediment are removed from the strontium signal. The correlation is shown to result from the common dependence of both signals on weathering and magmatic processes. Because the long-term evolution of carbon dioxide levels depends similarly on weathering and magmatism, the relative fluctuations of CO
2
levels are inferred from the shared fluctuations of the isotopic records. The resulting CO
2
signal exhibits no systematic correspondence with the geologic record of climatic variations at tectonic time scales.
Physical and genetic mapping of barley (
Hordeum vulgare
) germin-like cDNAs
Authors: Druka Arnis , Kudrna David , Kannangara C. Gamini , von Wettstein Diter , Kleinhofs Andris
Published: July 2002

Germin with oxalate oxidase and superoxide dismutase activity is a homohexamer of six manganese-containing interlocked β-jellyroll monomers with extreme resistance to heat and proteolytic degradation [Woo, E.-J., Dunwell, J. M., Goodenough, P. W., Marvier, A. C. & Pickersill, R. W. (2000)
Nat. Struct. Biol.
7, 1036–1038]. This structure is conserved in germin-like proteins (GLPs) with other enzymatic functions and characteristic for proteins deposited in plant cell walls in response to pathogen attack and abiotic stress. Comparative nucleotide and amino acid sequence analyses of 49,610 barley expressed sequence tags identified 124 germin and germin-like cDNAs, which distributed into five subfamilies designated
Hv
GER-I to
Hv
GER-V. Representative cDNAs for these subfamilies hybridized to 67 bacterial artificial chromosome (BAC) clones from a library containing 6.3 genomic equivalents. Twenty-six BAC clones hybridized to the subfamily IV probe and identified a gene-rich region including clone 418E1 of 96 kb encoding eight GLPs (i.e., 1 gene per 12 kb). This BAC clone lacked highly repeated sequences and mapped to the subtelomeric region of the long arm of chromosome 4(4H). Among the six genes of the contig expressed in leaves, one specifies a protein known to be associated with papilla formation in the epidermis upon powdery mildew infection. Three structural genes for oxalate oxidase are present in subfamily I and eight GLPs of various functions in the other subfamilies. These genes map at loci in chromosomes 1(7H), 2 (2H), 3(3H), 4(4H), and 7(5H). Some are present on a single BAC clone. The results are discussed in relation to cereal genome organization.
Human AML1/MDS1/EVI1 fusion protein induces an acute myelogenous leukemia (AML) in mice: A model for human AML
Authors: Cuenco Grace M. , Nucifora Giuseppina , Ren Ruibao
Published: July 2002

The human t(3;21)(q26;q22) translocation is found as a secondary mutation in some cases of chronic myelogenous leukemia during the blast phase and in therapy-related myelodysplasia and acute myelogenous leukemia. One result of this translocation is a fusion between the
AML1
,
MDS1
, and
EVI1
genes, which encodes a transcription factor of approximately 200 kDa. The role of the
AML1/MDS1/EVI1
(
AME
) fusion gene in leukemogenesis is largely unknown. In this study, we analyzed the effect of the
AME
fusion gene
in vivo
by expressing it in mouse bone marrow cells via retroviral transduction. We found that mice transplanted with
AME
-transduced bone marrow cells suffered from an acute myelogenous leukemia (AML) 5–13 mo after transplantation. The disease could be readily transferred into secondary recipients with a much shorter latency. Morphological analysis of peripheral blood and bone marrow smears demonstrated the presence of myeloid blast cells and differentiated but immature cells of both myelocytic and monocytic lineages. Cytochemical and flow cytometric analysis confirmed that these mice had a disease similar to the human acute myelomonocytic leukemia. This murine model for AME-induced AML will help dissect the molecular mechanism of AML and the molecular biology of the
AML1, MDS1,
and
EVI1
genes.
Adapter proteins SLP-76 and BLNK both are expressed by murine macrophages and are linked to signaling via Fcγ receptors I and II/III
Authors: Bonilla Francisco A. , Fujita Ross M. , Pivniouk Vadim I. , Chan Andrew C. , Geha Raif S.
Published: July 2002

The SLP-76 (Src homology 2 domain-containing leukocyte protein of 76 kDa) adapter protein is expressed in T cells and myeloid cells, whereas its homologue BLNK (B cell linker protein) is expressed in B cells. SLP-76 and BLNK link immunoreceptor tyrosine-based activation motif-containing receptors to signaling molecules that include phospholipase C-γ, mitogen-activated protein kinases, and the GTPases Ras and Rho. SLP-76 plays a critical role in T cell receptor, FcɛRI and gpVI collagen receptor signaling, and participates in signaling via FcγR and killer cell inhibitory receptors. BLNK plays a critical role in B cell receptor signaling. We show that murine bone marrow-derived macrophages express both SLP-76 and BLNK. Selective ligation of FcγRI and FcγRII/III resulted in tyrosine phosphorylation of both SLP-76 and BLNK. SLP-76−/−bone marrow-derived macrophages display FcγR-mediated tyrosine phosphorylation of Syk, phospholipase C-γ2, and extracellular signal regulated kinases 1 and 2, and normal FcγR-dependent phagocytosis. These data suggest that both SLP-76 and BLNK are coupled to FcγR signaling in murine macrophages.
Nitric oxide down-regulates brain-derived neurotrophic factor secretion in cultured hippocampal neurons
Authors: Canossa Marco , Giordano Emanuele , Cappello Silvia , Guarnieri Carlo , Ferri Sergio
Published: July 2002

The regulation of neurotrophin (NT) secretion is critical for many aspects of NT-mediated neuronal plasticity. Neurons release NTs by activity-regulated secretion pathways, initiated either by neurotransmitters and/or by existing NTs by a positive-feedback mechanism. This process depends on calcium release from intracellular stores. Little is known, however, about potential pathways that down-regulate NT secretion. Here we demonstrate that nitric oxide (NO) induces a rapid down-regulation of brain-derived neurotrophic factor (BDNF) secretion in cultured hippocampal neurons. Similar effects occur by activating a downstream target of intracellular NO, the soluble guanylyl cyclase, or by increasing the levels of its product, cGMP. Furthermore, down-regulation of BDNF secretion is mediated by cGMP-activated protein kinase G, which prevents calcium release from inositol 1,4,5-trisphosphate-sensitive stores. Our data indicate that the NO/cGMP/protein kinase G pathway represents a signaling mechanism by which neurons can rapidly down-regulate BDNF secretion and suggest that, in hippocampal neurons, NT secretion is finely tuned by both stimulatory and inhibitory signals.
Chains of magnetite crystals in the meteorite ALH84001: Evidence of biological origin
Authors: Friedmann E. Imre , Wierzchos Jacek , Ascaso Carmen , Winklhofer Michael
Published: July 2002

The presence of magnetite crystal chains, considered missing
evidence for the biological origin of magnetite in ALH84001
[Thomas-Keprta, K. L., Bazylinski, D. A., Kirschvink,
J. L., Clemett, S. J., McKay, D. S., Wentworth, S.
J., Vali, H., Gibson, E. K., Jr., & Romanek, C. S. (2000)
Geochim. Cosmochim. Acta
64, 4049–4081], is
demonstrated by high-power stereo backscattered scanning electron
microscopy. Five characteristics of such chains (uniform crystal size
and shape within chains, gaps between crystals, orientation of
elongated crystals along the chain axis, flexibility of chains, and a
halo that is a possible remnant of a membrane around chains), observed
or inferred to be present in magnetotactic bacteria but incompatible
with a nonbiological origin, are shown to be present. Although it is
unlikely that magnetotactic bacteria were ever alive in ALH84001,
decomposed remains of such organisms could have been deposited in
cracks in the rock while it was still on the surface on Mars.
Expression of the telomerase catalytic subunit, hTERT, induces resistance to transforming growth factor β growth inhibition in p16
INK4A
(−) human mammary epithelial cells
Authors: Stampfer Martha R. , Garbe James , Levine Gerri , Lichtsteiner Serge , Vasserot Alain P. , Yaswen Paul
Published: July 2002

Failures to arrest growth in response to senescence or
transforming growth factor β (TGF-β) are key derangements
associated with carcinoma progression. We report that activation of
telomerase activity may overcome both inhibitory pathways. Ectopic
expression of the human telomerase catalytic subunit, hTERT, in
cultured human mammary epithelial cells (HMEC) lacking both telomerase
activity and p16
INK4A
resulted in gaining the ability to
maintain indefinite growth in the absence and presence of TGF-β. The
ability to maintain growth in TGF-β was independent of telomere
length and required catalytically active telomerase capable of telomere
maintenance
in vivo
. The capacity of ectopic hTERT to
induce TGF-β resistance may explain our previously described gain of
TGF-β resistance after reactivation of endogenous
telomerase activity in rare carcinogen-treated HMEC. In those HMEC that
overcame senescence, both telomerase activity and TGF-β resistance
were acquired gradually during a process we have termed conversion.
This effect of hTERT may model a key change occurring during
in vivo
human breast carcinogenesis.
Modulation of protein–protein interactions by synthetic receptors: Design of molecules that disrupt serine protease–proteinaceous inhibitor interaction
Authors: Park Hyung Soon , Lin Qing , Hamilton Andrew D.
Published: July 2002

In the present article we describe the design and evaluation of a synthetic receptor that binds to the exterior surface of chymotrypsin and disrupts its interaction with proteinaceous inhibitors, such as soybean trypsin inhibitor, basic pancreatic trypsin inhibitor, ovomucoid turkey inhibitor, and Bowman-Birk inhibitor. Using enzyme kinetics, nondenaturing gel electrophoresis, and gel filtration chromatography we show that the receptor is particularly effective at blocking the chymotrypsin-soybean trypsin inhibitor complex and that the mechanism involves formation of an initial ternary complex followed by a time-dependent displacement of the proteinaceous inhibitor.
The fourth chromosome of
Drosophila melanogaster
: Interspersed euchromatic and heterochromatic domains
Authors: Sun Fang-Lin , Cuaycong Matthew H. , Craig Carolyn A. , Wallrath Lori L. , Locke John , Elgin Sarah C. R.
Published: July 2002

The small fourth chromosome of
Drosophila melanogaster
(3.5% of the genome) presents a puzzle. Cytological analysis suggests that the bulk of the fourth, including the portion that appears banded in the polytene chromosomes, is heterochromatic; the banded region includes blocks of middle repetitious DNA associated with heterochromatin protein 1 (HP1). However, genetic screens indicate 50–75 genes in this region, a density similar to that in other euchromatic portions of the genome. Using a P element containing an
hsp70
-
white
gene and a copy of
hsp26
(marked with a fragment of plant DNA designated
pt
), we have identified domains that allow for full expression of the
white
marker (R domains), and others that induce a variegating phenotype (V domains). In the former case, the
hsp26
-
pt
gene shows an accessibility and heat-shock-inducible activity similar to that seen in euchromatin, whereas in the latter case, accessibility and inducible expression are reduced to levels typical of heterochromatin. Mapping by
in situ
hybridization and by hybridization of flanking DNA sequences to a collection of cosmid and bacterial artificial chromosome clones shows that the R domains (euchromatin-like) and V domains (heterochromatin-like) are interspersed. Examination of the effect of genetic modifiers on the variegating transgenes shows some differences among these domains. The results suggest that heterochromatic and euchromatic domains are interspersed and closely associated within this 1.2-megabase region of the genome.
The biosynthetic gene cluster of the maytansinoid antitumor agent ansamitocin from
Actinosynnema
pretiosum
Authors: Yu Tin-Wein , Bai Linquan , Clade Dorothee , Hoffmann Dietmar , Toelzer Sabine , Trinh Khue Q. , Xu Jun , Moss Steven J. , Leistner Eckhard , Floss Heinz G.
Published: July 2002

Maytansinoids are potent antitumor agents found in plants and microorganisms. To elucidate their biosynthesis at the biochemical and genetic level and to set the stage for their structure modification through genetic engineering, we have cloned two gene clusters required for the biosynthesis of the maytansinoid, ansamitocin, from a cosmid library of
Actinosynnema pretiosum
ssp.
auranticum
ATCC 31565. This is a rare case in which the genes involved in the formation of a secondary metabolite are dispersed in separate regions in an Actinomycete. A set of genes,
asm22–24
,
asm43–45
, and
asm47
, was identified for the biosynthesis of the starter unit, 3-amino-5-hydroxybenzoic acid (AHBA). Remarkably, there are two AHBA synthase gene homologues, which may have different functions in AHBA formation. Four type I polyketide synthase genes,
asmA–D
, followed by the downloading
asm9
, together encode eight homologous sets of enzyme activities (modules), each catalyzing a specific round of chain initiation, elongation, or termination steps, which assemble the ansamitocin polyketide backbone. Another set of genes,
asm13–17
, encodes the formation of an unusual “methoxymalonate” polyketide chain extension unit that, notably, seems to be synthesized on a dedicated acyl carrier protein rather than as a CoA thioester. Additional ORFs are involved in postsynthetic modifications of the initial polyketide synthase product, which include methylations, an epoxidation, an aromatic chlorination, and the introduction of acyl and carbamoyl groups. Tentative functions of several
asm
genes were confirmed by inactivation and heterologous expression.
Autoimmunity to βIV spectrin in paraneoplastic lower motor neuron syndrome
Authors: Berghs Stanny , Ferracci Franco , Maksimova Elena , Gleason Shannon , Leszczynski Nancy , Butler Margaret , De Camilli Pietro , Solimena Michele
Published: July 2002

Paraneoplastic neurological disorders may result from autoimmunity directed against antigens shared by the affected neurons and the associated cancer cells. We have recently reported the case of a woman with breast cancer and paraneoplastic lower motor neuron syndrome whose serum contained autoantibodies directed against axon initial segments and nodes of Ranvier of myelinated axons, including the axons of motoneurons. Here, we show that major targets of the autoantibodies of this patient are βIVΣ1 spectrin and βIV spectrin 140, two isoforms of the novel βIV spectrin gene, as well as a neuronal surface epitope yet to be identified. Partial improvement of the neurological symptoms following cancer removal was associated with a drastic reduction in the titer of the autoantibodies against βIV spectrin and nodal antigens in general, consistent with the autoimmune pathogenesis of the paraneoplastic lower motor neuron syndrome. The identification of βIV spectrin isoforms and surface nodal antigens as novel autoimmune targets in lower motor neuron syndrome provide new insights into the pathogenesis of this severe neurological disease.
Unexpected signals in a system subject to kinetic proofreading
Authors: Liu Zhao-Jun , Haleem-Smith Hana , Chen Huaxian , Metzger Henry
Published: July 2002

When multivalent ligands attach to IgEs bound to the receptors with high affinity for IgE on mast cells, the receptors aggregate, tyrosines on the receptors become phosphorylated, and a variety of cellular responses are stimulated. Prior studies, confirmed here, demonstrated that the efficiency with which later events are generated from earlier ones is inversely related to the dissociation rate of the aggregating ligand. This finding suggests that the cellular responses are constrained by a “kinetic proofreading” regimen. We have now observed an apparent exception to this rule. Doses of the rapidly or slowly dissociating ligands that generated equivalent levels of tyrosine-phosphorylated receptors comparably stimulated a putatively distal event: transcription of the gene for monocyte chemoattractant protein 1. Possible explanations of this apparent anomaly were explored.
Bioavailability of organic matter in a highly disturbed estuary: The role of detrital and algal resources
Authors: Sobczak William V. , Cloern James E. , Jassby Alan D. , Müller-Solger Anke B.
Published: July 2002

The importance of algal and detrital food supplies to the planktonic food web of a highly disturbed, estuarine ecosystem was evaluated in response to declining zooplankton and fish populations. We assessed organic matter bioavailability among a diversity of habitats and hydrologic inputs over 2 years in San Francisco Estuary's Sacramento–San Joaquin River Delta. Results show that bioavailable dissolved organic carbon from external riverine sources supports a large component of ecosystem metabolism. However, bioavailable particulate organic carbon derived primarily from internal phytoplankton production is the dominant food supply to the planktonic food web. The relative importance of phytoplankton as a food source is surprising because phytoplankton production is a small component of the ecosystem's organic-matter mass balance. Our results indicate that management plans aimed at modifying the supply of organic matter to riverine, estuarine, and coastal food webs need to incorporate the potentially wide nutritional range represented by different organic matter sources.