bluuebunny/crossref_metadata_2025 huggingface dataset:
Decaying Kolmogorov turbulence in a model of superflow
Authors: Nore C. , Abid M. , Brachet M. E.
Published: July 2002

Superfluid turbulence is studied using numerical simulations of the nonlinear Schrödinger equation (NLSE), which is the correct equation of motion for superflows at low temperatures. This equation depends on two parameters: the sound velocity and the coherence length. It naturally contains nonsingular quantized vortex lines. The NLSE mass, momentum, and energy conservation relations are derived in hydrodynamic form. The total energy is decomposed into an incompressible kinetic part, and other parts that correspond to acoustic excitations. The corresponding energy spectra are defined and computed numerically in the case of the two-dimensional vortex solution. A preparation method, generating initial data reproducing the vorticity dynamics of any three-dimensional flow with Clebsch representation is given and is applied to the Taylor–Green (TG) vortex. The NLSE TG vortex is studied with resolutions up to 5123. The energetics of the flow is found to be remarkably similar to that of the viscous TG vortex. The rate of the (irreversible) transfer of kinetic energy into other energy components is comparable, both in magnitude and time scale, to the energy dissipation of the viscous flow. This transfer rate depends weakly on the coherence length. At the moment of maximum energy dissipation, the energy spectrum follows a power law compatible with Kolmogorov’s −5/3 value. Physical-space visualizations show that the vorticity dynamics of the superflow is similar to that of the viscous flow in which vortex reconnection events play a major role. It is argued that there may be some amount of universality of reconnection processes, because of topological constraints. Some preliminary support for this conjecture is given in the special case of secondary instabilities of round jets. The experimental implications of the close analogy between superfluid and viscous decaying turbulence are discussed.
Cross stream dependence of conditional averages in elliptic region of flows behind a bluff-body
Authors: Swaminathan N. , Dally B. B.
Published: July 2002

Data obtained using the Raman/Rayleigh/LIF technique in turbulent nonpremixed reacting flows behind a bluff-body are analyzed to study the behavior of conditionally averaged temperature and species mass fraction. In particular, their cross stream dependence in the elliptic region of the above flow fields is investigated from the conditional moment closure view. Analyses show that the conditional averages have a very weak dependence on the cross stream position in recirculation regions which are elliptic in nature. The weak cross stream dependence of the conditional averages has been established in previous studies for parabolic flows.
The Lagrangian spectral relaxation model for differential diffusion in homogeneous turbulence
Authors: Fox R. O.
Published: July 2002

The Lagrangian spectral relaxation (LSR) model is extended to treat turbulent mixing of two passive scalars (φα and φβ) with different molecular diffusivity coefficients (i.e., differential-diffusion effects). Because of the multiscale description employed in the LSR model, the scale dependence of differential-diffusion effects is described explicitly, including the generation of scalar decorrelation at small scales and its backscatter to large scales. The model is validated against DNS data for differential diffusion of Gaussian scalars in forced, isotropic turbulence at four values of the turbulence Reynolds number (Rλ=38, 90, 160, and 230) with and without uniform mean scalar gradients. The explicit Reynolds and Schmidt number dependencies of the model parameters allows for the determination of the Re (integral-scale Reynolds number) and Sc (Schmidt number) scaling of the scalar difference z=φα−φβ. For example, its variance is shown to scale like 〈z2〉∼Re−0.3. The rate of backscatter (βD) from the diffusive scales towards the large scales is found to be the key parameter in the model. In particular, it is shown that βD must be an increasing function of the Schmidt number for Sc⩽1 in order to predict the correct scalar-to-mechanical time-scale ratios, and the correct long-time scalar decorrelation rate in the absence of uniform mean scalar gradients.
Dynamical compensation of irradiation nonuniformities in a spherical hohlraum illuminated with tetrahedral symmetry by laser beams
Authors: Phillion D. W. , Pollaine S. M.
Published: July 2002

Indirect-drive inertial confinement fusion with laser beams requires focusing the beams through laser entrance holes (LEHs) onto the inside surface of the hi-Z case comprising the hohlraum. The problem is how to illuminate the hohlraum so that the x-ray flux upon the capsule is as highly symmetric as possible at all times. This approach involves putting four LEHs at the corners of an imaginary regular tetrahedron whose vertices lie on the spherical hohlraum and putting a multiple of three beams through each LEH. Strict tetrahedral symmetry is maintained, so that under any proper tetrahedral symmetry operation, beam cones map into beam cones and LEHs into LEHs. The radiation field can have no l=1, 2, or 5 spherical harmonic components. By using two sets of twelve beams with different pulse shapes, the single surviving l=3 and single surviving l=4 components of the radiation flux upon the capsule can be made to vanish at all times.
Propagation of electromagnetic waves in a rotating ultrarelativistic electron–positron plasma
Authors: Mamun A. A.
Published: July 2002

The nonlinear evaluation of the electromagnetic waves under the condition of extreme rotation of the plasma is studied. Solitons are found to generate in the electron–positron plasma of a rotating neutron star. The behavior of the solitons and pulsar radiation is discussed.
Magnetohydrodynamic processes in the solar corona: Flares, coronal mass ejections, and magnetic helicity*
Authors: Low B. C.
Published: July 2002

The magnetized, million-degree solar corona evolves in cycles of about 11 years, in dynamical response to newly generated magnetic fluxes emerging from below to eventually reverse the global magnetic polarity. Over the larger scales, the corona does not erupt violently all the time. Violent events like the flares and episodic ejections of material into interplanetary space occur frequently, several times a day, but they often originate in long-lived magnetic structures that form continually throughout the solar cycle. In this paper, the creation, stability, and eventual eruption of these structures are discussed from basic principles, drawing on recent advances in observation and theory. A global view is offered in which different pieces of observation relate physically, with distinct roles for the conservation of magnetic helicity and the release of magnetic energy in dissipated and ordered forms.
Improved stability condition for rotating plasmas
Authors: Hameiri Eliezer , Holties Hanno A.
Published: July 2002

It is shown that the conservation of flow circulation along magnetic field lines can be used to improve on the δW stability criterion for rotating plasmas by adding to the energy integral a positive definite term. The improvement is most effective for ballooning modes in systems with a closed-line magnetic field. Such systems are investigated, both when the flow is sheared and when it is unsheared. In the unsheared case, instabilities grow exponentially in time, while, if the flow is sheared, an instability eventually saturates. The time-asymptotic behavior of such solutions is obtained and is different from the asymptotic behavior when the magnetic field is sheared.
Nondimensional transport scaling in DIII-D: Bohm versus gyro-Bohm resolved
Authors: Petty C. C. , Luce T. C. , Burrell K. H. , Chiu S. C. , deGrassie J. S. , Forest C. B. , Gohil P. , Greenfield C. M. , Groebner R. J. , Harvey R. W. , Pinsker R. I. , Prater R. , Waltz R. E. , James R. A. , Wròblewski D.
Published: July 2002

The scaling of cross-field heat transport with relative gyroradius ρ* was measured in low (L) and high (H) mode tokamak plasmas using the technique of dimensionally similar discharges. The relative gyroradius scalings of the electron and ion thermal diffusivities were determined separately using a two-fluid transport analysis. For L-mode plasmas, the electron diffusivity scaled as χe∝χBρ1.1±0.3* (gyro-Bohm-like) while the ion diffusivity scaled as χi∝χBρ−0.5±0.3* (worse than Bohm-like). The results were independent of the method of auxiliary heating (radio frequency or neutral beam). Since the electron and ion fluids had different gyroradius scalings, the effective diffusivity and global confinement time scalings were found to vary from gyro-Bohm-like to Bohm-like depending upon whether the electron or ion channel dominated the heat flux. This last property can explain the previously disparate results with dimensionally similar discharges on different fusion experiments that have been published. Experiments in H mode were also done with the expected values of beta, collisionality, safety factor, and plasma shape for thermonuclear ignition experiments. For these dimensionally similar discharges, both the electron and ion diffusivities scaled gyro-Bohm-like, χe, χi∝χBρ*, as did the global thermal confinement time. This leads to a very favorable prediction for the confinement time of future ignition devices.
Development and applications of a plasma waveguide for intense laser pulses
Authors: Milchberg H. M. , Clark T. R. , Durfee C. G. , Antonsen T. M. , Mora P.
Published: July 2002

The demonstration of optical guiding of high-intensity laser pulses in a plasma fiber waveguide [C. G. Durfee III and H. M. Milchberg, Phys. Rev. Lett. 71, 2409 (1993)] has opened the way to new advances in the development of nonlinear optics-based short-wavelength light sources, soft x-ray lasers, and compact laser-driven charged particle accelerators, and offers a new practical realm in which to study, control, and apply nonperturbative laser–matter interactions at ultrahigh intensity. An overview of selected experimental and theoretical results and their applications is presented.
Equation of state measurements of hydrogen isotopes on Nova
Authors: Collins G. W. , Celliers P. , Da Silva L. B. , Cauble R. , Gold D. , Foord M. , Budil K. S. , Stewart R. , Holmes N. C. , Ross M. , Hammel B. A. , Kilkenny J. D. , Wallace R. J. , Ng A.
Published: July 2002

The Nova laser [E. M. Campbell, Laser Part. Beams 9, 209 (1991)] was used to shock-compress liquid deuterium and obtain new principal Hugoniot measurements of density and pressure between 0.3 and 2.1 Mbar. In this pressure-density region, deuterium is predicted to transform from a molecular insulating fluid to an atomic conducting fluid. Nova data show a rapid increase in density from 0.6 g/cc at 0.3 Mbar, to 1 g/cc at 0.6 Mbar, suggestive of such a transition. The observed sixfold compression near 1 Mbar is larger than predicted by many widely used equation of state models.
Damping of toroidal ion temperature gradient modes
Authors: Sugama H.
Published: July 2002

The temporal evolution of linear toroidal ion temperature gradient (ITG) modes is studied based on a kinetic integral equation including an initial condition. It is shown how to evaluate the analytic continuation of the integral kernel as a function of a complex-valued frequency, which is useful for investigating the asymptotic damping behavior of the ITG mode. In the presence of the toroidal magnetic drift, the potential perturbation consists of normal modes and a continuum mode, which correspond to contributions from poles and from an integral along a branch cut, respectively, of the Laplace-transformed potential function of the frequency. The normal modes have exponential time dependence while the continuum mode, which has a ballooning structure, shows a power law decay ∝t−2, where t is the time variable. Therefore, the continuum mode dominantly describes the long-time asymptotic behavior of the perturbation for the stable system. By performing proper analytic continuation for the dispersion relation, the normal modes’ growth rate, real frequency, and eigenfunction are numerically obtained for both stable and unstable cases.
Velocity shear stabilization of interchange modes in elongated plasma configurations
Authors: Hassam A. B.
Published: July 2002

Interchange modes in magnetized plasmas can be stabilized by cross-field velocity shear. This effect is re-examined for systems with elongated cross-sections. For large elongations, E, the interchange growth drops as E−1/2 while the velocity shear scale is still determined by the short scale size. Consequently, velocity shear stabilization of elongated plasmas is shown to be more efficient by E−1/2.
Collisionless and resistive ballooning stability
Authors: Connor J. W. , Hastie R. J.
Published: July 2002

It has been suggested [Kleva and Guzdar, Phys. Plasmas 6, 116 (1999)] that reconnecting ballooning modes in which electron inertia replaces resistivity in a nonideal magnetohydrodynamic Ohm’s law can have substantial growth rates in the low collisionality regime. Numerical calculation, albeit necessarily at unrealistically large values of the collisionless skin depth, showed that strongly growing ballooning modes exist at beta values which are below the ideal beta limit. In order to investigate stability at more realistic values of the skin depth we exploit an analytic approach. As in the case of resistive ballooning modes, we find that inertial ballooning modes are stabilized by favorable average curvature effects at moderate values of ΔB′, the stability index for resistive ballooning. Instability only becomes possible close to the ideal stability boundary (ΔB′→∞) or at unrealistically large values of the toroidal mode number n (e.g., n≳102). Another ballooning mode, the collisionless analogue of the Carreras–Diamond mode [Carreras, Diamond, Murakami, Dunlap et al., Phys. Rev. Lett. 50, 503 (1983)] can also be excited at larger values of the collisionless skin depth, but this mode is not valid for realistic parameters in a hot plasma.
A model of laser imprinting
Authors: Goncharov V. N. , Skupsky S. , Boehly T. R. , Knauer J. P. , McKenty P. , Smalyuk V. A. , Town R. P. J. , Gotchev O. V. , Betti R. , Meyerhofer D. D.
Published: July 2002

Irradiation nonuniformities in direct-drive (DD) inertial confinement fusion experiments generate, or “imprint,” surface modulations that degrade the symmetry of the implosion and reduce the target performance. To gain physical insight, an analytical model of imprint is developed. The model takes into account the hydrodynamic flow, the dynamics of the conduction zone, and the mass ablation. The important parameters are found to be the time scale for plasma atmosphere formation and the ablation velocity. The model is validated by comparisons to detailed two-dimensional (2D) hydrocode simulations. The results of the model and simulations are in good agreement with a series of planar-foil imprint experiments performed on the OMEGA laser system [T.R. Boehly, D.L. Brown, R.S. Craxton et al., Opt. Commun. 133, 495 (1997)]. Direct-drive National Ignition Facility’s [J.A. Paisner, J.D. Boyes, S.A. Kumpan, W.H. Lowdermilk, and M.S. Sorem, Laser Focus World 30, 75 (1994)] cryogenic targets are shown to have gains larger than 10 when the rms laser-irradiation nonuniformity is reduced by 2D smoothing by spectral dispersion (SSD) used in the current DD target designs.
Nonlinear bounce-gyrocenter Hamiltonian dynamics in general magnetic field geometry
Authors: Brizard Alain J.
Published: July 2002

Nonlinear bounce-gyrocenter Hamilton equations for full electromagnetic field fluctuations in general magnetic geometry are derived by the phase-space Lagrangian Lie-perturbation method. These reduced dynamical equations can be used to follow the orbits of magnetically trapped charged particles in the presence of low-frequency electromagnetic fluctuations in magnetic-field geometries suitable for applications in fusion and space plasma physics.
Outdiffusion and diffusion mechanism of oxygen in silicon
Authors: Lee S.-Tong , Nichols D.
Published: July 2002

The outdiffusion profiles of oxygen in Czochralski Si(111) within the temperature range 700–1160 °C and for three processing conditions (nitrogen atmosphere, steam oxidation, and phosphorus indiffusion) were measured by secondary ion mass spectrometry. The diffusivity and solubility of oxygen in Si were determined by fitting these profiles to a simple diffusion model. Oxygen diffusivity shows little or no dependence on processing conditions and can be expressed as D=0.14 exp(−2.53 eV/kT) cm2 s−1 for the temperature range studied. Our observations show that point defects in Si have little effect on oxygen diffusion and demonstrate that oxygen diffuses primarily via an interstitial mechanism. Oxygen solubility was the largest during steam oxidation.
Nanosecond photoacoustic studies on ultraviolet laser ablation of organic polymers
Authors: Dyer P. E. , Srinivasan R.
Published: July 2002

Wide bandwidth polyvinylidenefluoride film piezoelectric transducers have been used to make time-resolved measurements of stress waves generated by ablation and subthreshold thermoelastic mechanisms in excimer laser irradiated polymers. At high fluence, ablation commences within 4–6 ns of the start of the laser pulse and generates short acoustic impulses (∼20 ns) with peak stresses ≥107 Pa (∼100 atm).
Dependence of lattice parameter on elastic strain and composition in undoped Czochralski grown GaAs
Authors: Okada Yasumasa , Tokumaru Yozo , Kadota Yoshinori
Published: July 2002

By precise measurement of the spatial variation in the lattice parameters of {001} undoped Czochralski grown gallium arsenide wafers, it was found that the lattice parameters are strongly dependent upon elastic strain and not so much on the melt composition. Although a remarkable spatial variation in the lattice parameters of ±5×10−6 nm from the average value was observed in a wafer specimen, the variation was considerably reduced to ±2×10−6 nm by dividing the wafer into small specimens. The lattice parameter variation was smaller than 2×10−6 nm due to a change in the As composition ratio from 0.42 to 0.52 in the melt.
Origin of ‘‘residual’’ persistent photoconductivity in selectively doped GaAs/AlxGa1−xAs heterojunctions
Authors: Theis T. N. , Wright S. L.
Published: July 2002

We present experimental results which clearly separate the various physical mechanisms which cause persistent photoconductivity in GaAs/AlxGa1−xAs heterojunctions. For high Al mole fraction the major contribution is from the donor-related DX center. This contribution is eliminated by reducing the Al mole fraction x, but we observe a ‘‘residual’’ effect for x≲0.2. We show that this is due to the persistent photovoltage developed between channel and semi-insulating substrate. Charge trapping in the epitaxial GaAs buffer layer contributes negligibly, contrary to the assumptions of other workers. This is demonstrated by fabricating modulation-doped field-effect transistors of low Al mole fraction on conductive substrates. In these devices persistent photoconductivity is eliminated as long as the substrate (back gate) potential is fixed with respect to the channel.
dc performance of ballistic tunneling hot-electron transfer amplifiers
Authors: Heiblum M. , Anderson I. M. , Knoedler C. M.
Published: July 2002

We present new experimental results of ballistic electron transport through thin n+-GaAs layers. Measurements were done on tunneling hot-electron transfer amplifier devices composed of GaAs and AlGaAs layers. In devices with GaAs active regions (bases) of 300 and 800 Å, collisionless or ballistic transport was observed. By performing hot-electron energy spectroscopy we found that the collected ballistic distributions were similar in shape but differed in magnitude. This suggests the existence of a strong scattering mechanism which randomizes the otherwise ballistic electrons. The maximum differential current transfer ratio α was 0.9 in devices for which about 75% of the injected current traversed the base ballistically. The presence of ballistic transport has also allowed the measurement of the AlGaAs barrier height through observation of the onset of current collection in the devices. Barrier heights higher than those recently reported have been measured. In addition we show the effects of grading the collector barrier. The most noted effect in these cases was a higher transfer ratio.
Long wavelength InAs1−xSbx/GaAs detectors prepared by molecular beam epitaxy
Authors: Bethea C. G. , Yen M. Y. , Levine B. F. , Choi K. K. , Cho A. Y.
Published: July 2002

We prepared InAs0.02Sb0.98 on semi-insulating GaAs substrates with molecular beam epitaxy and measured the temperature dependence of the band gap. Photoconducting detectors were measured and found to have high internal quantum efficiency (47%) and high speed (10 ns).
Effect of Ga addition to NdFeCoB on their magnetic properties
Authors: Tsutai A. , Sakai I. , Mizoguchi T. , Inomata K.
Published: July 2002

It was found that the Ga addition to NdFeCoB magnets was very effective for improving their magnetic properties. Magnets with high boron concentration had a high coercive force and magnets with low boron concentration had a high-energy product. The following magnetic properties were obtained: (1) Nd14.5FebalCo16Ga1B9.5:Br=12.0 kG, IHc=15.3 kOe, (BH)max=34 MGOe, Tc=500 °C (2) Nd14.5FebalCo16Ga1B5.5:Br=13.1 kG, IHc=12.2 kOe, (BH)max=40 MGOe, Tc=500 °C. It was also found that NdFeCoGaB magnets with very low boron concentration still had a relatively high coercive force.
SiO2/Si interface probed with a variable-energy positron beam
Authors: Nielsen Bent , Lynn K. G. , Chen Yen-C , Welch D. O.
Published: July 2002

The annihilation characteristics of a monoenergetic beam of positrons, after implantation in Si with a 350-nm overlayer of SiO2, were measured as a function of mean implantation depth. Positrons implanted overlapping the SiO2/Si interface were observed to decay from a state with properties distinctively different from the state in bulk Si and the thermally grown SiO2, i.e., a positron interface state. The momentum distribution of the annihilating positron-electron pair, as observed in the Doppler broadening of the annihilation line, is much broader for this state than for either bulk Si or SiO2, in contrast to previously observed localized positron states in solids and at surfaces which show a narrower distribution.
Actively mode-locked GaInAsP laser with subpicosecond output
Authors: Corzine S. W. , Bowers J. E. , Przybylek G. , Koren U. , Miller B. I. , Soccolich C. E.
Published: July 2002

We actively mode lock a high-frequency GaInAsP laser at a rate of 16 GHz to obtain nearly transform-limited hyperbolic secant pulses with a pulse width of 0.58 ps. This is the shortest pulse width yet demonstrated for either passively or actively mode-locked semiconductor lasers.
Helix formation via conformation diffusion search
Authors: Huang Cheng-Yen , Getahun Zelleka , Zhu Yongjin , Klemke Jason W. , DeGrado William F. , Gai Feng
Published: July 2002

The helix-coil transition kinetics of an α-helical peptide were investigated by time-resolved infrared spectroscopy coupled with laser-induced temperature-jump initiation method. Specific isotope labeling of the amide carbonyl groups with
13
C at selected residues was used to obtain site-specific information. The relaxation kinetics following a temperature jump, obtained by probing the amide I′ band of the peptide backbone, exhibit nonexponential behavior and are sensitive to both initial and final temperatures. These data are consistent with a conformation diffusion process on the folding energy landscape, in accord with a recent molecular dynamics simulation study.
Involvement of striatal and extrastriatal DARPP-32 in biochemical and behavioral effects of fluoxetine (Prozac)
Authors: Svenningsson Per , Tzavara Eleni T. , Witkin Jeffrey M. , Fienberg Allen A. , Nomikos George G. , Greengard Paul
Published: July 2002

Fluoxetine (Prozac) is the most widely prescribed medication for the treatment of depression. Nevertheless, little is known about the molecular basis of its clinical efficacy, apart from the fact that fluoxetine increases the synaptic availability of serotonin. Here we show that,
in vivo
, fluoxetine, given either acutely or chronically, regulates the phosphorylation state of dopamine- and cAMP-regulated phosphoprotein of
M
r
32,000 (DARPP-32) at multiple sites in prefrontal cortex, hippocampus, and striatum. Acute administration of fluoxetine increases phosphorylation of DARPP-32 at the protein kinase A site, Thr-34, and at the casein kinase-1 site, Ser-137, and decreases phosphorylation at the cyclin-dependent kinase 5 site, Thr-75. Each of these changes contributes, through distinct signaling pathways, to increased inhibition of protein phosphatase-1, a major serine/threonine protein phosphatase in the brain. Fluoxetine also increases phosphorylation of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor subunit GluR1 at Ser-831 and Ser-845. Both the fluoxetine-mediated increase in AMPA receptor phosphorylation at Ser-845–GluR1 and the beneficial responsiveness to fluoxetine in an animal test of antidepressant efficacy were strongly reduced in DARPP-32 knockout mice, indicating a critical role for this phosphoprotein in the antidepressant actions of fluoxetine. Mice chronically treated with fluoxetine had increased levels of DARPP-32 mRNA and protein and a decreased ability to increase phospho-Ser-137–DARPP-32 and phospho-Ser-831–GluR1. These chronic changes may be relevant to the delayed onset of therapeutic efficacy of fluoxetine.
Complete pathway for protein disulfide bond formation encoded by poxviruses
Authors: Senkevich Tatiana G. , White Christine L. , Koonin Eugene V. , Moss Bernard
Published: July 2002

We show that three cytoplasmic thiol oxidoreductases encoded by vaccinia virus comprise a complete pathway for formation of disulfide bonds in intracellular virion membrane proteins. The pathway was defined by analyzing conditional lethal mutants and effects of cysteine to serine substitutions and by trapping disulfide-bonded heterodimer intermediates for each consecutive step. The upstream component, E10R, belongs to the ERV1/ALR family of FAD-containing sulfhydryl oxidases that use oxygen as the electron acceptor. The second component, A2.5L, is a small α-helical protein with a CxxxC motif that forms a stable disulfide-linked heterodimer with E10R and a transient disulfide-linked complex with the third component, G4L. The latter is a thioredoxin-like protein that directly oxidizes thiols of L1R, a structural component of the virion membrane with three stable disulfide bonds, and of the related protein F9L. These five proteins are conserved in all poxviruses, suggesting that the pathway is an ancestral mechanism for direct thiol-disulfide interchanges between proteins even in an unfavorable reducing environment.
IL-1-induced NFκB and c-Jun N-terminal kinase (JNK) activation diverge at IL-1 receptor-associated kinase (IRAK)
Authors: Li Xiaoxia , Commane Mairead , Jiang Zhengfan , Stark George R.
Published: July 2002

Mutant I1A cells, lacking IL-1 receptor-associated kinase (IRAK)
mRNA and protein, have been used to study the involvement of IRAK in
NFκB and c-Jun N-terminal kinase (JNK) activation. A series of IRAK
deletion constructs were expressed in I1A cells, which were then tested
for their ability to respond to IL-1. Both the N-terminal death domain
and the C-terminal region of IRAK are required for IL-1-induced NFκB
and JNK activation, whereas the N-proximal undetermined domain is
required for the activation of NFκB but not JNK. The phosphorylation
and ubiquitination of IRAK deletion mutants correlate tightly with
their ability to activate NFκB in response to IL-1, but IRAK can
mediate IL-1-induced JNK activation without being phosphorylated. These
studies reveal that the IL-1-induced signaling pathways leading to
NFκB and JNK activation diverge either at IRAK or at a point nearer
to the receptor.
Proteomic analysis of the bacterial cell cycle
Authors: Grünenfelder Björn , Rummel Gabriele , Vohradsky Jiri , Röder Daniel , Langen Hanno , Jenal Urs
Published: July 2002

A global approach was used to analyze protein synthesis and
stability during the cell cycle of the bacterium
Caulobacter
crescentus
. Approximately one-fourth (979) of the estimated
C. crescentus
gene products were detected by
two-dimensional gel electrophoresis, 144 of which showed differential
cell cycle expression patterns. Eighty-one of these proteins were
identified by mass spectrometry and were assigned to a wide variety of
functional groups. Pattern analysis revealed that coexpression groups
were functionally clustered. A total of 48 proteins were rapidly
degraded in the course of one cell cycle. More than half of these
unstable proteins were also found to be synthesized in a cell
cycle-dependent manner, establishing a strong correlation between rapid
protein turnover and the periodicity of the bacterial cell cycle. This
is, to our knowledge, the first evidence for a global role of
proteolysis in bacterial cell cycle control.
Hydrogen bonding and perhalometallate ions: A supramolecular synthetic strategy for new inorganic materials
Authors: Brammer Lee , Swearingen John K. , Bruton Eric A. , Sherwood Paul
Published: July 2002

A synthetic strategy for constructing ionic hydrogen-bonded materials by combining perhalometallate anions with cations able to serve as hydrogen bond donors is presented. The approach is based on identification of well defined hydrogen bond acceptor sites on the anions by a combination of experimental and theoretical approaches. Selective population of these sites by hydrogen bond donors has the potential to afford organized crystalline arrays in one, two, or three dimensions. The approach is applicable to a wide range of metal centers.
A neuronal network model of macaque primary visual cortex (V1): Orientation selectivity and dynamics in the input layer 4Cα
Authors: McLaughlin David , Shapley Robert , Shelley Michael , Wielaard D. J.
Published: July 2002

In this paper, we offer an explanation for how selectivity for
orientation could be produced by a model with circuitry that is based
on the anatomy of V1 cortex. It is a network model of layer 4Cα in
macaque primary visual cortex (area V1). The model consists of a large
number of integrate-and-fire conductance-based point neurons, both
excitatory and inhibitory, which represent dynamics in a small patch of
4Cα—1 mm
2
in lateral area—which contains four
orientation hypercolumns. The physiological properties and coupling
architectures of the model are derived from experimental data for layer
4C
α
of macaque. Convergent feed-forward input from
many neurons of the lateral geniculate nucleus sets up an orientation
preference, in a pinwheel pattern with an orientation preference
singularity in the center of the pattern. Recurrent cortical
connections cause the network to sharpen its selectivity. The pattern
of local lateral connections is taken as isotropic, with the spatial
range of monosynaptic excitation exceeding that of inhibition. The
model (
i
) obtains sharpening, diversity in selectivity,
and dynamics of orientation selectivity, each in qualitative agreement
with experiment; and (
ii
) predicts more sharpening near
orientation preference singularities.
Ectopic
scute
induces
Drosophila
ommatidia development without R8 founder photoreceptors
Authors: Sun Yan , Jan Lily Yeh , Jan Yuh Nung
Published: July 2002

During development of the
Drosophila
peripheral nervous system, different proneural genes encoding basic helix–loop–helix transcription factors are required for different sensory organs to form.
atonal
(
ato
) is the proneural gene required for chordotonal organs and R8 photoreceptors, whereas the
achaete
-
scute
complex contains proneural genes for external sensory organs such as the macrochaetae, large sensory bristles. Whereas ectopic
ato
expression induces chordotonal organ formation, ectopic
scute
expression produces external sensory organs but not chordotonal organs in the wing. Proneural genes thus appear to specify the sensory organ type. In the ommatidium, or unit eye, R8 is the first photoreceptor to form and appears to recruit other photoreceptors and support cells. In the
atonal
1
(
ato
1
) mutant, R8 photoreceptors fail to form, thereby resulting in the complete absence of ommatidia. To our surprise, we found that ectopic
scute
expression in the
ato
1
mutant induces the formation of ommatidia, which occasionally sprout ectopic macrochaetae. Remarkably, many
scute
-induced ommatidia lack R8 although they contain outer photoreceptors.
Germ line deletion of the CD1 locus exacerbates diabetes in the NOD mouse
Authors: Shi Fu-Dong , Flodström Malin , Balasa Balaji , Kim Soon Ha , Van Gunst Kurt , Strominger Jack L. , Wilson S. Brian , Sarvetnick Nora
Published: July 2002

Quantitative and qualitative defects in CD1-restricted natural killer T cells have been reported in several autoimmune-prone strains of mice, including the nonobese diabetic (NOD) mouse. These defects are believed to be associated with the emergence of spontaneous autoimmunity. Here we demonstrate that both CD1d-null NOD and CD1d-null NOD/BDC2.5 T cell receptor transgenic mice have an accelerated onset and increased incidence of diabetes when compared with CD1d+/−and CD1d+/+littermates. The acceleration of disease did not seem to result from changes in the T helper (Th)1/Th2 balance because lymphocytes purified from lymphoid organs and pancreatic islets of wild-type and CD1d-null mice secreted equivalent amounts of IFN-γ and IL-4 after stimulation. In contrast, the pancreata of CD1d-null mice harbored significantly higher numbers of activated memory T cells expressing the chemokine receptor CCR4. Notably, the presence of these T cells was associated with immunohistochemical evidence of increased destructive insulitis. Thus, CD1d-restricted T cells are critically important for regulation of the spontaneous disease process in NOD mice.
Antigen presentation subverted: Structure of the human cytomegalovirus protein US2 bound to the class I molecule HLA-A2
Authors: Gewurz Benjamin E. , Gaudet Rachelle , Tortorella Domenico , Wang Evelyn W. , Ploegh Hidde L. , Wiley Don C.
Published: July 2002

Many persistent viruses have evolved the ability to subvert MHC class I antigen presentation. Indeed, human cytomegalovirus (HCMV) encodes at least four proteins that down-regulate cell-surface expression of class I. The HCMV unique short (US)2 glycoprotein binds newly synthesized class I molecules within the endoplasmic reticulum (ER) and subsequently targets them for proteasomal degradation. We report the crystal structure of US2 bound to the HLA-A2/Tax peptide complex. US2 associates with HLA-A2 at the junction of the peptide-binding region and the α3 domain, a novel binding surface on class I that allows US2 to bind independently of peptide sequence. Mutation of class I heavy chains confirms the importance of this binding sitein vivo. Available data on class I-ER chaperone interactions indicate that chaperones would not impede US2 binding. Unexpectedly, the US2 ER-luminal domain forms an Ig-like fold. A US2 structure-based sequence alignment reveals that seven HCMV proteins, at least three of which function in immune evasion, share the same fold as US2. The structure allows design of further experiments to determine how US2 targets class I molecules for degradation.
Naïve CD4 T cells inhibit CD28-costimulated R5 HIV replication in memory CD4 T cells
Authors: Mengozzi Manuela , Malipatlolla Meena , De Rosa Stephen C. , Herzenberg Leonard A. , Herzenberg Leonore A. , Roederer Mario
Published: July 2002

Stimulation with antibodies to CD3 and CD28 coimmobilized on beads can be used to significantly expand T cellsex vivo. With CD4 T cells from HIV-infected patients, this expansion usually is accompanied by complete suppression of viral replication, presumed to be caused by down-regulation of the viral coreceptor CCR5 and up-regulation of CCR5 ligands. Here we show that this suppression occurs in total CD4 T cells acutely infected with R5 HIV, but not in purified CD62L−memory CD4 T cells. The lack of complete suppression in these memory cells, typically comprising 10–40% of total CD4 T cells, occurs despite high levels of CCR5 ligand secretion and down-regulation of CCR5. Significantly, adding back naïve or CD62L+memory CD4 T cells inhibits the viral replication in the CD62L−cells, with the naïve cells capable of completely repressing the virus. Although this inhibition was previously thought to be specific to bead-bound anti-CD3/CD28 stimulation, we show that the same suppression is obtained with sufficiently strong anti-CD3/B7.1 stimulation. Our results show that inhibitory mechanisms, expressed predominantly by strongly stimulated naïve CD4 T cells and mediated independently of CCR5-binding chemokines, play a role in the inhibition of R5 HIV replication in CD4 T cells upon CD28 costimulation.
Lipid rafts are required for GLUT4 internalization in adipose cells
Authors: Ros-Baró Anna , López-Iglesias Carmen , Peiró Sandra , Bellido David , Palacín Manuel , Zorzano Antonio , Camps Marta
Published: July 2002

It has been recently reported that insulin recruits a novel signaling machinery to lipid rafts required for insulin-stimulated GLUT4 translocation [Baumann, A., Ribon, V., Kanzaki, M., Thurmond, D. C., Mora, S., Shigematsu, S., Bickel, P. E., Pessin, J. E. & Saltiel, A. R. (2001)
Nature
407, 202–207, 2000; Chiang, S. H., Baumann, C. A., Kanzaki, M., Thurmond, D. C., Watson, R. T., Neudauer, C. L., Macara, I. G., Pessin, J. E. & Saltiel, A. R. (2001)
Nature
410, 944–948]. We have assessed the role of lipid rafts on GLUT4 traffic in adipose cells. High GLUT4 levels were detected in caveolae from adipocytes by two approaches, the mechanical isolation of purified caveolae from plasma membrane lawns and the immunogold analysis of plasma membrane lawns followed by freeze-drying. The role of lipid rafts in GLUT4 trafficking was studied by adding nystatin or filipin at concentrations that specifically disrupt caveolae morphology and inhibit caveolae function without altering clathrin-mediated endocytosis. These caveolae inhibitors did not affect the insulin-stimulated glucose transport. However, they blocked both the GLUT4 internalization and the down-regulation of glucose transport triggered by insulin removal in 3T3-L1 adipocytes. Our data indicate that lipid rafts are crucial for GLUT4 internalization after insulin removal. Given that high levels of GLUT4 were detected in caveolae from insulin-treated adipose cells, this transporter may be internalized from caveolae or caveolae may operate as an obligatory transition station before internalization.
Analysis of DNA microarrays using algorithms that employ rule-based expert knowledge
Authors: Pan Kuang-Hung , Lih Chih-Jian , Cohen Stanley N.
Published: July 2002

The ability to investigate the transcription of thousands of genes concurrently by using DNA microarrays offers both major scientific opportunities and significant analytical challenges. Here we describe
gabriel
, a rule-based system of computer programs designed to apply domain-specific and procedural knowledge systematically and uniformly for the analysis and interpretation of data from DNA microarrays.
gabriel
's problem-solving rules direct stereotypical tasks, whereas domain-specific knowledge pertains to gene functions and relationships or to experimental conditions. Additionally,
gabriel
can learn novel rules through genetic algorithms, which define patterns that best match the data being analyzed and can identify groupings in gene expression profiles preordered by chromosomal position or by a nonsupervised algorithm such as hierarchical clustering.
gabriel
subsystems explain the logic that underlies conclusions and provide a graphical interface and interactive platform for the acquisition of new knowledge. The present report compares
gabriel
's output with published findings in which expert knowledge has been applied post hoc to microarray groupings generated by hierarchical clustering.
A role for phospholipase D1 in neurotransmitter release
Authors: Humeau Yann , Vitale Nicolas , Chasserot-Golaz Sylvette , Dupont Jean-Luc , Du Guangwei , Frohman Michael A. , Bader Marie-France , Poulain Bernard
Published: July 2002

Phosphatidic acid produced by phospholipase D (PLD) as a result of
signaling activity is thought to play a role in membrane vesicle
trafficking, either as an intracellular messenger or as a cone-shaped
lipid that promotes membrane fusion. We recently described that, in
neuroendocrine cells, plasma membrane-associated PLD1 operates at a
stage of Ca
2+
-dependent exocytosis subsequent to
cytoskeletal-mediated recruitment of secretory granules to exocytotic
sites. We show here that PLD1 also plays a crucial role in
neurotransmitter release. Using purified rat brain synaptosomes
subjected to hypotonic lysis and centrifugation, we found that PLD1 is
associated with the particulate fraction containing the plasma
membrane. Immunostaining of rat cerebellar granule cells confirmed
localization of PLD1 at the neuronal plasma membrane in zones
specialized for neurotransmitter release (axonal neurites,
varicosities, and growth cone-like structures). To determine the
potential involvement of PLD1 in neurotransmitter release, we
microinjected catalytically inactive PLD1(K898R) into
Aplysia
neurons and analyzed its effects on evoked
acetylcholine (ACh) release. PLD1(K898R) produced a fast and potent
dose-dependent inhibition of ACh release. By analyzing paired-pulse
facilitation and postsynaptic responses evoked by high-frequency
stimulations, we found that the exocytotic inhibition caused by
PLD1(K898R) was not the result of an alteration in stimulus-secretion
coupling or in vesicular trafficking. Analysis of the fluctuations in
amplitude of the postsynaptic responses revealed that the PLD1(K898R)
blocked ACh release by reducing the number of active
presynaptic-releasing sites. Our results provide evidence that PLD1
plays a major role in neurotransmission, most likely by controlling the
fusogenic status of presynaptic release sites.
Mutation, specialization, and hypersensitivity in highly optimized tolerance
Authors: Zhou Tong , Carlson J. M. , Doyle John
Published: July 2002

We introduce a model of evolution in which competing organisms are represented by percolation lattice models. Fitness is based on the number of occupied sites remaining after removing a cluster connected to a randomly selected site. High-fitness individuals arising through mutation and selection must trade off density versus robustness to loss, and are characterized by cellular barrier patterns that prevent large cascading losses to common disturbances. This model shows that Highly Optimized Tolerance (HOT), which links complexity to robustness in designed systems, arises naturally through Darwinian mechanisms. Although the model is a severe abstraction of biology, it produces a surprisingly wide variety of micro- and macroevolutionary features strikingly similar to real biological evolution.
Mechanism of activation for Zap-70 catalytic activity.
Authors: LoGrasso P V , Hawkins J , Frank L J , Wisniewski D , Marcy A
Published: July 2002

There is a growing body of evidence, including data from human genetic and T-cell receptor function studies, which implicate a zeta-associated protein of M(r) 70,000 (Zap-70) as a critical protein tyrosine kinase in T-cell activation and development. During T-cell activation, Zap-70 becomes associated via its src homology type 2 (SH2) domains with tyrosine-phosphorylated immune-receptor tyrosine activating motif (ITAM) sequences in the cytoplasmic zeta chain of the T-cell receptor. An intriguing conundrum is how Zap-70 is catalytically activated for downstream phosphorylation events. To address this question, we have used purified Zap-70, tyrosine phosphorylated glutathione S-transferase (GST)-Zeta, and GST-Zeta-1 cytoplasmic domains, and various forms of ITAM-containing peptides to see what effect binding of zeta had upon Zap-70 tyrosine kinase activity. The catalytic activity of Zap-70 with respect to autophosphorylation increased approximately 5-fold in the presence of 125 nM phosphorylated GST-Zeta or GST-Zeta-1 cytoplasmic domain. A 20-fold activity increase was observed for phosphorylation of an exogenous substrate. Both activity increases showed a GST-Zeta concentration dependence. The increase in activity was not produced with nonphosphorylated GST-Zeta, phosphorylated zeta, or phosphorylated ITAM-containing peptides. The increase in Zap-70 activity was SH2 mediated and was inhibited by phenylphosphate, Zap-70 SH2, and an antibody specific for Zap-70 SH2 domains. Since GST-Zeta and GST-Zeta-1 exist as dimers, the data suggest Zap-70 is activated upon binding a dimeric form of phosphorylated zeta and not by peptide fragments containing a single phosphorylated ITAM. Taken together, these data indicate that the catalytic activity of Zap-70 is most likely activated by a trans-phosphorylation mechanism.
Mutations in copper-zinc superoxide dismutase that cause amyotrophic lateral sclerosis alter the zinc binding site and the redox behavior of the protein.
Authors: Lyons T J , Liu H , Goto J J , Nersissian A , Roe J A , Graden J A , Café C , Ellerby L M , Bredesen D E , Gralla E B , Valentine J S
Published: July 2002

A series of mutant human and yeast copper-zinc superoxide dismutases has been prepared, with mutations corresponding to those found in familial amyotrophic lateral sclerosis (ALS; also known as Lou Gehrig's disease). These proteins have been characterized with respect to their metal-binding characteristics and their redox reactivities. Replacement of Zn2+ ion in the zinc sites of several of these proteins with either Cu2+ or Co2+ gave metal-substituted derivatives with spectroscopic properties different from those of the analogous derivative of the wild-type proteins, indicating that the geometries of binding of these metal ions to the zinc site were affected by the mutations. Several of the ALS-associated mutant copper-zinc superoxide dismutases were also found to be reduced by ascorbate at significantly greater rate than the wild-type proteins. We conclude that similar alterations in the properties of the zinc binding site can be caused by mutations scattered throughout the protein structure. This finding may help to explain what is perhaps the most perplexing question in copper-zinc superoxide dismutase-associated familial ALS-i.e., how such a diverse set of mutations can result in the same gain of function that causes the disease.
Conformations and folding of lysozyme ions in vacuo.
Authors: Gross D S , Schnier P D , Rodriguez-Cruz S E , Fagerquist C K , Williams E R
Published: July 2002

Proton transfer reactivity of isolated charge states of the protein hen egg-white lysozyme shows that multiple distinct conformations of this protein are stable in the gas phase. The reactivities of the 9+ and 10+ charge state ions, formed by electrospray ionization of "native" (disulfide-intact) and "denatured" (disulfide-reduced) solutions, are consistent with values calculated for ions in their crystal structure and fully denatured conformations, respectively. Charge states below 8+ of both forms, formed by proton stripping, have similar or indistinguishable reactivities, indicating that the disulfide-reduced ions fold in the gas phase to a more compact conformation.