bluuebunny/crossref_metadata_2025 huggingface dataset:
Convection in a rotating spherical fluid shell with an inhomogeneous temperature boundary condition at finite Prandtl number
Authors: Zhang K. , Gubbins D.
Published: July 2002

We examine thermal convection in a rotating spherical shell with central gravity and a spatially non-uniformly heated outer surface at two values of the Prandtl number: Pr=7.0, appropriate for water at room temperature, and Pr=0.7, appropriate for air at standard temperature and pressure, by numerical calculation. Four calculations are performed in a sequence: the onset of convection with homogeneous temperature boundary condition, nonlinear boundary-forced steady convection, stability of the forced steady convection to infinitesimal disturbances, and time stepping of subsequent secondary convection. Unlike our previous study of the infinite Prandtl number limit [J. Fluid Mech. 250, 209 (1993)] inertial terms in the equation of motion for moderate Prandtl numbers play a key role in the dynamics. The effects of an inhomogeneous temperature boundary condition on nonlinear convection are illustrated by varying the wavelength and strength of the imposed boundary temperature. It is shown that even a slight inhomogeneity in the thermal boundary condition can lock azimuthally drifting convection and make it stationary, or modify the normal drifting convection rolls to a vacillating structure. In the infinite Prandtl number case, when inertial forces are absent from the equation of motion, resonance occurs when the wavelengths of boundary forcing and natural convection coincide. Fluid inertia destroys this resonance for finite Prandtl number fluids. The same effect reduces in size the stability region where steady convection is locked to the boundary, and steady convection becomes unstable to time-dependent convection. The period of the secondary convection is close to that obtained with uniform temperature boundaries but the spatial structure is dramatically changed, exhibiting vacillations between the wavelength of the boundary temperature and that of the natural convection.
Parametric instability of dielectric, slightly viscous liquid jets under ac electric fields
Authors: González H. , Ramos A. , Castellanos A.
Published: July 2002

The ac electric fields longitudinally tangential to a dielectric liquid column are able to excite capillary waves on the cylindrical surface. The phenomenon is theoretically predicted using a Lagrangian formulation of the dynamics of small amplitude perturbations of the free surface. As in the dc case, dielectric forces tend to stabilize those perturbations affected by the capillary instability, but if the field is periodic parametric resonance takes place for perturbations of shorter wavelength, otherwise stable with dc fields. A detailed description of the stability spectrum is included and the role of field intensity and frequency in the parametric resonance phenomenon is discussed. Non axisymmetric modes are also excited but they are always dominated by the axisymmetric one. The effect of a small viscosity is to diminish or even suppress unstable regions. The field necessary to observe parametric resonance is calculated.
Hydrodynamic pair diffusion in isotropic random velocity fields with application to turbulent coagulation
Authors: Brunk Brett K. , Koch Donald L. , Lion Leonard W.
Published: July 2002

Diffusion and coagulation are investigated in a random, isotropic flow in the presence of hydrodynamic interactions, interparticle forces, and Brownian diffusion. Different strain and rotation rate time scales characterize the velocity field and the particles are assumed small compared with the characteristic length of the flow, so that the velocity field is linear in the vicinity of the particles. The pair probability equation for the relative motion of two particles is written in terms of a diffusion tensor and a drift velocity. This technique is valid in the limit of small strain, i.e., when the product of the characteristic velocity gradient and time scale of the fluctuating velocity gradient is small. A consequence of the drift velocity is that, at steady state in a noncoagulating system, the pair probability distribution is nonuniform when hydrodynamic interactions are included, and there is a higher probability of particle pairs at close proximity. The pair probability conservation equation is used to determine the coagulation rate both without and with consideration of interparticle interactions. The stability factor, W, is the ratio of the coagulation rate in the absence and presence of interparticle forces, and W is calculated numerically for different size particles influenced by van der Waals attraction, electrostatic repulsion, hydrodynamic interactions, and Brownian motion. A semi-analytical expression is derived that is valid for large particles that are not influenced by Brownian motion and that experience weak van der Waals attraction. The analysis shows that colloidal stability increases with increasing particle size and shear rate as a result of the hydrodynamic resistance to particle–particle collision. Double layer repulsion can lead to stable colloidal suspensions, but increasing the fluid shear can reduce this effect. Colloid stability for the randomly varying flow considered here is comparable to that obtained for steady linear flows, such as simple shear when only van der Waals attraction is considered. Compared with the steady linear flows, double layer repulsion imparts additional resistance to aggregation in the randomly varying flow. The relevance of applying this analysis to coagulation in isotropic turbulent flows is discussed.
Comparisons of gyrofluid and gyrokinetic simulations*
Authors: Parker S. E. , Dorland W. , Santoro R. A. , Beer M. A. , Liu Q. P. , Lee W. W. , Hammett G. W.
Published: July 2002

The gyrokinetic and gyrofluid models show the most promise for large scale simulations of tokamak microturbulence. This paper discusses detailed comparisons of these two complementary approaches. Past comparisons with linear theory have been fairly good, therefore the emphasis here is on nonlinear comparisons. Simulations include simple two-dimensional slab test cases, turbulent three-dimensional slab cases, and toroidal cases, each modeling the nonlinear evolution of the ion temperature gradient instability. There is good agreement in both turbulent and coherent nonlinear slab comparisons in terms of the ion heat flux, both in magnitude and scaling with magnetic shear. However, the nonlinear saturation level for ‖Φ‖ in the slab comparisons shows differences of approximately 40%. Preliminary toroidal comparisons show agreement within 50%, in terms of ion heat flux and saturation level.
Study of selective heating at ion cyclotron resonance for the plasma separation process
Authors: Compant La Fontaine A. , Pashkovsky V. G.
Published: July 2002

The plasma separation process by ion cyclotron resonance heating (ICRH) is studied both theoretically and experimentally on two devices: the first one called ERIC (Ion Cyclotron Resonance Experiment) at Saclay (France) [P. Louvet, Proceedings of the 2nd Workshop on Separation Phenomena in Liquids and Gases, Versailles, France, 1989, edited by P. Louvet, P. Noe, and Soubbaramayer (Centre d’Etudes Nucléaires de Saclay and Cité Scientifique Parcs et Technopoles, Ile de France Sud, France, 1989), Vol. 1, p. 5] and the other one named SIRENA at the Kurchatov Institute, Moscow, Russia [A. I. Karchevskii et al., Plasma Phys. Rep. 19, 214 (1993)]. The radio frequency (RF) transversal magnetic field is measured by a magnetic probe both in plasma and vacuum and its Fourier spectrum versus the axial wave number kz is obtained. These results are in agreement with the electromagnetic (EM) field calculation model based on resolution of Maxwell equations by a time-harmonic scheme studied here. Various axial boundary conditions models used to compute the EM field are considered. The RF magnetic field is weakly influenced by the plasma while the electric field components are strongly disturbed due to space-charge effects. In the plasma the transversal electric field is enhanced and the kz spectrum is narrower than in vacuum. The calculation of the resonant isotope heating is made by the Runge–Kutta method. The influence of ion–ion collisions, inhomogeneity of the static magnetic field B0, and the RF transversal magnetic field component on the ion acceleration is examined. These results are successfully compared with experiments of a minor isotope 44Ca heating measurements, made with an energy analyzer.
A model for ideal m=1 internal kink stabilization by minority ion cyclotron resonant heating
Authors: Dendy R. O. , Hastie R. J. , McClements K. G. , Martin T. J.
Published: July 2002

A generalized energy principle is used to determine the effect of ion cyclotron resonant heating (ICRH) on the stability of m=1 internal kink displacements in the low-frequency limit: such displacements are associated with sawtooth oscillations. An integral expression is obtained for the contribution to the plasma energy of an ICRH-heated minority ion population with strong temperature anisotropy, which relates the former to the ICRH power input and its deposition profile. The link is provided by a realistic, but analytically tractable, new model for the distribution function of the heated ions, which is based on the approach of Stix [Nucl. Fusion 15, 737 (1975)]. Numerical evaluation of the integral expression is carried out using parameters inferred from ICRH experiments in the Joint European Torus (JET) [Campbell et al., Phys. Rev. Lett. 60, 2148 (1988)]. It is shown that the ideal m=1 internal kink is stable at values of the poloidal plasma beta βp which typically lie in the range 0.4–1, depending on the radio-frequency power input and the radius r1 of the q=1 surface. Stability is thus possible at values of βp lying significantly above the magnetohydrodynamic instability threshold (≂0.3). If the perpendicular temperature T⊥ of the hot ions exceeds the parallel temperature by a factor of 10 or more, and r1 is greater than about one-third of the plasma minor radius, trapped ions have a greater stabilizing effect than passing ions. Stabilization is most easily achieved, however, if r1 is small. The hot-ion plasma energy depends strongly on the value of T⊥, but for fixed T⊥ is insensitive to the degree of anisotropy.
Microinstability properties of small-aspect-ratio tokamaks
Authors: Rewoldt G. , Tang W. M. , Kaye S. , Menard J.
Published: July 2002

Advanced tokamak configurations can have improved stability properties for high-n microinstabilities such as the toroidal drift mode (trapped-electron-ηi mode) and the kinetically-calculated magnetohydrodynamic (MHD) ballooning mode. A promising means to achieve this end involves employing tokamak configurations with very small aspect ratio, as in the proposed National Spherical Tokamak Experiment (NSTX) [M. Ono et al., Bull. Am. Phys. Soc. 40, 1655 (1995)] or the existing Small Tight Aspect Ratio Tokamak (START) experiment [R. J. Colchin et al., Phys. Fluids B 5, 2481 (1993)]. Kinetic instabilities are analyzed here using a comprehensive toroidal eigenvalue code with realistic equilibria for cases based on NSTX and START along with artificial cases to study parametric sensitivities. It is found that, as the aspect ratio decreases, the amount of ‘‘bad’’ magnetic curvature decreases, causing stabilization of both electrostatic and electromagnetic high-n instabilities at sufficiently small aspect ratio.
Propagation of realistic beams in underdense plasma
Authors: Hinkel D. E. , Williams E. A. , Berger R. L. , Powers L. V. , Langdon A. B. , Still C. H.
Published: July 2002

The effect of beam structure on propagation through underdense plasma is examined in two different examples. First, it is shown that the distribution of intensities within a laser beam affects how the beam deflects in the presence of transverse plasma flow. A detailed analysis of beam deflection shows that the rate scales linearly with intensity and plasma density, and inversely with plasma temperature. When the plasma flow is subsonic, the deflection rate is proportional to the ion damping decrement, and scales as M/(1−M2)3/2, where M is the transverse flow Mach number. When the plasma flow is supersonic, the deflection rate scales as 1/[M(M2−1))1/2]. Next, the effect of beam structure on channel formation by very intense laser beams is studied. A diffraction-limited beam with ∼3 TW of input power forms a channel through 400 μm of plasma, whereas when this beam is phase aberrated, channel formation does not occur.
Effects of orbit distortion on classical transport
Authors: Shaing K. C. , Aydemir A. Y. , Hazeltine R. D.
Published: July 2002

It is well known that electrostatic fields in tokamaks can vary on relatively short scale lengths, approaching the ion banana width. The resulting “squeezed” ion orbits are associated with significantly reduced neoclassical transport. It is shown here that an analogous process occurs, for steeper field variation, at the level of particle gyration: potentials varying on a scale comparable to the ion gyro-radius distort gyro-orbits and thus modify classical transport. The gyro-distortion can take one of three forms, depending upon the sign and size of the electric field shear; reduction in orbit width occurs only in a potential well. In this case, and assuming that the ion density and temperature vary slowly on the scale of the shrunken orbit, the classical ion heat flux is computed. It is shown that this flux is reduced by a factor of S−2, where S≡1+cΦ″(r)/BΩ. The sharp potential variation required for large S might result from steep electron temperature gradients near the separatrix of a spherical tokamak (with comparable poloidal and toroidal field components) or reversed field pinch.
Momentum and heat conduction in highly ionizable plasmas
Authors: Whitney K. G.
Published: July 2002

Calculations of the pressure tensor and heat conductivity for highly ionizable plasmas are presented that differ in three main respects from Braginskii’s calculation [Reviews of Plasma Physics, edited by M. A. Leontovich (Consultants Bureau, New York, 1965), Vol. 1, pp. 205–311]. One, the atomic number dependence of the classical viscosity is explicitly calculated and used to demonstrate, for ionization states of 12 or more, that the magnitude of the electron viscosity can greatly exceed that of the ion viscosity. Two, additional nonlinear contributions to the electron pressure tensor, dependent on gradients in temperature and density, are calculated, which can become comparable to and larger than the classical viscosity when these (physically realizable) gradients are sufficiently large. Three, these calculations interrelate the transport of energy and momentum by electrons in a plasma. As a consequence, flux limits on local heat transport suggest similar limits on local momentum transport. A model calculation of both transported quantities shows that they increase nonlinearly in size before the flux limit is reached. This behavior, in turn, suggests that flux limiting onsets earlier than linear transport theory implies and that the fluid equations for a plasma with severe temperature and density gradients must be closed, in general, by employing a nonlocal treatment of energy and momentum transport by electrons.
Critical issues in space plasma physics
Authors: Baker Daniel N.
Published: July 2002

It has been shown that solar, magnetospheric, and ionospheric plasmas exhibit remarkable global coherence and collective behavior. On the small scale, it has been possible in space research to perform experiments in what has been characterized as a “laboratory without walls.” Wave–particle interactions, particle acceleration, and transport phenomena have been studied in revealing detail. There remain many outstanding issues in space plasma research such as the location, timing, and detailed mechanisms of magnetic reconnection; the processes of rapid particle acceleration to relativistic energies; the physics of thin current sheets; and the nature of a host of plasma instabilities in ionospheric, magnetospheric, and solar contexts. In this paper we provide a guide to special jargon and concepts employed in space plasma research. An assessment is made of the present state of observational and theoretical investigations in critical areas and possible future directions in space plasma research are considered.
Pulsed laser atom probe analysis of GaAs and InAs
Authors: Cerezo A. , Grovenor C. R. M. , Smith G. D. W.
Published: July 2002

A pulsed laser atom probe has been used to obtain the first stoichiometrically correct analysis of GaAs and InAs. These results are presented, together with a comparison of results obtained from conventional and pulsed laser atom probes.
Field-dependent transport of electrons in selectively doped AlGaAs/GaAs/AlGaAs double-heterojunction systems
Authors: Inoue Kaoru , Sakaki Hiroyuki , Yoshino Junji
Published: July 2002

The transport properties of high-mobility electrons in selectively doped AlGaAs/GaAs/AlGaAs double-heterojunction systems have been investigated for electric fields (E) up to several kV/cm by pulsed Hall and pulsed current-voltage measurements. It was found that electron mobilities began to decrease drastically in proportion to E−0.8 when the electric fields exceeded (6.2–6.6)×106 (cm/s)/μ0, where μ0 is the low field electron mobility. The saturation of electron velocity was observed at E≥ 2 kV/cm, and its estimated value of (1.5–1.7)×107 cm/s was found to be almost independent both of the temperature in the range below 100 K and the density of electrons in the GaAs well of 3.8×1011 and 1.2×1012/cm2.
A new one-dimensional quantum well structure
Authors: Chang Yia-Chung , Chang L. L. , Esaki L.
Published: July 2002

A new one-dimensional quantum well structure is proposed. The structure is created by converting one side of the potential barrier of an asymmetric quantum well into a periodically indented potential. Both the electron and hole states are confined in the one-dimensional channel adjacent to the indented region of the side potential barrier, making it possible to achieve enhanced exciton binding energies and oscillator strengths for optical properties.
Heterojunction band discontinuity control by ultrathin intralayers
Authors: Niles D. W. , Margaritondo G. , Perfetti P. , Quaresima C. , Capozi M.
Published: July 2002

We present evidence that the band lineup at a semiconductor-semiconductor heterojunction interface can be changed and potentially controlled by an ultrathin metal intralayer. Synchrotron-radiation photoemission experiments demonstrate that 0.5–2-Å-thick Al intralayers increase the valence-band discontinuity of CdS-Ge and CdS-Si heterojunctions by 0.15 eV on the average.
GaInAsSb metastable alloys grown by organometallic vapor phase epitaxy
Authors: Cherng M. J. , Stringfellow G. B. , Kisker D. W. , Srivastava A. K. , Zyskind J. L.
Published: July 2002

Ga1−xInxAs1−ySby alloys have been grown by organometallic vapor phase epitaxy using trimethyl compounds of Ga, In, As, and Sb(TMGa, TMIn, TMAs, and TMSb) plus AsH3 in an atmospheric pressure, horizontal, infrared heated reactor. For the first time, alloys near the center of the region of solid immiscibility have been grown. Alloys with room-temperature band gaps of 0.45 eV (Ga0.68In0.32As0.28Sb0.72) and 0.37 eV (Ga0.26In0.74As0.76Sb0.24) have been grown on GaSb substrates and alloys with larger band gaps (0.74 eV for Ga0.71In0.29As0.76Sb0.24) have been grown on InP substrates. The smaller band-gap alloys are grown at temperatures as low as 486 °C. The alloys on InP substrates are grown at higher temperatures of 600 °C, more typical of the GaAsSb and GaInAs alloys reported earlier. Solid composition was determined using energy dispersive x-ray analysis and combined x-ray diffraction and photoluminescence measurements. The low-temperature photoluminescence of these metastable alloys consists of a single, presumably band edge peak. The half-widths of the photoluminescence peaks, especially those near the center of the region of immiscibility, are broader than those for the metastable ternary alloy GaAsSb. This may indicate that a significant amount of compositional clustering occurs during growth.
Amorphous carbon films as resist masks with high reactive ion etching resistance for nanometer lithography
Authors: Kakuchi Masami , Hikita Makoto , Tamamura Toshiaki
Published: July 2002

We propose the application of carbon films as resist masks for practical nanometer lithography involving reactive ion etching (RIE). Amorphous carbon films prepared by room-temperature plasma chemical vapor deposition show a very high resistance against RIE, the etching rates being less than 1/2 of that of a novolak-based conventional photoresist. The carbon films can be finely patterned by O2 RIE in a bilayer resist process using a high-resolution silicone-based negative resist. Nanometer patterns as small as 40 nm are fabricated on a thick solid substrate, and can be transferred into the substrate layer directly by RIE.
Lanthanum hexaboride (LaB6) resistivity measurement
Authors: Williams M. D. , Jackson L. T. , Kippenhan D. O. , Leung K. N. , West M. K. , Crawford C. K.
Published: July 2002

In the development of high-power free-electron lasers, intense electron beams are required. Large area, directly heated lanthanum hexaboride cathodes have been proposed as the electron emitter. To aid in the design of the cathode, the resistivity of lanthanum hexaboride as a function of material density and temperature has been measured.
Polarization bistability in semiconductor laser: Rate equation analysis
Authors: Chen Y. C. , Liu J. M.
Published: July 2002

The bistable switching between the TE and TM modes in semiconductor lasers has been analyzed using the rate equations. The condition of bistability has been determined using linear and nonlinear gain constants. The observed bistable switching behavior can be explained by a numerical simulation.
Resonant tunneling via X-point states in AlAs-GaAs-AlAs heterostructures
Authors: Mendez E. E. , Wang W. I. , Calleja E. , Gonçalves da Silva C. E. T.
Published: July 2002

We have observed resonant tunneling of electrons in AlAs-GaAs-AlAs heterostructures, via a quantum state localized in AlAs. The resonance manifests itself as a distinct feature in the current-voltage characteristics, at 4 K. The confined energy state arises from a potential profile derived from the X point of the Brillouin zone, in which AlAs behaves as a quantum well and GaAs as a barrier.
Implantation damage and the anomalous transient diffusion of ion-implanted boron
Authors: Michel A. E. , Rausch W. , Ronsheim P. A.
Published: July 2002

The effect of the implantation of silicon ions on the anomalous transient diffusion of ion-implanted boron is investigated. It is found that silicon ion fluences well below that necessary to amorphize the lattice substantially reduce the anomalous transient diffusion of subsequently implanted boron. The sheet resistance, however, is increased by the additional silicon implant. The implantation of silicon ions into activated boron layers causes additional anomalous diffusion at substantial distances beyond the range of the silicon ions. The anomalous motion is also reduced in regions where the damage is greater. The effects can be explained in terms of the generation of point defect clusters which dissolve during anneal and the sinking of point defects in the regions of high damage by the formation of interstitial type extended defects.
Point defect generation and enhanced diffusion in silicon due to tantalum silicide overlays
Authors: Hu S. M.
Published: July 2002

Tantalum silicide deposited directly on monocrystalline silicon substrates and annealed at 950 °C causes enhanced diffusion of both boron and antimony in buried layers. The effect is taken as evidence of vacancy supersaturation, since it is known that antimony diffuses in silicon by an almost entirely vacancy mechanism. It also indicates a substantial vacancy component in boron diffusion, at least at 950 °C, or lower. The simultaneous occurrence of boron and antimony enhanced diffusion contrasts with the nitridation effect on diffusion previously reported. That the enhanced diffusion occurred in buried layers excludes the snow-plow mechanism. The Si:Ta ratio of the sputter-deposited tantalum silicide is slightly less than 2. The interpretation is that further silicidation generates vacancies by removing silicon atoms from the silicon substrate. Enhanced diffusion was not detectable when there was a 150-nm intervening layer of polycrystalline silicon film between the silicide and the monocrystalline silicon substrate, indicating that polycrystalline silicon is an effective sink for excess vacancies, perhaps more than it is for excess interstitials.
Disk hydrogen plasma assisted chemical vapor deposition of aluminum nitride
Authors: Sheng T. Y. , Yu Z. Q. , Collins G. J.
Published: July 2002

We employ a well-confined hydrogen plasma of disk shape both as a vacuum ultraviolet (VUV) lamp operating primarily at 121.5 nm and as a source of atomic hydrogen radicals. Both VUV photons and atomic hydrogen act to dissociate feedstock gases used in low-temperature (<400 °C) metalorganic chemical vapor deposition (MOCVD). Thin films have been deposited both with the confined hydrogen plasma and with an excimer laser operating at 193 nm in order to compare the two methods. Preliminary chemical and electrical properties of the films deposited via the two methods indicate the superiority of the atomic hydrogen assisted MOCVD technique.
Granular metal films as recording media
Authors: Liou S. H. , Chien C. L.
Published: July 2002

High-density recording media require materials with a high magnetization and high coercivity as well as chemical stability, wear, and corrosion resistance. We explore the potential of granular metal films for recording media. Films of Fe granules about 150 Å in size embedded in an amorphous SiO2 matrix exhibit coercivities as high as 3 kOe at low temperatures and 1.1 kOe at room temperature, and magnetizations of about 150 emu/g. The methods with which these materials are fabricated, the essential microstructure characterization, and magnetic measurements are described.
Estimating the probability for a protein to have a new fold: A statistical computational model
Authors: Portugaly Elon , Linial Michal
Published: July 2002

Structural genomics aims to solve a large number of protein structures that represent the protein space. Currently an exhaustive solution for all structures seems prohibitively expensive, so the challenge is to define a relatively small set of proteins with new, currently unknown folds. This paper presents a method that assigns each protein with a probability of having an unsolved fold. The method makes extensive use of
protomap
, a sequence-based classification, and
scop
, a structure-based classification. According to
protomap
, the protein space encodes the relationship among proteins as a graph whose vertices correspond to 13,354 clusters of proteins. A representative fold for a cluster with at least one solved protein is determined after superposition of all
scop
(release 1.37) folds onto
protomap
clusters. Distances within the
protomap
graph are computed from each representative fold to the neighboring folds. The distribution of these distances is used to create a statistical model for distances among those folds that are already known and those that have yet to be discovered. The distribution of distances for solved/unsolved proteins is significantly different. This difference makes it possible to use Bayes' rule to derive a statistical estimate that any protein has a yet undetermined fold. Proteins that score the highest probability to represent a new fold constitute the target list for structural determination. Our predicted probabilities for unsolved proteins correlate very well with the proportion of new folds among recently solved structures (new
scop
1.39 records) that are disjoint from our original training set.
CML66, a broadly immunogenic tumor antigen, elicits a humoral immune response associated with remission of chronic myelogenous leukemia
Authors: Yang Xiao-Feng , Wu Catherine J. , McLaughlin Stephen , Chillemi Antoinette , Wang Kathy S. , Canning Christine , Alyea Edwin P. , Kantoff Philip , Soiffer Robert J. , Dranoff Glenn , Ritz Jerome
Published: July 2002

This report describes a tumor-associated antigen, termed CML66, initially cloned from a chronic myelogenous leukemia (CML) cDNA expression library. CML66 encodes a 583-aa protein with a molecular mass of 66 kDa and no significant homology to other known genes. CML66 gene is localized to human chromosome 8q23, but the function of this gene is unknown. CML66 is expressed in leukemias and a variety of solid tumor cell lines. When examined by Northern blot, expression in normal tissues was restricted to testis and heart, and no expression was found in hematopoietic tissues. When examined by quantitative reverse transcription–PCR, expression in CML cells was 1.5-fold higher than in normal peripheral blood mononuclear cells. The presence of CML66-specific antibody in patient serum was confirmed by Western blot and the development of high titer IgG antibody specific for CML66 correlated with immune induced remission of CML in a patient who received infusion of normal donor lymphocytes for treatment of relapse. CML66 antibody also was found in sera from 18–38% of patients with lung cancer, melanoma, and prostate cancer. These findings suggest that CML66 may be immunogenic in a wide variety of malignancies and may be a target for antigen-specific immunotherapy.
Protection from superoxide damage associated with an increased level of the YggX protein in
Salmonella enterica
Authors: Gralnick Jeffrey , Downs Diana
Published: July 2002

The deleterious effect of superoxide radicals on cell growth and survival is predominately caused by rapid oxidation of labile [Fe-S] clusters in proteins. Oxidation of these clusters releases Fe(II) ions, which participate in Fenton chemistry that damages DNA. Here it is shown that elevated levels of the YggX protein increase the resistance of
Salmonella enterica
to superoxide stress, reverse enzymatic defects attributed to oxidized [Fe-S] clusters, and decrease the spontaneous mutation frequency. The data are consistent with a model in which YggX protects protein [Fe-S] clusters from oxidation.
DNA binding induces dissociation of the multimeric form of HIV-1 integrase: A time-resolved fluorescence anisotropy study
Authors: Deprez Eric , Tauc Patrick , Leh Hervé , Mouscadet Jean-François , Auclair Christian , Hawkins Mary E. , Brochon Jean-Claude
Published: July 2002

Self-assembly of HIV-1 integrase (IN) in solution has been studied previously by time-resolved fluorescence, using tryptophan anisotropy decay. This approach provides information on the size of macromolecules via the determination of rotational correlation times (θ). We have shown that, at submicromolar concentration, IN is characterized by a long rotational correlation time (θ
20°C
= 90–100 ns) corresponding to a high-order oligomeric form, likely a tetramer. In the present work, we investigated the self-assembly properties of the DNA-bound IN by using three independent fluorophores. Under enzymatic assay conditions (10
−7
M IN, 2 × 10
−8
M DNA), using either fluorescein-labeled or fluorescent guanosine analog-containing oligonucleotides that mimic a viral end long terminal repeat sequence, we found that the DNA–IN complex was characterized by shorter θ
20°C
values of 15.5–19.5 and 23–27 ns, calculated from experiments performed at 25°C and 37°C, respectively. These results were confirmed by monitoring the Trp anisotropy decay as a function of the DNA substrate concentration: the θ of IN shifted from 90–100 ns to lower values (<30 ns) upon increasing the DNA concentration. Again, the normalized θ
20°C
values were significantly higher when monitored at 37°C as compared with 25°C. These results indicate that upon binding the viral DNA end, the multimeric enzyme undergoes a dissociation, most likely into a homogenous monomeric form at 25°C and into a monomer–dimer equilibrium at 37°C.
Active acetyl-CoA synthase from
Clostridium thermoaceticum
obtained by cloning and heterologous expression of
acsAB
in
Escherichia coli
Authors: Loke Huay-Keng , Bennett George N. , Lindahl Paul A.
Published: July 2002

Acetyl-CoA synthase from
Clostridium thermoaceticum
(ACS
Ct
) is an α
2
β
2
tetramer
containing two novel Ni-X-Fe
4
S
4
active sites
(the A and C clusters) and a standard Fe
4
S
4
cluster (the B cluster). The
acsA
and
acsB
genes encoding the enzyme were cloned into
Escherichia coli
strain JM109 and overexpressed at
37
o
C under anaerobic conditions with Ni supplementation.
The isolated recombinant His-tagged protein (AcsAB) exhibited
characteristics essentially indistinguishable from those of
ACS
Ct
, from which Ni had been removed from the A
cluster. AcsAB migrated through nondenaturing electrophoretic gels as a
single band and contained a 1:1 molar ratio of subunits and 1.0–1.6
Ni/αβ and 14–22 Fe/αβ. AcsAB exhibited
100–250 units/mg CO oxidation activity but no CO/acetyl–CoA
exchange activity. Electronic absorption spectra of thionin-oxidized
and CO-reduced AcsAB were similar to those of ACS
Ct
, with
features typical of redox-active Fe
4
S
4
clusters. Partially oxidized and CO-reduced AcsAB exhibited EPR signals
with
g
values and low spin intensities indistinguishable
from those of the B
red
state of the B cluster and the
C
red1
and C
red2
states of the C cluster of
ACS
Ct
. Upon overnight exposure to NiCl
2
, the
resulting recombinant enzyme (ACS
Ec
) developed 0.06–0.25
units/mg exchange activity. The highest of these values is typical of
fully active ACS
Ct
. When reduced with CO, ACS
Ec
exhibited an EPR signal indistinguishable from the NiFeC signal of
Ni-replete ACS
Ct
. Variability of activities and signal
intensities were observed among different preparations. Issues
involving the assembly of these metal centers in
E. coli
are discussed.
Modifications of RNA processing modulate the expression of hemoglobin genes.
Authors: Kollia P , Fibach E , Najjar S M , Schechter A N , Noguchi C T
Published: July 2002

The developmental changes in hemoglobin gene expression known as "switching" involve both the sequential activation and silencing of the individual globin genes. We postulated that in addition to changes in transcription, posttranscriptional mechanisms may be involved in modulating globin gene expression. We studied globin RNA transcripts in human adult erythroid cells (hAEC to analyze the mechanism of silencing of the embryonic epsilon-globin gene in the adult stage and in K562 erythroleukemic cells to analyze the inactive state of their adult beta-globin genes. In hAEC, which express primarily the beta-globin gene, quantitative PCR analysis shows that beta-mRNA exon levels are high and comparable among the three exons; the RNA transcripts corresponding to exons of the gamma-globin gene are low, with slight differences among the three exons. Although epsilon-globin is not expressed, epsilon-globin RNA transcripts are detected, with exon I levels comparable to that of gamma-globin exon I and much higher than epsilon-exons II and III. As expected, in K562 cells that express high levels of epsilon- and gamma-globin, epsilon- and gamma-mRNA levels are high, with comparable levels of exons I, II, and III. In K562 cells beta-mRNA levels are very low but beta-exon I levels are much higher than that of exons II or III. Moreover, all or most of the globin transcripts for the highly expressed globin genes in both cell types (gamma and beta in hAEC, epsilon and gamma in K562 cells) found in the cytoplasm or nucleus are correctly processed. The globin transcripts that are detected both in the cytoplasm and nucleus of cells without expression of the corresponding protein are largely unspliced (containing one or two intervening sequences). These studies suggest that in addition to changes in transcription rates, changes in completion or processing of globin RNA transcripts may contribute to the developmental regulation of the hemoglobin phenotype.
Real-time detection of the surface delivery of newly synthesized membrane proteins.
Authors: Andreose J S , Fumagalli G , Sigworth F J , Caplan M J
Published: July 2002

Newly synthesized membrane proteins travel from the Golgi complex to the cell surface in transport vesicles. We have exploited the ion channel properties of the nicotinic acetylcholine receptor (AChR) to observe in real time the constitutive delivery of newly synthesized AChR proteins to the plasma membrane in cultured muscle cells. Whole-cell voltage clamp was employed to monitor the current fluctuations induced by carbamylcholine upon the insertion into the plasma membrane of newly synthesized AChRs, following release from a 20 degrees C temperature block. We find that the transit of vesicles to the cell surface occurs within a few minutes after release of the block. The time course of electrical signals is consistent with many of the fusion events being instantaneous, although some appear to reveal the flickering of a fusion pore. AChR-containing vesicles can fuse individually or as conglomerates. Intracellular application of guanosine 5'-[gamma-thio]triphosphate inhibits the constitutive traffic of AChRs in most cells. Individual exocytotic vesicles carry between 10 and 300 AChR molecules, suggesting that AChRs may be packed extremely densely.
New approach for inhibiting Rev function and HIV-1 production using the influenza virus NS1 protein.
Authors: Qian X Y , Chen Z Y , Zhang J , Rabson A B , Krug R M
Published: July 2002

The Rev protein of HIV-1, which facilitates the nuclear export of HIV-1 pre-mRNAs, has been a target for antiviral therapy. Here we describe a new strategy for inhibiting Rev function and HIV-1 replication. In contrast to previous approaches, we use a wild-type rather than a mutant Rev protein and covalently link this Rev sequence to the NS1 protein of influenza A virus, a protein that inhibits the nuclear export of mRNAs. The NS1 protein contains an RNA-binding domain mutation (RM), so that the only functional RNA-binding domain in the chimeric protein (NS1RM-Rev) is in the Rev protein sequence. In the presence of the NS1RM-Rev chimeric protein, HIV-1 pre-mRNAs were retained in, rather than exported from, the nucleus. In addition, this chimeric protein effectively inhibited Rev function in trans in transfection experiments and effectively inhibited the production of HIV-1 in tissue culture cells transfected with an infectious molecular clone of HIV-1 DNA. The inhibitory activities of the NS1RM-Rev chimera were at least equivalent to those of the Rev M10 mutant protein, which has been considered to be the prototype trans inhibitor of Rev function and is currently in phase I clinical trials for the treatment of AIDS patients. We discuss (i) the potential for increasing the inhibitory activity of NS1-Rev chimeras against HIV-1 and (ii) the need for additional studies to evaluate these chimeras for the treatment of AIDS.
Statistical analysis of shape of objects based on landmark data.
Authors: Rao C R , Suryawanshi S
Published: July 2002

Two objects with homologous landmarks are said to be of the same shape if the configurations of landmarks of one object can be exactly matched with that of the other by translation, rotation/reflection, and scaling. The observations on an object are coordinates of its landmarks with reference to a set of orthogonal coordinate axes in an appropriate dimensional space. The origin, choice of units, and orientation of the coordinate axes with respect to an object may be different from object to object. In such a case, how do we quantify the shape of an object, find the mean and variation of shape in a population of objects, compare the mean shapes in two or more different populations, and discriminate between objects belonging to two or more different shape distributions. We develop some methods that are invariant to translation, rotation, and scaling of the observations on each object and thereby provide generalizations of multivariate methods for shape analysis.
Aminoacylation identity switch of turnip yellow mosaic virus RNA from valine to methionine results in an infectious virus.
Authors: Dreher T W , Tsai C H , Skuzeski J M
Published: July 2002

The turnip yellow mosaic virus genomic RNA terminates at its 3' end in a tRNA-like structure that is capable of specific valylation. By directed mutation, the aminoacylation specificity has been switched from valine to methionine, a novel specificity for viral tRNA-like structures. The switch to methionine specificity, assayed in vitro under physiological buffer conditions with wheat germ methionyl-tRNA synthetase, required mutation of the anticodon loop and the acceptor stem pseudoknot. The resultant methionylatable genomes are infectious and stable in plants, but genomes that lack strong methionine acceptance (as previously shown with regard to valine acceptance) replicate poorly. The results indicate that amplification of turnip yellow mosaic virus RNA requires aminoacylation, but that neither the natural (valine) specificity nor interaction specifically with valyl-tRNA synthetase is crucial.
Production of identical sextuplet mice by transferring metaphase nuclei from four-cell embryos
Authors: Kwon O. Y. , Kono T.
Published: July 2002

Mouse clones were produced by serial nuclear transfer commencing
with the transfer of four-cell nuclei at metaphase into unfertilized
ooplasts. The donor four-cell-stage nuclei were synchronized in
metaphase with nocodazole. The oocytes receiving a four-cell nucleus at
metaphase formed two nuclei after artificial activation and inhibition
of cytokinesis with cytochalasin B. To obtain embryos with diploid sets
of chromosomes, nuclei from each reconstructed embryo were transferred
individually into separate enucleated fertilized one-cell embryos, thus
doubling the number of identical embryos. This procedure produced a
high frequency of development of reconstructed embryos to the
blastocyst stage. Of 11 sets of identical embryos produced by serial
nuclear transplantation, 83% developed into blastocysts, including
three sets of identical septuplet blastocysts. After transfer to
recipient mice, a total of 25 (57%) live young were obtained, which
included one set of identical sextuplet and two sets of identical
quadruplet mice.
Characterization of a replication-incompetent adenovirus type 5 mutant deleted for the preterminal protein gene
Authors: Schaack Jerome , Guo Xiaoling , Langer Stephen J.
Published: July 2002

An adenovirus type 5 mutant deleted for the preterminal protein
(pTP) gene was constructed using cell lines that express pTP. The pTP
deletion mutant virus is incapable of replicating in the absence of
complementation and does not express detectable levels of viral mRNAs
that are expressed only after the onset of replication. Accumulation of
early-region mRNAs, including that for E1A, exhibits a lag relative to
that observed from the wild-type virus. However, E1A mRNA accumulation
attains a steady-state level similar to the level of expression during
the early phase of infection with the wild-type virus. In 293-pTP cells
(human embryonic kidney cells that express pTP in addition to high
levels of adenovirus E1A and E1B proteins), the pTP deletion mutant
virus replicates efficiently and yields infectious titers within 5-fold
of that of the wild-type virus. The deletion of 1.2 kb of pTP-encoding
sequence increases the size of foreign DNA that can be introduced into
the virus and, with an absolute block to replication, makes this virus
an important tool for gene therapy.
The aphid transmission factor of cauliflower mosaic virus forms a stable complex with microtubules in both insect and plant cells
Authors: Blanc Stéphane , Schmidt Isabelle , Vantard Marilyn , Scholthof Herman B. , Kuhl Georges , Esperandieu Pascal , Cerutti Martine , Louis Claude
Published: July 2002

We analyzed the distribution of the cauliflower mosaic virus (CaMV)
aphid transmission factor (ATF), produced via a baculovirus
recombinant, within Sf9 insect cells. Immunogold labeling revealed that
the ATF colocalizes with an atypical cytoskeletal network. Detailed
observation by electron microscopy demonstrated that this network was
composed of microtubules decorated with paracrystalline formations,
characteristic of the CaMV ATF. A derivative mutant of the ATF, unable
to self-assemble into paracrystals, was also analyzed. This mutant
formed a net-like structure, with a mesh of four nanometers, tightly
sheathing microtubules. Both the ATF– and the derivative
mutant–microtubule complexes were highly stable. They resisted
dilution-, cold-, and calcium-induced microtubule disassembly as well
as a combination of all three for over 6 hr. CaMV ATF cosedimented with
microtubules and, surprisingly, it bound to Taxol-stabilized
microtubules at high ionic strength, thus suggesting an atypical
interaction when compared with that usually described for
microtubule-binding proteins. Using immunofluorescence double labeling
we also demonstrated that the CaMV ATF colocalizes with the microtubule
network when expressed in plant cells.
Suppression of glucocorticoid secretion and antipsychotic drugs have similar effects on the mesolimbic dopaminergic transmission
Authors: Piazza Pier Vincenzo , Barrot Michel , Rougé-Pont Françoise , Marinelli Michela , Maccari Stefania , Abrous Djoher Nora , Simon Hervé , Le Moal Michel
Published: July 2002

Specific antagonists of central dopaminergic receptors constitute
the major class of antipsychotic drugs (APD). Two principal effects of
APD are used as criteria for the pre-clinical screening of their
antipsychotic action: (
i
) inhibition of basal and
depolarization-induced activity of mesolimbic dopaminergic neurons;
(
ii
) antagonism of the locomotor effects of dopaminergic
agonists. Given that glucocorticoid hormones in animals increase
dopamine release and dopamine-mediated behaviors and that high levels
of glucocorticoids can induce psychotic symptoms in humans, these
experiments examined whether inhibition of endogenous
glucocorticoids might have APD-like effects on mesolimbic dopaminergic
transmission in rats. It is shown that suppression of glucocorticoid
secretion by adrenalectomy profoundly decreased (by greater than 50%):
(
i
) basal dopaminergic release and the release of
dopamine induced by a depolarizing stimulus such as morphine (2
mg/kg, s.c.), as measured in the nucleus accumbens of freely moving
animals by microdialysis; (
ii
) the locomotor activity
induced by the direct dopaminergic agonist apomorphine. The effects of
adrenalectomy were glucocorticoid specific given that they were
reversed by the administration of glucocorticoids at doses
within the physiological range. Despite its profound diminution of
dopaminergic neurotransmission, adrenalectomy neither modified the
number of mesencephalic dopaminergic neurons nor induced gliosis in the
mesencephalon or in the nucleus accumbens, as shown by tyrosine
hydroxylase and glial fibrillary acidic protein immunostaining. In
conclusion, these findings suggest that blockade of central effects of
glucocorticoids might open new therapeutic strategies of behavioral
disturbances.