bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental investigation on the history force acting on oscillating fluid spheres at low Reynolds number
Authors: Abbad M. , Souhar M.
Published: September 2004

This paper reports an experimental investigation of isolated fluid particles rising (or falling) in a quiescent viscous liquid placed in an oscillating frame. Our goal is to carry out the first quantitative analysis of the effect of the history force on clean and spherical drops and bubbles. The average terminal Reynolds number is less than 0.5, the Strouhal number ranges from 1 to 25, and the Weber number ranges from 0.006 to 0.5. The particle motion is tracked by using a high-speed video camera and an accurate image processing facility. The average terminal velocity, the oscillation magnitude, and the phase shift with the oscillating frame are measured and compared with theoretical predictions. The comparison is made by solving the equation of motion of the sphere with and without the history force. Agreement between experiments and theory is observed when the history force corresponding to the creeping flow limit is taken into account. This experimental setup provides credible results, which confirm the fact that the history force given by the creeping flow theory remains still valid in these conditions, and brings non-negligible contribution into the momentum balance of small fluid inclusions moving in unsteady flows.
Nonparallel linear stability analysis of unconfined vortices
Authors: Herrada M. A. , Barrero A.
Published: September 2004

Parabolized stability equations [F. P. Bertolotti, Th. Herbert, and P. R. Spalart, J. Fluid. Mech. 242, 441 (1992)] have been used to study the stability of a family of swirling jets at high Reynolds numbers whose velocity and pressure fields decay far from the axis as rm−2 and r2(m−2), respectively [M. Pérez-Saborid, M. A. Herrada, A. Gómez-Barea, and A. Barrero, J. Fluid. Mech. 471, 51 (2002)]; r is the radial distance and m is a real number in the interval 0<m<2. Results show that the nonparallel effects of the basic flow play an important role in the development of both axisymmetric and nonaxisymmetric unstable perturbations upstream of the vortex breakdown station. A complementary local nonparallel analysis shows the convective nature of these instabilities. Therefore, a criterion based on the transition from convective to absolute instabilities cannot be applied to predict the vortex breakdown of this kind of swirling jets. On the contrary, the failure of the quasicylindrical approximation used to compute the downstream evolution of the basic flow gives a clear breakdown criterion based on the catastrophic transition between slender and nonslender flows.
On the behavior of the velocity-scalar cross correlation spectrum in the inertial range
Authors: Bos W. J. T. , Touil H. , Shao L. , Bertoglio J.-P.
Published: September 2004

The velocity-scalar cross spectrum (or scalar flux spectrum) is generally presumed to have a K−7/3 wavenumber dependence in the inertial range, in agreement with the dimensional analysis proposed by Lumley [Phys. Fluids 10, 855 (1967)]. Such a behavior is, however, clearly not observed in experiments in which spectra closer to K−2 (or even less steep) are generally found. It is shown in the paper that dimensional analysis is compatible with a K−2 scaling if a spectral flux of the velocity-scalar cross correlation is introduced. An analysis of the different terms in the equation of the scalar flux spectrum shows that two nonlinear contributions can be identified: a transfer term and the pressure contribution. Direct numerical simulations and large eddy simulation calculations are performed to obtain spectral information about the scalar flux spectrum and to analyze some key properties of the associated nonlinear transfer and pressure terms.
Analysis of convective hydrodynamic instabilities in a symmetric wavy channel
Authors: Blancher S. , Creff R. , Le Quéré P.
Published: September 2004

The dynamic development of a laminar flow in a two-dimensional symmetric wavy channel is studied numerically by numerical integration of the unsteady Navier–Stokes equations. It is shown that beyond a critical Reynolds number the flow is convectively unstable and exhibits an exponential spatial growth of the velocity fluctuations. The amplification factor for these “natural instabilities” increases with Reynolds number. It is characteristic of the geometry but independent of the number of the periods chosen for the simulation and other numerical parameters. The amplitude of velocity fluctuations saturates at a distance from the entry that decreases with increasing Reynolds number. The structure of the developing unsteady flow is compared with the most unstable modes of the fully developed laminar steady flow obtained by linear stability analysis. Although visual inspection would tend to favor the assumption of a single mode disturbance, it is found that the disturbances are wave packets centered around a dominant wavenumber which does not correspond to the geometrical periodicity. Spatial amplification factors computed with the theoretical group velocities determined from linear stability of the fully developed flow are in very good agreement with the numerically measured values, both for the sinuous and varicous modes.
Standing shocks in a rotating channel
Authors: Jacobson Tivon E. , Tabak Esteban G.
Published: September 2004

This paper discusses the stationary shallow water shocks occurring in a reentrant rotating channel with wind stress and topography. Asymptotic predictions for the shock location, strength, and associated energy dissipation are developed by taking the topographic perturbation to be small. It is shown that under appropriate conditions, a mean flow develops under the action of the wind stress, with a transverse profile determined by the need to support stationary shocks. The scaling arguments for the asymptotics are developed by demanding integrated energy and momentum balance, with the result that the free surface perturbation is of the order of the square root of the topographic perturbation. Shock formation requires that linear waves be nondispersive, which sets a solvability condition on the mean flow and which leads to a class of generalized Kelvin waves. Two-dimensional shock-resolving numerical simulations validate the asymptotic expressions and demonstrate the presence of stationary separated flow shocks in some cases.
Velocity slip and temperature jump coefficients for gaseous mixtures.  III. Diffusion slip coefficient
Authors: Sharipov Felix , Kalempa Denize
Published: September 2004

The diffusion slip coefficient is calculated for binary gaseous mixtures on the basis of the McCormack kinetic model of the Boltzmann equation, which is solved by the discrete velocity method. The calculations are carried out for the three mixtures of noble gases: neon–argon, helium–argon, and helium–xenon. Two models of the intermolecular interaction potential were considered. It was shown that this coefficient strongly depends on the potential. It was concluded that the use of the rigid spheres model does not provide physical results. An example of application of the diffusion slip coefficient is given.
Combining optical tweezers and patch clamp for studies of cell membrane electromechanics
Authors: Qian Feng , Ermilov Sergey , Murdock David , Brownell William E. , Anvari Bahman
Published: September 2004

We have designed and implemented a novel experimental setup which combines optical tweezers with patch-clamp apparatus to investigate the electromechanical properties of cellular plasma membranes. In this system, optical tweezers provide measurement of forces at piconewton scale, and the patch-clamp technique allows control of the cell transmembrane potential. A micron-size bead trapped by the optical tweezers is brought in contact with the membrane of a voltage-clamped cell, and subsequently moved away to form a plasma membrane tether. Bead displacement from the trapping center is monitored by a quadrant photodetector for dynamic measurements of tether force. Fluorescent beads and the corresponding fluorescence imaging optics are used to eliminate the shadow of the cell projected on the quadrant photodetector. Salient information associated with the mechanical properties of the membrane tether can thus be obtained. A unique feature of this setup is that the patch-clamp headstage and the manipulator for the recording pipette are mounted on a piezoelectric stage, preventing relative movements between the cell and the patch pipette during the process of tether pulling. Tethers can be pulled from the cell membrane at different holding potentials, and the tether force response can be measured while changing transmembrane potential. Experimental results from mammalian cochlear outer hair cells and human embryonic kidney cells are presented.
On-chip manipulation of levitated femtodroplets
Authors: Lyuksyutov I. F. , Naugle D. G. , Rathnayaka K. D. D.
Published: September 2004

We report diamagnetic levitation of droplets and∕or particles of pico–femtoliter volume and demonstrate their on-chip storage and high precision manipulation (translation, merging, assembling and rotation). We also demonstrate a levitation based microfluidic processor to process droplets∕particles with up to a billion times smaller volume than in typical microfluidic devices. The levitated particles can be positioned with up to 300nm accuracy and precisely rotated and assembled, providing a different physical approach for micro-electro-mechanical systems. Force can be applied to the droplets∕particles via magnetic, electric, and gravitational fields with up to femto-Newton accuracy, and potential energy can be controlled with up to 0.2zeptoJ(0.05kBT) precision, thus providing experimental tools for fundamental studies.
Nonequilibrium Bhatnagar–Gross–Krook model for nitrogen shock structure
Authors: Xu Kun , Tang Lei
Published: September 2004

This Brief Communication is about the study of diatomic gas shock structure based on the nonequilibrium gas-kinetic Bhatnagar–Gross–Krook (BGK) model, where an additional rotational energy relaxation equation is added. The BGK Navier–Stokes flow solver is extended to solve the nonequilibrium gas kinetic model. The numerical solutions are compared with the experiment measurements and direct simulation Monte Carlo solutions.
Damping of Alfvén eigenmodes on localized electrons in stellarators
Authors: Kolesnichenko Ya. I. , Marchenko V. S. , Wobig H.
Published: September 2004

The electron collisional damping of various kinds of Alfvén eigenmodes (AE) in stellarators is studied. Simple expressions for the damping rates of various well-localized AEs are obtained and applied to evaluating the damping rates in the Helias reactor [H. Wobig et al., Fusion Energy 1998, 17th Conference Proceedings, Yokohama, Japan (IAEA, Vienna, 1999), Vol. 4, p. 1235] and quasi-poloidal stellarator [J. F. Lyon et al., Fusion Energy 2002, 19th Conference Proceedings, Lyon, France (IAEA, Vienna, 2002), Paper IC/P-05]. The estimates made indicate that the collisional damping prevents the destabilization of AEs localized at the plasma periphery of the Helias reactor. A new mechanism that can considerably affect the collisional damping of Alfvén waves in stellarators is predicted: it is found that under certain conditions the collisionless orbit transformations between the locally trapped states and locally passing states significantly change the damping rate, so that the latter becomes weakly (logarithmically) dependent on the collision frequency.
Electrical characterization of Cd∕CdTe Schottky barrier diodes
Authors: Mason Whitney , Almeida L. A. , Kaleczyc A. W. , Dinan J. H.
Published: September 2004

We have deposited Cd metal contacts on molecular-beam epitaxy CdTe(112)B on Si(112) and have made electronic transport measurements to deduce the properties of the Schottky barrier diode thus formed. We find a room-temperature barrier height ϕB=0.92eV and an ideality factor n≈2. We suggest that the high value of n is due to generation–recombination currents associated with dislocations in the CdTe epilayer.
Ageostrophic, anticyclonic instability of a geostrophic, barotropic boundary current
Authors: McWilliams James C. , Molemaker M. Jeroen , Yavneh Irad
Published: September 2004

After having previously demonstrated the occurrence of ageostrophic, anticyclonic instability (AAI) for several other steady flows, in this paper we further test the hypothesis that rotating, stably stratified, shear flows are generally subject to AAI at finite Rossby (Ro) and Froude (Fr) numbers by calculating the inviscid, incompressible normal modes of a geostrophic, barotropic boundary current that vanishes toward the interior of the domain. We focus on a background current profile with no inflection point and nonvanishing absolute vorticity to exclude other known instability types. The hypothesis is again confirmed. The instability occurs for finite Ro only in an anticyclonic background flow. Its modal growth rate steeply decreases (approximately inverse exponentially, ∼e−c/Ro) as Ro→0. The downstream phase velocity of the unstable mode lies within the speed range for the background current, so the eigenmode has a near-critical layer within the zone of strong background shear. Its unstable eigenmode has an aspect ratio of downstream and vertical wave numbers, l/m, on the order of the ratio of the Coriolis and Brünt-Väisällä frequencies (as is typical for rotating, stratified flows). The maximum growth rate is independent of Fr for small Fr (the usual geophysical regime), and it decreases with large Fr, disappearing when there is no stratification. The eigenmode has a weakly decaying, oscillatory, interior far-field structure similar to an inertia-gravity wave. This supports the interpretation that the modal instability arises through the coalescence (i.e., resonance) of two stable normal-mode branches, one associated with the background shear flow and the other an inertia-gravity or Kelvin wave mode.
Fluctuation threshold and profile resilience in weakly ionized plasma in a curved, unsheared magnetic field
Authors: Rypdal K. , Ratynskaia S.
Published: September 2004

A study of electrostatic fluctuations in a weakly ionized plasma confined by a purely toroidal magnetic field B is presented. At low B field the plasma is quiescent and transport is provided by stationary E×B flows along open equipotential surfaces. For B above a certain threshold, strong electrostatic fluctuations are excited, and the electron pressure profile on the low-field side is resilient with scale length much shorter than the threshold scale length for flute instability. At threshold the fluctuations exhibit the signatures of a monochromatic drift mode, and above threshold they are dominated by flute modes growing on the low-field side. Threshold behavior and profile resilience are explained as a two-stage process, where drift waves act as a seed for the unstable flute modes, and where a negative feedback mechanism involving anomalous transport regulates the electron pressure profile to maintain the imposed particle flux.
Phase-resolved optical Doppler tomography for imaging flow dynamics in microfluidic channels
Authors: Wang Lei , Xu Wei , Bachman Mark , Li G. P. , Chen Zhongping
Published: September 2004

Phase-resolved optical Doppler tomography (ODT), an imaging technique based on low coherence interferometry, is presented as a tool to perform high-resolution cross-sectional imaging of fluidic flow in microchannels with high velocity sensitivity. To demonstrate ODT as a tool, electro-osmotic flow (EOF) was investigated, observing cross-sectional images of bidirectional flow within a microfluidic channel and pulsating flow when driven by a pulsed electrical field. ODT demonstrates great promise as a tool for studying the effects of microchannel surface modifications on biological sample flow and optimizing microfluidic device design.
Simple ortho-para hydrogen and para-ortho deuterium converter for matrix isolation spectroscopy
Authors: Andrews Lester , Wang Xuefeng
Published: September 2004

A copper tube containing catalyst immersed in the cold gas above liquid helium is used to convert normal H2 and D2 to high purity J=0 samples. The converted samples are sublimed directly from 12–16 K catalyst to the 4 K matrix substrate for recording infrared spectra. The decrease of infrared absorptions due to J=1 isomer perturbations on the major J=0 species bands show that solid samples >99% in the J=0 species are formed. Such high purity p-H2 and o-D2 subjected to Tesla coil discharge during condensation at 4 K sustain a 2%–8% decrease in the J=0 species population depending on the discharge pressure. We also show that orthodeuterium is an excellent matrix host.
On the drag of two-dimensional flow about a circular cylinder
Authors: Wen C.-Y. , Yeh C.-L. , Wang M.-J. , Lin C.-Y.
Published: September 2004

The drag force experienced by a circular cylinder in a two-dimensional (2D) flow is investigated experimentally. Both horizontal and vertical soap film tunnels are used to set up the 2D flow with Reynolds numbers Re ranging from 35 to 560 (based on the diameter of the circular cylinder). Momentum defect measurements are used to obtain the time averaged drag coefficients, via laser Doppler velocimetry. It is found that the drag curve is in good agreement with the 2D computations of Henderson [Phys. Fluids 7, 2102 (1995)]. Two separate three-dimensional instabilities of the natural wake at Re≅180 and 260 are not observed in the present data. Flow visualization of the characteristic wake patterns behind a circular cylinder, as Reynolds number increases, is also presented.
A numerical study of the generation and propagation of thermoacoustic waves in water
Authors: Aktas Murat K. , Farouk Bakhtier , Narayan Padma , Wheatley Margaret A.
Published: September 2004

The generation and propagation of thermoacoustic waves in water are investigated by solving the fully compressible form of the Navier–Stokes equations. A square enclosure filled with water is considered as the computational domain. Thermally induced pressure waves are generated by rapidly heating the left wall. The thermodynamic properties of water are calculated via an accurate equation of state. The effect of the rapidity of the heating process on the production of thermoacoustic waves is studied, using both impulse (sudden) and gradual changes in the left wall temperature. The thermoacoustic waves are significantly stronger for impulse heating and are found to eventually damp out with time due to viscous losses. Gradual change of the left wall temperature reduced the strength of the pressure wave peaks.
Marek's disease is a natural model for lymphomas overexpressing Hodgkin's disease antigen (CD30)
Authors: Burgess S. C. , Young J. R. , Baaten B. J. G. , Hunt L. , Ross L. N. J. , Parcells M. S. , Kumar P. M. , Tregaskes C. A. , Lee L. F. , Davison T. F.
Published: September 2004

Animal models are essential for elucidating the molecular mechanisms of carcinogenesis. Hodgkin's and many diverse non-Hodgkin's lymphomas overexpress the Hodgkin's disease antigen CD30 (CD30hi), a tumor necrosis factor receptor II family member. Here we show that chicken Marek's disease (MD) lymphoma cells are also CD30hiand are a unique natural model for CD30hilymphoma. Chicken CD30 resembles an ancestral form, and we identify a previously undescribed potential cytoplasmic signaling domain conserved in chicken, human, and mouse CD30. Our phylogeneic analysis defines a relationship between the structures of human and mouse CD30 and confirms that mouse CD30 represents the ancestral mammalian gene structure. CD30 expression by MD virus (MDV)-transformed lymphocytes correlates with expression of the MDVMeqputative oncogene (ac-Junhomologue)in vivo. The chicken CD30 promoter has 15 predicted high-stringencyMeq-binding transcription factor recognition motifs, andMeqenhances transcription from the CD30 promoterin vitro. Plasma proteomics identified a soluble form of CD30. CD30 overexpression is evolutionarily conserved and defines one class of neoplastic transformation events, regardless of etiology. We propose that CD30 is a component of a critical intracellular signaling pathway perturbed in neoplastic transformation. Specific anti-CD30 Igs occurred after infection of genetically MD-resistant chickens with oncogenic MDV, suggesting immunity to CD30 could play a role in MD lymphoma regression.
Kinase peptide specificity: Improved determination and relevance to protein phosphorylation
Authors: Fujii Koichi , Zhu Guozhi , Liu Yin , Hallam John , Chen Lin , Herrero Juan , Shaw Stephen
Published: September 2004

Specificity of phosphorylation is critical to signal transduction. Recent emphasis on colocalization of substrate and kinase has eclipsed emphasis on peptide specificity, i.e., kinase preference for particular amino acids surrounding the phosphorylation site. We describe an approach to determining peptide specificity by using positional scanning of biotinylated oriented peptide libraries and insights emerging from those determinations. We accurately determine preference (or disfavor) for residues at a given substrate position (such as P+2) by comparison of
in vitro
phosphorylation of peptide libraries differing by a single residue at that position. By analysis of all positions near the phosphorylation site, position-specific scoring matrices are generated and used both to understand the basis of specificity and to predict phosphorylation. PKC-δ and -ζ predictions have been validated rigorously by comparisons with measured phosphorylation. The results demonstrate specificity and sensitivity (80–90%) much better than the previous predictive method. These predictions can be accessed at
http://mpr.nci.nih.gov
. The accuracy of the specificity determination allows identification of an important difference in peptide specificity between these closely related kinases; Ile/Leu at the P–1 position is disfavored by PKC-ζ but not PKC-δ. Our findings and visual representation of peptide specificity highlight the importance of disfavored residues. Finally, analysis of 124 experimentally determined PKC sites from the literature demonstrates a very strong role of peptide specificity in many of those sites. Thus, position-specific scoring matrices generated by this method provide a foundation for quantitative analyses of kinase specificity and improved predictions of previously determined physiologically relevant phosphorylation sites.
The influence of sulfur and iron on dissolved arsenic concentrations in the shallow subsurface under changing redox conditions
Authors: O'Day Peggy A. , Vlassopoulos Dimitri , Root Robert , Rivera Nelson
Published: September 2004

The chemical speciation of arsenic in sediments and porewaters of aquifers is the critical factor that determines whether dissolved arsenic accumulates to potentially toxic levels. Sequestration of arsenic in solid phases, which may occur by adsorption or precipitation processes, controls dissolved concentrations. We present synchrotron x-ray absorption spectra of arsenic in shallow aquifer sediments that indicate the local structure of realgar (AsS) as the primary arsenic-bearing phase in sulfate-reducing conditions at concentrations of 1–3 mmol·kg
–1
, which has not previously been verified in sediments at low temperature. Spectroscopic evidence shows that arsenic does not substitute for iron or sulfur in iron sulfide minerals at the molecular scale. A general geochemical model derived from our field and spectroscopic observations show that the ratio of reactive iron to sulfur in the system controls the distribution of solid phases capable of removing arsenic from solution when conditions change from oxidized to reduced, the rate of which is influenced by microbial processes. Because of the difference in solubility of iron versus arsenic sulfides, precipitation of iron sulfide may remove sulfide from solution but not arsenic if precipitation rates are fast. The lack of incorporation of arsenic into iron sulfides may result in the accumulation of dissolved As(III) if adsorption is weak or inhibited. Aquifers particularly at risk for such geochemical conditions are those in which oxidized and reduced waters mix, and where the amount of sulfate available for microbial reduction is limited.
Learning increases human electroencephalographic coherence during subsequent slow sleep oscillations
Authors: Mölle Matthias , Marshall Lisa , Gais Steffen , Born Jan
Published: September 2004

Learning is assumed to induce specific changes in neuronal activity during sleep that serve the consolidation of newly acquired memories. To specify such changes, we measured electroencephalographic (EEG) coherence during performance on a declarative learning task (word pair associations) and subsequent sleep. Compared with a nonlearning control condition, learning performance was accompanied with a strong increase in coherence in several EEG frequency bands. During subsequent non-rapid eye movement sleep, coherence only marginally increased in a global analysis of EEG recordings. However, a striking and robust increase in learning-dependent coherence was found when analyses were performed time-locked to the occurrence of slow oscillations (<1 Hz). Specifically, the surface-positive half-waves of the slow oscillation resulting from widespread cortical depolarization were associated with distinctly enhanced coherence after learning in the slow-oscillatory, delta, slow-spindle, and gamma bands. The findings identify the depolarizing phase of the slow oscillations in humans as a time period particularly relevant for a reprocessing of memories in sleep.
Visualization of plasma membrane compartmentalization with patterned lipid bilayers
Authors: Wu Min , Holowka David , Craighead Harold G. , Baird Barbara
Published: September 2004

Micrometer-size patterned lipid bilayers containing liganded lipids are used to control the location and size of receptor clusters and enable direct visualization of structural reorganization of cellular components. Subsequent to concentration of Fcε receptor I, the mast cell receptor for IgE, and colocalized tyrosine phosphorylation activity, Lyn kinase and other proteins anchored to the inner leaflet of the plasma membrane redistribute selectively with the receptor clusters in a process that depends on actin polymerization. Surprisingly, outer leaflet components characteristically associated with lipid rafts do not detectably coredistribute with these inner leaflet components. Cell activation using patterned surfaces provides unique insights into cell membrane structural organization, revealing dynamic, large-scale uncoupling of inner and outer leaflet components of lipid rafts.
Carcinoma and stromal enzyme activity profiles associated with breast tumor growth
in vivo
Authors: Jessani Nadim , Humphrey Mark , McDonald W. Hayes , Niessen Sherry , Masuda Kim , Gangadharan Beena , Yates John R. , Mueller Barbara M. , Cravatt Benjamin F.
Published: September 2004

Cancer research depends on the use of human cell lines for both the
in vitro
(culture) and
in vivo
(xenograft) analysis of tumor progression and treatment. However, the extent to which cultured preparations of human cancer lines display similar properties
in vivo
, where important host factors may influence tumor biology, remains unclear. Here, we address this question by conducting a functional proteomic analysis of the human breast cancer line MDA-MB-231 grown in culture and as orthotopic xenograft tumors in the mammary fad pad of immunodeficient mice. Using a suite of activity-based chemical probes, we identified carcinoma (human) enzyme activities that were expressed selectively in culture or in xenograft tumors. Likewise, distinct groups of stromal (mouse) enzyme activities were found that either infiltrated or were excluded from xenograft tumors, indicating a contribution by specific host components to breast cancer development. MDA-MB-231 cells isolated from tumors exhibited profound differences in their enzyme activity profiles compared with the parent cell line, including the dramatic posttranscriptional up-regulation of the serine proteases urokinase plasminogen activator and tissue plasminogen activator and down-regulation of the glycolytic enzyme phosphofructokinase. These altered enzyme activity profiles correlated with significantly greater tumor growth rates and metastases for xenograft-derived MDA-MB-231 cells upon reintroduction into mice. Collectively, these data indicate that the
in vivo
environment of the mouse mammary fat pad cultivates the growth of human breast cancer cells with elevated tumorigenic properties and highlight the value of activity-based protein profiling for identifying proteomic signatures that depict such changes in cancer cell biology.
Structural analysis uncovers a role for redox in regulating FKBP13, an immunophilin of the chloroplast thylakoid lumen
Authors: Gopalan Gayathri , He Zengyong , Balmer Yves , Romano Patrick , Gupta Rajeev , Héroux Annie , Buchanan Bob B. , Swaminathan Kunchithapadam , Luan Sheng
Published: September 2004

Change in redox status has long been known to link light to the posttranslational regulation of chloroplast enzymes. So far, studies have been conducted primarily with thioredoxin-linked members of the stroma that function in a broad array of biosynthetic and degradatory processes. Consequently, little is known about the role of redox in regulating the growing number of enzymes found to occur in the lumen, the site of oxygen evolution in thylakoid membranes. To help fill this gap, we have studied AtFKBP13, an FKBP-type immunophilin earlier shown to interact with a redox-active protein of the lumen, and found the enzyme to contain a pair of disulfide bonds in x-ray structural studies. These disulfides, which in protein mutagenesis experiments were shown to be essential for the associated peptidyl-prolyl isomerase activity, are unique to chloroplast FKBPs and are absent in animal and yeast counterparts. Both disulfide bonds were redox-active and were reduced by thioredoxin from either chloroplast or bacterial sources in a reaction that led to loss of enzyme activity. The results suggest a previously unrecognized paradigm for redox regulation in chloroplasts in which activation by light is achieved in concert with oxygen evolution by the oxidation of sulfhydryl groups (conversion of SH to S—S). Such a mechanism, occurring in the thylakoid lumen, is in direct contrast to regulation of enzymes in the stroma, where reduction of disulfides targeted by thioredoxin (S—S converted to SH) leads to an increase in activity in the light.
RETRACTED: Protein tyrosine phosphatase receptor-type O (PTPRO) exhibits characteristics of a candidate tumor suppressor in human lung cancer
Authors: Motiwala Tasneem , Kutay Huban , Ghoshal Kalpana , Bai Shoumei , Seimiya Hiroyuki , Tsuruo Takashi , Suster Saul , Morrison Carl , Jacob Samson T.
Published: September 2004

Previous study in our laboratory demonstrated suppression of the gene for protein tyrosine phosphatase receptor-type O (
PTPRO
) in primary and established rat hepatomas. The present study showed methylation-mediated silencing of this gene in primary human lung tumors and in several human lung cancer cell lines, one of the characteristics of many tumor-suppressor genes. The reduced expression of
PTPRO
in the primary lung tumors correlated with the methylation status of its CpG island. Demethylation of the gene by deoxy-5-azacytidine treatment led to its reactivation in a lung cancer line (A549). Overexpression of PTPRO in A549 cells inhibited anchorage-independent growth, delayed reentry of the cells into the cell cycle after release from cell-cycle arrest, and increased susceptibility of the cells to apoptosis. These data have demonstrated the growth-suppressor characteristics of PTPRO that are unique to a classical tumor suppressor.
Factors Associated with Readiness to Stop Smoking among Patients in Treatment for Alcohol Use Disorder
Authors: Joseph Anne , Lexau Ben , Willenbring Mark , Nugent Sean , Nelson Dave
Published: September 2004

The Timing of Alcohol and Smoking Cessation (TASC) Study is a randomized controlled trial that examines the optimal timing of intervention for nicotine dependence in patients with alcohol use disorders. A cross‐sectional analysis of baseline characteristics of study participants was used to identify characteristics associated with readiness of patients in intensive treatment for alcohol abuse or dependence to quit smoking. Baseline characteristics of 499 subjects enrolled in the TASC trial were analyzed. Readiness to quit was assessed by two self‐rated measures: being in the preparation) action stages of change and scoring at least an 8 on the Contemplation Ladder. Univariate analyses showed a higher prevalence of African‐Americans and other minorities than Caucasian, among participants planning to quit in the next month (p = 0.005). There were no other differences between groups. Participants in the preparation/ action action stages of change experienced significantly lower rates of current (p = 0.011) and past (p = 0.014) major depressive disorder and displayed significantly less current depressive symptoms on the Beck Depression Inventory (p= 0.008). Patients with Contemplation Ladder ratings between 8 and 10 showed similar results. Logistic regression models consistently confirmed that the degree of depression was negatively associated with the intention to quit, but different models suggested that increasing age, shorter duration of smoking history, race other than white, and a greater number of past quit attempts were positively associated with readiness to quit. Among patients in intensive treatment for alcohol use disorders who smoke, a history of depressive disorder and depressive symptoms predict less interest in quitting smoking.
Cocaine Induces Apoptosis in Primary Cultured Rat Aortic Vascular Smooth Muscle Cells: Possible Relationship to Aortic Dissection, Atherosclerosis, and Hypertension
Authors: Su Jialin , Li Jianfeng , Li Wenyan , Altura Bella T. , Altura Burton M.
Published: September 2004

Cocaine abuse is known to induce many adverse cardiovascular effects, including hypertension, atherosclerosis, and aortic dissection. A major physiological event leading to these pathophysiological actions of cocaine could be apoptosis. This study was designed to investigate if primary cultured rat aortic vascular smooth muscle cells (VSMCs) can undergo apoptosis when treated with cocaine. After treatment with cocaine (10−6 to 10−4 M), morphological analysis of aortic VSMCs using confocal fluoresence microscopy showed that the percentage of apoptotic aortic VSMCs increased after cocaine (10−6 to 10−4 M) treatment for 12, 24, and 48 h. These results demonstrate that aortic VSMCs can undergo rapid apoptosis in response to cocaine in a concentration-dependent manner. Cocaine-induced apoptosis may thus play a major role in cocaine abuse-induced aortic dissection, atherosclerosis, and hypertension.
Impact of 30-Day Oral Dosing with N-acetyl-l-cysteine on Sprague-Dawley Rat Physiology
Authors: Arfsten Darryl P. , Johnson Eric W. , Thitoff Angie R. , Jung Anne E. , Wilfong Erin R. , Lohrke Scott M. , Bausman Tim A. , Eggers Jeffrey S. , Bobb Andrew J.
Published: September 2004

A number of studies have demonstrated a protective effect associated with N-acetyl-l-cysteine (NAC) against toxic chemical exposure. However, the impact of long-term oral dosing on tissue pathology has not been determined. In this study, the authors assessed the impact of long-term oral NAC administration on organ histopathology and tissue glutathione (GSH) and total glutathione- S-transferase (GST) activity levels in Sprague-Dawley (SD) rats. Groups of 20 SD rats (10 males, 10 females), 8 weeks of age, were dosed daily by oral gavage with deionized H2O (negative controls) or NAC solution at a rate of 600 or 1200 mg/kg/day for 30 days. Animals were euthanized 6 h after treatment on study day 30. There were no significant differences in final body weights or weekly average weight gain between treatment groups. Serum alanine amino-transferase (ALT) activities were significantly elevated ( p ≤.05) in NAC-treated animals compared to controls when measured on study day 30. Histopathologic evaluation of the stomach, small intestine, liver, kidneys, spleen, thymus, and lungs revealed no lesions associated with NAC administration. When measured on study day 30, total GST activity for kidney and skin from NAC-treated animals were increased 39% to 131% as compared to controls. Tissue GSH concentrations from NAC-treated animals were increased 24% to 81% as compared with negative controls. Further studies are needed to determine if the observed increase in tissue GSH concentration and GST activity provide a degree of chemoprotection against dermal and systemic chemical toxicants.
Perfluoro-n-Butyl Iodide: Acute Toxicity, Subchronic Toxicity and Genotoxicity Evaluations
Authors: Dodd Darol E. , Hoffman Gary M. , Hardy Colin J.
Published: September 2004

Perfluoro-n-butyl iodide (PFBI) is a promising alternative to chlorofluorocarbon solvents used in aircraft ground maintenance operations and other military and commercial operations, because it cleans well, has zero ozone depletion potential, and has extremely low global warming properties. Toxicity tests were performed with PFBI to determine and evaluate its health hazard. Using standard testing guidelines (e.g., Organization for Economic Cooperation and Development [OECD]), tests included acute (4-h) and 4-week (6 h/day, 5 days/week) inhalation (nose-only) toxicity studies in rats, acute (10-min) inhalation cardiac sensitization study in dogs, in vitro chromosomal aberrations experiments in human lymphocytes, and in vitro mutagenic experiments in Salmonella typhimurium and Escherichia coli. There were no mortalities in rats ( n = 10) exposed for 4 h to 10,000 ppm PFBI, but all rats ( n = 10) died within 2 h when exposed to 20,000 ppm PFBI. The 4-h LC50 (95% confidence limits) was 14,000 ppm (13,000 ppm to 16,000 ppm). Signs (nasal discharge and labored breathing) observed in the rats exposed to 10,000 ppm returned to normal within 48 h. PFBI has the potential to cause cardiac sensitization in epinephrine-challenged dogs at 6200 ppm. A concentration of 3900 ppm was a no-observed-adverse-effect level (NOAEL) in the cardiac sensitization study. In the 4-week inhalation study (5 rats/sex/group), respiratory mucosal hypertrophy/hyperplasia was observed in rats of the 10,000-ppm group. A NOAEL of 1000 ppm was selected for the 4-week study on the basis that the mild increase in T4 observed at 1000 ppm was considered adaptive, not adverse, because of the absence of frank effects in the thyroid. In the in vitro studies, PFBI showed no evidence of either mutagenic or clastogenic activity. The toxicity profile of PFBI was compared to trifluoroiodomethane. In conclusion, the results of these studies indicate a low order of general toxicity and an absence of genotoxicity following PFBI exposure.
Early-Phase Alcoholic Liver Disease: An Update on Animal Models, Pathology, and Pathogenesis
Authors: Ramaiah Shashi K. , Rivera Chantal , Arteel Gavin E.
Published: September 2004

Alcoholic liver disease (ALD) remains to be one of the most common etiology of liver disease and is a major cause of morbidity and mortality worldwide. The pathologic stages of ALD comprises of steatosis, steatohepatitis, and fibrosis/cirrhosis. Steatosis and steatohepatitis represents the early phase of ALD and are precursor stages for fibrosis/cirrhosis. Numerous research efforts have been directed at recognizing cofactors interacting with alcohol in the pathogenesis of steatosis and steatohepatitis. This review will elucidate the constellation of complex pathogenesis, available animal models, and microscopic pathologic findings mostly in the early-phase of ALD. The role of endotoxin, reactive oxygen species, alcohol metabolism, and cytokines are discussed. Understanding the mechanisms of early-phase ALD should provide insight into the development of therapeutic strategies and thereby decrease the morbidity and mortality associated with ALD.
Organophosphorus Compound–Induced Delayed Neurotoxicity in White Leghorn Hens Assessed by Fluoro-Jade
Authors: Carlson Kent , Ehrich Marion
Published: September 2004

Certain organophosphorus (OP) compounds can induce a delayed neuropathy, termed OPIDN, that involves central and peripheral nervous system axons, terminals, and perikarya. Historically, OPIDN has been characterized by staining neural sections with silver or hematoxylin and eosin (H&E). This study utilized a novel staining method, Fluoro-Jade, for evaluating the distribution and extent of OPIDN in the central nervous system of hens. Results were then compared to synoptically sectioned and stained H&E preparations. White Leghorn hens were injected with phenyl saligenin phosphate (PSP, 2.5 mg/kg, intramuscular [im]), triphenyl phosphite (TPPi, 500 mg/kg, subcutaneous [sc]), or dimethyl sulfoxide vehicle (DMSO, 0.5 ml/kg, im or sc) and evaluated clinically for signs of neurological dysfunction associated with OPIDN. Hens were sacrificed 7, 14, and 21 days post dosing. Brains and spinal cords were removed immediately following sacrifice, fixed in formalin, and embedded in paraffin. Microtomecut sections (7 μm) were then stained with Fluoro-Jade (0.001%, w/ v) or H&E. Staining with Fluoro-Jade revealed time-dependent degeneration of nerve fibers and terminals (with PSP and TPPi), or cell bodies (with TPPi) in lamina VII, spinocerebellar, and medial pontine-spinal tracts of the lumbar spinal cord, in white matter and mossy fibers of foliae I–V and IX of the cerebellum, and in medullary, pontine, and midbrain nuclei and paleostriatal fibers surrounding the optic tract. TPPi-induced degeneration was more extensive than that induced by PSP and affected additional cerebellar folia, medullary, pontine, midbrain, and forebrain nuclei and fiber tracts. H&E-stained sections revealed fewer sites of neurodegeneration when compared to Fluoro-Jade. These results demonstrate that Fluoro-Jade is a sensitive method for staining neural tissue affected by OPIDN.
Acute Renal Injury Following Methanol Poisoning: Analysis of a Case Series
Authors: Verhelst David , Moulin Pierre , Haufroid Vincent , Wittebole Xavier , Jadoul Michel , Hantson Philippe
Published: September 2004

The objective of this paper is to document the prevalence of indicators of acute renal injury in a series of methanol-poisoned patients treated in an intensive care unit and to discuss the possible mechanisms. This is a retrospective analysis of the medical records of 25 consecutive patients admitted to the intensive care unit after severe intentional methanol poisoning. Acute renal impairment was defined as a serum creatinine concentration higher than 177 μmol/L and/or a urinary output on admission and for the first 24 h below 0.5 ml/kg/h. Clinical pathological signs of acute renal injury were found in 15 patients. In comparison with the 10 other patients taken as control group, the patients who developed renal injury had a lower blood pH value on admission, a higher serum osmolality, and a higher peak formate concentration. Two factors contributing to renal injury could be identified: hemolysis and myoglobinuria. The role of osmotic changes (“osmotic nephrosis”) or of a direct cytotoxic effect of formic acid remains speculative. Analysis of proteinuria suggests that proximal tubular cells may be preferentially affected. Results of histopathological evaluation of the kidney on a limited sample size ( n = 5) were inconclusive but suggestive of possible hydropic changes in the proximal tubule secondary to methanol toxicity. Acute renal injury may be associated with other signs of severity in methanol poisoning, but it is almost always reversible in survivors. Indicators of acute renal injury were identified. The pathophysiology of this acute renal injury is multifactorial and far more complex than shock-related tubular necrosis.
Catch bonds govern adhesion through L-selectin at threshold shear
Authors: Yago Tadayuki , Wu Jianhua , Wey C. Diana , Klopocki Arkadiusz G. , Zhu Cheng , McEver Rodger P.
Published: September 2004

Flow-enhanced cell adhesion is an unexplained phenomenon that might result from a transport-dependent increase in on-rates or a force-dependent decrease in off-rates of adhesive bonds. L-selectin requires a threshold shear to support leukocyte rolling on P-selectin glycoprotein ligand-1 (PSGL-1) and other vascular ligands. Low forces decrease L-selectin–PSGL-1 off-rates (catch bonds), whereas higher forces increase off-rates (slip bonds). We determined that a force-dependent decrease in off-rates dictated flow-enhanced rolling of L-selectin–bearing microspheres or neutrophils on PSGL-1. Catch bonds enabled increasing force to convert short-lived tethers into longer-lived tethers, which decreased rolling velocities and increased the regularity of rolling steps as shear rose from the threshold to an optimal value. As shear increased above the optimum, transitions to slip bonds shortened tether lifetimes, which increased rolling velocities and decreased rolling regularity. Thus, force-dependent alterations of bond lifetimes govern L-selectin–dependent cell adhesion below and above the shear optimum. These findings establish the first biological function for catch bonds as a mechanism for flow-enhanced cell adhesion.
Good orbital integrals
Authors: Cunningham Clifton , Hales Thomas
Published: September 2004

This paper concerns a class of orbital integrals in Lie algebras over

p
p

-adic fields. The values of these orbital integrals at the unit element in the Hecke algebra count points on varieties over finite fields. The construction, which is based on motivic integration, works both in characteristic zero and in positive characteristic. As an application, the Fundamental Lemma for this class of integrals is lifted from positive characteristic to characteristic zero. The results are based on a formula for orbital integrals as distributions inflated from orbits in the quotient spaces of the Moy-Prasad filtrations of the Lie algebra. This formula is established by Fourier analysis on these quotient spaces.