bluuebunny/crossref_metadata_2025 huggingface dataset:
Transient Responses in a Piezoelectric Spherically Isotropic Hollow Sphere for Symmetric Problems
Authors: Ding H. J. , Wang H. M. , Chen W. Q.
Published: June 2003

By virtue of the separation of variables technique, the spherically symmetric electroelastic dynamic problem of a spherically isotropic hollow sphere is transformed to an integral equation about a function with respect to time, which can be solved successfully by means of the interpolation method. Then the solution of displacements, stresses, electric displacements, and electric potential are obtained. The present method is suitable for a piezoelectric hollow sphere with an arbitrary thickness subjected to spherically symmetric electric potential and radial mechanical loads, that both can be arbitrary functions about the time variable, at the internal and external surfaces.
Zeroth-Order Shear Deformation Theory for Laminated Composite Plates
Authors: Ray M. C.
Published: June 2003

In this paper a zeroth-order shear deformation theory has been derived for static and dynamic analysis of laminated composite plates. The responses obtained by the theory for symmetric and antisymmetric laminates are compared with the existing solutions. The comparison firmly establishes that this new shear deformation theory can be used for both thick and thin laminated composite plates with high accuracy.
Load Distribution in Cylindrical Worm Gears
Authors: Simon Vilmos
Published: June 2003

A method for the determination of load sharing between the instantaneously engaged worm threads and gear teeth, for the calculation of load distribution along the teeth and transmission errors in different types of cylindrical worm gears is presented. The method covers both cases—that of the theoretical line and point contact. The bending and shearing deflections of worm thread and gear tooth, the local contact deformations of the mating surfaces, the axial deformations of worm body, gear body bending and torsion, deflections of the supporting shafts, and the manufacturing and alignment errors of worm and gear are included. Based on the real load distribution the tooth contact pressure is calculated, in the case of point contact in two different ways, and the obtained results are compared. Also, the total transmission error, consisting of the kinematical transmission error due to the mismatch of the worm gear drive and of the transmission error caused by the deflections of worm thread and gear teeth, is calculated. The method is implemented by a computer program. By using this program the influence of the type of worm gear drive and of design and manufacturing parameters on load distribution and transmission errors is investigated and discussed.
Dynamics of Hypoid Gear Transmission With Nonlinear Time-Varying Mesh Characteristics
Authors: Cheng Yuping , Lim Teik C.
Published: June 2003

The coupled translation-rotation vibratory response of hypoid geared rotor system due to loaded transmission error excitation is studied by employing a generalized 3-dimensional dynamic model. The formulation includes the effects of backlash nonlinearity as well as time-dependent mesh position and line-of-action vectors. Its mesh coupling is derived from a quasi-static, 3-dimensional, loaded tooth contact analysis model that accounts for the precise gear geometry and profile modifications. The numerical simulations show significant tooth separation and occurrence of multi-jump phenomenon in the predicted response spectra under certain lightly loaded operating conditions. Also, resonant modes contributing to the response spectra are identified, and cases with super-harmonics are illustrated. The computational results are then analyzed to quantify the extent of non-linear and time-varying factors.
Analysis for the Effect of Inverter Ripple Current on Fuel Cell Operating Condition
Authors: Gemmen Randall S.
Published: June 2003

The effect of inverter ripple current on fuel cell stack performance and stack lifetime remains uncertain. This paper provides a first attempt to examine the impact of inverter load dynamics on the fuel cell. Since reactant utilization is known to impact the mechanical nature of a fuel cell, it is suggested that the varying reactant conditions surrounding the cell govern, at least in part, the lifetime of the cells. This paper investigates these conditions through the use of a dynamic model for the bulk conditions within the stack, as well as a one-dimensional model for the detailed mass transport occurring within the electrode of a cell. These two independent modeling approaches are used to verify their respective numerical procedures. In this work, the inverter load is imposed as a boundary condition to the models. Results show the transient behavior of the reactant concentrations within the stack, and of the mass diffusion within the electrode under inverter loads with frequencies between 30 Hz and 1250 Hz.
Experiments and Modeling in Bubbly Flows at Elevated Pressures
Authors: Kumar Ranganathan , Trabold Thomas A. , Maneri Charles C.
Published: June 2003

Measurements of local void fraction, rise velocity, and bubble diameter have been obtained for cocurrent, wall-heated, upward bubbly flows in a pressurized refrigerant. The instrumentation used are the gamma densitometer and the hot-film anemometer. Departure bubble size is correlated in terms of liquid subcooling and bulk bubble size in terms of void fraction. Flow visualization techniques have also been used to understand the two-phase flow structure and the behavior of the bubbly flow for different bubble shapes and sizes, and to obtain the bubble diameter and rise velocity. The lift model is provided explicitly in terms of Eotvos number which is changed by changing the system pressure. In general, Eotvos number plays a strong role in determining both bubbly lift and drag. Such insight coupled with quantitative local and averaged data on void fraction and bubble size at different pressures has aided in developing bubbly flow models applicable to heated two-phase flows at high pressure.
Computations of the Compressible Multiphase Flow Over the Cavitating High-Speed Torpedo
Authors: Owis F. M. , Nayfeh Ali H.
Published: June 2003

For high-speed cavitating flows, compressibility becomes significant in the liquid phase as well as in the vapor phase. In addition, the compressible energy equation is required for studying the effects of the propulsive jet on the cavity. Therefore, a numerical method is developed to compute cavitating flows over high-speed torpedoes using the full unsteady compressible Navier-Stokes equations. The multiphase system of equations is preconditioned for low-speed flow computations. Using the mass fraction form, we derive an eigensystem for both the conditioned and the nonconditioned system of equations. This eigensystem provides stability for the numerical discretization of the convective flux and increases the convergence rate. This method can be used to compute single as well as multiphase flows. The governing equations are discretized on a structured grid using an upwind flux difference scheme with flux limits. Single as well as multiphase flows are computed over a cavitating torpedo. The results indicate that the preconditioned system of equations converges rapidly to the required solution at very low speeds. The theoretical results are in good agreement with the measurements.
Modeling of Combustion in Gasoline Direct Injection Engines for the Optimization of Engine Management System Through Reduction of Three-Dimensional Models to (n × One-Dimensional) Models
Authors: Emery P. , Maroteaux F. , Sorine M.
Published: June 2003

Gasoline direct injection (GDI) spark ignition engines may be able to run over a wide range of operating conditions. The GDI process allows combustion with lean mixtures which may lead to improved fuel economy and emissions relative to homogeneous spark ignition (SI) engines. To satisfy the different modes of operation, the tuning of GDI engines requires a large number of engine tests which are time-consuming and very expensive. To reduce the number of tests, a model with a very short computational time to simulate the engines in the whole operating range is needed; therefore the objective of this paper is to present a reduced model to analyze the combustion process in GDI engines, applied to a homogeneous stoichiometric mode. The objective of the model is to reproduce the same tendencies as those obtained by three-dimensional models, but with a reduced computational time. The one-dimensional model is obtained thanks to a reduction methodology based on the geometry of the combustion front computed with three-dimensional models of the KIVA-GSM code, a modified version of KIVA-II code including a CFM combustion model. The model is a set of n one-dimensional equations (i.e., for n rays), taking into account a thin flame front, described with the flamelet assumption. It includes a CFM combustion model and a (k,ε)-model including the mean air motions (swirl and tumble). The results of the one-dimensional model are compared to those obtained by the KIVA IIGSM under different engine conditions. The comparison shows that the one-dimensional model overestimates the maximum cylinder pressure, which has an insignificant effect on the net indicated work per cycle. The results obtained by the numerical simulations are close to those given by the three-dimensional model, with a much reduced computation time.
Investigation of Variable Frequency Microwave Processing for Electronic Packaging Applications
Authors: Mead Patricia F. , Ramamoorthy Aravind , Pal Shapna
Published: June 2003

This paper summarizes the effects of the variable frequency microwave (VFM) technique for rapid cure of polymeric encapsulants (such as flip-chip underfills) on the performance and reliability of electronic devices. Initial electrical performance of selected commercial IC packages following the application of VFM radiation stress has been recorded, and the performance has been compared to packages that were treated with comparable temperature cycles as applied in a convection oven. Failure analysis was performed on packages that showed electrical degradation to identify likely degradation and failure modes of the packaged ICs. Overall, our results show that VFM technology can safely be applied as an electronic packaging technology. However, proper control of VFM operating parameters is needed to ensure favorable performance of electronic devices.
Michell’s General Solutions for Torsionless Axisymmetric Problems With Body Forces in Elasticity
Authors: Lou Y. C. , Wang M. Z.
Published: June 2003

In this note, it is pointed out that simple modified Michell’s general solutions may treat the torsionless axisymmetric problems with both axial and radial body forces in elasticity and are more convenient in some cases contrast to Love’s solutions.
Analysis of Laminated Anisotropic Cylindrical Shell by Chebyshev Collocation Method
Authors: Lin C.-H. , Jen M.-H. R.
Published: June 2003

The governing equations of a laminated anisotropic cylindrical shell problem are a system of partial differential equations. The boundary conditions will complicate the problem. Thus, it is hard to handle the governing equations in the form of functions of independent variables. Herein, Chebyshev collocation method is proposed to achieve the exact solution theoretically of such a difficult problem. Finally, two examples with numerical results are presented. The preciseness and efficiency of the proposed Chebyshev collocation method for laminated anisotropic shell problem are highlighted.
A Sub-Domain Inverse Finite Element Characterization of Hyperelastic Membranes Including Soft Tissues
Authors: Seshaiyer Padmanabhan , Humphrey Jay D.
Published: June 2003

Quantification of the mechanical behavior of hyperelastic membranes in their service configuration, particularly biological tissues, is often challenging because of the complicated geometry, material heterogeneity, and nonlinear behavior under finite strains. Parameter estimation thus requires sophisticated techniques like the inverse finite element method. These techniques can also become difficult to apply, however, if the domain and boundary conditions are complex (e.g. a non-axisymmetric aneurysm). Quantification can alternatively be achieved by applying the inverse finite element method over sub-domains rather than the entire domain. The advantage of this technique, which is consistent with standard experimental practice, is that one can assume homogeneity of the material behavior as well as of the local stress and strain fields. In this paper, we develop a sub-domain inverse finite element method for characterizing the material properties of inflated hyperelastic membranes, including soft tissues. We illustrate the performance of this method for three different classes of materials: neo-Hookean, Mooney Rivlin, and Fung-exponential.
Alterations in the Mechanical Properties of the Human Chondrocyte Pericellular Matrix With Osteoarthritis
Authors: Alexopoulos Leonidas G. , Haider Mansoor A. , Vail Thomas P. , Guilak Farshid
Published: June 2003

In articular cartilage, chondrocytes are surrounded by a pericellular matrix (PCM), which together with the chondrocyte have been termed the “chondron.” While the precise function of the PCM is not known there has been considerable speculation that it plays a role in regulating the biomechanical environment of the chondrocyte. In this study, we measured the Young’s modulus of the PCM from normal and osteoarthritic cartilage using the micropipette aspiration technique, coupled with a newly developed axisymmetric elastic layered half-space model of the experimental configuration. Viable, intact chondrons were extracted from human articular cartilage using a new microaspiration-based isolation technique. In normal cartilage, the Young’s modulus of the PCM was similar in chondrons isolated from the surface zone (68.9±18.9 kPa) as compared to the middle and deep layers (62.0±30.5 kPa). However, the mean Young’s modulus of the PCM (pooled for the two zones) was significantly decreased in osteoarthritic cartilage (66.5±23.3 kPa versus 41.3±21.1 kPa, p<0.001). In combination with previous theoretical models of cell-matrix interactions in cartilage, these findings suggest that the PCM has an important influence on the stress-strain environment of the chondrocyte that potentially varies with depth from the cartilage surface. Furthermore, the significant loss of PCM stiffness that was observed in osteoarthritic cartilage may affect the magnitude and distribution of biomechanical signals perceived by the chondrocytes.
Automatic three‐dimensional model for protontherapy of the eye: Preliminary results
Authors: Bondiau Pierre‐Yves , Malandain Gregoire , Chauvel Pierre , Peyrade Frédérique , Courdi Adel , Iborra Nicole , Caujolle Jean‐Pierre , Gastaud Pierre
Published: June 2003

Recently, radiotherapy possibilities have been dramatically increased by software and hardware developments. Improvements in medical imaging devices have increased the importance of three‐dimensional (3D) images as the complete examination of these data by a physician is not possible. Computer techniques are needed to present only the pertinent information for clinical applications. We describe a technique for an automatic 3D reconstruction of the eye and CT scan merging with fundus photographs (retinography). The final result is a “virtual eye” to guide ocular tumor protontherapy. First, we make specific software to automatically detect the position of the eyeball, the optical nerve, and the lens in the CT scan. We obtain a 3D eye reconstruction using this automatic method. Second, we describe the retinography and demonstrate the projection of this modality. Then we combine retinography with a reconstructed eye, using a CT scan to get a virtual eye. The result is a computer 3D scene rendering a virtual eye into a skull reconstruction. The virtual eye can be useful for the simulation, the planning, and the control of ocular tumor protontherapy. It can be adapted to treatment planning to automatically detect eye and organs at risk position. It should be highlighted that all the image processing is fully automatic to allow the reproduction of results, this is a useful property to conduct a consistent clinical validation. The automatic localization of the organ at risk in a CT scan or an MRI by automatic software could be of great interest for radiotherapy in the future for comparison of one patient at different times, the comparison of different treatments centers, the possibility of pooling results of different treatments centers, the automatic generation of doses–volumes histograms, the comparison between different treatment planning for the same patient and the comparison between different patients at the same time. It will also be less time consuming.
Beta voxel S values for internal emitter dosimetry
Authors: Franquiz J. M. , Chigurupati S. , Kandagatla K.
Published: June 2003

Monte Carlo volume integration of dose point kernels was used for calculating voxel S values of beta emissions of radionuclides of interest for internal radiotherapy. The method was verified by comparing our results with others derived from Monte Carlo radiation transport simulation. The algorithm has been implemented in a C++ program that can be used by any laboratory to calculate voxel S values of beta emissions from tabulated dose point kernels and for any combination of pixel edges and the thickness of SPECT and PET images without the complexity and expertise needed for direct Monte Carlo radiation transport simulations.
The theoretical benefit of beam fringe compensation and field size reduction for iso‐normal tissue complication probability dose escalation in radiotherapy of lung cancer
Authors: Engelsman Martijn , Remeijer Peter , van Herk Marcel , Mijnheer Ben , Damen Eugène
Published: June 2003

To assess the benefit of beam fringe (50%–90% dose level) sharpening for lung tumors, we performed a numerical simulation in which all geometrical errors (breathing motion, random and systematic errors) are included. A 50 mm diameter lung tumor, located centrally in a lung‐equivalent phantom was modeled. Treatment plans were designed with varying number and direction of beams, both with and without the use of intensity modulation to sharpen the beam fringe. Field size and prescribed dose were varied under the constraint of a constant mean lung dose of 20 Gy, which yields a predicted complication probability of about 10%. After numerical simulation of the effect of setup errors and breathing, the resulting dose distribution was evaluated using the minimum dose and the equivalent uniform dose (EUD) in the moving clinical target volume (CTV). When the dose in the CTV was constrained between 95% and 107% of the prescribed dose, the maximum attainable EUD was 71 Gy for a four‐field noncoplanar technique with simple conformal beams. When penumbra sharpening was applied using a single beam segment at the edge of the open field, this EUD could be raised to 87 Gy. For a hypothetical infinitely steep penumbra, further escalation to an EUD of 104 Gy was possible. When the dose in the CTV was not constrained, a large escalation of the EUD was possible compared to the constrained case. In this case, the maximum attainable EUD for open fields was 115 Gy, using the four‐field noncoplanar technique. The benefit of penumbra sharpening was only modest, with no increase of the EUD for the single‐segment technique and a small increase to 125 Gy for the infinitely steep penumbra. From these results we conclude that beam fringe sharpening in combination with field‐size reduction leads to a large increase in EUD when a homogeneous target dose is pursued. Further escalation of the EUD is possible when the homogeneity constrained is relaxed, but the relative benefit of beam‐fringe sharpening then decreases.
A new local multiscale Fourier analysis for medical imaging
Authors: Zhu H. , Goodyear B. G. , Lauzon M. L. , Brown R. A. , Mayer G. S. , Law A. G. , Mansinha L. , Mitchell J. R.
Published: June 2003

The Stockwell transform (ST), recently developed for geophysics, combines features of the Fourier, Gabor and wavelet transforms; it reveals frequency variation over time or space. This valuable information is obtained by Fourier analysis of a small segment of a signal at a time. Localization of the Fourier spectrum is achieved by filtering the signal with frequency‐dependent Gaussian scaling windows. This multi‐scale time–frequency analysis provides information about which frequencies occur and more importantly when they occur. Furthermore, the Stockwell domain can be directly inferred from the Fourier domain andvice versa. These features make the ST a potentially effective tool to visualize, analyze, and process medical imaging data. The ST has proven useful in noise reduction and tissue texture analysis. Herein, we focus on the theory and effectiveness of the ST for medical imaging. Its effectiveness and comparison with other linear time–frequency transforms, such as the Gabor and wavelet transforms, are discussed and demonstrated using functional magnetic resonance imaging data.
Requirement of AMPA Receptor GluR2 Phosphorylation for Cerebellar Long-Term Depression
Authors: Chung Hee Jung , Steinberg Jordan P. , Huganir Richard L. , Linden David J.
Published: June 2003

Cerebellar long-term depression (LTD) is a model of synaptic memory that requires protein kinase C (PKC) activation and is expressed as a reduction in the number of postsynaptic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) receptors. LTD was absent in cultured cerebellar Purkinje cells from mutant mice lacking the AMPA receptor GluR2 subunit and could be rescued by transient transfection with the wild-type GluR2 subunit. Transfection with a point mutant that eliminated PKC phosphorylation of Ser
880
in the carboxy-terminal PDZ ligand of GluR2 failed to restore LTD. In contrast, transfection with a point mutant that mimicked phosphorylation at Ser
880
occluded subsequent LTD. Thus, PKC phosphorylation of GluR2 Ser
880
is a critical event in the induction of cerebellar LTD.
Certainly Nondeterministic
Authors: Schultz Wolfram
Published: June 2003

Decisions, Uncertainty, and the Brain
The Science of Neuroeconomics. Paul W. Glimcher. MIT Press, Cambridge, MA, 2003. 395 pp. $37.95, £25.50. ISBN 0-262-07244-0.

Glimcher outlines an economics-based model for studying the neural processes that connect sensation and action.
Sex-Dependent Gene Expression and Evolution of the
Drosophila
Transcriptome
Authors: Ranz José M. , Castillo-Davis Cristian I. , Meiklejohn Colin D. , Hartl Daniel L.
Published: June 2003

Comparison of the gene-expression profiles between adults of
Drosophila melanogaster
and
Drosophila simulans
has uncovered the evolution of genes that exhibit sex-dependent regulation. Approximately half the genes showed differences in expression between the species, and among these, ∼83% involved a gain, loss, increase, decrease, or reversal of sex-biased expression. Most of the interspecific differences in messenger RNA abundance affect male-biased genes. Genes that differ in expression between the species showed functional clustering only if they were sex-biased. Our results suggest that sex-dependent selection may drive changes in expression of many of the most rapidly evolving genes in the
Drosophila
transcriptome.
Nota Bene: You Want To Build It with What?
Authors: Lavine Marc
Published: June 2003

Materials and Design
The Art and Science of Material Selection in Product Design. Mike Ashby and Kara Johnson. Butterworth-Heinemann (Elsevier Science) Oxford, 2002. 348 pp. Paper, $49.99, £24.99. ISBN 0-7506-5554-2.

Demonstrating how important the selection of materials is to the design of objects, the authors discuss the impact of aspects from strength and toughness to texture and color.
Identification of Pyrene-Induced Proteins in
Mycobacterium
sp. Strain 6PY1: Evidence for Two Ring-Hydroxylating Dioxygenases
Authors: Krivobok Serge , Kuony Sylvain , Meyer Christine , Louwagie Mathilde , Willison John C. , Jouanneau Yves
Published: June 2003

In this study, the enzymes involved in polycyclic aromatic hydrocarbon (PAH) degradation were investigated in the pyrene-degrading
Mycobacterium
sp. strain 6PY1. [
14
C]pyrene mineralization experiments showed that bacteria grown with either pyrene or phenanthrene produced high levels of pyrene-catabolic activity but that acetate-grown cells had no activity. As a means of identifying specific catabolic enzymes, protein extracts from bacteria grown on pyrene or on other carbon sources were analyzed by two-dimensional gel electrophoresis. Pyrene-induced proteins were tentatively identified by peptide sequence analysis. Half of them resembled enzymes known to be involved in phenanthrene degradation, with closest similarity to the corresponding enzymes from
Nocardioides
sp. strain KP7. The genes encoding the terminal components of two distinct ring-hydroxylating dioxygenases were cloned. Sequence analysis revealed that the two enzymes, designated Pdo1 and Pdo2, belong to a subfamily of dioxygenases found exclusively in gram-positive bacteria. When overproduced in
Escherichia coli
, Pdo1 and Pdo2 showed distinctive selectivities towards PAH substrates, with the former enzyme catalyzing the dihydroxylation of both pyrene and phenanthrene and the latter preferentially oxidizing phenanthrene. The catalytic activity of the Pdo2 enzyme was dramatically enhanced when electron carrier proteins of the phenanthrene dioxygenase from strain KP7 were coexpressed in recombinant cells. The Pdo2 enzyme was purified as a brown protein consisting of two types of subunits with
M
r
s of about 52,000 and 20,000. Immunoblot analysis of cell extracts from strain 6PY1 revealed that Pdo1 was present in cells grown on benzoate, phenanthrene, or pyrene and absent in acetate-grown cells. In contrast, Pdo2 could be detected only in PAH-grown cells. These results indicated that the two enzymes were differentially regulated depending on the carbon source used for growth.
NikAB- or NikB-Dependent Intracellular Recombination between Tandemly RepeatedoriTSequences of Plasmid R64 in Plasmid or Single-Stranded Phage Vectors
Authors: Furuya Nobuhisa , Komano Teruya
Published: June 2003

The origin of transfer (oriT) of a bacterial plasmid plays a key role in both the initiation and termination of conjugative DNA transfer. We have previously shown that a conjugation-dependent recombination between the tandem R64oriTsequences cloned into pHSG398 occurred, resulting in the deletion of the intervening sequence during DNA transfer. In this study, we tandemly cloned twooriTsequences of IncI1 plasmid R64 into pUC18. Specific recombination between the twooriTsequences in pUC18 was observed withinEscherichia colicells harboring mini-R64. This recombination was found to be independent of both therecAgene and conjugative DNA transfer. The R64 genesnikAandnikB, required for conjugal DNA processing, were essential for this recombination. Although a fully active 92-bporiTsequence was required at one site for the recombination, the 44-bporiTcore sequence was sufficient at the other site. Furthermore, when twooriTsequences were tandemly cloned into the single-stranded phage vector M13 and propagated withinE. colicells, recombination between the twooriTsequences was observed, depending on thenikBgene. These results suggest that the R64 relaxase protein NikB can execute cleavage and rejoining of single-strandedoriTDNA withinE. colicells, whereas such a reaction in double-strandedoriTDNA requires collaboration of the two relaxosome proteins, NikA and NikB.
Transcriptional Regulation of the Gene Encoding an Alcohol Dehydrogenase in the Archaeon
Sulfolobus solfataricus
Involves Multiple Factors and Control Elements
Authors: Fiorentino Gabriella , Cannio Raffaele , Rossi Mosè , Bartolucci Simonetta
Published: June 2003

A transcriptionally active region has been identified in the 5′ flanking region of the alcohol dehydrogenase gene of the crenarchaeon
Sulfolobus solfataricus
through the evaluation of the activity of putative transcriptional regulators and the role of the region upstream of the gene under specific metabolic circumstances. Electrophoretic mobility shift assays with crude extracts revealed protein complexes that most likely contain TATA box-associated factors. When the TATA element was deleted from the region, binding sites for both DNA binding proteins, such as the small chromatin structure-modeling Sso7d and Sso10b (Alba), and transcription factors, such as the repressor Lrs14, were revealed. To understand the molecular mechanisms underlying the substrate-induced expression of the
adh
gene, the promoter was analyzed for the presence of
cis
-acting elements recognized by specific transcription factors upon exposure of the cell to benzaldehyde. Progressive dissection of the identified promoter region restricted the analysis to a minimal responsive element (PAL) located immediately upstream of the transcription factor B-responsive element-TATA element, resembling typical bacterial regulatory sequences. A benzaldehyde-activated transcription factor (Bald) that specifically binds to the PAL
cis
-acting element was also identified. This protein was purified from heparin-fractionated extracts of benzaldehyde-induced cells and was shown to have a molecular mass of ∼16 kDa. The correlation between
S. solfataricus adh
gene activation and benzaldehyde-inducible occupation of a specific DNA sequence in its promoter suggests that a molecular signaling mechanism is responsible for the switch of the aromatic aldehyde metabolism as a response to environmental changes.
Bradyrhizobium japonicumNnrR, a Denitrification Regulator, Expands the FixLJ-FixK2Regulatory Cascade
Authors: Mesa Socorro , Bedmar Eulogio J. , Chanfon Astrid , Hennecke Hauke , Fischer Hans-Martin
Published: June 2003

InBradyrhizobium japonicum, a gene namednnrRwas identified which encodes a protein with high similarity to FNR/CRP-type transcriptional regulators. Mutant strains carrying annnrRnull mutation were unable to grow anaerobically in the presence of nitrate or nitrite, and they lacked both nitrate and nitrite reductase activities. Anaerobic activation of annnrR′-′lacZfusion required FixLJ and FixK2. In turn, N oxide-mediated induction ofnirandnorgenes encoding nitrite and nitric oxide reductase, respectively, depended on NnrR. Thus, NnrR expands the FixLJ-FixK2regulatory cascade by an additional control level which integrates the N oxide signal required for maximal induction of the denitrification genes.
Hepatitis B Virus Core Protein Stimulates the Proteasome-Mediated Degradation of Viral X Protein
Authors: Kim Jung-Hwan , Kang Seongman , Kim Joon , Ahn Byung-Yoon
Published: June 2003

Hepatitis B virus (HBV) X protein (HBx) plays an essential role in viral replication and in the development of hepatocellular carcinoma. HBx has the ability to transactivate the expression of all HBV proteins, including the viral core protein HBc. Consistent with its regulatory role, HBx is relatively unstable and is present at low levels in the cell. We report here that the level of HBx was significantly reduced by the coexpression of HBc in cultured human hepatoma cells, whereas the level of HBx mRNA was unaffected. The repression of HBx by HBc was relieved by treating cells with the proteasome inhibitor MG132, indicating that HBc acts by stimulating the proteasome-mediated degradation of HBx. Moreover, the inhibitory effect of HBc was specific to HBx and did not affect other proteins, including p53, a known target of the proteasome. Although no direct physical interaction between HBc and HBx could be demonstrated, mutational analysis indicated that the C-terminal half of HBc is responsible for its inhibitory effect. These results suggest that HBc functions as a novel regulator of the HBV life cycle and of hepatocellular carcinogenesis through control of the HBx level via an inhibitory feedback type of mechanism.
Flexibility of the Adenovirus Fiber Is Required for Efficient Receptor Interaction
Authors: Wu Eugene , Pache Lars , Von Seggern Dan J. , Mullen Tina-Marie , Mikyas Yeshi , Stewart Phoebe L. , Nemerow Glen R.
Published: June 2003

The adenovirus (Ad) fiber protein mediates Ad binding to the coxsackievirus and Ad receptor (CAR) and is thus a major determinant of viral tropism. The fiber contains three domains: an N-terminal tail that anchors the fiber to the viral capsid, a central shaft region of variable length and flexibility, and a C-terminal knob domain that binds to cell receptors. Ad type 37 (Ad37), a subgroup D virus associated with severe ocular infections, is unable to use CAR efficiently to infect host cells, despite containing a CAR binding site in its fiber knob. We hypothesized that the relatively short, inflexible Ad37 fiber protein restricts interactions with CAR at the cell surface. To test this hypothesis, we analyzed the infectivity and binding of recombinant Ad particles containing modified Ad37 or Ad5 fiber proteins. Ad5 particles equipped with a truncated Ad5 fiber or with a chimeric fiber protein comprised of the Ad5 knob fused to the short, rigid Ad37 shaft domain had significantly reduced infectivity and attachment. In contrast, placing the Ad37 knob onto the long, flexible Ad5 shaft allowed CAR-dependent virus infection and cell attachment, demonstrating the importance of the shaft domain in receptor usage. Increasing fiber rigidity by substituting the predicted flexibility modules in the Ad5 shaft with the corresponding regions of the rigid Ad37 fiber dramatically reduced both virus infection and cell attachment. Cryoelectron microscopy (cryo-EM) single-particle analysis demonstrated the increased rigidity of this chimeric fiber. These studies demonstrate that both length and flexibility of the fiber shaft regulate CAR interaction and provide a molecular explanation for the use of alternative receptors by subgroup D Ad with ocular tropism. We present a molecular model for Ad-CAR interactions at the cell surface that explains the significance of fiber flexibility in cell attachment.
Viral Escape from Dominant Simian Immunodeficiency Virus Epitope-Specific Cytotoxic T Lymphocytes in DNA-Vaccinated Rhesus Monkeys
Authors: Barouch Dan H. , Kunstman Jennifer , Glowczwskie Jennifer , Kunstman Kevin J. , Egan Michael A. , Peyerl Fred W. , Santra Sampa , Kuroda Marcelo J. , Schmitz Jörn E. , Beaudry Kristin , Krivulka Georgia R. , Lifton Michelle A. , Gorgone Darci A. , Wolinsky Steven M. , Letvin Norman L.
Published: June 2003

Virus-specific cytotoxic T lymphocytes (CTL) are critical for control of human immunodeficiency virus type 1 replication. However, viral escape from CTL recognition can undermine this immune control. Here we demonstrate the high frequency and pattern of viral escape from dominant epitope-specific CTL in SIVgagDNA-vaccinated rhesus monkeys following a heterologous simian immunodeficiency virus (SIV) challenge. DNA-vaccinated monkeys exhibited initial effective control of the SIV challenge, but this early control was lost by serial breakthroughs of viral replication over a 3-year follow-up period. Increases in plasma viral RNA correlated temporally with declines of dominant SIV epitope-specific CD8+T-lymphocyte responses and the emergence of viral mutations that escaped recognition by dominant epitope-specific CTL. Viral escape from CTL occurred in a total of seven of nine vaccinated and control monkeys, including three animals that initially controlled viral replication to undetectable levels of plasma viral RNA. These data suggest that CTL exert selective pressure on viral replication and that viral escape from CTL may be a limitation of CTL-based AIDS vaccine strategies.
The Herpes Simplex Virus Type 1 Alkaline Nuclease and Single-Stranded DNA Binding Protein Mediate Strand Exchange In Vitro
Authors: Reuven Nina Bacher , Staire Amy E. , Myers Richard S. , Weller Sandra K.
Published: June 2003

The replication of herpes simplex virus type 1 (HSV-1) DNA is associated with a high degree of homologous recombination. While cellular enzymes may take part in mediating this recombination, we present evidence for an HSV-1-encoded recombinase activity. HSV-1 alkaline nuclease, encoded by the UL12 gene, is a 5′→3′ exonuclease that shares homology with Redα, commonly known as λ exonuclease, an exonuclease required for homologous recombination by bacteriophage lambda. The HSV-1 single-stranded DNA binding protein ICP8 is an essential protein for HSV DNA replication and possesses single-stranded DNA annealing activities like the Redβ synaptase component of the phage lambda recombinase. Here we show that UL12 and ICP8 work together to effect strand exchange much like the Red system of lambda. Purified UL12 protein and ICP8 mediated the complete exchange between a 7.25-kb M13mp18 linear double-stranded DNA molecule and circular single-stranded M13 DNA, forming a gapped circle and a displaced strand as final products. The optimal conditions for strand exchange were 1 mM MgCl
2
, 40 mM NaCl, and pH 7.5. Stoichiometric amounts of ICP8 were required, and strand exchange did not depend on the nature of the double-stranded end. Nuclease-defective UL12 could not support this reaction. These data suggest that diverse DNA viruses appear to utilize an evolutionarily conserved recombination mechanism.
Cytokine Profiles in Adult Mink Infected with Aleutian Mink Disease Parvovirus
Authors: Jensen P. V. , Castelruiz Y. , Aasted B.
Published: June 2003

The aim of this study was to examine the levels of gamma interferon (IFN-γ)-, interleukin 4 (IL-4)-, and IL-8-producing cells in peripheral blood mononuclear cells from mink infected with the Aleutian mink disease parvovirus (ADV). As expected, ADV-infected mink developed high plasma gamma globulin values (hypergammaglobulinemia) and enhanced quantities of CD8-positive (CD8+) cells in the blood during the infection. We quantified the percentages of IFN-γ- and IL-4-positive lymphocytes and IL-8-positive monocytes up to week 38 after virus challenge. The results clearly indicated marked increases in the percentages of IFN-γ- and IL-4-producing lymphocytes during ADV infection. The total number of IL-8-producing monocytes in the blood of ADV-infected mink stayed fairly constant during the infection. In order to characterize the phenotype of the cytokine-producing cells, we performed double-labeling fluorescence-activated cell sorter (FACS) experiments with CD8 surface labeling in one channel and cytokine intracellular staining in the other. We found that most IFN-γ and IL-4 in ADV-infected mink was produced by CD8+cells, while in the uninfected mink, these cytokines were primarily produced by a cell type that was not CD8 (possibly CD4-positive cells). We also observed that IL-8 was almost exclusively produced by monocytes. All of the above findings led us to conclude that both Th1- and Th2-driven immune functions are found in mink plasmacytosis.
Functional Analysis of the Endogenous Retroviral Promoter of the Human Endothelin B Receptor Gene
Authors: Landry Josette-Renée , Mager Dixie L.
Published: June 2003

We previously reported that the long terminal repeats (LTRs) of retroviral elements belonging to the HERV-E family contribute to the expression of the human apolipoprotein C1 (
APOC1
) and endothelin B receptor (
EDNRB
) genes by providing alternative promoters. While both LTRs were shown to promote transcription in vivo and in vitro, their respective activity and tissue specificity appeared to differ even though they shared a high degree of sequence identity. In the present study, we further characterized the promoter of the
EDNRB
LTR and delineated the regions and motifs required for strong activity. We confirmed the placenta-restricted expression of the LTR by transient transfections and quantitative real-time PCR and determined that the retroviral promoter contributes significantly to the level of
EDNRB
transcripts in placenta, where chimeric mRNAs were found to represent 15% of overall
EDNRB
mRNAs. Transient transfection of 5′ deletion constructs in cells of placental origin identified a motif, named LPE1, between positions 111 and 122 of the
EDNRB
LTR necessary for transcriptional activity. Removal of this region, which contains a putative SP1 binding site, abolished promoter activity. A second enhancing region resides between positions 175 and 215 of the LTR and was termed LPE2. Interestingly, this section contained three binding sites that were not present in the
APOC1
LTR due to minor nucleotide differences. The predicted motifs in the
EDNRB
LTR were found to likely act in symbiosis as modifications to any of the three sites reduced transcription by one-third while alterations to all three eliminated promoter activity. The results from this study illustrate how slight variations in transcriptional regulatory sequences can have a profound effect on promoter activity and demonstrate the complex regulatory effects of human endogenous retrovirus elements on human gene expression.
Poxvirus Orthologous Clusters: toward Defining the Minimum Essential Poxvirus Genome
Authors: Upton Chris , Slack Stephanie , Hunter Arwen L. , Ehlers Angelika , Roper Rachel L.
Published: June 2003

Increasingly complex bioinformatic analysis is necessitated by the plethora of sequence information currently available. A total of 21 poxvirus genomes have now been completely sequenced and annotated, and many more genomes will be available in the next few years. First, we describe the creation of a database of continuously corrected and updated genome sequences and an easy-to-use and extremely powerful suite of software tools for the analysis of genomes, genes, and proteins. These tools are available free to all researchers and, in most cases, alleviate the need for using multiple Internet sites for analysis. Further, we describe the use of these programs to identify conserved families of genes (poxvirus orthologous clusters) and have named the software suite POCs, which is available at
www.poxvirus.org
. Using POCs, we have identified a set of 49 absolutely conserved gene families—those which are conserved between the highly diverged families of insect-infecting entomopoxviruses and vertebrate-infecting chordopoxviruses. An additional set of 41 gene families conserved in chordopoxviruses was also identified. Thus, 90 genes are completely conserved in chordopoxviruses and comprise the minimum essential genome, and these will make excellent drug, antibody, vaccine, and detection targets. Finally, we describe the use of these tools to identify necessary annotation and sequencing updates in poxvirus genomes. For example, using POCs, we identified 19 genes that were widely conserved in poxviruses but missing from the vaccinia virus strain Tian Tan 1998 GenBank file. We have reannotated and resequenced fragments of this genome and verified that these genes are conserved in Tian Tan. The results for poxvirus genes and genomes are discussed in light of evolutionary processes.
Effects of Charged Cluster Mutations on the Function of Herpes Simplex Virus Type 1 U
L
34 Protein
Authors: Bjerke Susan L. , Cowan John M. , Kerr Jelani K. , Reynolds Ashley E. , Baines Joel D. , Roller Richard J.
Published: June 2003

Herpes simplex virus type 1 (HSV-1) is a DNA virus that acquires an envelope by budding into the inner nuclear membrane of an infected cell. Recombinant HSV-1 lacking the U
L
34 gene cannot undergo this event. U
L
34 and U
L
31, another viral protein, colocalize in an infected cell and are necessary and sufficient to target both proteins to the inner nuclear envelope. In order to define and characterize sequences of U
L
34 that are necessary for primary envelopment to occur, a library of 19 U
L
34 charged cluster mutants and a truncation mutant lacking the putative transmembrane domain (ΔTM) were generated. Mutants in this library were analyzed in a complementation assay for their ability to function in the production of infectious virus. Seven of the mutants failed to complement a U
L
34-null virus. The remainder of the mutants complemented at or near wild-type U
L
34 levels. Failure of a mutant protein to function might be the result of incorrect subcellular localization. To address this possibility, confocal microscopy was used to determine the localization of the U
L
34 protein in charged cluster mutants and ΔTM. In transfection-infection experiments, all of the functional U
L
34 mutants and four of the six noncomplementing mutants localized to the inner nuclear envelope in a manner indistinguishable from that of wild-type U
L
34. All of the noncomplementing U
L
34 mutants mediated proper localization of U
L
31. Charged clusters critical for U
L
34 function are dispersed throughout the protein sequence and do not correlate well with highly conserved regions of the protein. These data suggest that U
L
34 has at least one function in addition to mediating proper localization of U
L
31 in infected cells and provide further support for the role of U
L
34 in mediating proper localization of U
L
31 in infected cells.
High Frequency of Syncytium-Inducing and CXCR4-Tropic Viruses among Human Immunodeficiency Virus Type 1 Subtype C-Infected Patients Receiving Antiretroviral Treatment
Authors: Johnston Elizabeth R. , Zijenah Lynn S. , Mutetwa Solomon , Kantor Rami , Kittinunvorakoon Chonticha , Katzenstein David A.
Published: June 2003

Human immunodeficiency virus type 1 (HIV-1) subtype C viruses have been found to almost exclusively use the chemokine receptor CCR5 as a coreceptor for entry, even in patients with advanced AIDS. We have characterized subtype C virus isolates from 28 patients from Harare, Zimbabwe, 20 of whom were receiving antiretroviral treatment. Virus from 10 of the treated patients induced syncytium formation (SI virus) when cultured with MT2 cells. Only non-syncytium-inducing (NSI) virus was cultured from the peripheral blood mononuclear cells of the eight patients who had not received treatment. The majority of these subtype C SI viruses were capable of using both CCR5 and CXCR4 as coreceptors for viral entry, and the consensus V3 loop sequences from the SI viruses displayed a high net charge compared to those of NSI viruses. While those on treatment had reverse transcriptase (RT) and protease mutations, there was no clear association between RT and protease drug resistance mutations and coreceptor tropism. These results suggest that CXCR4-tropic viruses are present within the quasispecies of patients infected with subtype C virus and that antiretroviral treatment may create an environment for the emergence of CXCR4 tropism.
Electrical Conductivity of Chloro(phenyl)glyoxime and Its Co(II), Ni(II) and Cu(II) Complexes
Authors: Turkoglu Orhan , Soylak Mustafa , Belenli Ibrahim
Published: June 2003

Chloro(phenyl)glyoxime, a vicinal dioxime, and its Ni(II), Cu(II) and Co(II) complexes were prepared. XRD patterns of the complexes point to similar crystal structures. IR and elemental analysis data revealed the 1:2 metal-ligand ratio in the complexes. The Co(II) complex is a dihydrate. Temperature dependence of electrical conductivity of the solid ligand and its complexes was measured in the temperature range 25-250 °C; it ranged between 10-14-10-6 Ω-1 cm-1 and increased with rising temperature. The activation energies were between 0.61-0.80 eV. The Co(II) complex has lower electric conductivity than the Ni(II) and Cu(II) complexes. This difference in the conductivity has been attributed to differences in the stability of the complexes.