bluuebunny/crossref_metadata_2025 huggingface dataset:
A Method for Planar Biaxial Mechanical Testing That Includes In-Plane Shear
Authors: Sacks M. S.
Published: February 2008

A limitation in virtually all planar biaxial studies of soft tissues has been the inability to include the effects of in-plane shear. This is due to the inability of current mechanical testing devices to induce a state of in-plane shear, due to the added cost and complexity. In the current study, a straightforward method is presented for planar biaxial testing that induces a combined state of in-plane shear and normal strains. The method relies on rotation of the test specimen’s material axes with respect to the device axes and on rotating carriages to allow the specimen to undergo in-plane shear freely. To demonstrate the method, five glutaraldehyde treated bovine pericardium specimens were prepared with their preferred fiber directions (defining the material axes) oriented at 45 deg to the device axes to induce a maximum shear state. The test protocol included a wide range of biaxial strain states, and the resulting biaxial data re-expressed in material axes coordinate system. The resulting biaxial data was then fit to the following strain energy function W: W=c/2[exp(A1E′112+A2E′222+2A3E′11E′22+A4E′122+2A5E′11E′12+2A6E′22E′12)−1]where E′ij is the Green’s strain tensor in the material axes coordinate system and c and Ai are constants. While W was able to fit the data very well, the constants A5 and A6 were found not to contribute significantly to the fit and were considered unnecessary to model the shear strain response. In conclusion, while not able to control the amount of shear strain independently or induce a state of pure shear, the method presented readily produces a state of simultaneous in-plane shear and normal strains. Further, the method is very general and can be applied to any anisotropic planar tissue that has identifiable material axes.
Dynamic Lumped Element Response of the Human Fingerpad
Authors: Pawluk D. T. V. , Howe R. D.
Published: February 2008

The dynamic response of the fingerpad plays an important role in the tactile sensory response and precision manipulation, as well as in ergonomic design. This paper investigates the dynamic lumped element response of the human fingerpad in vivo to a compressive load. A flat probe indented the fingerpad at a constant velocity, then held a constant position. The resulting force (0–2 N) increased rapidly with indentation, then relaxed during the hold phase. A quasilinear viscoelastic model successfully explained the experimental data. The instantaneous elastic response increased exponentially with position, and the reduced relaxation function included three decaying exponentials (with time constants of approximately 4 ms, 70 ms, and 1.4 s) plus a constant. The model was confirmed with data from sinusoidal displacement trajectories.
Standardization of a Method for Characterizing Low-Concentration Biogels: Elastic Properties of Low-Concentration Agarose Gels
Authors: Benkherourou M. , Rochas C. , Tracqui P. , Tranqui L. , Gume´ry P. Y.
Published: February 2008

Low-concentration biogels, which provide an extracellular matrix for cells in vitro, are involved in a number of important cell biological phenomena, such as cell motility and cell differentiation. In order to characterize soft tissues, which collapse under their own weight, we developed and standardized a new experimental device that enabled us to analyze the mechanical properties of floating biogels with low concentrations, i.e., with values ranging from 2 g/L to 5 g/L. In order to validate this approach, the mechanical responses of free floating agarose gel samples submitted to compression as well as stretching tests were quantified. The values of the Young’s moduli, measured in the range of 1000 to 10,000 Pa, are compared to the values obtained from other experimental techniques. Our results showed indeed that the values we obtained with our device closely match those obtained independently by performing compression tests on an Instron device. Thus, the floating gel technique is a useful tool first to characterize and then to model soft tissues that are used in biological science to study the interaction between cell and extracellular matrix.
Centering Mechanism for Soft Contact Lenses
Authors: Funkenbusch Guo Ming T. , Benson Richard C.
Published: February 2008

A soft contact lens, because of its elasticity, can re-center itself over the cornea after it has been displaced by a blink. In this paper, a potential energy method is used to simulate the centering mechanism. Specifications for commercially available soft contact lenses and realistic eye shapes are used for the examples. With this technique we can compare the centering attributes of different lens and eye geometries.
An Energy Theorem for Developing Testing Functions for Numerical Simulations of Dynamic Systems
Authors: Liu C. Q. , Huston R. L.
Published: February 2008

This paper presents a kinetic energy theorem, applicable with simple nonholonomic systems. The theorem provides a basis for developing testing functions for measuring the accuracy of numerical simulations—even where no classical conservation principle is applicable. The theorem is established using Kane’s equations for general mechanical systems. A set of general testing functions are then developed. Several examples are presented.
Optimization of a Tire Traction Model for Antilock Brake System Simulations
Authors: Wagner J. R.
Published: February 2008

The cost effective design of antilock brake systems for automobiles requires the use of computer aided design and analysis techniques, as well as traditional invehicle testing. An important consideration in the simulation of the vehicle and brake dynamics is the generation of the shear forces and aligning torques at the tire/road interface. Frequently, experimental tire data gathered over a limited number of road surfaces is extrapolated to test antilock brake systems on a variety of roads. However, this approach may lead to problems in correlating the simulated system performance with actual vehicle tests. In this study, nonlinear programming strategies are applied to an analytical tire model to facilitate the selection of system variables. The formulation of an optimization problem to determine these variables permits the generation of shear forces which correspond fairly well with the empirical data. Simulation results are presented and discussed for five road surfaces to indicate the overall performance of this technique.
Modeling of Twofold Flame Behavior of Ceramic Foam Surface Burners
Authors: Severens P. F. J. , Bouma P. H. , van de Ven C. J. H. , de Goey L. P. H. , van der Drift A.
Published: February 2008

A model for the flame behavior of a ceramic foam surface gas burner is developed. The burner plate is divided into small segments. Each segment is assumed to behave independently and the transport phenomena in each segment are assumed to be one-dimensional. Relations between the local gas velocity and global pressure drop are derived. The model predicts the pressure drop over the hot burner plate and the radiating fraction of the plate reasonably well.
A Study of Parameters Influencing Wall-to-Bed Heat Transfer in Low-Temperature Rotary Desorbers
Authors: Cook C. A. , Cundy V. A.
Published: February 2008

Heat transfer between a rotating wall and a bed of granular material is investigated. Three specific areas of this problem are studied. First, a Stefan-type model is used to evaluate the importance of evaporation near the wall on the wall-to-bed heat transfer coefficient. Next, a heat-balance integral method is used to model wall-to-bed heat transfer, including both evaporation within the bed and a thermal contact resistance between the wall and the first layer of particles. The method is evaluated and then compared to an approximate means with which to include the thermal contact resistance. Thirdly, the wall-to-bed heat transfer problem is solved under the condition of a linearly changing wall temperature. This solution is used to evaluate the consequences of the common isothermal wall assumption.
Effect of Design and Operating Parameters on the Performance of Two-Bed Sorption Heat Pump Systems
Authors: Zheng W. , Worek W. M. , Nowakowski G.
Published: February 2008

The effect of design and operating parameters on the performance of closed-cycle, two-bed sorption heat pump systems were investigated. The parameters studied in this paper included the effects of bed switching frequency (i.e., the switching speed), the sorbent bed NTU, the thermal resistance within the sorbent, the contact resistance between the sorbent and the tube wall of the heat transfer fluid, the fraction of inert mass within the sorbent bed heat exchanger, and the amount of fluid resident within the heat exchanger. The results show that the performance of a sorption heat pump system is extremely sensitive to the switching speed. In fact, the value of the switching speed that optimizes the COP is different from the value that optimizes the overall cooling capacity. Such a performance characteristic allows the design of multispeed sorbent bed heat pumps to be operated in such a way to follow the load while still maximizing the system COP. However, operation of the system at switching speeds away from the optimum values can cause a dramatic deterioration in system performance.
Nitric Oxide Emission From Pulverized Coal Blend Flames
Authors: Kopparthi V. , Gollahalli S. R.
Published: February 2008

An experimental study of the nitric oxide emission from pulverized blended coal flames as a function of blending mass ratio is presented. Coals of three ranks (anthracite, bituminous, and lignite), and of the same rank (bituminous), but of different origin (Oklahoma and Wyoming mines), were used as fuels. Also, their blends (anthracite-bituminous, anthracite-lignite, lignite-bituminous, and Oklahoma-Wyoming coals) at mass ratios of 20:80, 40:60, 60:40, and 80:20 were studied. Correlations of nitric oxide emission index (mass/unit energy release) with blend mass ratio are presented.
Optimal Second-Law Efficiency for a Brayton Cycle With an Internal Heat Source
Authors: Woodward J. B.
Published: February 2008

Net work of an endoreversible Brayton cycle and its second-law efficiency are examined for a heat source (hot air) that is initially at a temperature typical of adiabatic and stoichiometric combustion. That temperature is taken to be well above maximum cycle temperature. When heat is transferred to the cycle via a heat exchanger, maximum work per unit of heat source mass and per unit of heat source availability (second-law efficiency) are found to occur at a cycle pressure ratio that differs from the pressure ratio for maximum cycle first-law efficiency. When the heat source is internal, i.e., a fraction of the cycle working fluid, maximum work per unit of heat source mass is found to occur at the pressure ratio found for the external source; on the other hand, maximum work per unit of heat source availability is found to occur at the highest possible cycle pressure ratio, which is the same point at which cycle first-law efficiency is a maximum.
Endothelial Nitric Oxide Synthase and Calcium Production in Arterial Geometries: An Integrated Fluid Mechanics/Cell Model
Authors: Comerford A. , Plank M. J. , David T.
Published: February 2008

It is well known that atherosclerosis occurs at very specific locations throughout the human vasculature, such as arterial bifurcations and bends, all of which are subjected to low wall shear stress. A key player in the pathology of atherosclerosis is the endothelium, controlling the passage of material to and from the artery wall. Endothelial dysfunction refers to the condition where the normal regulation of processes by the endothelium is diminished. In this paper, the blood flow and transport of the low diffusion coefficient species adenosine triphosphate (ATP) are investigated in a variety of arterial geometries: a bifurcation with varying inner angle, and an artery bend. A mathematical model of endothelial calcium and endothelial nitric oxide synthase cellular dynamics is used to investigate spatial variations in the physiology of the endothelium. This model allows assessment of regions of the artery wall deficient in nitric oxide (NO). The models here aim to determine whether 3D flow fields are important in determining ATP concentration and endothelial function. For ATP transport, the effects of a coronary and carotid wave form on mass transport is investigated for low Womersley number. For the carotid, the Womersley number is then increased to determine whether this is an important factor. The results show that regions of low wall shear stress correspond with regions of impaired endothetial nitric oxide synthase signaling, therefore reduced availability of NO. However, experimental work is required to determine if this level is significant. The results also suggest that bifurcation angle is an important factor and acute angle bifurcations are more susceptible to disease than large angle bifurcations. It has been evidenced that complex 3D flow fields play an important role in determining signaling within endothelial cells. Furthermore, the distribution of ATP in blood is highly dependent on secondary flow features. The models here use ATP concentration simulated under steady conditions. This has been evidenced to reproduce essential features of time-averaged ATP concentration over a cardiac cycle for small Womersley numbers. However, when the Womersley number is increased, some differences are observed. Transient variations are overall insignificant, suggesting that spatial variation is more important than temporal. It has been determined that acute angle bifurcations are potentially more susceptible to atherogenesis and steady-state ATP transport reproduces essential features of time-averaged pulsatile transport for small Womersley number. Larger Womersley numbers appear to be an important factor in time-dependent mass transfer.
Stiffness Evaluation for Solids Containing Dilute Distributions of Inclusions and Microcracks
Authors: Huang Y. , Hu K. X. , Chandra A.
Published: February 2008

Materials, such as ceramics, intermetallics, and rocks, contain varying amounts of inhomogeneities, and the matrix material is vulnerable to microcracking in the neighborhood around these inhomogeneities. In an attempt to model the micromechanical aspects of this type of material, a solid containing dilute inclusions surrounded by cracks is investigated in this paper. The dilute-inclusion assumption neglects any interactions among different inclusion-crack clusters, but local inclusion-crack and crack-crack interactions are taken into account fully. It is shown that additional strain due to microcracking in a solid containing inclusions can be represented by an integral of crack opening displacements weighted by a nonuniform stress field induced by inclusions alone (in the absence of microcracking). An effective numerical approach is then developed to evaluate the effective moduli and additional macroscopic strain due to microcracking in composites. It is found that an increase in the number of hard inclusions may not always lead to expected strengthening of the materials, if the matrix material is vulnerable to microcracking around inclusions and a relatively large microcracking zone develops. The limited calculations show that a quasi-static crack-growing process can lead to an actively growing crack being arrested or to a stationary crack starting to grow. This suggests that self-similar crack growth may not be enough to describe the behavior of microcracked composites.
Analysis of a Crack Embedded in a Linear Elastic Half-Plane Solid
Authors: Sung J. C. , Liou J. Y.
Published: February 2008

A crack embedded in a half-plane solid traction-free on the infinite straight boundary is analyzed. The response of the material is linear elastic. A system of singular integral equations for the unknown dislocation densities defined on the crack faces is derived. These equations are then specialized to the problem of a crack located arbitrarily in an orthotropic material which are found to depend on two material parameters only. For a crack oriented either perpendicular or parallel to the infinite straight boundary, the kernel functions appearing in the singular integral equations are obtained in real form which are valid for arbitrary alignment of the orthotropic material. Furthermore, these kernel functions are found to be valid even for degenerate materials and can directly lead to those kernel functions for isotropic materials. Numerical results have been carried out for horizontal or vertical crack problems to elucidate the effect of material parameters on the stress intensity factors. The effect of the alignment of the material on the stress intensity factors is also presented for degenerate materials.
Vibration Modes and Frequencies of Timoshenko Beams With Attached Rigid Bodies
Authors: White M. W. D. , Heppler G. R.
Published: February 2008

The equations of motion and boundary conditions for a free-free Timoshenko beam with rigid bodies attached at the endpoints are derived. The natural boundary conditions, for an end that has an attached rigid body, that include the effects of the body mass, first moment of mass, and moment of inertia are included. The frequency equation for a free-free Timoshenko beam with rigid bodies attached at its ends which includes all the effects mentioned above is presented and given in terms of the fundamental frequency equations for Timoshenko beams that have no attached rigid bodies. It is shown how any support / rigid-body condition may be easily obtained by inspection from the reported frequency equation. The mode shapes and the orthogonality condition, which include the contribution of the rigid-body masses, first moments, and moments of inertia, are also developed. Finally, the effect of the first moment of the attached rigid bodies is considered in an illustrative example.
Line Force, Charge, and Dislocation in Anisotropic Piezoelectric Composite Wedges and Spaces
Authors: Chung M. Y. , Ting T. C. T.
Published: February 2008

Two-dimensional problems of anisotropic piezoelectric composite wedges and spaces are studied. The Stroh formalism is employed to obtain the basic real-form solution in terms of two arbitrary constant vectors for a particular wedge. Explicit real-form solutions are then obtained for (i) a composite wedge subjected to a line force and a line charge at the apex of the wedge and (ii) a composite space subjected to a line force, line charge, line dislocation, and an electric dipole at the center of the composite space. For the composite wedge the surface traction on any radial plane θ = constant and the electric displacement Dθ normal to the radial plane θ = constant vanish everywhere. For the composite space these quantities may not vanish but they are invariant with the choice of the radial plane.
Galerkin Projection for Geometrically Exact Sandwich Beams Allowing for Ply Drop-off
Authors: Vu-Quoc Loc , Deng H.
Published: February 2008

A Galerkin projection of the equations of equilibrium for a recent theory of geometrically exact sandwich beams that allow finite rotations and shear deformation in each layer is presented. The continuity of the displacement across the layers is exactly satisfied. The resulting finite element formulation can accommodate large deformation. The number of layers is variable, with layer lengths and thicknesses not required to be the same, thus allowing the modeling of sandwich structures with ply drop-off. Numerical examples are presented which underline the salient features of the formulation. Saint-Venant principle is demonstrated for very short sandwich beams.
Noise-Induced Transitions in Weakly Nonlinear Oscillators Near Resonance
Authors: Roy R. V.
Published: February 2008

We investigate the noise-induced transitions between the oscillatory steady states of a class of weakly nonlinear oscillators excited by resonant harmonic forcing. We begin by deriving a set of averaged equations governing slow variables of the system when the latter is perturbed by both additive white Gaussian noise and by random phase fluctuations of the resonant excitation. We then examine in detail the behavior of the reduced system in the case of cubic stiffness and viscous damping forces. Three regimes are examined: the case of weak damping, the case of near-bifurcation and the more general case when neither of the first two situations apply. In each case we predict the quasi-stationary probability density of the response and the mean time taken by the trajectories to pass from one basin of attraction to the other. These theoretical predictions are based on averaging of a near-Hamiltonian system in the weak damping limit, on center-manifold theory in the near-bifurcation case, or on Wentzell-Kramers-Brillouin (WKB) singular perturbation expansions in the more general case. These predictions are compared with digital simulations which show excellent agreement. We can then determine the probability of a transition for each state and for all parameter values. For this, we compute contour curves of the activation energy of each attractor in the parameter plane to yield a complete picture of the survivability of the system subject to random perturbations.
Distributional Concept of the Elastic-Viscoelastic Correspondence Principle
Authors: Kovarik V.
Published: February 2008

Distribution concept of physical variables in viscoelasticity theory enables to represent the stress-strain relations in the form of convolution equations, that is algebraic equations in the convolution algebra of right-sided distributions. These equations can be handled in much the same way that one handles matrix equations. Distributional correspondence principle is formulated as a transition process from the algebra of numbers (elastic solution) to the convolution algebra of distributions (viscoelastic solution). Corresponding elements and operations, respectively, in both algebras are established. Applications to a wide class of problems of the plate and shell theory are shown.
On the Transformation Properties of the Nonlinear Hamel Equations
Authors: Papastavridis J. G.
Published: February 2008

This paper discusses the transformation properties of the famous Johnsen-Hamel equations of motion of discrete mechanical systems in general nonlinear nonholonomic coordinates and constraints (i.e., the nonlinear extension of the well-known Boltzmann-Hamel equations), under general nonlinear (local) quasi-velocity transformations. It is shown that the individual kinematico-inertial terms making up the system inertia force, or system acceleration, such as the nonlinear nonholonomic Euler-Lagrange operator and nonholonomic correction (or deviation) terms, in general, do not transform as nonholonomic covariant vectors; although taken as a whole they do, as expected. This work extends and completes the work of Papastavridis (1994), and it is strongly recommended that it be read after that paper.
A Shape Design Sensitivity Approach for Two-Dimensional Mixed-Mode Fracture Analysis Under General Loading
Authors: Lee Tae Won , Grosse I. R.
Published: February 2008

Under general loadings including body forces and crack-face traction, the energy release rate equation for a two-dimensional cracked body is derived by a shape design sensitivity approach. Defining the virtual crack extension (VCE) as the variation of the geometry, the virtual work principle and the material derivative concept are used to obtain the final analytical equation for the energy release rate. In contrast to the results of other researchers, the functionals which appear in the derived energy release rate equation do not involve the derivative of the displacement field on the crack surface, thereby improving the numerical accuracy in the computation of the energy release rate. Although the finite element method (FEM) is applied to crack problems in this paper, any numerical analysis method can be applied to the resulting equation. In addition, if body forces and crack-face traction are constant with respect to VCE, i.e., their material derivatives are identically zero, then the energy release rate equation is domain independent for domains which exclude the crack-tip region. Three example problems are treated which demonstrate the generality, accuracy, and domain-independent nature of the derived energy release rate equation.
Stability of Cohesive Crack Model: Part I—Energy Principles
Authors: Bazˇant Z. P. , Li Yuan-Neng
Published: February 2008

The paper deals with a cohesive crack model in which the cohesive (crack-bridging) stress is a specified decreasing function of the crack-opening displacement. Under the assumption that no part of the crack undergoes unloading, the complementary energy and potential energy of an elastic structure which has a cohesive crack and is loaded by a flexible elastic frame is formulated using continuous influence functions representing compliances or stiffnesses relating various points along the crack. By variational analysis, in which the derivatives of the compliance or stiffness functions with respect to the crack length are related to the crack-tip stress intensity factors due to various unit loads, it is shown that the minimizing conditions reduce to the usual compatibility or equilibrium equations for the cohesive cracks. The variational equations obtained can be used as a basis for approximate solutions. Furthermore, the conditions of stability loss of a structure with a growing cohesive crack are obtained from the condition of vanishing of the second variation of the complementary energy or the potential energy. They have the form of a homogeneous Fredholm integral equation for the derivatives of the cohesive stresses or crack opening displacements with respect to the crack length. Loadings with displacement control, load control, or through a flexible loading frame are considered. Extension to the analysis of size effect on the maximum load or maximum displacement are left to a subsequent companion paper.
Combination Resonances of a Circular Plate With Three-Mode Interaction
Authors: Lee Won Kyoung , Kim Cheol Hong
Published: February 2008

A nonlinear analysis is presented for combination resonances in the symmetric responses of a clamped circular plate with the internal resonance, ω3≈ω1+2ω2. The combination resonances occur when the frequency of the excitation are near a combination of the natural frequencies, that is, when Ω≈2ω1+ω2. By means of the internal resonance condition, the frequency of the excitation is also near another combination of the natural frequencies, that is, Ω≈ω1−ω2+ω3. The effect of two near combination resonance frequencies on the response of the plate is examined. The method of multiple scales is used to solve the nonlinear nonautonomous system of equations governing the generalized coordinates in Galerkin’s procedure. For steady-state responses, we determine the equilibrium points of the autonomous system transformed from the nonautonomous system and examine their stability. It has been found that in some cases resonance responses with nonzero-amplitude modes don’t exist, and the amplitudes of the responses decrease with the excitation amplitude. We integrate numerically the nonautonomous system to find the long-term behaviors of the plate and to check the validity of the analytical solution. It is found that there exist multiple stable responses resulting in jumps. In this case the long-term response of the plate depends on the initial condition. In order to visualize total responses depending on the initial conditions, we draw the deflection curves of the plate.
The Fires of Aging
Authors: Holmes Donna J.
Published: February 2008

The Biology of Human Longevity
. Inflammation, Nutrition, and Aging in the Evolution of Life-spans.

By Caleb E. Finch

. Academic (Elsevier), Amsterdam, 2007. 640 pp. $69.95, £39.99, €58.95. ISBN 9780123736574.

Drawing on findings from a wide range of disciplines, the author identifies reduced levels of inflammation as a crucial factor in the recent increase in human life-spans.
In Vivo Therapeutic Effect of Gatifloxacin on BALB/c Mice Infected with
Nocardia brasiliensis
Authors: Daw-Garza Alejandra , Welsh Oliverio , Said-Fernández Salvador , Lozano-Garza Hector Gerardo , Waksman de Torres Noemi , Rocha Norma Cavazos , Ocampo-Candiani Jorge , Vera-Cabrera Lucio
Published: February 2008

In the present work, we evaluated the effect of gatifloxacin on the evolution of experimental murine infection with
Nocardia brasiliensis
using linezolid as a control. Gatifloxacin was injected subcutaneously at 100 mg/kg body weight every 8 h for 4 weeks. This compound was equally as efficient as linezolid in reducing the production of lesions.
Synergy between Polyethylenimine and Different Families of Antibiotics against a Resistant Clinical Isolate of
Pseudomonas aeruginosa
Authors: Khalil Hayssam , Chen Tao , Riffon Renée , Wang Rutao , Wang Zhao
Published: February 2008

The in vitro activities of 10 families of antimicrobial agents alone and in combination with a synthetic polycationic polymer, polyethylenimine (PEI), against a resistant clinical isolate of
Pseudomonas aeruginosa
were investigated by MIC assays, checkerboard testing, and killing curve studies. At a concentration of 250 nM, PEI (10 kDa) was not directly bactericidal or bacteriostatic; but when it was used in combination with novobiocin, ceftazidime, ampicillin, ticarcillin, carbenicillin, piperacillin, cefotaxime, chloramphenicol, rifampin, or norfloxacin, it significantly reduced the MICs of these antibiotics by 1.5- to 56-fold. However, the MICs of aminoglycosides, polymyxins, and vancomycins were increased by 1.2- to 5-fold when these drugs were combined with PEI; and the MICs of tetracycline, erythromycin, ciprofloxacin, and ofloxacin were not affected when these drugs were combined with PEI. In the killing curve studies, combinations of PEI with novobiocin, ceftazidime, chloramphenicol, or rifampin resulted in 5- to 8-log
10
CFU/ml reductions in bacterial counts when 25% of the MIC of each antibiotic was used. These results indicate that infections due to resistant
Pseudomonas
strains could be treated by the use of a synergistic combination of PEI and antimicrobial drugs.
erm
(B)-Carrying Elements in Tetracycline-Resistant Pneumococci and Correspondence between Tn
1545
and Tn
6003
Authors: Cochetti Ileana , Tili Emily , Mingoia Marina , Varaldo Pietro E. , Montanari Maria Pia
Published: February 2008

This study investigated the genetic organization of
erm
(B)-carrying transposons of
Streptococcus pneumoniae
and their distribution in tetracycline-resistant clinical isolates. By comparatively analyzing reference pneumococci carrying
erm
(B)/
tet
(M) transposon Tn
1545
, Tn
6003
, Tn
6002
, or Tn
3872
, we demonstrated a substantial correspondence between Tn
1545
and Tn
6003
, which have the same resistance gene combination [
tet
(M) (tetracycline),
erm
(B) (erythromycin), and
aphA
-
3
(kanamycin)]; share the macrolide-aminoglycoside-streptothricin element, containing a second
erm
(B); and only differ by a ca. 1.2-kb insertion (containing a putative IS
1239
insertion sequence) detected in Tn
1545
from
S. pneumoniae
reference strain BM4200. These results enabled elucidation of the structure of Tn
1545
, the first
erm
(B)-carrying transposon described in
S. pneumoniae
. A collection of 83 erythromycin- and tetracycline-resistant clinical pneumococci, representative of recent Italian isolates carrying
erm
(B) as the sole erythromycin resistance gene, was used to investigate the distribution of the different transposons. All 83 organisms were positive for
tet
(M) and bore an
erm
(B)/
tet
(M) transposon that could be characterized by using a specific set of primer pairs; Tn
3872
was detected in 18 isolates, Tn
6002
in 59 isolates, and Tn
6003
in 6 (the sole kanamycin-resistant) isolates. The genetic organization of transposon Tn
1545
, with its specific insertion, was not detected in any of the isolates tested. The
erm
(B)-carrying elements of tetracycline-resistant pneumococci substantially corresponded to those [bearing a silent
tet
(M) gene] recently detected in tetracycline-susceptible pneumococci. Overall, in
erm
(B)-positive pneumococci, Tn
6003
was the least common
erm
(B)-carrying Tn
916
-related element and Tn
6002
the most common.
Rapid Clinical Induction of Hepatic Cytochrome P4502B6 Activity by Ritonavir
Authors: Kharasch Evan D. , Mitchell Darain , Coles Rebecka , Blanco Roberto
Published: February 2008

Ritonavir is the most potent and efficacious inhibitor of cytochrome P4503A (CYP3A), and it is used accordingly for the pharmacoenhancement of other antiretrovirals. Paradoxically, ritonavir induces the clinical metabolism and clearance of many drugs. The mechanism by which ritonavir inhibits and induces clinical drug metabolism is unknown. Ritonavir induces CYP2B6 in human hepatocytes. This investigation tested the hypothesis that ritonavir induces human CYP2B6 in vivo. Thirteen healthy human immunodeficiency virus-negative volunteers underwent a three-way sequential crossover protocol, receiving racemic bupropion after nothing (control), 3 days of treatment with ritonavir, and 2.5 weeks of treatment with ritonavir (400 mg twice a day). Stereoselective bupropion hydroxylation was used as an in vivo probe for CYP2B6 activity. Plasma and urine (R)- and (S)-bupropion and (R,R)- and (S,S)-hydroxybupropion concentrations were measured by liquid chromatography-mass spectrometry. Racemic, (R)-, and (S)-bupropion plasma ratios of the area under the concentration-time curve from 0 h to infinity (AUC0-∞) (ritonavir/control) were significantly reduced to 0.84, 0.86, and 0.80, respectively, after 3 days of ritonavir treatment and to 0.67, 0.69, and 0.60 after steady-state ritonavir treatment. Apparent oral clearances for racemic, (R)-, and (S)-bupropion all were significantly increased by 1.2-fold after 3 days of ritonavir treatment and by 1.4-, 1.7-, and 1.5-fold after steady-state ritonavir treatment. The plasma (S,S)-hydroxybupropion/(S)-bupropion AUC0-72ratio was significantly increased by ritonavir. Formation clearances of both (R,R)- and (S,S)-hydroxybupropion were increased 1.8-fold after 3 days of ritonavir treatment and 2.1-fold after steady-state ritonavir treatment. These results show that ritonavir induces human CYP2B6 activity. Induction is rapid, occurring after only 3 days of ritonavir, and is sustained for at least 2 weeks. The ritonavir induction of CYP2B6 activity may have significant implications for drug interactions and clarify previously unexplained interactions.
LipL32 Is an Extracellular Matrix-Interacting Protein of
Leptospira
spp. and
Pseudoalteromonas tunicata
Authors: Hoke David E. , Egan Suhelen , Cullen Paul A. , Adler Ben
Published: February 2008

LipL32 is the major outer membrane protein in pathogenic
Leptospira
. It is highly conserved throughout pathogenic species and is expressed in vivo during human infection. While these data suggest a role in pathogenesis, a function for LipL32 has not been defined. Outer membrane proteins of gram-negative bacteria are the first line of molecular interaction with the host, and many have been shown to bind host extracellular matrix (ECM). A search for leptospiral ECM-interacting proteins identified the major outer membrane protein, LipL32. To verify this finding, recombinant LipL32 was expressed in
Escherichia coli
and was found to bind Matrigel ECM and individual components of ECM, including laminin, collagen I, and collagen V. Likewise, an orthologous protein found in the genome of
Pseudoalteromonas tunicata
strain D2 was expressed and found to be functionally similar and immunologically cross-reactive. Lastly, binding activity was mapped to the C-terminal 72 amino acids. These studies show that LipL32 and an orthologous protein in
P. tunicata
are immunologically cross-reactive and function as ECM-interacting proteins via a conserved C-terminal region.
Enhancement of Antibody Responses toBacillus anthracisProtective Antigen Domain IV by Use of Calreticulin as a Chimeric Molecular Adjuvant
Authors: Park Yong Sung , Lee Jin Hyup , Hung Chien-Fu , Wu T.-C. , Kim Tae Woo
Published: February 2008

The generation of protective humoral immune responses against the receptor-binding domain (domain IV) of protective antigen [PA(dIV)] ofBacillus anthracisrepresents a plausible approach against anthrax toxin. In the current study, we have developed a naked DNA vaccine encoding calreticulin (CRT) linked to PA(dIV) ofBacillus anthracis[CRT/PA(dIV)]. We transfected a human embryonic kidney cell line (HEK 293) with CRT/PA(dIV) DNA and performed Western blotting and confocal microscopy analysis. We found that linkage of CRT to PA(dIV) targets PA(dIV) to the endoplasmic reticulum, resulting in secretion of the chimeric CRT/PA(dIV) protein. We then evaluated the ability of CRT/PA(dIV) DNA to generate PA(dIV)-specific antibody responses and protective immunity against lethal anthrax toxin (PA plus lethal factor) challenge. We found that mice immunized with CRT/PA(dIV) DNA were capable of rapidly inducing significantly higher PA(dIV)-specific antibody responses than mice immunized with PA(dIV) DNA alone. Furthermore, we observed that this enhanced antibody response generated by CRT/PA(dIV) DNA was CD4 dependent, since CD4 knockout mice demonstrated a significant reduction in antibody responses. In addition, analysis of the titers and avidity maturation of the induced PA-specific antibodies revealed that vaccination with CRT/PA(dIV) DNA vaccine accelerated the avidity maturation of antibodies to PA(dIV) compared to vaccination with PA(dIV) DNA. Importantly, the enhanced antibody responses correlated to protective immunity against lethal anthrax toxin challenge. Thus, DNA vaccines encoding CRT linked to PA(dIV) may dramatically enhance PA-specific protective antibody responses. Our results have significant clinical applications for biodefense against anthrax toxin.
Prevalence of Virulence Genes and Cytolethal Distending Toxin Production inCampylobacter jejuniIsolates from Diarrheal Patients in Bangladesh
Authors: Talukder Kaisar A. , Aslam Mohammad , Islam Zhahirul , Azmi Ishrat J. , Dutta Dilip K. , Hossain Sabir , Nur-E-Kamal Alam , Nair Gopinath B. , Cravioto Alejandro , Sack David A. , Endtz Hubert P.
Published: February 2008

From 300 stool samples, 58Campylobacterstrains were isolated by standard microbiological and biochemical methods. Of these, 40 strains were identified asCampylobacter jejuniand 5 asCampylobacter coli. The presence offlaA(100%),cadF(100%),racR(100%),dnaJ(100%),pldA(100%),ciaB(95%),virB11(0%),ceuE(82.5%),cdtA(97.5%),cdtB(97.5%),cdtC(97.5%), andwlaN(7.5%) genes was detected inC. jejuniby PCR. AllC. jejunistrains but one produced cytolethal distending toxin in a HeLa cell assay.
Proteomic Studies Reveal Coordinated Changes in T-Cell Expression Patterns upon Infection with Human Immunodeficiency Virus Type 1
Authors: Ringrose Jeffrey H. , Jeeninga Rienk E. , Berkhout Ben , Speijer Dave
Published: February 2008

We performed an extensive two-dimensional differential in-gel electrophoresis proteomic analysis of the cellular changes in human T cells upon human immunodeficiency virus type 1 (HIV-1) infection. We detected 2,000 protein spots, 15% of which were differentially expressed at peak infection. A total of 93 proteins that changed in relative abundance were identified. Of these, 27 were found to be significantly downregulated and 66 were upregulated at peak HIV infection. Early in infection, only a small group of proteins was changed. A clear and consistent program of metabolic rerouting could be seen, in which glycolysis was downregulated and mitochondrial oxidation enhanced. Proteins that participate in apoptotic signaling were also significantly influenced. Apart from these changes, the virus also strongly influenced levels of proteins involved in intracellular transport. These and other results are discussed in light of previous microarray and proteomic studies regarding the impact of HIV-1 infection on cellular mRNA and protein content.
XBP-1, a Novel Human T-Lymphotropic Virus Type 1 (HTLV-1) Tax Binding Protein, Activates HTLV-1 Basal and Tax-Activated Transcription
Authors: Ku Sebastian C. Y. , Lee Jialing , Lau Joanne , Gurumurthy Meera , Ng Raymond , Lwa Siew Hui , Lee Joseph , Klase Zachary , Kashanchi Fatah , Chao Sheng-Hao
Published: February 2008

X-box binding protein 1 (XBP-1), a basic leucine zipper transcription factor, plays a key role in the cellular unfolded protein response (UPR). There are two XBP-1 isoforms in cells, spliced XBP-1S and unspliced XBP-1U. XBP-1U has been shown to bind to the 21-bp Tax-responsive element of the human T-lymphotropic virus type 1 (HTLV-1) long terminal repeat (LTR) in vitro and transactivate HTLV-1 transcription. Here we identify XBP-1S as a transcription activator of HTLV-1. Compared to XBP-1U, XBP-1S demonstrates stronger activating effects on both basal and Tax-activated HTLV-1 transcription in cells. Our results show that both XBP-1S and XBP-1U interact with Tax and bind to the HTLV-1 LTR in vivo. In addition, elevated mRNA levels of the gene for XBP-1 and several UPR genes were detected in the HTLV-1-infected C10/MJ and MT2 T-cell lines, suggesting that HTLV-1 infection may trigger the UPR in host cells. We also identify Tax as a positive regulator of the expression of the gene for XBP-1. Activation of the UPR by tunicamycin showed no effect on the HTLV-1 LTR, suggesting that HTLV-1 transcription is specifically regulated by XBP-1. Collectively, our study demonstrates a novel host-virus interaction between a cellular factor XBP-1 and transcriptional regulation of HTLV-1.
Adenovirus E3/19K Promotes Evasion of NK Cell Recognition by Intracellular Sequestration of the NKG2D Ligands Major Histocompatibility Complex Class I Chain-Related Proteins A and B
Authors: McSharry Brian P. , Burgert Hans-Gerhard , Owen Douglas P. , Stanton Richard J. , Prod'homme Virginie , Sester Martina , Koebernick Katja , Groh Veronika , Spies Thomas , Cox Steven , Little Ann-Margaret , Wang Eddie C. Y. , Tomasec Peter , Wilkinson Gavin W. G.
Published: February 2008

The adenovirus (Ad) early transcription unit 3 (E3) encodes multiple immunosubversive functions that are presumed to facilitate the establishment and persistence of infection. Indeed, the capacity of E3/19K to inhibit transport of HLA class I (HLA-I) to the cell surface, thereby preventing peptide presentation to CD8+T cells, has long been recognized as a paradigm for viral immune evasion. However, HLA-I downregulation has the potential to render Ad-infected cells vulnerable to natural killer (NK) cell recognition. Furthermore, expression of the immediate-early Ad gene E1A is associated with efficient induction of ligands for the key NK cell-activating receptor NKG2D. Here we show that while infection with wild-type Ad enhances synthesis of the NKG2D ligands, major histocompatibility complex class I chain-related proteins A and B (MICA and MICB), their expression on the cell surface is actively suppressed. Both MICA and MICB are retained within the endoplasmic reticulum as immature endoglycosidase H-sensitive forms. By analyzing a range of cell lines and viruses carrying mutated versions of the E3 gene region, E3/19K was identified as the gene responsible for this activity. The structural requirements within E3/19K necessary to sequester MICA/B and HLA-I are similar. In functional assays, deletion of E3/19K rendered Ad-infected cells more sensitive to NK cell recognition. We report the first NK evasion function in theAdenoviridaeand describe a novel function for E3/19K. Thus, E3/19K has a dual function: inhibition of T-cell recognition and NK cell activation.
Rapid Adaptive Amplification of Preexisting Variation in an RNA Virus
Authors: Dutta Ranendra N. , Rouzine Igor M. , Smith Sarah D. , Wilke Claus O. , Novella Isabel S.
Published: February 2008

The amount and nature of preexisting variation in a population of RNA viruses is an important determinant of the virus's ability to adapt rapidly to a changed environment. However, direct quantification of this preexisting variation may be cumbersome, because potentially beneficial alleles are typically rare, and isolation of a large number of subclones is required. Here, we propose a simpler method. We infer the initial population structure of vesicular stomatitis virus (VSV) by fitting a mathematical model of asexual evolution to an extensive set of measurements of VSV fitness dynamics under various conditions, including new and previously published data. The inferred variation of fitness in the initial population agrees very well with the results of direct experiments with subclone fitness quantification. From the same procedure, we also estimate the mean fitness effect of beneficial mutations (selection coefficient
s
), the percentage of sites in the genome that are under moderate positive or negative selection, and the percentage of sites where beneficial mutations may potentially occur. For VSV strain MARM U evolving in BHK-21 cells, the three parameters have values of 0.39, 9%, and 0.06%, respectively. The method can be generalized and applied easily to other rapidly evolving microbes, including both asexual microorganisms and those with recombination.
Autographa californica
Multiple Nucleopolyhedrovirus Nucleocapsid Protein BV/ODV-C42 Mediates the Nuclear Entry of P78/83
Authors: Wang Yun , Wang Qian , Liang Changyong , Song Jianhua , Li Ni , Shi Hui , Chen Xinwen
Published: February 2008

Autographa californica
multiple nucleopolyhedrovirus (AcMNPV)
BV/ODV-c42
(
orf101
;
c42
), which encodes a 41.5-kDa viral nucleocapsid protein with a putative nuclear localization signal (NLS) motif at the C terminus, is a highly conserved gene among members of the
Baculoviridae
family. C42 is demonstrated to be essential for AcMNPV propagation and can bind to nucleocapsid protein P78/83, a viral activator for the actin-related protein 2/3 (ARP2/3) complex to initiate nuclear actin polymerization, which is essential for viral nucleocapsid morphogenesis during AcMNPV infection. Here, we report the identification of a novel pathway through which
c42
functions in nucleocapsid assembly. Cotransfection of Sf9 cells with
c42
and
p78/83
plasmids demonstrated that C42 was capable of recruiting P78/83 to the nuclei of uninfected cells and that the NLS motif of C42 was essential for this process. To validate this nuclear relocation mode in bacmid-transfected cells, a
c42
-disrupted bacmid (vAc
c42ko-gfp
) and rescued bacmids with wild-type
c42
(vAc
c42res-gfp
) or with NLS coding sequence-mutated
c42
(vAc
c42nls-gfp
) were prepared. By immuno-staining, P78/83 was found to be localized in the cytoplasm of either vAc
c42ko-gfp
- or vAc
c42nls-gfp
-transfected cells, whereas P78/83 was relocated to the nuclei of vAc
c42res-gfp
-transfected cells. Furthermore, F-actin-specific staining confirmed that there was no actin polymerization activity in the nuclei of either vAc
c42ko-gfp
- or vAc
c42nls-gfp
-transfected cells, which might be attributed to the absence of nuclear P78/83, an activator of the ARP2/3 complex to initiate nuclear actin polymerization. We therefore hypothesize a mode of action where C42 binds to P78/83 in the cytoplasm to form a protein complex and cotransports to the nucleus under the direction of the NLS motif in C42 during AcMNPV infection.