bluuebunny/crossref_metadata_2025 huggingface dataset:
Complex structures in galaxy cluster fields: implications for gravitational lensing mass models
Authors: King Lindsay , Corless Virginia
Published: November 2006

The distribution of mass on galaxy cluster scales is an important test of structure formation scenarios, providing constraints on the nature of dark matter itself. Several techniques have been used to probe the mass distributions of clusters, sometimes yielding results which are discrepant, or at odds with clusters formed in simulations – for example giving Navarro–Frenk–White (NFW) concentration parameters much higher than expected in the standard cold dark matter (CDM) model. In addition, the velocity fields of some well-studied galaxy clusters reveal the presence of several structures close to the line of sight, often not dynamically bound to the cluster itself. We investigate what impact such neighbouring but unbound massive structures would have on the determination of cluster profiles using weak gravitational lensing. Depending on its concentration and mass ratio to the primary halo, one secondary halo close to the line-of-sight can cause the estimated NFW concentration parameter to be significantly higher than that of the primary halo, and also cause the estimated mass to be biased high. Although it is difficult to envisage how this mechanism alone could yield concentrations as high as reported for some clusters, multiple haloes close to the line-of-sight, such as in the case of Abell 1689, can substantially increase the concentration parameter estimate. Together with the fact that clusters are triaxial, and that including baryonic physics also leads to an increase in the concentration of a dark matter halo, the tension between observations and the standard CDM model is eased. Additionally, we note that if the alignment with the secondary structure is imprecise, then the estimated concentration parameter can also be even lower than that of the primary halo, reinforcing the importance of identifying structures in cluster fields.
The magnetic field of the planet-hosting star τ Bootis
Authors: Catala C. , Donati J.-F. , Shkolnik E. , Bohlender D. , Alecian E.
Published: November 2006

We have obtained high-resolution spectropolarimetric data for the planet-hosting star τ Bootis, using the ESPaDOnS spectropolarimeter at the Canada–France–Hawaii Telescope (CFHT). A weak but clear Stokes V signature is detected on three of the four nights of 2006 June during which we have recorded data. This polarimetric signature indicates with no ambiguity the presence of a magnetic field at the star's surface, with intensity of just a few gauss.

The analysis of the photospheric lines of τ Boo at ultra-high signal-to-noise ratio reveals the presence of an 18 per cent relative differential rotation. Tentative Zeeman–Doppler imaging, using our spectropolarimetric observations covering only a fraction of the star's rotational phase, indicates a magnetic field with a dominant potential field component. The data are best fitted when a 3.1-d period of modulation and an intermediate inclination are assumed. Considering the level of differential rotation of τ Boo, this implies a rotation period of 3.0 d at the equator and of 3.7 d at the pole, and a topology of the magnetic field where its main non-axisymmetric part is located at low latitudes.

The planet is probably synchronized with the star's rotation at intermediate latitudes, while the non-axisymmetric part of the magnetic field seems located at lower latitudes. Our limited data do not provide sufficient constraints on the magnetic field to study a possible interaction of the planet with the star's magnetosphere. Investigating this issue will require data with much better phase coverage. Similar studies should also be performed for other stars hosting close-in giant planets.
MEASUREMENT OF FLUID FOOD VISCOSITY USING MICROFABRICATED RADIO FREQUENCY COILS
Authors: MCCARTHY MICHAEL J. , CHOI YOUNG JIN , GOLOSHEVSKY ARTEM G. , DE ROPP JEFFREY S. , COLLINS SCOTT D. , WALTON JEFFREY H.
Published: November 2006

We report on the use and applicability of microfabricated radio frequency (r.f.) coils for viscosity measurements of fluid foods. The viscosity of fluid milk and milklike products was measured using nuclear magnetic resonance imaging based on microfabricated r.f. coils coupled to in‐line tubing with an inner diameter of 1.4 × 10‐3 m. The fluid's apparent viscosity ranged from 0.002 to 0.08 Pa·s. The magnetic resonance‐based measurements were limited in shear rate range because of the small size of the coil. Magnetic resonance‐based measurements from 2 to 15 s‐1 were obtained and were equivalent to off‐line rotational rheometry.
ANALYSIS OF COMPRESSION, TENSION AND TORSION FOR TESTING FOOD GEL FRACTURE PROPERTIES*
Authors: HAMANN DONALD D. , ZHANG JUNHUA , DAUBERT CHRISTOPHER R. , FOEGEDING E. ALLEN , DIEHL KENNETH C.
Published: November 2006

Three fracture test methods: uniaxial compression, uniaxial tension and torsion were examined by interpreting results using theories upon which the methods were based. In each of these tests, the fracture of gels can occur as a result of shear, compression or tension. The fracture properties determined from uniaxial compression and tension were compared with torsion testing, a suitable reference technique. Shear stress and strain in uniaxial compression were comparable with shear stress and strain in torsion. However, the tensile stress in compression is not in agreement with that in torsion. Tensile stress or shear stress values in uniaxial tension were generally comparable with tensile or shear stress values in torsion, while the strain levels in uniaxial tension were typically much lower than those in uniaxial compression or torsion. This result could be related to the fracture strain being a function of elongation necessary to reduce the specimen cross section to an area producing the critical fracture stress. The comparison among different methods revealed shear stress and strain can be the fracture criteria for uniaxial compression, and tensile stress can be the fracture criterion for uniaxial tension, whereas the fracture strain criterion in uniaxial tension cannot be specified. Possible mechanisms for differences among methods are discussed in the manuscript.
RELATIONSHIP BETWEEN THE BOSTWICK MEASUREMENT AND FLUID PROPERTIES
Authors: MILCZAREK REBECCA R. , MCCARTHY KATHRYN L.
Published: November 2006

Consistency of tomato concentrates was evaluated in a Bostwick consistometer. The concentrates were produced in a semibatch evaporator at soluble solids content from 5.3 to 24.0°Brix. The apparent viscosity, yield stress and density were measured at 20C. With respect to the gravity current analysis, the Bostwick measurement correlated well with the theoretical ratio of the apparent viscosity to density (R2 = 0.96). For the concentrates with yield stress values in the range of 60–200 Pa, the predicted extent of flow based on the slump analysis was within 2% of the measured extent of flow in the Bostwick consistometer.
MEASUREMENT OF YIELD STRESS IN DARK CHOCOLATE USING CONTROLLED STRESS VANE METHOD
Authors: BAKER BRIAN S. , BROWN B. DOUGLAS , ANANTHESWARAN RAMASWAMY C.
Published: November 2006

The controlled stress vane method was used to measure the yield stress in dark chocolate. Three vanes with different L/D ratios and five different stress rates were used in three different chocolate formulations. The vane displacement data did not indicate a definite yield phenomenon. When the vane displacement data were transformed into a ratio of vane velocity to elapsed time, the square root of vane velocity (SV) or the cube root of displacement, a definite yield phenomenon was observed. The SV was preferred on the basis of physical considerations and the linear regression of its derived yield stress on vane dimensions, stress rate and chocolate particle size. The value of the yield stress was the least when determined for a vane height to diameter ratio of 2 and at a stress rate of 3 Pa/min using the SV transformation.
RHEOLOGICAL CHARACTERIZATION OF ASEPTICALLY PACKAGED PUDDING
Authors: ANDERSON M.C. , SHOEMAKER C.F. , SINGH R.P.
Published: November 2006

The flow behavior of commercially available, aseptically packaged vanilla pudding was measured using a Thermo Haake RheoStress rheometer (RS1, Thermo Electron Corporation, Waltham, MA) with a concentric cylinder system. Six different shear rates, ranging from 1 to 100/s, and three reasonable serving temperatures were investigated using constant shear rate tests. A time‐dependent, Herschel–Bulkley model characterized the thixotropic nature of pudding. The model's five parameters were related to temperature. The model was validated at three constant shear rates and at two different temperatures, and was found to predict viscosity well as a function of time, shear rate and temperature.
DYNAMIC VISCOELASTIC PROPERTIES OF PASTA AS A FUNCTION OF TEMPERATURE AND WATER CONTENT*
Authors: TAKHAR PAWAN SINGH , KULKARNI MANISH V. , HUBER KERRY
Published: November 2006

Pasta samples were tested in the linear viscoelasticity range using a dynamic mechanical thermal analyzer over the temperature range of 25 to 95C and the water content range of 12 to 20% (weight of water/weight of solids). To obtain wholesome pasta samples at different moisture levels, the intermittent sorption technique was used. The behavior of G′ and tanδversus temperature curves exhibited a transition, which was determined to be the glass transition by making comparisons to the literature values of glass transition for starch and semolina extrudates. At 12.5% water content, glass transition initiated at 48.7C. With increase in water content values, the initiating glass transition temperature decreased. At 19.7% water content, glass transition was observed in the temperature range of 36.9 to 57.3C. Although pasta contains about 13% protein fraction, it did not seem to affect the major part of glass transition range because the pasta proteins become mobile at temperatures greater than 80C and water content greater than 17%.
Religion in the Public Square
Authors: Langerak Edward
Published: November 2006

This article gives an overview of the debate about the “restraint principle” that political liberals urge on those who are inclined to use distinctive moral and theological doctrines in public square debates about politics. It clarifies such central concepts as “public reason” while surveying the main arguments and highlighting three different proposals for possible convergence in this conflict.
Analytic Epistemology and Experimental Philosophy
Authors: Alexander Joshua , Weinberg Jonathan M.
Published: November 2006

It has been standard philosophical practice in analytic philosophy to employ intuitions generated in response to thought‐experiments as evidence in the evaluation of philosophical claims. In part as a response to this practice, an exciting new movement –experimental philosophy– has recently emerged. This movement is unified behind both a common methodology and a common aim: the application of methods of experimental psychology to the study of the nature of intuitions. In this paper, we will introduce two different views concerning the relationship that holds between experimental philosophy and the future of standard philosophical practice (what we call, theproper foundation viewand therestrictionist view), discuss some of the more interesting and important results obtained by proponents of both views, and examine the pressure these results put on analytic philosophers to reform standard philosophical practice. We will also defend experimental philosophy from some recent objections, suggest future directions for work in experimental philosophy, and suggest what future lines of epistemological response might be available to those wishing to defend analytic epistemology from the challenges posed by experimental philosophy.
Real-Time Tip-Over Prevention and Path Following Control for Redundant Nonholonomic Mobile Modular Manipulators via Fuzzy and Neural-Fuzzy Approaches
Authors: Li Yangmin , Liu Yugang
Published: November 2006

This paper presents a practical method for automatic tip-over prevention and path following control of a redundant nonholonomic mobile modular manipulator. According to modular robot concept, the mobile platform is treated as a special module attached to the base of the modular manipulator, then an integrated structure is constructed and its dynamic modeling is performed. A new tip-over stability criterion based on the supporting forces is proposed in consideration of inertia, gravity, and acceleration. An online fuzzy logic (FL) self-motion planner and an adaptive neural-fuzzy controller (ANFC) are presented: The former is used to generate desired self-motions in a real-time manner, and the latter is used to prevent the robot from tipping over and to control the end-effector to follow a desired spacial trajectory at the same time. The proposed algorithm does not need any a priori knowledge of dynamic parameters and can suppress bounded external disturbances effectively. Simulation results for a real robot validate the dynamic modeling method and the controller design algorithm.
High Precision Hydrostatic Actuation Systems for Micro- and Nanomanipulation of Heavy Loads
Authors: Habibi Saeid , Burton Richard , Sampson Eric
Published: November 2006

In this paper reports on an important finding, that is, hydrostatic actuation systems are able to manipulate heavy loads with submicron precision and a large stroke. In this relation, the design of a high-precision hydrostatic actuation system referred to as the ElectroHydraulic Actuator (EHA) is presented. A laboratory prototype of this system has achieved an unprecedented level of performance by being able to move a large load of 20Kg with a precision of 100nm and a stroke of 12cm. This level of performance places the hydrostatic actuation concept in competition with piezoelectric platforms in terms of positional accuracy. Experimental results from this prototype are reported and analyzed.
Scan Planning Strategy for a General Digitized Surface
Authors: Mehdi-Souzani Charyar , Thiébaut François , Lartigue Claire
Published: November 2006

As new functional requirements of products lead to the definition of more complicated shapes, reverse engineering is playing a more important role. The process consists in defining a CAD model of the object surfaces from the measurement of the real object. Reverse engineering takes advantage of new advances in noncontact measuring systems leading to a representation of the surfaces as large clouds of points. Nevertheless, scanning without path planning may affect completeness and accuracy of the measured data. This paper addresses the problem of intelligent scan planning within the context of reverse engineering. A measuring system allows us to acquire a cloud of points, which represents the first measurement of the free-form object. This incomplete and locally inaccurate cloud of points is used as a basis to generate an intelligent scan planning. A pretreatment of the point cloud is performed to determine the quality of the first scan and to find out the characteristic edges. The method relies on a voxel representation of the data. According to given thresholds of quality criteria (noise and completeness), unsatisfactory quality zones and digitizing gaps are identified. The new scan paths for an optimal digitizing are then calculated including optimal orientation search. An experimental application of the presented work is described through the digitizing of a face mask.
New Results on Robot Modeling and Simulation
Authors: Celentano Laura , Iervolino Raffaele
Published: November 2006

In this paper the possibility of simulating the robot forward dynamics by making use of the inertia matrix and of the kinetic energy gradient only is demonstrated. Such method is shown to be simpler and numerically more efficient than the classical approaches. In the case of planar robots with revolute joints and link centers of mass belonging to the plane containing the rotating axes of the joints, theorems are formulated and demonstrated providing a relatively fast and simple method of calculation for both the inertia matrix and the gradient of the kinetic energy. This allows obtaining a simple and efficient tool to simulate practical robots with rigid links and can also be particularly useful for studying robots with flexible links. By using the proposed approach, the model of a practical planar robot, designed by the computer aided design software package CATIA™, is easily developed and implemented. The simulation results when the gradient of the kinetic energy is computed analytically versus numerically are compared to illustrate that the computational costs are relatively low and the accuracy is high.
Intelligent Modeling of Thrust Force in Drilling Process
Authors: Sheng Ye , Tomizuka Masayoshi
Published: November 2006

In this paper, an intelligent modeling strategy for thrust force in drilling process is proposed. First of all, neural network (NN) models are developed to model the thrust force in drilling process. Second, drill head position information is included in the NN model to get better force prediction accuracy for entrance and exit drilling stages. Third, a fuzzy switching strategy is proposed to deal with the gain variation problem due to transitions from one drilling stage to another. Finally, gain variation due to drill wear is studied and the related modeling strategy is developed. Simulation and experimental results show that the proposed model works well over a wide operating range.
An Error Space Controller for a Resonating Fiber Scanner: Simulation and Implementation
Authors: Smithwick Quinn Y. J. , Vagners Juris , Reinhall Per G. , Seibel Eric J.
Published: November 2006

A robust error-space controller for an amplitude modulated resonating fiber scanner is developed and implemented. Using a nonlinear dynamics model, the system’s open loop temporal response for a spiral scan pattern is simulated and compared to experiments to understand scan distortions, such as, toroid, swirl, and beating. A feedback linearized linear quadratic regulator based on error dynamics drives the tracking error to zero. Controller simulations determine robustness limits, and effects of fiber nonlinearities and actuator time delay. Using real-time hardware, the controller asymptotically tracks and is capable of removing the scan distortions. Image acquisition with the controlled scanner produces nearly pixel accurate images.
A μ-Synthesis Based Control for Compliant Maneuvers
Authors: Uchimura Yutaka , Kazerooni H.
Published: November 2006

This paper deals with a system, which is subjected to very uncertain factors: human and environment. These independent uncertainties are dealt with explicitly on the framework of μ-synthesis. We also describe a controller design, which enables a robust force feedback without using a force sensor. The model of human dynamics, environments, and actuators are modeled associated with uncertainties described in the form of weighting functions. A controller is designed based on the μ-synthesis so that it maintains robust performance against uncertainties in both environment and human dynamics, which contributes to dexterous manipulation. The controller described here is implemented on the human power extender, which is worn by a human and amplifies the human’s physical strength, while the human’s intelligence remains as the central control system for manipulation. Experimental results conducted on the extender showed that the force estimation worked fine and the control system performed as desired.
Structurally Stable Regulation for a Class of Nonlinear Systems: Application to a Rotary Inverted Pendulum
Authors: Castillo-Toledo B. , Obregón-Pulido G. , Espinosa-Guerra O.
Published: November 2006

This paper presents a structurally stable scheme for nonlinear systems which do not satisfy the so-called FIB conditions for the existence of a linear solution to the structurally stable regulator solution, namely, the case when some necessary detectability condition with respect to the original system’s output does not hold. Under certain additional conditions, it is shown that the proposed scheme guarantees zero output tracking error between the actual output and the desired reference signal, in spite of the presence of parameter variations. Application to the model of a rotary inverted pendulum shows the effectiveness of the proposed scheme.
Unidrive Modular Robot: Dynamics, Control, and Experiments
Authors: Karbasi Hamidreza , Khajepour Amir , Huissoon Jan Paul
Published: November 2006

In this paper, a control design methodology for the new class of modular robots so-called “unidrive modular robots” is introduced. Unidrive modular robots because of employing only a single drive for operating all the joints have a substantial advantage over regular modular robots in terms of the mass of each module. The drive is mounted at the robot base and all joints tap power from the single drive using clutches. By controlling the engagement time of the clutches, the position and velocity of the joints are regulated. In this work, a general state space model of the robot is first developed and then based on the theory of variable structure systems and sliding mode control a design methodology for local controllers is introduced. The control design technique is validated by experimental results.
Adaptive Synchronized Control for a Planar Parallel Manipulator: Theory and Experiments
Authors: Ren Lu , Mills James K. , Sun Dong
Published: November 2006

In this paper, we develop a new control method, termed adaptive synchronized (A-S) control, for improving tracking accuracy of a P-R-R type planar parallel manipulator with parametric uncertainty. The novelty of A-S control, a combination of synchronized control and adaptive control, is in the application of synchronized control to a single parallel manipulator so that tracking accuracy is improved during high-speed, high-acceleration tracking motions. Through treatment of each chain as a submanipulator; the P-R-R manipulator is thus modeled as a multi-robot system comprised of three submanipulators grasping a common payload. Considering the geometry of the platform, these submanipulators are kinematically constrained and move in a synchronous manner. To solve this synchronization control problem, a synchronization error is defined, which represents the coupling effects among the submanipulators. With the employment of this synchronization error, tracking accuracy of the platform is improved. Simultaneously, the estimated unknown parameters converge to their true values through the use of a bounded-gain-forgetting estimator. Experiments conducted on the P-R-R manipulator demonstrate the validity of the approach.
Multi-Degree-of-Freedom Precision Position Sensing and Motion Control Using Two-Axis Hall-Effect Sensors
Authors: Kawato Yusuke , Kim Won-jong
Published: November 2006

This paper presents a novel precision position-sensing methodology using two-axis Hall-effect sensors, where the absolute multi-degree-of-freedom (DOF) positioning of a device above any magnet matrix is possible. Magnet matrices have a periodic magnetic field about each of its orthogonal axes, which can be modeled using Fourier series. This position-sensing methodology was implemented on a Halbach-magnet-matrix-based magnetic-levitation (maglev) stage. It enables unrestricted translational and rotational ranges in planar motions with a potential 6-DOF motion-measuring capability. A Gaussian least-squares differential-correction (GLSDC) algorithm was developed and implemented to estimate the maglev stage’s position and orientation in three planar DOFs from raw Hall-effect-sensor measurements. Experimental results show its position resolution of better than 10μm in translation and 100μrad in rotation. The maximum rotational range achieved so far is 16deg, a factor of 100 improvement of a typical laser interferometers’ rotational range of a few milliradians. Classical lead-lag compensators were designed and implemented on a digital signal processor (DSP) to close the control loop at a sampling frequency of 800Hz for the three planar DOFs using the GLSDC outputs. Calibration was performed by comparing the Hall-effect sensors’ outputs against the laser-interferometer readings, which improved the positioning accuracy by correcting the GLSDC error. The experimental results exhibit better than a micrometer repeatability. This multi-DOF sensing mechanism is an excellent cost-effective solution to planar micro-positioning applications with unrestricted three-axis travel ranges.
Predictive Control for Time-Delayed Switching Control Systems
Authors: Shields Bobby L. , Barth Eric J. , Goldfarb Michael
Published: November 2006

A methodology is proposed for the control of switching systems characterized by linear system dynamics with a time delay in the input channel. The method incorporates a state predictor that at each switching period determines the effect that the next control input will have on the future output of the system, and chooses the input that will take the system closest to the desired future state. The resulting control action is suboptimal, but is computationally tractable and shown to provide a bounded tracking error for stable plants. The proposed predictive control methodology is demonstrated on a hot gas pressurization system that tracks a desired pressure trajectory via an on/off solenoid valve.
Output Feedback Adaptive Robust Control of Uncertain Linear Systems
With Disturbances
Authors: Yao Bin , Xu Li
Published: November 2006

In this paper, a discontinuous projection based output feedback adaptive robust control (ARC) scheme is constructed for a class of linear systems subjected to both parametric uncertainties and disturbances that might be output dependent. An observer is first designed to provide exponentially convergent estimates of the unmeasured states. This observer has an extended filter structure so that on-line parameter adaptation can be utilized to reduce the effect of possible large disturbances that have known shapes but unknown amplitudes. Estimation errors that come from initial state estimates and uncompensated disturbances are dealt with via certain robust feedback at each step of the backstepping design. Compared to other existing output feedback robust adaptive control schemes, the proposed method explicitly takes into account the effect of disturbances and uses both parameter adaptation and robust feedback to attenuate their effects for an improved tracking performance. Experimental results on the control of an iron core linear motor are presented to illustrate the effectiveness and achievable performance of the proposed scheme.
Induced Master Motion in Force-Reflecting Teleoperation
Authors: Kuchenbecker Katherine J. , Niemeyer Günter
Published: November 2006

Telerobotic systems have persistently struggled to provide users with realistic force feedback; high-frequency contact transients convey important information about the remote environment but are typically attenuated to avoid the contact instability they incite. This undesirable behavior can be traced to high-frequency induced master motion, movement of the master device that is caused by force feedback rather than user intention. Such motion is interpreted as a position command to the slave, closing an internal control loop that is unstable under high gain. This paper examines the phenomenon of induced master motion in position-force teleoperation, presenting a new approach for achieving stable, high-gain force reflection using model-based cancellation. Requirements for the model of the induced motion dynamics and methods for its characterization are described, focusing on successive isolation of inertial and connecting elements. The sixth-order nonlinear model obtained for a one-degree-of-freedom user-master system is validated and then tested in a cancellation controller. Canceling high-frequency induced master motion during teleoperation is shown to improve the stability of impacts, allowing significantly higher force reflection levels and a more authentic user experience.
Comparative DNA Analysis of Two
vanA
Plasmids from
Enterococcus faecium
Strains Isolated from Poultry and a Poultry Farmer in Norway
Authors: Sletvold H. , Johnsen P. J. , Simonsen G. S. , Aasnæs B. , Sundsfjord A. , Nielsen K. M.
Published: November 2006

The DNA sequences of two plasmids carrying
vanA
, pVEF1 (39,626 bp) and pVEF2 (39,714 bp), were determined. Forty-three shared coding sequences were identified, and the only nucleotide difference was an 88-bp indel. A postsegregational killing system was identified. This system possibly explains the persistence of the
vanA
gene cluster in Norwegian poultry farms.
RNAIII-Inhibiting-Peptide-Loaded Polymethylmethacrylate Prevents In Vivo
Staphylococcus aureus
Biofilm Formation
Authors: Anguita-Alonso Paloma , Giacometti Andrea , Cirioni Oscar , Ghiselli Roberto , Orlando Fiorenza , Saba Vittorio , Scalise Giorgio , Sevo Milica , Tuzova Marina , Patel Robin , Balaban Naomi
Published: November 2006

Staphylococci, common orthopedic pathogens, form antibiotic-resistant biofilms. Polymethylmethacrylate (PMMA) beads loaded with the quorum-sensing inhibitor RNAIII-inhibiting peptide (RIP) were implanted in rats and shown to prevent methicillin-resistant
Staphylococcus aureus
infection. RIP release was bimodal, typical of previously-tested antibiotics. These results suggest that RIP-PMMA warrants further evaluation for management of orthopedic infections caused by staphylococci.
Dual Targeting of GyrB and ParE by a Novel Aminobenzimidazole Class of Antibacterial Compounds
Authors: Grossman Trudy H. , Bartels Douglas J. , Mullin Steve , Gross Christian H. , Parsons Jonathan D. , Liao Yusheng , Grillot Anne-Laure , Stamos Dean , Olson Eric R. , Charifson Paul S. , Mani Nagraj
Published: November 2006

A structure-guided drug design approach was used to optimize a novel series of aminobenzimidazoles that inhibit the essential ATPase activities of bacterial DNA gyrase and topoisomerase IV and that show potent activities against a variety of bacterial pathogens. Two such compounds, VRT-125853 and VRT-752586, were characterized for their target specificities and preferences in bacteria. In metabolite incorporation assays, VRT-125853 inhibited both DNA and RNA synthesis but had little effect on protein synthesis. Both compounds inhibited the maintenance of negative supercoils in plasmid DNA in
Escherichia coli
at the MIC. Sequencing of DNA corresponding to the GyrB and ParE ATP-binding regions in VRT-125853- and VRT-752586-resistant mutants revealed that their primary target in
Staphylococcus aureus
and
Haemophilus influenzae
was GyrB, whereas in
Streptococcus pneumoniae
it was ParE. In
Enterococcus faecalis
, the primary target of VRT-125853 was ParE, whereas for VRT-752586 it was GyrB. DNA transformation experiments with
H. influenzae
and
S. aureus
proved that the mutations observed in
gyrB
resulted in decreased susceptibilities to both compounds. Novobiocin resistance-conferring mutations in
S. aureus
,
H. influenzae
, and
S. pneumoniae
were found in
gyrB
, and these mutants showed little or no cross-resistance to VRT-125853 or VRT-752586 and vice versa. Furthermore,
gyrB
and
parE
double mutations increased the MICs of VRT-125853 and VRT-752586 significantly, providing evidence of dual targeting. Spontaneous frequencies of resistance to VRT-752586 were below detectable levels (<5.2 × 10
−10
) for wild-type
E. faecalis
but were significantly elevated for strains containing single and double target-based mutations, demonstrating that dual targeting confers low levels of resistance emergence and the maintenance of susceptibility in vitro.
Quantitative Immunoassay To Measure Plasma and Intracellular Atazanavir Levels: Analysis of Drug Accumulation in Cultured T Cells
Authors: Roucairol Camille , Azoulay Stéphane , Nevers Marie-Claire , Créminon Christophe , Lavrut Thibault , Garraffo Rodolphe , Grassi Jacques , Burger Alain , Duval Danièle
Published: November 2006

We have developed an enzyme immunoassay to measure atazanavir (ATV) levels in plasma and cells. Anti-ATV polyclonal antibodies were raised in rabbits by using a synthetic ATV derivative coupled to bovine serum albumin as the immunogen, and the enzyme tracer was prepared by chemically coupling the ATV derivative with acetylcholinesterase. These reagents were used to develop a sensitive competitive enzyme immunoassay performed in microtitration plates, and the lowest limit of quantification was 150 pg/ml, which is about 10 times more sensitive than previously published techniques. The plasma assay was performed, after a simple methanol extraction, with a minimum of 30 μl of plasma. This assay showed good precision and efficiency, since the rates of recovery from human plasma and cell extracts spiked with ATV ranged form 93 to 113%, with coefficients of variation of less than 10%. ATV concentrations were measured in peripheral blood mononuclear cells incubated with various ATV concentrations and in CEM cells in the absence or presence of antiretroviral drugs and drug transporter inhibitors. The results indicated a dose-dependent uptake (intracellular concentration/extracellular concentration ratio range, 0.04 to 19). A significant increase in the accumulation of ATV was noticed in the presence of P-glycoprotein and MRP1 inhibitors (dipyridamole, inter alia). Interestingly, efavirenz significantly increased the baseline accumulation of ATV, whereas nevirapine induced a marked reduction. This new enzyme immunoassay for measuring plasma and intracellular ATV levels was fully validated and provides an inexpensive and useful tool for routine therapeutic drug monitoring. Moreover, in vitro results suggested the implication of drug transporters and interactions with other antiviral drugs that should be further explored in human immunodeficiency virus-infected patients.
Development of a New Methodology for Screening of Human Immunodeficiency Virus Type 1 Microbicides Based on Real-Time PCR Quantification
Authors: Aguiar Renato S. , Costa Luciana J. , Pereira Helena S. , Brindeiro Rodrigo M. , Tanuri Amilcar
Published: November 2006

Potential topical retrovirucides or vaginal microbicides against human immunodeficiency virus type 1 (HIV-1) include nonnucleoside reverse transcriptase inhibitors (NNRTIs). To be successful, such agents have to be highly active against cell-free virions. In the present study, we developed a new real-time PCR-based assay to measure the natural endogenous reverse transcription (NERT) activity directly on intact HIV-1 particles in the presence of reverse transcriptase (RT) inhibitors. We further evaluated the permeability to nevirapine (NVP) and efavirenz (EFV) and their retention within nascent viral particles. We also demonstrated the NVP and EFV inhibitory effects on NERT activity and the impact of resistance mutations measured directly by this new strategy. Furthermore, the results showed a clear correlation between NERT activity and classical infectivity assays. The 50% inhibitory concentrations (IC
50
s) of NVP and EFV were demonstrated to be up to 100-fold higher for cell-free than for cell-associated virions, suggesting that cell-free virions are less permeable to these drugs. Our results suggest that NVP and EFV penetrate both the envelope and the capsid of HIV-1 particles and readily inactivate cell-free virions. However, the characteristics of these NNRTIs, such as lower permeability and lower retention during washing procedures, in cell-free virions reduce their efficacies as microbicides. Here, we demonstrate the usefulness of the NERT real-time PCR as an assay for screening novel antiretroviral compounds with unique mechanisms of action.
Natural Polymorphisms in the Human Immunodeficiency Virus Type 2 Protease Can Accelerate Time to Development of Resistance to Protease Inhibitors
Authors: Ntemgwa Michel , Brenner Bluma G. , Oliveira Maureen , Moisi Daniela , Wainberg Mark A.
Published: November 2006

Human immunodeficiency virus type 2 (HIV-2) contains numerous natural polymorphisms in its protease (PR) gene that are implicated in drug resistance in the case of HIV-1. This study evaluated emergent PR resistance in HIV-2. Three HIV-2 isolates were selected for resistance to amprenavir (APV), nelfinavir (NFV), indinavir (IDV), and tipranavir (TPV) in cell culture. Genotypic analysis determined the time to the appearance of protease inhibitor (PI)-associated mutations compared to HIV-1. Phenotypic drug susceptibility assays were used to determine the levels of drug resistance. Within 10 to 15 weeks of serial passage, three major mutations—I54M, I82F, and L90M—arose in HIV-2 viral cultures exposed to APV, NFV, and IDV, whereas I82L was selected with TPV. After 25 weeks, other cultures had developed I50V and I84V mutations. In contrast, no major PI mutations were selected in HIV-1 over this period except for D30N in the context of NFV selective pressure. The baseline phenotypes of wild-type HIV-2 isolates were in the range observed for HIV-1, except for APV and NFV for which a lower degree of sensitivity was seen. The acquisition of the I54M, I84V, L90M, and L99F mutations resulted in multi-PI-resistant viruses, conferring 10-fold to more than 100-fold resistance. Of note, we observed a 62A/99F mutational motif that conferred high-level resistance to PIs, as well as novel secondary mutations, including 6F, 12A, and 21K. Thus, natural polymorphisms in HIV-2 may facilitate the selection of PI resistance. The increasing incidence of such polymorphisms in drug-naive HIV-1- and HIV-2-infected persons is of concern.
First Characterization of Fluoroquinolone Resistance in
Streptococcus suis
Authors: Escudero Jose Antonio , San Millan Alvaro , Catalan Ana , de la Campa Adela G. , Rivero Estefania , Lopez Gema , Dominguez Lucas , Moreno Miguel Angel , Gonzalez-Zorn Bruno
Published: November 2006

We have identified and sequenced the genes encoding the quinolone-resistance determining region (QRDR) of ParC and GyrA in fluoroquinolone-susceptible and -resistant
Streptococcus suis
clinical isolates. Resistance is the consequence of single point mutations in the QRDRs of ParC and GyrA and is not due to clonal spread of resistant strains or horizontal gene transfer with other bacteria.
Novel Ambler Class A β-Lactamase LAP-1 and Its Association with the Plasmid-Mediated Quinolone Resistance Determinant QnrS1
Authors: Poirel Laurent , Cattoir Vincent , Soares Ana , Soussy Claude-James , Nordmann Patrice
Published: November 2006

The plasmid-mediated quinolone resistance determinant QnrS1 was identified in non-clonally related
Enterobacter cloacae
isolates in association with a transferable narrow-spectrum β-lactam resistance marker. Cloning experiments allowed the identification of a novel Ambler class A β-lactamase, named LAP-1. It shares 62 and 61% amino acid identity with the most closely related β-lactamases, TEM-1 and SHV-1, respectively. It has a narrow-spectrum hydrolysis of β-lactams and is strongly inhibited by clavulanic acid and sulbactam and, to a lesser extent, by tazobactam. Association of the
bla
LAP-1
gene with the
qnrS1
gene was identified in
E. cloacae
isolates from France and Vietnam. These genes were plasmid located and associated with similar insertion sequences but were not associated with
sul1
-type class 1 integrons, as opposed to the
qnrA
genes.
High-Throughput
Plasmodium falciparum
Growth Assay for Malaria Drug Discovery
Authors: Baniecki Mary Lynn , Wirth Dyann F. , Clardy Jon
Published: November 2006

New therapeutic agents for the treatment of malaria, the world's most deadly parasitic disease, are urgently needed. Malaria afflicts 300 to 500 million people and results in 1 to 2 million deaths annually, and more than 85% of all malaria-related mortality involves young children and pregnant women in sub-Saharan Africa. The emergence of multidrug-resistant parasites, especially in
Plasmodium falciparum
, has eroded the efficacy of almost all currently available therapeutic agents. The discovery of new drugs, including drugs with novel cellular targets, could be accelerated with a whole-organism high-throughput screen (HTS) of structurally diverse small-molecule libraries. The standard whole-organism screen is based on incorporation of [
3
H]hypoxanthine and has liabilities, such as limited throughput, high cost, multiple labor-intensive steps, and disposal of radioactive waste. Recently, screens have been reported that do not use radioactive incorporation, but their reporter signal is not robust enough for HTS. We report a
P. falciparum
growth assay that is technically simple, robust, and compatible with the automation necessary for HTS. The assay monitors DNA content by addition of the fluorescent dye 4′,6-diamidino-2-phenylindole (DAPI) as a reporter of blood-stage parasite growth. This DAPI
P. falciparum
growth assay was used to measure the 50% inhibitory concentrations (IC
50
s) of a diverse set of known antimalarials. The resultant IC
50
s compared favorably with those obtained in the [
3
H]hypoxanthine incorporation assay. Over 79,000 small molecules have been tested for antiplasmodial activity using the DAPI
P. falciparum
growth assay, and 181 small molecules were identified as highly active against multidrug-resistant parasites.
Fitness Costs of Fluoroquinolone Resistance in
Streptococcus pneumoniae
Authors: Rozen Daniel E. , McGee Lesley , Levin Bruce R. , Klugman Keith P.
Published: November 2006

The fitness cost of the genes responsible for resistance to fluoroquinolones in clinical isolates of
Streptococcus pneumoniae
were estimated in vitro in a common genetic background. Naturally occurring
parC
,
parE
, and
gyrA
loci containing mutations in the quinolone-resistance-determining regions were introduced by transformation into
S. pneumoniae
strain R6 individually and in combinations. The fitness of these transformants was estimated by pairwise competition experiments with a common R6 strain. On average, single
par
and
gyr
mutants responsible for low-level MIC resistance (first-step resistance) impose a fitness burden of approximately 8%. Some of these mutants engender no measurable cost, while one, a
parE
mutant, reduces the fitness of these bacteria by more than 40%. Most interestingly, the addition of the second
par
or
gyr
mutations required for clinically significant, high-MIC fluoroquinolone resistance does not increase the fitness burden imposed by these single genes and can even reduce it. We discuss the implications of these results for the epidemiology of fluoroquinolone resistance and the evolution of acquired resistance in treated patients.
Treatment and Outcomes of Infections by Methicillin-Resistant
Staphylococcus aureus
at an Ambulatory Clinic
Authors: Szumowski John D. , Cohen Daniel E. , Kanaya Fumihide , Mayer Kenneth H.
Published: November 2006

Community-acquired methicillin-resistant
Staphylococcus aureus
(MRSA) skin and soft tissue infections (SSTI) have become increasingly common. This study's objectives were to describe the clinical spectrum of MRSA in a community health center and to determine whether the use of specific antimicrobials correlated with increased probability of clinical resolution of SSTI. A retrospective chart review of 399 sequential cases of culture-confirmed
S. aureus
SSTI, including 227 cases of MRSA SSTI, among outpatients at Fenway Community Health (Boston, MA) from 1998 to 2005 was done. The proportion of
S. aureus
SSTI due to MRSA increased significantly from 1998 to 2005 (
P
< 0.0001). Resistance to clindamycin was common (48.2% of isolates). At the beginning of the study period, most patients with MRSA SSTI empirically treated with antibiotics received a beta-lactam, whereas by 2005, 76% received trimethoprim-sulfamethoxazole (TMP-SMX) (
P
< 0.0001). Initially, few MRSA isolates were sensitive to the empirical antibiotic, but 77% were susceptible by 2005 (
P
< 0.0001). A significantly higher percentage of patients with MRSA isolates had clinical resolution on the empirical antibiotic by 2005 (
P
= 0.037). Use of an empirical antibiotic to which the clinical isolate was sensitive was associated with increased odds of clinical resolution on empirical therapy (odds ratio = 5.91), controlling for incision and drainage and HIV status. MRSA now accounts for the majority of SSTI due to
S. aureus
at Fenway, and improved rates of clinical resolution on empirical antibiotic therapy have paralleled increasing use of empirical TMP-SMX for these infections. TMP-SMX appears to be an appropriate empirical antibiotic for suspected MRSA SSTI, especially where clindamycin resistance is common.
Proinflammatory and Antimicrobial Nitric Oxide in Gingival Fluid of Diabetic Patients with Periodontal Disease
Authors: Skaleric Uros , Gaspirc Boris , McCartney-Francis Nancy , Masera Andrej , Wahl Sharon M.
Published: November 2006

Abnormal nitric oxide (NO) synthesis has been implicated in the pathogenesis of both periodontal disease and diabetes mellitus. In diabetic patients, increased inducible NO synthase in inflamed gingiva correlated with NO in gingival crevicular fluid. Although increased NO reflected more-severe inflammation, it was associated with reductions in CFU ofPrevotella intermedia, a major periodontopathogen, highlighting dual roles for NO.
Toll-Like Receptors Differentially Regulate CC and CXC Chemokines in Skeletal Muscle via NF-κB and Calcineurin
Authors: Boyd John H. , Divangahi Maziar , Yahiaoui Linda , Gvozdic Dusanka , Qureshi Salman , Petrof Basil J.
Published: November 2006

Immunologically active molecules such as cytokines and chemokines have been implicated in skeletal muscle weakness during sepsis as well as recovery from muscle injury. In sepsis, Toll-like receptors (TLRs) act as key sentinel molecules of the innate immune system. Here we determined skeletal muscle cell responses of two prototypical CC and CXC chemokine genes (monocyte chemoattractant protein 1 [MCP-1] and KC, respectively), to stimulation with specific TLR ligands. In addition, we examined whether NF-κB and calcineurin signaling are involved in these responses. Differentiated myotubes and intact whole muscles expressed TLR2, TLR4, TLR5, and TLR9. Stimulation with ligands for TLR2 (peptidoglycan) or TLR4 (LPS) elicited robust and equivalent levels of MCP-1 and KC mRNA expression, whereas stimulation of TLR5 (by flagellin) required gamma interferon priming to induce similar effects. Although both TLR2 and TLR4 ligands activated the NF-κB pathway, NF-κB reporter activity was approximately 20-fold greater after TLR4 stimulation than after TLR2 stimulation. Inhibitory effects of NF-κB blockade on TLR-mediated chemokine gene expression, by either pharmacological (pyrrolidine dithiocarbamate) or molecular (IKKβ dominant-negative transfection) methods, were also more pronounced during TLR4 stimulation. In contrast, inhibitory effects on TLR-mediated chemokine expression of calcineurin blockade (by FK506) were greater for TLR2 than for TLR4 stimulation. MCP-1 and KC mRNA levels also demonstrated differential responses to NF-κB and calcineurin blockade during stimulation with specific TLR ligands. We conclude that skeletal muscle cells differentially utilize the NF-κB and calcineurin pathways in a TLR-specific manner to enable complex regulation of CC and CXC chemokine gene expression.