bluuebunny/crossref_metadata_2025 huggingface dataset:
Feedforward Tracking Controller Design Based on the Identification of Low Frequency Dynamics
Authors: Tung E. D. , Tomizuka M.
Published: March 2008

Several methodologies are proposed for identifying the dynamics of a machine tool feed drive system in the low frequency region. An accurate identification is necessary for the design of a feedforward tracking controller, which achieves unity gain and zero phase shift for the overall system in the relevant frequency band. In machine tools and other mechanical systems, the spectrum of the reference trajectory is composed of low frequency signals. Standard least squares fits are shown to heavily penalize high frequency misfit. Linear models described by the output-error (OE) and Autoregressive Moving Average with eXogenous Input (ARMAX) models display better closeness-of-fit properties at low frequency. Based on the identification, a feedforward compensator is designed using the Zero Phase Error Tracking Controller (ZPETC). The feedforward compensator is experimentally shown to achieve near-perfect tracking and contouring of high-speed trajectories on a machining center X-Y bed.
Approximate Optimal Trajectories for Flexible-Link Manipulator Slewing Using Recursive Quadratic Programming
Authors: Eisler G. R. , Robinett R. D. , Segalman D. J. , Feddema J. D.
Published: March 2008

The method of recursive quadratic programming, coupled with a homotopy method, has been used to generate approximate minimum-time and minimum tracking-error tip trajectories for two-link flexible manipulator movements in the horizontal plane. The manipulator is modeled with an efficient finite-element scheme for a multi-link, multi-joint system with bending only in the horizontal-plane. Constraints on the trajectory include boundary conditions on link tip position, final joint velocities, accelerations and torque inputs to complete a rest-to-rest maneuver, straight-line tip tracking between boundary positions, and motor torque limits. Trajectory comparisons demonstrate the impact of torque input smoothness on structural mode excitation. Applied torques retain much of the qualitative character of rigid-body slewing motion with alterations for energy dissipation.
Dynamic Properties of Load-Sensing Systems With Interacting Complex Mechanical Loads
Authors: Lantto Birgitta , Krus Petter , Palmberg Jan-Ove
Published: March 2008

A load-sensing fluid power system is a feedback system with several types of instability modes. This paper deals with one of them, where load interaction through a mechanical structure and the fluid power system may cause instability, e.g. in a lorry crane. Criteria for instability are evaluated. This paper also proposes some methods how to avoid this type of instability.
Output Feedback Stabilizing Control With an H∞ Bound on Disturbance Attenuation
Authors: Fabien B. C.
Published: March 2008

This paper considers the design of direct output static and dynamic stabilizing controllers for linear systems. Here, the controllers that stabilize the closed-loop system must satisfy an H∞ disturbance attenuation constraint. Sufficient conditions for the existence of such controllers are presented in the form of two coupled nonlinear matrix equations. These conditions are derived by solving a mixed-norm H2/H∞ optimal control problem. The solution of these equations via a continuation method is also presented. Using the solution algorithm, a fixed order stabilizing controller gain matrix that minimizes the H∞ norm of the closed-loop transfer function can be computed. The controller design technique is applied to the vertical dynamics of an aircraft. It is shown that the performance of the reduced order controllers designed using the technique proposed in this paper is superior to that of full order controllers obtained using the standard LQG approach.
Control of Nonlinear Systems Using Terminal Sliding Modes
Authors: Venkataraman S. T. , Gulati S.
Published: March 2008

Many robotic systems would, in the future, be reuqired to operate in environments that are highly unstructured and active, i.e., possessing means of self-actuation. Although a significant volume of results exist in model-based, robust and adaptive control literature, general issues pertinent to the performance of such control systems remain unresolved, e.g., feasibility of implementing high gain switches for control robustness. It is also pointed out that in certain applications, control switching can be very detrimental to the overall system. The primary focus of this paper is development of a new approach to control synthesis for robust robot operations in unstructured environments. To enhance control performance with full model information, we introduce the notion of terminal convergence, and develop control laws based upon a new class of sliding modes, denoted terminal sliders. We demonstrate that terminal sliders provide robustness to parametric uncertainty without having to resort to high frequency control switching, as in the case of conventional sliders [2]. In addition, stability analysis that is conducted to demonstrate terminal slider approach results in improved control performance and allows for simple robust design of control parameters. Further, improved (guaranteed) precision of terminal sliders is argued for through an analysis of steady state behavior.
Experimental Study of Friction in a Pneumatic Actuator at Constant Velocity
Authors: Schroeder Lee E. , Singh Rajendra
Published: March 2008

This paper describes an experimental method of determining sliding friction forces in a pneumatic actuator. Several empirical and semi-empirical friction models are evaluated using measured friction force data. A repeatability study is also performed to qualitatively assess friction randomness and a change in friction regimes.
Parameter Identification of Compressor Dynamics During Closed-Loop Operation
Authors: Paduano J. , Valavani L. , Epstein A. H.
Published: March 2008

A low-speed axial research compressor has been fitted with movable inlet guide vanes to allow for feedback stabilization of rotating stall. A model exists whose structure captures the input-output behavior, and stabilization of rotating stall is possible using this model. Quantitative identification of the parameters in the rotating stall model requires the ability to identify MIMO dynamics, which may be unstable, during closed loop operation. The ‘instrumental variable’ technique is presented as the basic approach to this problem. The necessary extensions to the basic technique are discussed, and the resulting algorithm is applied. Experimental results are presented which verify that the methodology yields useful estimates.
An Iterative Approach to Multibody Simulation Dynamics Suitable for Parallel Implementation
Authors: Sharf I. , D’Eleuterio G. M. T.
Published: March 2008

This paper presents a new solution procedure for simulation dynamics of multibody systems. The method is applicable to open chains with general interbody constraints. It is based on obtaining an explicit solution for the joint constraint forces by means of iterative techniques. We show that the algorithm possesses a parallel structure which matches the topology of the system. Numerical results for an anthropomorphic manipulator indicate that the conjugate-gradient Jacobi iteration is computationally most efficient. An estimate for the parallel efficiency of this scheme is obtained by combining the theoretical bound for parallel complexity with an approximate overhead cost associated with parallel implementation.
Resolved-Mode Teleoperated Control of Heavy-Duty Hydraulic Machines
Authors: Sepehri N. , Lawrence P. D. , Sassani F. , Frenette R.
Published: March 2008

This paper addresses the control problem for a class of heavy-duty hydraulic machines in order to achieve coordinated motion control of the implement. A model and sensor-based control algorithm is proposed which is applied in conjunction with closed-loop components. The algorithm is basically a feedforward load compensating scheme which uses the measured hydraulic line pressures along with the appropriate portion of the hydraulic model to control the joint velocities. The effects of nonlinear dynamic coupling between the links, loading, coupled actuation and power limitations are compensated in this technique. The closed-loop part consists of PD components. A knowledge of some hydraulic parameters is the only requirement of this control scheme. The proposed approach has been examined through simulation and is supported by experimental evidence. The experiments were performed on a Caterpillar 215B excavator. The control program is written in the C language, running on a computer system which is interfaced between the human operator and the machine.
The Dynamic Effects of Tire Lag on Simulation Yaw Rate Predictions
Authors: Heydinger G. J. , Garrott W. R. , Chrstos J. P. , Guenther D. A.
Published: March 2008

Two vehicle stability and control simulations, IDSFC and VDANL, are shown to have substantial discrepancies in predicted yaw rate transient response. J-turn and sinusoidal sweep steering maneuvers, at 25 and 50 miles per hour, were used to study simulated vehicle behavior. Comparisons of predicted yaw rates with experimental measurements are made in both frequency and time domains. Differing predictions for transient yaw rate are shown to be strongly influenced by differences in the tire models used in the simulations, specifically the dynamics portion of these tire models. A modified tire dynamics model, consisting of a second-order system lag in slip angle, was implemented into one of the simulations. Lagging slip angle causes all force and moment outputs to be lagged, better representing the actual physical system. Modified tire dynamics are shown to improve yaw rate predictions at handwheel frequencies above six radians per second.
A Decentralized Controller for the Robust Stabilization of a Class of MIMO Dynamical Systems
Authors: Tornambe` A. , Valigi P.
Published: March 2008

This work deals with the problem of the robust stabilization of a class of multi-input multi-output (MIMO) dynamical systems. A simple decentralized controller is proposed, which reduces to the classical PID controller in case of single-input single-output dynamical systems. Such a controller includes integral actions for the compensation of the entire dynamics of the system. The paper is completed with an application to robotic systems.
A Surface Integral Approach to the Motion Planning of Nonholonomic Systems
Authors: Mukherjee Ranjan , Anderson David P.
Published: March 2008

Nonholonomic mechanical systems are governed by constraints of motion that are nonintegrable differential expressions. Unlike holonomic constraints, these constraints do not reduce the number of dimensions of the configuration space of a system. Therefore a nonholonomic system can access a configuration space of dimension higher than the number of the degrees of freedom of the system. In this paper, we develop an algorithm for planning admissible trajectories for nonholonomic systems that will take the system from one point in its configuration space to another. In our algorithm the independent variables are first converged to their desired values. Subsequently, closed trajectories of the independent variables are used to converge the dependent variables. We use Green’s theorem in our algorithm to convert the problem of finding a closed path into that of finding a surface area in the space of the independent variables such that the dependent variables converge to their desired values as the independent variables traverse along the boundary of this surface area. Using this approach, we specifically address issues related to the reachability of the system, motion planning amidst additional constraints, and repeatable motion of nonholonomic systems. The salient features of our algorithm are quite apparent in the two examples we discuss: a planar space robot and a disk rolling without slipping on a flat surface.
Coupled Stability of Multiport Systems—Theory and Experiments
Authors: Colgate J. E.
Published: March 2008

This paper presents both theoretical and experimental studies of the stability of dynamic interaction between a feedback controlled manipulator and a passive environment. Necessary and sufficient conditions for “coupled stability”—the stability of a linear, time-invariant n-port (e.g., a robot, linearized about an operating point) coupled to a passive, but otherwise arbitrary, environment—are presented. The problem of assessing coupled stability for a physical system (continuous time) with a discrete time controller is then addressed. It is demonstrated that such a system may exhibit the coupled stability property; however, analytical, or even inexpensive numerical conditions are difficult to obtain. Therefore, an approximate condition, based on easily computed multivariable Nyquist plots, is developed. This condition is used to analyze two controllers implemented on a two-link, direct drive robot. An impedance controller demonstrates that a feedback controlled manipulator may satisfy the coupled stability property. A LQG/LTR controller illustrates specific consequences of failure to meet the coupled stability criterion; it also illustrates how coupled instability may arise in the absence of force feedback. Two experimental procedures—measurement of endpoint admittance and interaction with springs and masses—are introduced and used to evaluate the above controllers. Theoretical and experimental results are compared.
A Novel PID Configuration for Speed and Position Control
Authors: De Santis Romano M.
Published: March 2008

A Proportional-Integral-Derivative (PID) configuration for speed and position control, of which the gains influence input/output and sensitivity properties with a higher degree of decoupling than in current PIDs, is presented. Performing the same global function as its classical counterpart, this novel configuration offers, in addition, a better understanding, an easier implementation, and a promising extension of the available tuning procedures. The presentation unfolds through a combination of theoretical analysis, practical considerations and test-bench results.
Design of Finite Time Settling Regulators for Linear Systems
Authors: Choura Slim
Published: March 2008

Earlier development of finite time settling controllers focused on the structure of the control law which consists of feedback and feedforward parts. In this structure, the feedback part is designed separately to satisfy certain performance specifications in the frequency and/or the time domain. The feedforward part is determined from the feedback control law, and therefore, there exists one-way coupling of both parts. In this paper, we propose a modification in the control structure that enables the designer to regulate the bounds of the control input and the state responses. We show that the finite time settling control problem can be transformed into a linear quadratic regulator one. This transformation results in a two-way coupling of the feedback and the feedforward control laws. We verify that the robustness property of the control strategy is preserved despite its structural change. In addition, we give guidelines for the selection of the feedforward control law.
Coordinate Transformations and Logical Operations for Minimizing Conservativeness in Coupled Stability Criteria
Authors: Colgate J. E.
Published: March 2008

Often it is desirable to guarantee that a manipulator will remain stable when contacting any member of some set of environments. Coupled stability criteria based on passivity may be used to provide such a guarantee, but may be arbitrarily conservative depending on the environment set. In this paper, two techniques for reducing conservativeness are introduced. The first is based on a canonical coordinate transformation which enables an environment set viewed in the frequency domain to be conformally mapped to the interior of the unit circle. A stability criterion is then derived via the small gain theorem. The second technique uses logical combinations of such criteria to reduce conservativeness further. Both techniques are illustrated with nontrivial examples.
Control of General Dynamic Systems With Periodically Varying Parameters Via Liapunov-Floquet Transformation
Authors: Sinha S. C. , Joseph P.
Published: March 2008

A new technique in the design of controllers for linear dynamic systems with periodically varying coefficients is presented. The idea is to utilize the well-known Liapunov-Floquet (L-F) transformation such that the original time-varying system can be reduced to a form suitable for the application of standard time-invariant methods of control theory. For this purpose, a procedure for computing the L-F matrices for general linear periodic systems is outlined. In this procedure, the state transition matrices are expressed in terms of Chebyshev polynomials which permits the computation of L-F matrices as explicit functions of time. Further, it is shown that controllers can be designed in the transformed domain via full state or observer based feedback using principles of pole placement and optimal control theory. The effectiveness of the proposed technique is demonstrated through two examples. The first example belongs to the class of commutative systems while in the second example a triple inverted pendulum subjected to a periodic follower load is considered. It is found that both types of controllers can be successfully designed.
Modeling Requirements for the Parallel Simulation of Hydraulic Systems
Authors: Burton J. D. , Edge K. A. , Burrows C. R.
Published: March 2008

Parallel simulation of systems offers the benefit of increased speed of execution, but requires the system model to be partitioned to enable numerical tasks to be performed concurrently. Hydraulic systems are characterized by a transport delay in the pipelines connecting physical components, which is due to the propagation of waves at the speed of sound through the fluid medium. The transmission delay allows component models to be decoupled for the current time step, enabling a parallel solution; the inputs to each component model are delayed outputs from connected models. This paper describes a simulation environment suitable for the simulation of hydraulic system performance, using the transmission line modeling approach for the pipelines, decoupling the component models in a hydraulic circuit simulation. Computationally efficient models for cavitation and friction are developed and evaluated. In addition, partitioning strategies for parallel operation are outlined, although these have yet to be implemented.
The Variation of Oil Effective Bulk Modulus With Pressure in Hydraulic Systems
Authors: Jinghong Yu , Zhaoneng Chen , Yuanzhang Lu
Published: March 2008

The paper presents theoretical modeling and an experimental investigation of the variation of oil effective bulk modulus (βe) with pressure in hydraulic systems. A pressure sensitive model of βe and its several simplified forms have been derived. In addition, a method for parameter identification has been formulated. In an actual hydraulic system, values for βe at different load pressures were obtained, model parameters identified and modelling errors evaluated.
Cancellation of Discrete Time Unstable Zeros by Feedforward Control
Authors: Gross Eric , Tomizuka Masayoshi , Messner William
Published: March 2008

This paper presents a design methodology for the cancellation of unstable zeros in linear discrete time systems with tracking control objectives. Unstable zeros are defined to be those zeros of the rational transfer function that occur outside the unit circle. Unstable zeros cannot be canceled by feedback without compromising stability. In light of this fact, a feedforward scheme is used. Future desired trajectory information is required because the feedforward scheme is noncausal. The amount of future desired trajectory information that is required depends upon the zero locations and design specifications. It is shown that for a known plant with no zeros on the unit circle one can obtain a frequency response arbitrarily close to 1. Robustness issues and simulation results are discussed.
Formulation of Equations of Motion for a Chain of Flexible Links Using Hamilton’s Principle
Authors: Benati M. , Morro A.
Published: March 2008

The dynamic equations of a chain of flexible links are determined by means of Hamilton’s principle. First a continuous model is adopted and the boundary conditions are determined, along with the partial differential equations of motion. Then a model with a finite number of degrees of freedom is set up. The configuration of each link is described through the line which joins the end points and the relative deformation is described in terms of appropriate trial functions. The boundary conditions are incorporated into a set of basic trial functions. The time-dependent coefficients of the remaining shape functions play the role of Lagrangian coordinates. The dynamic equations are then derived and the procedure is contrasted with other methods for reduction of a system of links to a system with a finite number of degrees of freedom.
Response to Comment on "Physical Model for the Decay and Preservation of Marine Organic Carbon"
Authors: Rothman Daniel H. , Forney David C.
Published: March 2008

Fast enzyme deactivation rates are not required by our physical model of organic matter decay. Instead, low effective diffusivities arising from sorption of enzymes and physical protection by minerals are sufficient. Our model predicts observed temporal trends in organic-matter decay rather than specific rate constants. Existing statistical models of intrinsic reactivity explain observed trends empirically but not theoretically.
Pattern Separation in the Human Hippocampal CA3 and Dentate Gyrus
Authors: Bakker Arnold , Kirwan C. Brock , Miller Michael , Stark Craig E. L.
Published: March 2008

Pattern separation, the process of transforming similar representations or memories into highly dissimilar, nonoverlapping representations, is a key component of many functions ascribed to the hippocampus. Computational models have stressed the role of the hippocampus and, in particular, the dentate gyrus and its projections into the CA3 subregion in pattern separation. We used high-resolution (1.5-millimeter isotropic voxels) functional magnetic resonance imaging to measure brain activity during incidental memory encoding. Although activity consistent with a bias toward pattern completion was observed in CA1, the subiculum, and the entorhinal and parahippocampal cortices, activity consistent with a strong bias toward pattern separation was observed in, and limited to, the CA3/dentate gyrus. These results provide compelling evidence of a key role of the human CA3/dentate gyrus in pattern separation.
Orrorin tugenensis
Femoral Morphology and the Evolution of Hominin Bipedalism
Authors: Richmond Brian G. , Jungers William L.
Published: March 2008

Bipedalism is a key human adaptation and a defining feature of the hominin clade. Fossil femora discovered in Kenya and attributed to
Orrorin tugenensis
, at 6 million years ago, purportedly provide the earliest postcranial evidence of hominin bipedalism, but their functional and phylogenetic affinities are controversial. We show that the
O. tugenensis
femur differs from those of apes and
Homo
and most strongly resembles those of
Australopithecus
and
Paranthropus
, indicating that
O. tugenensis
was bipedal but is not more closely related to
Homo
than to
Australopithecus
. Femoral morphology indicates that
O. tugenensis
shared distinctive hip biomechanics with australopiths, suggesting that this complex evolved early in human evolution and persisted for almost 4 million years until modifications of the hip appeared in the late Pliocene in early
Homo
.
The Female Equally with the Male I Sing
Authors: Balaban Evan
Published: March 2008

Sex Differences in the Brain
. From Genes to Behavior.
Jill B. Becker, Karen J. Berkley, Nori Geary, Elizabeth Hampson, James P. Herman, and Elizabeth A. Young, Eds.
. Oxford University Press, New York, 2008. 504 pp. $98.50, £54. ISBN 9780195311587.

Offering a comprehensive introduction for researchers, students, and clinicians, the contributors cover background and methodology, sex differences in neurobiology and behavior, and sex differences in the neurobiology of disease.
A Morpholino Oligomer Targeting Highly Conserved Internal Ribosome Entry Site Sequence Is Able To Inhibit Multiple Species of Picornavirus
Authors: Stone Jeffrey K. , Rijnbrand Rene , Stein David A. , Ma Yinghong , Yang Yan , Iversen Patrick L. , Andino Raul
Published: March 2008

Members of the genera
Enterovirus
and
Rhinovirus
(family
Picornaviridae
) cause a wide range of human diseases. An established vaccine is available only for poliovirus, and no effective therapy is available for the treatment of infections caused by any pathogenic picornavirus. Peptide-conjugated phosphorodiamidate morpholino oligomers (PPMO) are single-stranded DNA-like antisense agents that readily enter cells. A panel of PPMO was tested for their antiviral activities against various picornaviruses. PPMO targeting conserved internal ribosome entry site (IRES) sequence were highly active against human rhinovirus type 14, coxsackievirus type B2, and poliovirus type 1 (PV1), reducing PV1 titers by up to 6 log
10
in cell cultures. Comparative sequence analysis led us to design a PPMO (EnteroX) targeting 22 nucleotides of IRES sequence that are perfectly conserved across greater than 99% of all human enteroviruses and rhinoviruses. EnteroX reduced PV1 replication in cell culture to an extent similar to that of other IRES-specific PPMO. Resistant PV1 arose in cell cultures after 12 passages in the presence of EnteroX and were found to have two mutations within the EnteroX target sequence. Nevertheless, cPVR transgenic mice treated once daily by intraperitoneal (i.p.) injection with EnteroX before and/or after i.p. infection with 3 × 10
8
PFU (three times the 50% lethal dose) of PV1 had an approximately 80% higher rate of survival than the controls. The viral titer in tissues taken at day 5 postinfection showed that animals in the EnteroX-treated group averaged over 3, 4, and 5 log
10
less virus in the small intestine, spinal cord, and brain, respectively, than the amount in the control animals. These results suggest that EnteroX may have broad therapeutic potential against entero- and rhinoviruses.
Phase I Dose-Escalation Study of a Monovalent Heat Shock Protein 70-Herpes Simplex Virus Type 2 (HSV-2) Peptide-Based Vaccine Designed To Prime or Boost CD8 T-Cell Responses in HSV-Naïve and HSV-2-Infected Subjects
Authors: Koelle David M. , Magaret Amalia , McClurkan Christopher L. , Remington Michael L. , Warren Terri , Teofilovici Florentina , Wald Anna
Published: March 2008

This was a phase I study to assess the safety, tolerability, and immunogenicity of escalating doses of AG-702, a noncovalent complex of an HLA A*0201-restricted epitope in the glycoprotein B protein of herpes simplex virus type 2 (gB2) and truncated human constitutive heat shock protein 70. Similar vaccines have been immunogenic in animals. Three injections of 10 to 250 μg were administered intradermally to HLA A*0201-bearing subjects who were either herpes simplex virus type 2 (HSV-2)-infected or HSV uninfected. Sixty-two participants received the vaccine, 60 completed the protocol, and T-cell data were accrued for 56 subjects. The vaccine was safe and well tolerated. New or boosted responses to the HSV-2 CD8 epitope were not detected. Baseline responses to an epitope in virion proteins 13/14 were higher than responses to the gB2 epitope. A heat shock protein vaccine with an HSV-2 peptide appears to be safe at the doses studied in healthy adults with or without HSV infection. Modifications of the dose, adjuvant, route, schedule, or HSV antigen may be required to improve responses.
A Neutralizing Antibody to the A Chain of Abrin Inhibits Abrin Toxicity both In Vitro and In Vivo
Authors: Surendranath Kalpana , Karande Anjali A.
Published: March 2008

Plant ribosome-inactivating proteins (RIPs) are RNA N-glycosidases that inhibit protein synthesis in cells. Abrin, a type II RIP, is an AB type toxin, which is one of the most lethal types of toxin known. The B chain facilitates the entry of the molecule into the cell, whereas the A chain exerts the toxic effect. We have generated hybridomas secreting antibodies of the immunoglobulin G class specific to the recombinant A chain of abrin. One monoclonal antibody, namely, D6F10, rescued cells from abrin toxicity. Importantly, the antibody also protected mice from lethal doses of the toxin. The neutralizing effect of the antibody was shown to be due to interference with abrin attachment to the cell surface.
Kinesin Motor Domain ofLeishmania donovanias a Future Vaccine Candidate
Authors: Dey Ayan , Sharma Pawan , Redhu Naresh Singh , Singh Sarman
Published: March 2008

Visceral leishmaniasis (VL) is one of the important parasitic diseases, with approximately 350 million people at risk. Due to the nonavailability of an ideal drug, development of a safe, effective, and affordable vaccine could be a solution for control and prevention of this disease. The present study was carried out to examine the immunological potential of kinesin protein from the microtubule locus ofLeishmania donovanias a suitable vaccine candidate. In silico analysis of this region revealed clusters of major histocompatibility complex class I and II binding epitopes in its motor domain region. A recombinant protein was expressed from this region and named rLvacc. The antigenicity and immunogenicity studies of this protein by Western blot analysis revealed that rLvacc is strongly recognized by sera from acute VL patients. To evaluate its immunogenicity, peripheral blood mononuclear cells from cured VL patients were separated, and a lymphocyte proliferation assay was carried out in the presence of rLvacc. After lymphocyte proliferation, the pooled culture supernatant was assayed for anti-rLvacc antibody titers using an enzyme-linked immunosorbent assay. The results showed that immunoglobulin G2 (IgG2) subtype antibodies were predominant, while IgG1 subtype antibodies were produced in very low titers. On the basis of these ex vivo preliminary findings, its immunogenicity was studied in BALB/c mice. Vaccination with the DNA construct generated a good cellular immune response with significant increases in gamma interferon and interleukin-2 (IL-2) cytokine levels (Th1), but no increase in IL-4 levels (Th2). Taken together, our findings suggest the kinesin motor domain region ofL. donovanias a potential vaccine candidate against visceral leishmaniasis.
EmaA, a Potential Virulence Determinant of
Aggregatibacter actinomycetemcomitans
in Infective Endocarditis
Authors: Tang Gaoyan , Kitten Todd , Munro Cindy L. , Wellman George C. , Mintz Keith P.
Published: March 2008

The gram-negative fastidious human oropharyngeal
Aggregatibacter actinomycetemcomitans
is implicated in the etiology of infective endocarditis. EmaA, an oligomeric coiled-coil adhesin homologous to YadA of
Yersinia enterocolitica
, was hypothesized to mediate the interaction of
A. actinomycetemcomitans
with collagen. Collagen, the most abundant protein in human bodies and the main component of extracellular matrix (ECM), predominates in the supporting tissue of cardiac valves. To extend our earlier studies using purified collagen to determine bacterial binding activities, we developed a tissue model using rabbit cardiac valves to investigate the interaction of
A. actinomycetemcomitans
with native collagen. The resected mitral valves, with or without removal of the endothelium, were incubated with equivalent numbers of the wild type and the isogenic
emaA
mutant defective in collagen binding. There was no difference in binding between the wild-type and the mutant strains when the endothelium remained intact. However, the
emaA
mutant was fivefold less effective than the wild-type strain in colonizing the exposed ECM. A 10-fold increase in the binding of the wild-type strain to ECM was observed compared with the intact endothelium. Similar observations were replicated in an in vivo endocarditis rabbit model; the
emaA
mutant was 10-fold less effective in the initial infection of the traumatized aortic valve. Colocalization studies indicated that
A. actinomycetemcomitans
bound to type I collagen.
A. actinomycetemcomitans
preferentially colonized the ECM and, together with the evidence that EmaA interacts with the native collagen, suggested that the adhesin is likely a potential virulence determinant of the bacterium in the initiation of infective endocarditis.
Staphylococcus aureus
CcpA Affects Biofilm Formation
Authors: Seidl Kati , Goerke Christiane , Wolz Christiane , Mack Dietrich , Berger-Bächi Brigitte , Bischoff Markus
Published: March 2008

Biofilm formation in
Staphylococcus aureus
under in vitro growth conditions is generally promoted by high concentrations of sugar and/or salts. The addition of glucose to routinely used complex growth media triggered biofilm formation in
S. aureus
strain SA113. Deletion of
ccpA
, coding for the catabolite control protein A (CcpA), which regulates gene expression in response to the carbon source, abolished the capacity of SA113 to form a biofilm under static and flow conditions, while still allowing primary attachment to polystyrene surfaces. This suggested that CcpA mainly affects biofilm accumulation and intercellular aggregation.
trans
-Complementation of the mutant with the wild-type
ccpA
allele fully restored the biofilm formation. The biofilm produced by SA113 was susceptible to sodium metaperiodate, DNase I, and proteinase K treatment, indicating the presence of polysaccharide intercellular adhesin (PIA), protein factors, and extracellular DNA (eDNA). The investigation of several factors which were reported to influence biofilm formation in
S. aureus
(
arlRS
,
mgrA
,
rbf
,
sarA
,
atl
,
ica
,
citZ
,
citB
, and
cidABC
) showed that CcpA up-regulated the transcription of
cidA
, which was recently shown to contribute to eDNA production. Moreover, we showed that CcpA increased
icaA
expression and PIA production, presumably over the down-regulation of the tricarboxylic acid cycle genes
citB
and
citZ
.
TheChlamydia trachomatisPlasmid Is a Transcriptional Regulator of Chromosomal Genes and a Virulence Factor
Authors: Carlson John H. , Whitmire William M. , Crane Deborah D. , Wicke Luke , Virtaneva Kimmo , Sturdevant Daniel E. , Kupko John J. , Porcella Stephen F. , Martinez-Orengo Neysha , Heinzen Robert A. , Kari Laszlo , Caldwell Harlan D.
Published: March 2008

Chlamydia trachomatispossesses a cryptic 7.5-kb plasmid of unknown function. Here, we describe a comprehensive molecular and biological characterization of the naturally occurring plasmidless humanC. trachomatisstrain L2(25667R). We found that despite minimal chromosomal polymorphisms, the LGV strain L2(25667R) was indistinguishable from plasmid-positive strain L2(434) with regard to its in vitro infectivity characteristics such as growth kinetics, plaquing efficiency, and plaque size. The only in vitro phenotypic differences between L2(434) and L2(25667R) were the accumulation of glycogen granules in the inclusion matrix and the lack of the typical intrainclusion Brownian-like movement characteristic ofC. trachomatisstrains. Conversely, we observed a marked difference between the two strains in their abilities to colonize and infect the female mouse genital tract. The 50% infective dose of plasmidless strain L2(25667R) was 400-fold greater (4 × 106inclusion-forming units [IFU]) than that of plasmid-bearing strain L2(434) (1 × 104IFU). Transcriptome analysis of the two strains demonstrated a decrease in the transcript levels of a subset of chromosomal genes for strain L2(25667R). Among those genes wasglgA, encoding glycogen synthase, a finding consistent with the failure of L2(25667R) to accumulate glycogen granules. These findings support a primary role for the plasmid in in vivo infectivity and suggest that virulence is controlled, at least in part, by the plasmid's ability to regulate the expression of chromosomal genes. Our findings have important implications in understanding a role for the plasmid in the pathogenesis of human infection and disease.
Burkholderia pseudomallei
Infection of T Cells Leads to T-Cell Costimulation Partially Provided by Flagellin
Authors: Ye Zhiyong , Lee Cheryl Mei Ling , Sun Guang Wen , Gan Yunn-Hwen
Published: March 2008

Burkholderia pseudomallei
is the causative agent of melioidosis. While adaptive immunity has been shown to be important for host resistance to
B. pseudomallei
, the direct interaction of the bacteria with adaptive immune cells such as T and B cells is not well known. To address this question, we infected Jurkat T cells, as well as human primary CD4
+
and CD8
+
T cells, with live
B. pseudomallei
. We found that live bacterial infection could costimulate T cells to produce interleukin-2 (IL-2) and gamma interferon (IFN-γ) in the presence of anti-CD3 cross-linking antibodies. Bacterial supernatant could also costimulate T cells, and this was due to the presence of flagellin in the supernatant. However, T cells infected with bacterial mutants lacking flagellin showed strong impairment in IL-2 but only a slight impairment in IFN-γ production. When cross-linking of CD3 is replaced by IL-2, live bacterial infection was still able to costimulate human primary T cells to produce IFN-γ and flagellin is only a minor ligand contributing to this costimulation. Thus, live
B. pseudomallei
could potentially costimulate T cells not only in an antigen-specific manner but also in a nonspecific manner through bystander activation via IL-2.
Dominant Role of Paraoxonases in Inactivation of the
Pseudomonas aeruginosa
Quorum-Sensing Signal
N
-(3-Oxododecanoyl)-
l
-Homoserine Lactone
Authors: Teiber John F. , Horke Sven , Haines Donovan C. , Chowdhary Puneet K. , Xiao Junhui , Kramer Gerald L. , Haley Robert W. , Draganov Dragomir I.
Published: March 2008

The pathogenic bacterium
Pseudomonas aeruginosa
causes serious infections in immunocompromised patients.
N
-(3-Oxododecanoyl)-
l
-homoserine lactone (3OC12-HSL) is a key component of
P
.
aeruginosa
's quorum-sensing system and regulates the expression of many virulence factors. 3OC12-HSL was previously shown to be hydrolytically inactivated by the paraoxonase (PON) family of calcium-dependent esterases, consisting of PON1, PON2, and PON3. Here we determined the specific activities of purified human PONs for 3OC12-HSL hydrolysis, including the common PON1 polymorphic forms, and found they were in the following order: PON2 ≫ PON1
192R
> PON1
192Q
> PON3. PON2 exhibited a high specific activity of 7.6 ± 0.4 μmols/min/mg at 10 μM 3OC12-HSL, making it the best PON2 substrate identified to date. By use of class-specific inhibitors, approximately 85 and 95% of the 3OC12-HSL lactonase activity were attributable to PON1 in mouse and human sera, respectively. In mouse liver homogenates, the activity was metal dependent, with magnesium- and manganese-dependent lactonase activities comprising 10 to 15% of the calcium-dependent activity. In mouse lung homogenates, all of the activity was calcium dependent. The calcium-dependent activities were irreversibly inhibited by extended EDTA treatment, implicating PONs as the major enzymes inactivating 3OC12-HSL. In human HepG2 and EA.hy 926 cell lysates, the 3OC12-HSL lactonase activity closely paralleled the PON2 protein levels after PON2 knockdown by small interfering RNA treatment of the cells. These findings suggest that PONs, particularly PON2, could be an important mechanism by which 3OC12-HSL is inactivated in mammals.
Optimizing Screening for Acute Human Immunodeficiency Virus Infection with Pooled Nucleic Acid Amplification Tests
Authors: Westreich Daniel J. , Hudgens Michael G. , Fiscus Susan A. , Pilcher Christopher D.
Published: March 2008

Recent studies have shown the public health importance of identifying individuals with acute human immunodeficiency virus infection (AHI); however, the cost of nucleic acid amplification testing (NAAT) makes individual testing of at-risk individuals prohibitively expensive in many settings. Pooled NAAT (or group testing) can improve efficiency and test performance of testing for AHI, but optimizing the pooling algorithm can be difficult. We developed simple, flexible biostatistical models of specimen pooling with NAAT for the identification of AHI cases; these models incorporate group testing theory, operating characteristics of biological assays, and a model of viral dynamics during AHI. Pooling algorithm sensitivity, efficiency (test kits used per individual specimen evaluated), and positive predictive value (PPV) were modeled and compared for three simple pooling algorithms: two-stage minipools (D2), three-stage hierarchical pools (D3), and square arrays with master pools (A2m). We confirmed the results by stochastic simulation and produced reference tables and a Web calculator to facilitate pooling by investigators without specific biostatistical expertise. All three pooling strategies demonstrated improved efficiency and PPV for AHI case detection compared to individual NAAT. D3 and A2m algorithms generally provided better efficiency and PPV than D2; additionally, A2m generally exhibited better PPV than D3. Used selectively and carefully, the simple models developed here can guide the selection of a pooling algorithm for the detection of AHI cases in a wide variety of settings.
Assessing Proficiency of Interpretation of Rapid Human Immunodeficiency Virus Assays in Nonlaboratory Settings: Ensuring Quality of Testing
Authors: Learmonth Kate M. , McPhee Dale A. , Jardine Darren K. , Walker Sandy K. , Aye Thein-Thein , Dax Elizabeth M.
Published: March 2008

Rapid antibody tests for the detection of human immunodeficiency virus (HIV) offer an effective means of providing a timely result of HIV serostatus to individuals. The increased use of rapid HIV antibody tests outside the laboratory has highlighted the need for new, cost-effective quality assurance methods to be developed for use in nonlaboratory-based and resource-limited settings. Photographed rapid HIV test results were used in a modified external quality assessment scheme to assess the interpretation proficiency and, therefore, to assess the feasibility of using this method as a basis for a quality assessment program for nonlaboratory-based testing. Participants (
n
= 148), both experienced and inexperienced in the performance and interpretation of rapid HIV testing, interpreted the photographed results of five rapid HIV assays. These were scored according to the degree of technical discordance. Error scores were grouped according to each participant's technical experience. The accuracy of interpretation for four of the five assays was between 80 and 97%, indicating that the photographed results of samples, including those difficult to read or borderline difficult to read, can be used to assess the proficiency of test operators in interpreting results. Participants had greater difficulty in interpreting samples of weak reactivity; this was consistent across the five assays. Experience played an important role in accurate interpretation, with experienced laboratory participants exhibiting greater proficiency (
P
< 0.05) in interpreting the results of three of the five rapid HIV assays. It was established that photographed results of rapid HIV assays could be interpreted with accuracy and demonstrated that prior experience resulted in a more accurate interpretation performance.
Automated and Manual Methods of DNA Extraction for
Aspergillus fumigatus
and
Rhizopus oryzae
Analyzed by Quantitative Real-Time PCR
Authors: Francesconi Andrea , Kasai Miki , Harrington Susan M. , Beveridge Mara G. , Petraitiene Ruta , Petraitis Vidmantas , Schaufele Robert L. , Walsh Thomas J.
Published: March 2008

Quantitative real-time PCR (qPCR) may improve the detection of fungal pathogens. Extraction of DNA from fungal pathogens is fundamental to optimization of qPCR; however, the loss of fungal DNA during the extraction process is a major limitation to molecular diagnostic tools for pathogenic fungi. We therefore studied representative automated and manual extraction methods for
Aspergillus fumigatus
and
Rhizopus oryzae
. Both were analyzed by qPCR for their ability to extract DNA from propagules and germinated hyphal elements (GHE). The limit of detection of
A. fumigatus
and
R. oryzae
GHE in bronchoalveolar lavage (BAL) fluid with either extraction method was 1 GHE/ml. Both methods efficiently extracted DNA from
A. fumigatus
, with a limit of detection of 1 × 10
2
conidia. Extraction of
R. oryzae
by the manual method resulted in a limit of detection of 1 × 10
3
sporangiospores. However, extraction with the automated method resulted in a limit of detection of 1 × 10
1
sporangiospores. The amount of time to process 24 samples by the automated method was 2.5 h prior to transferring for automation, 1.3 h of automation, and 10 min postautomation, resulting in a total time of 4 h. The total time required for the manual method was 5.25 h. The automated and manual methods were similar in sensitivity for DNA extraction from
A. fumigatus
conidia and GHE. For
R. oryzae
, the automated method was more sensitive for DNA extraction of sporangiospores, while the manual method was more sensitive for GHE in BAL fluid.
Triple Gene Block Protein Interactions Involved in Movement of
Barley Stripe Mosaic Virus
Authors: Lim Hyoun-Sub , Bragg Jennifer N. , Ganesan Uma , Lawrence Diane M. , Yu Jialin , Isogai Masimachi , Hammond John , Jackson Andrew O.
Published: March 2008

Barley stripe mosaic virus
(BSMV) encodes three movement proteins in an overlapping triple gene block (TGB), but little is known about the physical interactions of these proteins. We have characterized a ribonucleoprotein (RNP) complex consisting of the TGB1 protein and plus-sense BSMV RNAs from infected barley plants and have identified TGB1 complexes in planta and in vitro. Homologous TGB1 binding was disrupted by site-specific mutations in each of the first two N-terminal helicase motifs but not by mutations in two C-terminal helicase motifs. The TGB2 and TGB3 proteins were not detected in the RNP, but affinity chromatography and yeast two-hybrid experiments demonstrated that TGB1 binds to TGB3 and that TGB2 and TGB3 form heterologous interactions. These interactions required the TGB2 glycine 40 and the TGB3 isoleucine 108 residues, and BSMV mutants containing these amino acid substitution were unable to move from cell to cell. Infectivity experiments indicated that TGB1 separated on a different genomic RNA from TGB2 and TGB3 could function in limited cell-to-cell movement but that the rates of movement depended on the levels of expression of the proteins and the contexts in which they are expressed. Moreover, elevated expression of the wild-type TGB3 protein interfered with cell-to-cell movement but movement was not affected by the similar expression of a TGB3 mutant that fails to interact with TGB2. These experiments suggest that BSMV movement requires physical interactions of TGB2 and TGB3 and that substantial deviation from the TGB protein ratios expressed by the wild-type virus compromises movement.