bluuebunny/crossref_metadata_2025 huggingface dataset:
Vibration Control Based on a Probabilistic Nonlinear Processing of the Piezoelement Output Voltage
Authors: Guyomar Daniel , Badel Adrien , Richard Claude , Lefeuvre Elie
Published: June 2008

This paper deals with the so-called SSDI technique which is a semi-passive approach developed to address the problem of structural vibration damping. This technique takes advantage of an original non-linear processing of the voltage generated by piezoelements. It was shown that the original control law corresponding to the SSDI technique was optimal in the case of mono-modal solicitations. In the case of wide band multi-modal solicitation it is not ever true. This paper proposes a novel multi-modal control law for the SSDI technique. It is based on a probabilistic description of the piezovoltage and results in an optimization of the energy dissipated in the nonlinear device connected to the piezoelectric elements.
Dynamic Anti-Plane Characteristic of an Infinite Piezoelectric Medium With a Non-Circular Cavity
Authors: Song Tianshu , Sun Lili , Liu Diankui
Published: June 2008

In this paper, dynamic stress concentrations are studied in an infinite piezoelectric medium with a non-circular cavity under time harmonic incident anti-plane shear wave and inplane electric field. Based on complex variable and conformal mapping method, the dynamic stress concentration factors and the electric field concentration factors at the boundary of the non-circular cavity are obtained by applying the orthogonal function expansion technique. Numerical examples about an infinite piezoelectric medium with an elliptic cavity are provided with different elliptic axial length ratios, different wave numbers and different piezoelectric characteristic parameters. The calculating results show that dynamic analyses are very important to an infinite piezoelectric medium with a non-circular cavity at lower frequencies and larger piezoelectric characteristic parameters.
Numerical Assessment of Nonlinear Electric Field of HVDC Wall Bushing
Authors: Luo L. , Dai L.
Published: June 2008

A numerical model is established in the present research on the basis of a theoretical analysis, for describing and analyzing the electric field of High Voltage Direct Current (HVDC) wall bushing that demonstrates highly nonlinear characteristics. The relationship between the electric field intensity and the resistance of the insulators of the wall bushing is highly nonlinear and the wall bushing is subjected high voltage with nonlinear electric field. A numerical iteration technique is developed with the Parameter Design Language (PDL) of a Finite Element Analysis software package for carrying out the numerical calculations. The nonlinear characteristics of the HVDC wall bushing are investigated with the model and the iteration technique established. The methodology presented in the research provides a new approach for designing and manufacturing the HVDC wall bushing.
Towards a Better Understanding of the Methodological Characteristics of Engineering Design Research
Authors: Horva´th Imre , Duhovnik Jozˇe
Published: June 2008

The goal of this paper is to interpret the methodological characteristics of design research. Design science is in a specific epistemic relationship with natural, formal, human, social, and applied sciences. Although design science explores and generates knowledge on its own, these sciences are the major sources of design knowledge. Therefore, design research shares many characteristics with the source sciences, but it also has its own features. First, the platform of reasoning of the study is clarified. Afterwards, the various underpinning philosophical assumptions, and the nature of research conducted in the source sciences and in design science are analyzed. It has been found that the distinguishing characteristics of design research are that it is view-dependent, largely purpose-driven, usually done with a compound focus, normatively instrumental, and strongly influenced by participatory approaches.
A Nonlinear Fuzzy Logic Controller Developed for an Autonomous Surface Boat
Authors: Bean Thomas A. , Okamoto Akira , Canning John R. , Edwards Dean B.
Published: June 2008

This paper presents an optimized nonlinear fuzzy logic controller designed for an autonomous surface craft and describes the process by which it was found. The nonlinear fuzzy logic controller described herein was developed to maintain the linear feedback control of an optimal set of controller gains when the state is near the operating point. The simplex optimization method was utilized to find the optimal fuzzy logic parameters that define the shape of the control law away from the normal operating point. The resultant controller showed approximately a 20% improvement over the optimal linear controller.
Analysis of Nonlinear Vibration for the Cracked Rotors With Unsymmetrical Viscoelastic Supported Conditions
Authors: Chen Changping , Dai Liming , Fu Yiming
Published: June 2008

The nonlinear governing equations of motion for the cracked rotor system with unsymmetrical viscoelastic supported condition are derived and the nonlinear vibrations of the system are analyzed. The effects of the cracked depth, the cracked position and the disc position on the response curves of the rotational speed-the nonlinear vibration amplitude and the response curve of the nonlinear amplitude-frequency are discussed in detail. The results can be used for the on-line crack monitor of the rotor system.
Experimental Identification of a Fractional Derivative Linear Model for Viscoelastic Materials
Authors: Catania Giuseppe , Sorrentino Silvio
Published: June 2008

Non integer, fractional order derivative rheological models are known to be very effective in describing the linear viscoelastic dynamic behaviour of mechanical structures made of polymers [1]. The application of fractional calculus to viscoelasticity can be physically consistent [2][3][4] and the resulting non integer order differential stress-strain constitutive relation provides good curve fitting properties, requires only a few parameters and leads to causal behaviour [5]. When using such models the solution of direct problems, i.e. the evaluation of time or frequency response from a known excitation can still be obtained from the equations of motion using standard tools such as modal analysis [6]. But regarding the inverse problem, i.e. the identification from measured input-output vibrations, no general technique has so far been established, since the current methods do not seem to easily work with differential operators of non integer order. In this paper a frequency domain method is proposed for the experimental identification of a linear viscoelastic model, namely the Fractional Zener also known as Fractional Standard Linear Solid [5], to compute the frequency dependent complex stress-strain relationship parameters related to the material. The procedure is first checked with respect to numerically generated frequency response functions for testing its accuracy, and then to experimental inertance data from a free-free homogeneous beam made of High Density Polyethylene (HDPE) in plane flexural and axial vibration.
Nonlinear Multi-Mode Dynamics of a Microbeam for Noncontact Atomic Force Microscopy in Ultra-High Vacuum
Authors: Wu W. , Pragai S. , Gottlieb O.
Published: June 2008

We study the nonlinear multi-mode dynamics of a microbeam for noncontact atomic force microscopy in ultra-high vacuum. A boundary-value problem that includes a coupled linear thermo- and viscoelastic field with a localized nonlinear atomic interaction force, augmented by the linearized heat equation, is reduced to a modal dynamical system via Galerkin’s method. An equivalent linear thermoelastic quality factor is obtained and compared with a closed form solution. A numerically obtained escape curve defines valid operating parameters for low damping conditions. Primary, secondary and coupled internal resonances of a three-mode system are examined to reveal a rich bifurcation structure.
Dosimetry in an IMRT phantom designed for a remote monitoring program
Authors: Han Youngyih , Shin Eun Hyuk , Lim Chunil , Kang Se‐Kwon , Park Sung Ho , Lah Jeong‐Eun , Suh Tae‐suk , Yoon Myonggeun , Lee Se Byeong , Cho Sang Hyun , Ibbott Geoffrey S. , Ju Sang Gyu , Ahn Yong Chan
Published: June 2008

An accurate delivery of prescribed dose is essential to ensure the most successful outcome from advanced radiation treatments such as intensity modulated radiation therapy (IMRT). An anthropomorphic phantom was designed and constructed to conduct a remote‐audit program for IMRT treatments. The accuracy of the dosimetry in the phantom was assessed by comparing the results obtained from different detectors with those from Monte Carlo calculations. The developed phantom has a shape of a cylinder with one target and three organs at risk (OARs) inside the unit. The target and OARs were shaped similar to those of nasopharyngeal cancer patients, and manufactured for their identification during computed tomography imaging. The phantom was designed with thermoluminescent dosimeter (TLD) holders that were inserted inside the target and the OARs for the measurements of absolute dose. In addition, the phantom allowed measurements with ionization chambers placed at the TLD locations. As a result, an inter‐comparison between the two types of dosimeters was possible. For the measurement of the relative dose distribution across the target and OARs, two film slots were orthogonally placed near the center of the phantom, which also enabled the insertion of inhomogeneities near the target. Measurements with TLDs, provided by Korea Food and Drug Administration and Radiological Physics Center, and measurements with an ionization chamber (IC) were performed in four cases. The first case was one anterior field of x rays delivered to the phantom; the second case used the same anterior field, but with inhomogeneities inserted into the phantom. The third case was three fields of beams at an equi‐gantry angle for the homogeneous phantom, and the fourth case was IMRT delivery to the phantom without inhomogeneities. For each case, measurements with both TLDs and IC were performed. For cases 1–3, theoretical predictions were obtained by using the Monte Carlo (MC) codes (BEAMnrc and DOSXYZnrc6.0). The TLD measurements were larger than the IC readings by 2.2% (1.3–2.5%), 2.2% (1.2–2.9%), and 2.1% (0–3.3%) on average for case 1, case 2 and case 3, respectively. The average deviation between TLDs and MC results was 0.97% for the first case, 1.27% (0.34–2.18%) for the second case, and 1.13% (0.31–1.94%) for the third case. The IC reading was less than the MC results; the average deviations were , and for the first, second, and third cases, respectively. For the IMRT case, the average deviation between IC readings and TLD measurements was 0.5% . In conclusion, the TLD measurements in the developed phantom agreed with IC and MC results with less than 3% of an average difference. The developed phantom with TLD dosimeters should be useful for remote monitoring of IMRT.
A statistical approach to infer the minimum setup distance of a well chamber to the wall or to the floor for HDR calibration
Authors: Chang Liyun , Ho Sheng‐Yow , Chui Chen‐Shou , Lee Jeng‐Hung , Du Yi‐Chun , Chen Tainsong
Published: June 2008

We propose a new method based on statistical analysis technique to determine the minimum setup distance of a well chamber used in the calibration of high dose rate (HDR). The chamber should be placed at least this distance away from any wall or from the floor in order to mitigate the effect of scatter. Three different chambers were included in this study, namely, Sun Nuclear Corporation, Nucletron, and Standard Imaging. The results from this study indicated that the minimum setup distance varies depending on the particular chamber and the room architecture in which the chamber was used. Our result differs from that of a previous study by Podgorsak et al. [Med. Phys. 19, 1311–1314 (1992)], in which was suggested, and also differs from that of the International Atomic Energy Agency (IAEA)‐TECDOC‐1079 report, which suggested . The new method proposed in this study may be considered as an alternative approach to determine the minimum setup distance of a well‐type chamber used in the calibration of HDR.
Delivery verification using 3D dose reconstruction based on fluorescence measurement in a carbon beam scanning irradiation system
Authors: Furukawa Takuji , Saotome Naoya , Inaniwa Taku , Sato Shinji , Noda Koji , Kanai Tatsuaki
Published: June 2008

The authors have developed a method to reconstruct the 3D dose distribution in a particle beam scanning irradiation system. In this scheme, 3D dose distribution is reconstructed by using the measured images of fluence distribution, which are taken for each iso‐energy slice (i.e., the unit of the depth scanning). A fluorescent screen with a CCD camera is used to measure the fluence distribution. This system was installed at the HIMAC experimental port and tested by using carbon ion beams. Since a maximum difference between the reconstructed dose and the ionization chamber measurement was around in the target volume, this system can be useful for quick verification of 3D dose distribution.
Automated computer optimization for 3D treatment planning of breast irradiation
Authors: Chen Guang‐Pei , Ahunbay Ergun , Li X. Allen
Published: June 2008

A software package, capable of optimizing beam energy and weight and wedge angle and orientation in conjunction with commercial treatment planning system, has been developed to effectively generate three‐dimensional conformal radiation therapy (3DCRT) plans for breast irradiation with complicated dosimetry requirements. A nonlinear optimization procedure was utilized for the optimization. The study with 15 patient cases shows that the technique can reduce treatment planning time and effort significantly and can give comparable or slightly better dosimetry results. The package can also be used to optimize the beam weights of 3DCRT plans for other treatment sites.
Accuracy of dose measurements and calculations within and beyond heterogeneous tissues for photon fields smaller than produced by Cyberknife
Authors: Wilcox Ellen E. , Daskalov George M.
Published: June 2008

For the small radiation field sizes used in stereotactic radiosurgery, lateral electronic disequilibrium and steep dose gradients exist in a large portion of these fields, requiring the use of high‐resolution measurement techniques. These relatively large areas of electronic disequilibrium make accurate dosimetry as well as dose calculation more difficult, and this is exacerbated in regions of tissue heterogeneity. Tissue heterogeneity was considered insignificant in the brain where stereotactic radiosurgery was first used. However, as this technique is expanded to the head and neck and other body sites, dose calculations need to account for dose perturbations in and beyond air cavities, lung, and bone. In a previous study we have evaluated EBT Gafchromic film (International Specialty Products, Wayne, NJ) for dosimetry and characterization of the Cyberknife radiation beams and found that it was comparable to other common detectors used for small photon beams in solid water equivalent phantoms. In the present work EBT film is used to measure dose in heterogeneous slab phantoms containing lung and bone equivalent materials for the radiation beams of diameter 7.5 to produced by the Cyberknife (Accuray, Sunnyvale, CA). These measurements are compared to calculations done with both the clinically utilized Raytrace algorithm as well as the newly developed Monte Carlo based algorithm available on the Cyberknife treatment planning system. Within the low density material both the measurements and Monte Carlo calculations correctly model the decrease in dose produced by a loss of electronic equilibrium, whereas the Raytrace algorithm incorrectly predicts an enhancement of dose in this region. Beyond the low density material an enhancement of dose is correctly calculated by both algorithms. Within the high density bone heterogeneity the EBT film measurements represent dose to unit density tissue in bone and agree with the Monte Carlo results when corrected to dose to unit density tissue in bone. We conclude that EBT film is an appropriate dosimeter for measuring dose in heterogeneous materials and these measurements agree with Monte Carlo calculations of dose as implemented in the Cyberknife treatment planning system.
Feasibility studies of a passive scatter proton therapy nozzle without a range modulator wheel
Authors: Harvey Mark C. , Polf Jerimy C. , Smith Alfred R. , Mohan Radhe
Published: June 2008

The purpose of this work was to determine the feasibility of producing a spread out Bragg peak (SOBP) without a range modulation wheel (RMW) using the passive scattering beam delivery technique. For this study, a comprehensive Monte Carlo model of a passive scattering treatment nozzle was used. The RMW was removed from the model leaving only the initial fixed scatterer (RMW‐free configuration). Range modulation was achieved by directly changing the energy of the proton beam entering the nozzle. To produce a uniform SOBP, the number of protons injected into the nozzle at each beam energy was “dose weighted.” To do so, the effective number of protons was calculated for the individual initial energies using an analytical dose‐weighting function, and the resulting weighted Bragg curves were summed together to produce an SOBP of the desired width. We found that SOBPs calculated using the RMW‐free nozzle configuration were in very good agreement to those calculated with the standard nozzle configuration containing the RMW for the 250, 180, and maximum beam energies. The depth of the distal 90% dose and the 80%–20% distal dose falloff of SOBPs calculated with the two different nozzle configurations agreed to within a millimeter for the three beam energy options considered in this study. In addition, the 80%–20% lateral penumbra for the cross‐field dose profiles calculated with the RMW‐free delivery method agreed with results calculated using the standard RMW technique to less than one millimeter. For an equal number of protons injected into the nozzle, an increase of up to 10% in the delivered dose and a significant reduction in both the in‐air secondary neutron fluence and dose equivalent (H/D) were observed at the isocenter by removing the RMW from the treatment nozzle and modulating the initial proton beam energy. However, increases in delivery time of up to 70% were also estimated with this method. Our results suggest that it is feasible to deliver a passively scattered dose distribution with an RMW‐free nozzle configuration with clinical characteristics comparable to those using standard methods.
Reducing monitor units for robotic radiosurgery by optimized use of multiple collimators
Authors: Pöll Johan J. , Hoogeman Mischa S. , Prévost Jean‐Briac , Nuyttens Joost J. , Levendag Peter C. , Heijmen Ben J.
Published: June 2008

Advances in image guidance and dose delivery techniques, and increased use of hypofractionation, have led to prolonged radiotherapy fraction duration. This is also the case with robotic radiosurgery, as extensive on‐line image guidance procedures, many beams, and usually high fraction doses are used for tumor irradiation. At this institution, early stage non‐small‐cell lung cancer patients are treated with image guided tumor tracking for respiratory motion compensation. Approximately 130 circular beams and up to monitor units (MUs) are used for delivery of a total treatment dose of 60 Gy. The large number of MUs leads to long treatment times and the radiation leakage increases with the number of MUs. Generally, per patient, a single (small) cone is used. To substantially reduce the number of MUs, the authors have developed a new planning strategy for combined use of a small and a large cone. The large cone aims at dose delivery around the PTV center, while the small cone shapes the dose around the (irregular) PTV edges. The authors systematically investigated relationships between the number of MUs, the plan quality, the selected cone diameters, and the beam‐direction setup. Plan quality was assessed with the conformity index, mean lung dose (MLD), V20 of the lungs, and by visual inspection. The reduction in MUs was determined by comparing two‐cone plans with corresponding one‐cone plans that yielded equal MLD, i.e., equal predicted lung toxicity. With the proposed two‐cone approach, the required number of MUs reduced by on average (range ). The beam‐on time per treatment fraction reduced by on average 8 min (range 1–15.2 min). All plans obeyed the clinically applied constraints and were considered clinically acceptable by an involved physician.
Dosimetric characterization of CyberKnife radiosurgical photon beams using polymer gels
Authors: Pantelis E. , Antypas C. , Petrokokkinos L. , Karaiskos P. , Papagiannis P. , Kozicki M. , Georgiou E. , Sakelliou L. , Seimenis I.
Published: June 2008

Dose distributions registered in water equivalent, polymer gel dosimeters were used to measure the output factors and off‐axis profiles of the radiosurgical photon beams employed for CyberKnife radiosurgery. Corresponding measurements were also performed using a shielded silicon diode commonly employed for CyberKnife commissioning, the PinPoint ion chamber, and Gafchromic EBT films, for reasons of comparison. Polymer gel results of this work for the output factors of the 5, 7.5, and 10 mm diameter beams are , , and , respectively. Comparison of polymer gel and diode measurements shows that the latter overestimate output factors of the two small beams ( for the 5 mm beam and for the 7.5 mm beams). This is attributed to the nonwater equivalence of the high atomic number silicon material of the diode detector. On the other hand, the PinPoint chamber is found to underestimate output factors up to for the 5 mm beam due to volume averaging effects. Polymer gel and EBT film output factor results are found in close agreement for all beam sizes, emphasizing the importance of water equivalence and fine detector sensitive volume for small field dosimetry. Relative off‐axis profile results are in good agreement for all dosimeters used in this work, with noticeable differences observed only in the PinPoint estimate of the penumbra width, which is relatively overestimated.
Comparison of slot scanning digital mammography system with full‐field digital mammography system
Authors: Lai Chao‐Jen , Shaw Chris C. , Geiser William , Chen Lingyun , Arribas Elsa , Stephens Tanya , Davis Paul L. , Ayyar Geetha P. , Dogan Basak E. , Nguyen Victoria A. , Whitman Gary J. , Yang Wei T.
Published: June 2008

The purpose of this study was to evaluate and compare microcalcification detectability of two commercial full‐field digital mammography (DM) systems. The first unit was a flat panel based DM system (FFDM) which employed an anti‐scatter grid method to reject scatter, and the second unit was a charge‐coupled device‐based DM system (SSDM) which used scanning slot imaging geometry to reduce scatter radiation. Both systems have comparable scatter‐to‐primary ratios. In this study, 125–160 and calcium carbonate grains were used to simulate microcalcifications and imaged by both DM systems. The calcium carbonate grains were overlapped with a ‐thick 50% adipose/50% glandular simulated breast tissue slab and an anthropomorphic breast phantom (RMI 165, Gammex) for imaging at two different mean glandular dose levels: 0.87 and . A reading study was conducted with seven board certified mammographers with images displayed on review workstations. A five‐point confidence level rating was used to score each detection task. Receiver operating characteristic (ROC) analysis was performed and the area under the ROC curve was used to quantify and compare the performances of these two systems. The results showed that with the simulated breast tissue slab (uniform background), the SSDM system resulted in higher 's than the FFDM system at both MGD levels with the difference statistically significant at only. With the anthropomorphic breast phantom (tissue structure background), the SSDM system performed better than the FFDM system at but worse at . However, the differences were not found to be statistically significant.
3D ultrasound for prostate localization in radiation therapy: A comparison with implanted fiducial markers
Authors: Johnston H. , Hilts M. , Beckham W. , Berthelet E.
Published: June 2008

This study compares prostate localization using three‐dimensional ultrasound (3D US) to a standard technique using implanted fiducial markers (FMs) for prostate image guided radiation therapy (IGRT). Two methods to determine prostate position on US were evaluated: Assisted segmentation (prospectively) and manual segmentation (retrospectively). Daily couch shifts to align the prostate into treatment position were measured using each technique. A total of 278 FM couch shifts and 255 and 218 corresponding assisted and manual segmentation US couch shifts were analyzed in each direction: Anterior‐posterior, right‐left, and superior‐inferior. Ninety five percent “limits‐of‐agreement” (LOA) were used to analyze paired couch shifts and to determine if US can reliably replace FMs. We chose an error tolerance of for the LOA analysis. For FM vs assisted‐segmentation US, 35.3%, 51.0%, and 48.2% of couch shifts (anterior‐posterior, right‐left, and superior‐inferior, respectively) agreed within . Agreement improved using manual segmentation US (corresponding agreements were 45.3%, 64.1%, and 55.2%), however, results still lie markedly below the 95% we consider to indicate clinical equivalence. Based on these results, our experience indicates US cannot replace FMs for prostate IGRT, using either assisted or manual segmentation. US couch shifts showed considerably greater variability than FM measures and US image quality is shown to affect agreement. Planning target volume margins for use with the US system were found to be 15.8, 8.7, and for assisted segmentation and 13.1, 7.6, and for manual segmentation. Comparison of these margins to those reported in recent studies for use with FM IGRT indicate FMs offer greater sparing of the rectum and bladder than the US system.
From laser cooling to aging: A unified Lévy flight description
Authors: Bertin Eric , Bardou François
Published: June 2008

What phenomena such as the subrecoil laser cooling of atoms and aging in glasses have in common is that these systems do not reach steady state during experimental observations, although the observation times are very large compared to microscopic time scales. We discuss some standard models that describe these phenomena and reformulate them in a unified framework in terms of the occupation times of the microscopic states of the system. A universal dynamical mechanism emerges, leading to a generic time-dependent distribution of occupation times, independent of the physical system considered.
An experiment on the dynamics of thermal diffusion
Authors: Sullivan M. C. , Thompson B. G. , Williamson A. P.
Published: June 2008

We present an experiment that demonstrates thermal diffusion in metals via a dynamic measurement of the temperature in a metal rod as a function of position and time. From this single measurement and using simple heat flow equations, we can extract the thermal conductivity and the specific heat of the metal to within 5% of the accepted values. This experiment can be extended for advanced students, who can model the heat flow by including heat losses and finite heater models via a numerical solution of a partial differential equation.
Explaining irreversibility
Authors: Swendsen Robert H.
Published: June 2008

I describe an approach that helps students understand why the behavior of macroscopic systems distinguishes between past and future, even though the underlying classical or quantum microscopic equations are time-reversal invariant. This approach provides a qualitative understanding of irreversibility by an explicit calculation of irreversible behavior for a simple, time-reversal-invariant model system. The mathematics involved is accessible to upper-level undergraduate students.
Precise measurements of Faraday rotation using ac magnetic fields
Authors: Valev V. K. , Wouters J. , Verbiest T.
Published: June 2008

We discuss several important issues concerning the use of a lock-in amplifier and the experimental procedure that need to be addressed to obtain accurate measurements of the Faraday rotation using ac magnetic fields. Our study was conducted on BK7 glass. We show that if electronic interference is avoided and the dependence of the signal on the average light intensity is taken into account, an accurate value of the Verdet constant for thin samples can be determined.
Reforming Cost-Benefit Calculations
Authors: Pilkey Orrin H.
Published: June 2008

Retaking Rationality
. How Cost-Benefit Analysis Can Better Protect the Environment and Our Health.
By Richard L. Revesz and Michael A. Livermore
. Oxford University Press, New York, 2008. 262 pp. $34.95, £18.99. ISBN 9780195368574.

The authors argue that despite the biased way cost-benefit analyses have been applied to environmental and health regulations, the approach can and should be used to further the public good.
Impact of Nucleoside Reverse Transcriptase Inhibitors on Mitochondrial DNA and RNA in Human Skeletal Muscle Cells
Authors: Saitoh Akihiko , Haas Richard H. , Naviaux Robert K. , Salva Neurita G. , Wong Justine K. , Spector Stephen A.
Published: June 2008

We previously reported that 2′,3′-dideoxyinosine (didanosine, or ddI) significantly altered mitochondrial DNA (mtDNA) in peripheral blood mononuclear cells in human immunodeficiency virus type 1 (HIV-1)-infected children who had undetectable plasma HIV-1 RNA for more than 2 years while receiving highly active antiretroviral therapy. This research examines the in vitro effects of nucleoside reverse transcriptase inhibitors (NRTIs) on mitochondria of human skeletal muscle cells (HSMCs), including myoblasts and differentiated myotubes. mtDNA, mitochondrial RNA (mtRNA), and mRNA levels for nuclear mitochondrial regulatory factors were quantified in vitro using HSMCs, including myoblasts and differentiated myotubes, treated with NRTIs singly and in combination. After 5 days of treatment, mtDNA was significantly decreased in myoblasts and myotubes treated with ddI (P< 0.001 andP= 0.01, respectively) and ddI-containing regimens (P< 0.001 andP< 0.001, respectively) compared to levels in untreated cells. mtRNA (MTCYB) was also significantly decreased in the myoblasts and myotubes treated with ddI (P= 0.004) and ddI-containing regimens (P< 0.001). Regardless of the NRTI regimens examined, NRTI combinations significantly decreased mtRNA (MTCO3) in myoblasts and myotubes (P= 0.02 andP= 0.01, respectively). No significant differences were observed for nuclear mitochondrial regulatory factor mRNA in myoblasts or myotubes when treated with NRTIs (P> 0.07). ddI and ddI-containing regimens significantly decrease mtDNA and mtRNA in HSMCs, most notably in myoblasts. These findings may be of particular importance in developing countries, where ddI is widely used for first-line treatment of HIV-infected children.
Phenotypic and Genotypic Analyses of
Neisseria gonorrhoeae
Isolates That Express Frequently Recovered PorB PIA Variable Region Types Suggest that Certain P1a Porin Sequences Confer a Selective Advantage for Urogenital Tract Infection
Authors: Garvin Lotisha E. , Bash Margaret C. , Keys Christine , Warner Douglas M. , Ram Sanjay , Shafer William M. , Jerse Ann E.
Published: June 2008

Typing of the
porB
variable region (VR) is an epidemiological tool that classifies gonococcal strains based on sequence differences in regions of the
porB
gene that encode surface-exposed loops. The frequent isolation of certain
porB
VR types suggests that some porin sequences confer a selective advantage during infection and/or transmission. Alternatively, certain porin types may be markers of strains that are successful due to factors unrelated to porin. In support of the first hypothesis, here we show urogenital tract isolates representing the most common PIA VR types identified in an urban clinic in Baltimore, MD, over a 10-year period belonged to several different clonal types, as determined by pulsed-field gel electrophoresis (PFGE). Serum resistance, which was confirmed by factor H and C4b-binding protein binding studies, was more often associated with gonococcal the most common VR types. In contrast, three porin-independent phenotypes, namely, lactoferrin utilization, β-lactamase production, and multiple transferable resistance (Mtr), were segregated with the PFGE cluster and not with the VR type. Data combined with another PIA strain collection showed a strong correlation between serum resistance and the most common VR types. A comparison of VR typing hybridization patterns and nucleotide sequences of 12
porB1a
genes suggests that certain porin loop 1, 3, 6, and/or 7 sequences may play a role in the serum resistance phenotype. We conclude that some PorB PIA sequences confer a survival or transmission advantage in the urogenital tract, perhaps via increased resistance to complement-mediated killing. The capacity of some porin types to evade a porin-specific adaptive immune response must also be considered.
Rat Pneumonia and Soft-Tissue Infection Models for the Study of
Acinetobacter baumannii
Biology
Authors: Russo Thomas A. , Beanan Janet M. , Olson Ruth , MacDonald Ulrike , Luke Nicole R. , Gill Steven R. , Campagnari Anthony A.
Published: June 2008

Acinetobacter baumannii
is a bacterial pathogen of increasing medical importance. Little is known about its mechanisms of pathogenesis, and safe reliable agents with predictable activity against
A. baumannii
are presently nonexistent. The availability of relevant animal infection models will facilitate the study of
Acinetobacter
biology. In this report we tested the hypothesis that the rat pneumonia and soft-tissue infection models that our laboratory had previously used for studies of extraintestinal pathogenic
Escherichia coli
were clinically relevant for
A. baumannii
. Advantages of these models over previously described models were that the animals were not rendered neutropenic and they did not receive porcine mucin with bacterial challenge. Using the
A. baumannii
model pathogen 307-0294 as the challenge pathogen, the pneumonia model demonstrated all of the features of infection that are critical for a clinically relevant model: namely, bacterial growth/clearance, an ensuing host inflammatory response, acute lung injury, and, following progressive bacterial proliferation, death due to respiratory failure. We were also able to demonstrate growth of 307-0294 in the soft-tissue infection model. Next we tested the hypothesis that the soft-tissue infection model could be used to discriminate between the inherent differences in virulence of various
A. baumannii
clinical isolates. The ability of
A. baumannii
to grow and/or be cleared in this model was dependent on the challenge strain. We also hypothesized that complement is an important host factor in protecting against
A. baumannii
infection in vivo. In support of this hypothesis was the observation that the serum sensitivity of various
A. baumannii
clinical isolates in vitro roughly paralleled their growth/clearance in the soft-tissue infection model in vivo. Lastly we hypothesized that the soft-tissue infection model would serve as an efficient screening mechanism for identifying gene essentiality for drug discovery. Random mutants of 307-0294 were initially screened for lack of growth in human ascites in vitro. Selected mutants were subsequently used for challenge in the soft-tissue infection model to determine if the disrupted gene was essential for growth in vivo. Using this approach, we have been able to successfully identify a number of genes essential for the growth of 307-0294 in vivo. In summary, these models are clinically relevant and can be used to study the innate virulence of various
Acinetobacter
clinical isolates and to assess potential virulence factors, vaccine candidates, and drug targets in vivo and can be used for pharmacokinetic and chemotherapeutic investigations.
Impaired Opsonization with C3b and Phagocytosis ofStreptococcus pneumoniaein Sera from Subjects with Defects in the Classical Complement Pathway
Authors: Yuste Jose , Sen Ashwin , Truedsson Lennart , Jönsson Göran , Tay Liang-Seah , Hyams Catherine , Baxendale Helen E. , Goldblatt Fiona , Botto Marina , Brown Jeremy S.
Published: June 2008

Results from studies using mice deficient in specific complement factors and clinical data on patients with an inherited deficiency of the classical complement pathway component C2 suggest that the classical pathway is vital for immunity toStreptococcus pneumoniae. However, the consequences of defects in classical pathway activity for opsonization with C3b and the phagocytosis of differentS. pneumoniaeserotypes in human serum are not known, and there has not been a systematic analysis of the abilities of sera from subjects with a C2 deficiency to opsonizeS. pneumoniae. Hence, to investigate the role of the classical pathway in immunity toS. pneumoniaein more detail, flow cytometry assays of opsonization with C3b and the phagocytosis of three capsular serotypes ofS. pneumoniaewere performed using human sera depleted of the complement factor C1q or B or sera obtained from C2-deficient subjects. The results demonstrate that, in human serum, the classical pathway is vital for C3b-iC3b deposition onto cells of all three serotypes ofS. pneumoniaeand seems to be more important than the alternative pathway for phagocytosis. Compared to the results for sera from normal subjects, C3b-iC3b deposition and total anti-S. pneumoniaeantibody activity levels in sera obtained from C2−/−subjects were reduced and the efficiency of phagocytosis of all threeS. pneumoniaestrains was impaired. Anticapsular antibody levels did not correlate with phagocytosis or C3b-iC3b deposition. These data confirm that the classical pathway is vital for complement-mediated phagocytosis ofS. pneumoniaeand demonstrate why subjects with a C2 deficiency have a marked increase in susceptibility toS. pneumoniaeinfections.
The Fibrinogen- and Fibronectin-Binding Domains of
Staphylococcus aureus
Fibronectin-Binding Protein A Synergistically Promote Endothelial Invasion and Experimental Endocarditis
Authors: Piroth Lionel , Que Yok-Ai , Widmer Eleonora , Panchaud Alexandre , Piu Stéphane , Entenza José M. , Moreillon Philippe
Published: June 2008

Staphylococcus aureus
experimental endocarditis relies on sequential fibrinogen binding (for valve colonization) and fibronectin binding (for endothelial invasion) conferred by peptidoglycan-attached adhesins. Fibronectin-binding protein A (FnBPA) reconciles these two properties—as well as elastin binding—and promotes experimental endocarditis by itself. Here we attempted to delineate the minimal subdomain of FnBPA responsible for fibrinogen and fibronectin binding, cell invasion, and in vivo endocarditis. A large library of truncated constructs of FnBPA was expressed in
Lactococcus lactis
and tested in vitro and in animals. A 127-amino-acid subdomain spanning the hinge of the FnBPA fibrinogen-binding and fibronectin-binding regions appeared necessary and sufficient to confer the sum of these properties. Competition with synthetic peptides could not delineate specific fibrinogen- and fibronectin-binding sites, suggesting that dual binding arose from protein folding, irrespective of clearly defined binding domains. Moreover, coexpressing the 127-amino-acid subdomain with remote domains of FnBPA further increased fibrinogen binding by ≥10 times, confirming the importance of domain interactions for binding efficacy. In animals, fibrinogen binding (but not fibronectin binding) was significantly associated with endocarditis induction, whereas both fibrinogen binding and fibronectin binding were associated with disease severity. Moreover, fibrinogen binding also combined with fibronectin binding to synergize the invasion of cultured cell lines significantly, a feature correlating with endocarditis severity. Thus, while fibrinogen binding and fibronectin binding were believed to act sequentially in colonization and invasion, they appeared unexpectedly intertwined in terms of both functional anatomy and pathogenicity (in endocarditis). This unforeseen FnBPA subtlety might bear importance for the development of antiadhesin strategies.
A Novel Immunoprecipitation Strategy Identifies a Unique Functional Mimic of the Glial Cell Line-Derived Neurotrophic Factor Family Ligands in the PathogenTrypanosoma cruzi
Authors: Lu Bo , PereiraPerrin Mercio
Published: June 2008

The journey of the Chagas' disease parasiteTrypanosoma cruziin the human body usually starts in the skin after an insect bite, when trypomastigotes get through the extracellular matrix to bind specific surface receptors in the epidermis and dermis to enter cells, where they differentiate and replicate. As the infection spreads to the heart, nervous system, and other parts of the body via the circulatory system, the parasite must also cope with additional receptors in the immune system and vascular endothelium. The molecular underpinnings that govern host cell receptor recognition byT. cruzicounterreceptors remain largely unknown. Here, we describe an immunoprecipitation strategy designed to concurrently identify host receptors and complementing parasite counterreceptors. Extracellular domains of growth factor receptors fused to human immunoglobulin G (IgG) Fc were incubated with parasite lysates, immunoprecipitated on protein G-Sepharose, and eluted with Laemmli sample buffer. PossibleT. cruzicounterreceptors pulled down by the receptor-Fc bait were visualized on immunoblots probed with multispecific high-affinity IgG from chronic chagasic sera and on sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels stained with silver or Coomassie blue. In screening receptors important for nervous system repair, this parasite counterreceptor immunoprecipitation (PcIP) assay identified 7 to 11 polypeptides (molecular masses, 14 kDa to 55 kDa) that bound to the coreceptors of glial cell line-derived neurotrophic factor (GDNF) family ligands (GFLs) GFRα-1, -2, and -3. Binding was specific because theT. cruzimimic of host GFLs, named TGFL, did not react with GFL coreceptor tyrosine kinase RET and with other neurotrophic receptors. The polypeptides were located on the parasite outer membrane and bound noncovalently to each other. TGFL eluted from the GFL receptor/protein G affinity column with 0.5 M NaCl, pH 7.5, and potently promoted neurite outgrowth and cell survival in a GFL-sensitive mouse pheochromocytoma cell line. Given that GFLs are neuron survival factors crucial for development and maintenance of central and peripheral nervous systems, it may be thatT. cruzimimicry of host GFLs helps in mutually beneficial host repair of infected and damaged nervous tissue. As there are >30 growth factor receptor-Fc chimeras commercially available, this PcIP assay can be readily adapted to identify receptors/counterreceptors in otherT. cruziinvasion sites and in other infections such as Lyme disease, amebiasis, and schistosomiasis.
Screen for Leukotoxin Mutants in
Aggregatibacter actinomycetemcomitans
: Genes of the Phosphotransferase System Are Required for Leukotoxin Biosynthesis
Authors: Isaza Maria P. , Duncan Matthew S. , Kaplan Jeffrey B. , Kachlany Scott C.
Published: June 2008

Aggregatibacter
(formerly
Actinobacillus
)
actinomycetemcomitans
is a pathogen that causes localized aggressive periodontitis and extraoral infections including infective endocarditis. Recently, we reported that
A. actinomycetemcomitans
is beta-hemolytic on certain growth media due to the production of leukotoxin (LtxA). Based on this observation and our ability to generate random transposon insertions in
A. actinomycetemcomitans
, we developed and carried out a rapid screen for LtxA mutants. Using PCR, we mapped several of the mutations to genes that are known or predicted to be required for LtxA production, including
ltxA, ltxB, ltxD
, and
tdeA
. In addition, we identified an insertion in a gene previously not recognized to be involved in LtxA biosynthesis,
ptsH. ptsH
encodes the protein HPr, a phosphocarrier protein that is part of the sugar phosphotransferase system. HPr results in the phosphorylation of other proteins and ultimately in the activation of adenylate cyclase and cyclic AMP (cAMP) production. The
ptsH
mutant showed only partial hemolysis on blood agar and did not produce LtxA. The phenotype was complemented by supplying wild-type
ptsH
in
trans
, and real-time PCR analysis showed that the
ptsH
mutant produced approximately 10-fold less
ltxA
mRNA than the wild-type strain. The levels of cAMP in the
ptsH
mutant were significantly lower than in the wild-type strain, and LtxA production could be restored by adding exogenous cAMP to the culture.
Identification of Two Translocon Proteins of
Vibrio parahaemolyticus
Type III Secretion System 2
Authors: Kodama Toshio , Hiyoshi Hirotaka , Gotoh Kazuyoshi , Akeda Yukihiro , Matsuda Shigeaki , Park Kwon-Sam , Cantarelli Vlademir V. , Iida Tetsuya , Honda Takeshi
Published: June 2008

The type III secretion system (T3SS) translocon complex is composed of several associated proteins, which form a translocation channel through the host cell plasma membrane. These proteins are key molecules that are involved in the pathogenicity of many T3SS-positive bacteria, because they are necessary to deliver effector proteins into host cells. A T3SS designated T3SS2 of
Vibrio parahaemolyticus
is thought to be related to the enterotoxicity of this bacterium in humans, but the effector translocation mechanism of T3SS2 is unclear because there is only one gene (the VPA1362 gene) in the T3SS2 region that is homologous to other translocon protein genes. It is also not known whether the VPA1362 protein is functional in the translocon of T3SS2 or whether it is sufficient to form the translocation channel of T3SS2. In this study, we identified both VPA1362 (designated VopB2) and VPA1361 (designated VopD2) as T3SS2-dependent secretion proteins. Functional analysis of these proteins showed that they are essential for T3SS2-dependent cytotoxicity, for the translocation of one of the T3SS2 effector proteins (VopT), and for the contact-dependent activity of pore formation in infected cells in vitro. Their targeting to the host cell membrane depends on T3SS2, and furthermore, they are necessary for T3SS2-dependent enterotoxicity in vivo. These results indicate that VopB2 and VopD2 act as translocon proteins of
V. parahaemolyticus
T3SS2 and hence have a critical role in the T3SS2-dependent enterotoxicity of this bacterium.
Pattern Identification in the Microstructure of Sockeye Salmon (Oncorhynchus nerka) Otoliths
Authors: Marshall Scott L. , Parker Steven S.
Published: June 2008

Otoliths of sockeye salmon (Oncorhynchus nerka) display daily rings in the microstructure when reared in temperatures above ~ 5 °C. Otolith formation ceases in fed fry held at or below 5 °C, although body growth continues at a much reduced rate. Foraging periodicity is not a significant factor in ring periodicity; rather, the existence of an entrained biological rhythm is supported. Subdaily rings are present on some otoliths, but they are faint and poorly defined. A noticeable and consistent ring corresponding to the date of first feeding is identified. The otolith diameter—body length relationship varies significantly between fed and starved experimental groups. The relation measured for starved groups is thought to be a short-term response to brief periods of starvation.Key words: otoliths, daily rings, sockeye salmon, environmental factors