bluuebunny/crossref_metadata_2025 huggingface dataset:
An EPID response calculation algorithm using spatial beam characteristics of primary, head scattered and MLC transmitted radiation
Authors: Rosca Florin , Zygmanski Piotr
Published: June 2008

We have developed an independent algorithm for the prediction of electronic portal imaging device (EPID) response. The algorithm uses a set of images [open beam, closed multileaf collimator (MLC), various fence and modified sweeping gap patterns] to separately characterize the primary and head‐scatter contributions to EPID response. It also characterizes the relevant dosimetric properties of the MLC: Transmission, dosimetric gap, MLC scatter [P. Zygmansky et al., J. Appl. Clin. Med. Phys. 8(4) (2007)], inter‐leaf leakage, and tongue and groove [F. Lorenz et al., Phys. Med. Biol. 52, 5985–5999 (2007)]. The primary radiation is modeled with a single Gaussian distribution defined at the target position, while the head‐scatter radiation is modeled with a triple Gaussian distribution defined downstream of the target. The distances between the target and the head‐scatter source, jaws, and MLC are model parameters. The scatter associated with the EPID is implicit in the model. Open beam images are predicted to within 1% of the maximum value across the image. Other MLC test patterns and intensity‐modulated radiation therapy fluences are predicted to within 1.5% of the maximum value. The presented method was applied to the Varian aS500 EPID but is designed to work with any planar detector with sufficient spatial resolution.
Robust surface registration using salient anatomical features for image‐guided liver surgery: Algorithm and validation
Authors: Clements Logan W. , Chapman William C. , Dawant Benoit M. , Galloway Robert L. , Miga Michael I.
Published: June 2008

A successful surface‐based image‐to‐physical space registration in image‐guided liver surgery (IGLS) is critical to provide reliable guidance information to surgeons and pertinent surface displacement data for use in deformation correction algorithms. The current protocol used to perform the image‐to‐physical space registration involves an initial pose estimation provided by a point based registration of anatomical landmarks identifiable in both the preoperative tomograms and the intraoperative presentation. The surface based registration is then performed via a traditional iterative closest point (ICP) algorithm between the preoperative liver surface, segmented from the tomographic image set, and an intraoperatively acquired point cloud of the liver surface provided by a laser range scanner. Using this more conventional method, the registration accuracy can be compromised by poor initial pose estimation as well as tissue deformation due to the laparotomy and liver mobilization performed prior to tumor resection. In order to increase the robustness of the current surface‐based registration method used in IGLS, we propose the incorporation of salient anatomical features, identifiable in both the preoperative image sets and intraoperative liver surface data, to aid in the initial pose estimation and play a more significant role in the surface‐based registration via a novel weighting scheme. Examples of such salient anatomical features are the falciform groove region as well as the inferior ridge of the liver surface. In order to validate the proposed weighted patch registration method, the alignment results provided by the proposed algorithm using both single and multiple patch regions were compared with the traditional ICP method using six clinical datasets. Robustness studies were also performed using both phantom and clinical data to compare the resulting registrations provided by the proposed algorithm and the traditional method under conditions of varying initial pose. The results provided by the robustness trials and clinical registration comparisons suggest that the proposed weighted patch registration algorithm provides a more robust method with which to perform the image‐to‐physical space registration in IGLS. Furthermore, the implementation of the proposed algorithm during surgical procedures does not impose significant increases in computation or data acquisition times.
Determination of time‐course change rate for arterial xenon using the time course of tissue xenon concentration in xenon‐enhanced computed tomography
Authors: Sase Shigeru , Takahashi Hideaki , Ikeda Hiroki , Kobayashi Minoru , Matsumoto Nobuyuki , Suzuki Michihiro
Published: June 2008

In calculating tissue blood flow (TBF) according to the Fick principle, time‐course information on arterial tracer concentration is indispensable and has a considerable influence on the accuracy of calculated TBF. In TBF measurement by xenon‐enhanced computed tomography (Xe‐CT), nonradioactive xenon gas is administered by inhalation as a tracer, and end‐tidal xenon is used as a substitute for arterial xenon. There has been the assumption that the time‐course change rate for end‐tidal xenon concentration and that for arterial xenon concentration are substantially equal. Respiratory gas sampling is noninvasive to the patient and can be easily measured by exponential curve fitting to end‐tidal xenon concentrations. However, it is pointed out that there would be a large difference between and in many cases. The purpose of this work was to develop a method of determining the value using the time course of tissue xenon concentration in Xe‐CT. The authors incorporated into the Kety autoradiographic equation as a parameter to be solved, and developed a method of least‐squares to obtain the solution for from the time‐course changes in xenon concentration in the tissue. The authors applied this method of least‐squares to the data from Xe‐CT abdominal studies performed on 17 patients; the solution for was found pixel by pixel in the spleen, and its map was created for each patient. On the one hand, the authors obtained the average value of the map of the spleen as the calculated for each patient. On the other hand, the authors measured using the time‐course changes in CT enhancement in the abdominal aorta for each patient. There was a good correlation between and (, ), and these two values were close to each other . This demonstrates that would be close to the true value. Accuracy of TBF by Xe‐CT can be improved with use of the average value of the map of an organ like the spleen that has a single blood supply (only arterial inflow).
Optimization of exposure parameters in full field digital mammography
Authors: Williams Mark B. , Raghunathan Priya , More Mitali J. , Seibert J. Anthony , Kwan Alexander , Lo Joseph Y. , Samei Ehsan , Ranger Nicole T. , Fajardo Laurie L. , McGruder Allen , McGruder Sandra M. , Maidment Andrew D. A. , Yaffe Martin J. , Bloomquist Aili , Mawdsley Gordon E.
Published: June 2008

Optimization of exposure parameters (target, filter, and kVp) in digital mammography necessitates maximization of the image signal‐to‐noise ratio (SNR), while simultaneously minimizing patient dose. The goal of this study is to compare, for each of the major commercially available full field digital mammography (FFDM) systems, the impact of the selection of technique factors on image SNR and radiation dose for a range of breast thickness and tissue types. This phantom study is an update of a previous investigation and includes measurements on recent versions of two of the FFDM systems discussed in that article, as well as on three FFDM systems not available at that time. The five commercial FFDM systems tested, the Senographe 2000D from GE Healthcare, the Mammomat Novation DR from Siemens, the Selenia from Hologic, the Fischer Senoscan, and Fuji's 5000MA used with a Lorad M‐IV mammography unit, are located at five different university test sites. Performance was assessed using all available x‐ray target and filter combinations and nine different phantom types (three compressed thicknesses and three tissue composition types). Each phantom type was also imaged using the automatic exposure control (AEC) of each system to identify the exposure parameters used under automated image acquisition. The figure of merit (FOM) used to compare technique factors is the ratio of the square of the image SNR to the mean glandular dose. The results show that, for a given target/filter combination, in general FOM is a slowly changing function of kVp, with stronger dependence on the choice of target/filter combination. In all cases the FOM was a decreasing function of kVp at the top of the available range of kVp settings, indicating that higher tube voltages would produce no further performance improvement. For a given phantom type, the exposure parameter set resulting in the highest FOM value was system specific, depending on both the set of available target/filter combinations, and on the receptor type. In most cases, the AECs of the FFDM systems successfully identified exposure parameters resulting in FOM values near the maximum ones, however, there were several examples where AEC performance could be improved.
Assessing the future of diffuse optical imaging technologies for breast cancer management
Authors: Tromberg Bruce J. , Pogue Brian W. , Paulsen Keith D. , Yodh Arjun G. , Boas David A. , Cerussi Albert E.
Published: June 2008

Diffuse optical imaging (DOI) is a noninvasive optical technique that employs near‐infrared(NIR) light to quantitatively characterize the optical properties of thick tissues. Although NIR methods were first applied to breast transillumination (also called diaphanography) nearly 80 years ago, quantitative DOI methods employing time‐ or frequency‐domain photon migration technologies have only recently been used for breast imaging(i.e., since the mid‐1990s). In this review, the state of the art in DOI for breast cancer is outlined and a multi‐institutional Network for Translational Research in Optical Imaging (NTROI) is described, which has been formed by the National Cancer Institute to advance diffuse optical spectroscopy and imaging (DOSI) for the purpose of improving breast cancer detection and clinical management. DOSI employs broadband technology both in near‐infrared spectral and temporal signal domains in order to separate absorption from scattering and quantify uptake of multiple molecular probes based on absorption or fluorescence contrast. Additional dimensionality in the data is provided by integrating and co‐registering the functional information of DOSI with x‐ray mammography and magnetic resonance imaging(MRI), which provide structural information or vascular flow information, respectively. Factors affecting DOSI performance, such as intrinsic and extrinsic contrast mechanisms, quantitation of biochemical components, image formation/visualization, and multimodality co‐registration are under investigation in the ongoing research NTROI sites. One of the goals is to develop standardized DOSI platforms that can be used as stand‐alone devices or in conjunction with MRI, mammography, or ultrasound. This broad‐based, multidisciplinary effort is expected to provide new insight regarding the origins of breast disease and practical approaches for addressing several key challenges in breast cancer, including: Detecting disease in mammographically dense tissue, distinguishing between malignant and benign lesions, and understanding the impact of neoadjuvant chemotherapies.
Experimental evaluation of an online gamma‐camera imaging of permanent seed implantation (OGIPSI) prototype for partial breast irradiation
Authors: Ravi Ananth , Caldwell Curtis B. , Pignol Jean‐Philippe
Published: June 2008

Previously, our team used Monte Carlo simulation to demonstrate that a gamma camera could potentially be used as an online image guidance device to visualize seeds during permanent breast seed implant procedures. This could allow for intraoperative correction if seeds have been misplaced. The objective of this study is to describe an experimental evaluation of an online gamma‐camera imaging of permanent seed implantation (OGIPSI) prototype. The OGIPSI device is intended to be able to detect a seed misplacement of or more within an imaging time of or less. The device was constructed by fitting a custom built brass collimator ( height, hole pitch, septal thickness) on a 64 pixel linear array CZT detector (eValuator‐2000, eV Products, Saxonburg, PA). Two‐dimensional projection images of seed distributions were acquired by the use of a digitally controlled translation stage. Spatial resolution and noise characteristics of the detector were measured. The ability and time needed for the OGIPSI device to image the seeds and to detect cold spots was tested using an anthropomorphic breast phantom. Mimicking a real treatment plan, a total of 52 seeds of each were placed on three different layers at appropriate depths within the phantom. The seeds were reliably detected within with a median error in localization of . In conclusion, an OGIPSI device can potentially be used for image guidance of permanent brachytherapy applications in the breast and, possibly, other sites.
Noninvasive in vivo tomographic optical imaging of cellular morphology in the breast: Possible convergence of microscopic pathology and macroscopic radiology
Authors: Li Changqing , Grobmyer Stephen R. , Massol Nicole , Liang Xiaoping , Zhang Qizhi , Chen Lin , Fajardo Laurie L. , Jiang Huabei
Published: June 2008

This article presents a pilot study of multispectral diffuse optical tomography for noninvasively imaging volume fraction and mean size of cellular scattering components in the breast. Cellular morphology images for a total of 14 cases (four malignant breast and ten benign lesions) were obtained. Analyzing the images based on the pathological findings of the cases studied, we found that light scattering in the breast was contributed from both the nucleus and organelles such as mitochondria and nucleolus. Based on the image analysis of these 14 cases, we found that the differences in the mean size and volume fraction between the malignant and benign lesions are significant. The contrast ratio of the average mean size and volume fraction between malignant and benign lesions were calculated to be 3.38 and 2.63. These initial results suggest that cellular mean size and volume fraction may be two new criteria that could be used to differentiate malignant from benign lesions.
Scatter rejection and low‐contrast performance of a slot‐scan digital chest radiography system with electronic aft‐collimation: A chest phantom study
Authors: Liu Xinming , Shaw Chris C. , Lai Chao‐Jen , Altunbas Mustafa C. , Chen Lingyun , Han Tao , Wang Tianpeng
Published: June 2008

Anti‐scatter grids have been widely used to reject scatter and increase the perceptibility of low‐contrast object in chest radiography; however they also attenuate the primary x‐rays, resulting in a substantial degradation of primary information. Compensation for this degradation requires the use of higher exposure technique hence higher dose to the patient. A more efficient approach to reject scatter is the slot‐scan imaging technique which employs a narrow scanning x‐ray fan beam in conjunction with a slit or slot shaped solid state detector or an area detector used with an aft‐collimator. With this approach, scatter can be rejected effectively without the need to attenuate primary x‐rays. This paper demonstrates an electronic aft‐collimation method, referred to as the alternate line erasure and readout (ALER) technique, for implementing the slot‐scan digital radiography with a modern flat‐panel detector. With this technique, instead of first exposing the detector and then reading the image line by line, the image line on the leading edge of the scanning fan beam is reset to erase the scatter accumulated prior to the arrival of the fan beam x‐rays, while the image line on the trailing edge of the scanning fan beam is read out to acquire the image signals following the fan‐beam exposure. These reset and readout processes are alternated and repeated as the x‐ray fan beam scans across the detector. An anthropomorphic chest phantom was imaged to evaluate the scatter rejection ability and the low‐contrast performance for the ALER technique and compare them with those for the anti‐scatter grid method in full‐field chest imaging. With a projected beam width of , the slot‐scan/ALER technique resulted in an average reduction of the scatter‐to‐primary ratios by 81%, 84%, 82%, and 86% versus 65%, 73%, 74%, and 73% with the anti‐scatter grid method in the lungs, mediastinum, retrocardium, and subdiaphragm, respectively. The average CNR for the slot‐scan/ALER technique was found to improve by 135%, 133%, 176%, and 87% versus 15%, 15%, 38%, and with the anti‐scatter grid method in the mediastinum, retrocardium, subdiaphragm, and lungs, respectively. These results demonstrated that the slot‐scan/ALER technique can be used to achieve equally effective scatter rejection but substantially higher low‐contrast performance than the anti‐scatter grid method.
Monte Carlo evaluation of in infinitely long cylinders of water, polyethylene and PMMA with diameters from to
Authors: Zhou Hong , Boone John M.
Published: June 2008

Monte Carlo simulations were used to evaluate the radiation dose to infinitely long cylinders of water, polyethylene, and poly(methylmethacrylate) (PMMA) from 10 to in diameter. Radiation doses were computed by simulating a divergent primary beam striking the cylinder at , and the scattered radiation in the and directions was integrated out to infinity. Doses were assessed using the total energy deposited divided by the mass of the volume of material in the primary beam. This approach is consistent with the notion of the computed tomography dose index (CTDI) integrated over infinite , which is equivalent to the dose near the center of an infinitely long CT scan. Monoenergetic x‐ray beams were studied from 5 to , allowing polyenergetic x‐ray spectra to be evaluated using a weighted average. The radiation dose for a CT slice was assessed at the center, edge, and over the entire diameter of the phantom. The geometry of a commercial CT scanner was simulated, and the computed results were in good agreement with measured doses. The absorbed dose in water for x‐ray spectrum with no bow tie filter for a cylinder diameter was about per mGy air kerma at isocenter for both the peripheral and center regions, and dropped to for a water phantom at the periphery, where the corresponding value for the center location was . The influence of phantom composition was studied. For a diameter of , the dose coefficients were 1.23 for water, 1.02 for PMMA, and 0.94 for polyethylene (at ). For larger diameter phantoms, the order changed—for a phantom, the dose coefficient of polyethylene (0.25) was greater than water (0.21) and PMMA (0.16). The influence of the head and body bow tie filters was also studied. For the peripheral location, the dose coefficients when no bow tie filter was used were high (e.g., for a water phantom at at a diameter of , the dose coefficient was 0.97). The body bow tie filter reduces this value to 0.62, and the head bow tie filter (which is not actually designed to be used for a object) reduces the dose coefficient to 0.42. The dose in CT is delivered both by the absorption of primary and scattered x‐ray photons, and at the center of a water cylinder the ratio of scatter to primary (SPR) doses increased steadily with cylinder diameter. For water, a spectrum and a cylinder diameter of , the SPR was 4, and this value grew to 9 for a diameter of and to over 16 for a cylinder. A freely available spreadsheet was developed to allow the computation of radiation dose as a function of object diameter , composition (water, polyethylene, PMMA), and beam energy .
Focused beam‐stop array for the measurement of scatter in megavoltage portal and cone beam CT imaging
Authors: Maltz Jonathan S. , Gangadharan Bijumon , Vidal Marie , Paidi Ajay , Bose Supratik , Faddegon Bruce A. , Aubin Michele , Morin Olivier , Pouliot Jean , Zheng Zirao , Svatos Michelle M. , Bani‐Hashemi Ali R.
Published: June 2008

We describe a focused beam‐stop array (BSA) for the measurement of object scatter in imaging systems that utilize x‐ray beams in the megavoltage (MV) energy range. The BSA consists of 64 doubly truncated tungsten cone elements of maximum diameter that are arranged in a regular array on an acrylic slab. The BSA is placed in the accessory tray of a medical linear accelerator at a distance of approximately from the focal spot. We derive an expression that allows us to estimate the scatter in an image taken without the array present, given image values in a second image with the array in place. The presence of the array reduces fluence incident on the imaged object. This leads to an object‐dependent underestimation bias in the scatter measurements. We apply corrections in order to address this issue. We compare estimates of the flat panel detector response to scatter obtained using the BSA to those derived from Monte Carlo simulations. We find that the two estimates agree to within 10% in terms of RMS error for water slabs in the thickness range of . Larger errors in the scatter estimates are encountered for thinner objects, probably owing to extrafocal radiation sources. However, RMS errors in the estimates of primary images are no more than 5% for water slab thicknesses in the range of . The BSA scatter estimates are also used to correct cone beam tomographic projections. Maximum deviations of central profiles of uniform water phantoms are reduced from 193 to after application of corrections for scatter, beam hardening, and lateral truncation that are based on the BSA‐derived scatter estimate. The same corrections remove the typical cupping artifact from both phantom and patient images. The BSA proves to be a useful tool for quantifying and removing image scatter, as well as for validating models of MV imaging systems.
Monte Carlo simulation of MOSFET dosimeter for electron backscatter using the GEANT4 code
Authors: Chow James C. L. , Leung Michael K. K.
Published: June 2008

The aim of this study is to investigate the influence of the body of the metal–oxide–semiconductor field effect transistor (MOSFET) dosimeter in measuring the electron backscatter from lead. The electron backscatter factor (EBF), which is defined as the ratio of dose at the tissue‐lead interface to the dose at the same point without the presence of backscatter, was calculated by the Monte Carlo simulation using the GEANT4 code. Electron beams with energies of 4, 6, 9, and 12 MeV were used in the simulation. It was found that in the presence of the MOSFET body, the EBFs were underestimated by about for electron beam energies of , respectively. The trend of the decrease of EBF with an increase of electron energy can be explained by the small MOSFET dosimeter, mainly made of epoxy and silicon, not only attenuated the electron fluence of the electron beam from upstream, but also the electron backscatter generated by the lead underneath the dosimeter. However, this variation of the EBF underestimation is within the same order of the statistical uncertainties as the Monte Carlo simulations, which ranged from 1.3% to 0.8% for the electron energies of , due to the small dosimetric volume. Such small EBF deviation is therefore insignificant when the uncertainty of the Monte Carlo simulation is taken into account. Corresponding measurements were carried out and uncertainties compared to Monte Carlo results were within . Spectra of energy deposited by the backscattered electrons in dosimetric volumes with and without the lead and MOSFET were determined by Monte Carlo simulations. It was found that in both cases, when the MOSFET body is either present or absent in the simulation, deviations of electron energy spectra with and without the lead decrease with an increase of the electron beam energy. Moreover, the softer spectrum of the backscattered electron when lead is present can result in a reduction of the MOSFET response due to stronger recombination in the gate. It is concluded that the MOSFET dosimeter performed well for measuring the electron backscatter from lead using electron beams. The uncertainty of EBF determined by comparing the results of Monte Carlo simulations and measurements is well within the accuracy of the MOSFET dosimeter provided by the manufacturer.
SU‐FF‐J‐25: Quality Control Procedure for the PET‐Guided Interventions
Authors: Beylin D , Sherry S , Anashkin E , Narayanan D , Stepanov P , Zavarzin V
Published: June 2008

Objectives: Positron Emission Mammography (PEM) with F18‐FDG has been useful in breast cancer diagnosis and characterization [1]. Clinical PEM scanners produce high resolution (2mm) PET images of immobilized breasts in 5–10 minutes. This allows the PEM scanner to guide breast interventions, with the help of a localization accessory including software for procedure planning and hardware for needle support. We report the development of a quality control procedure to test the performance of the accessory in a clinical setting on a daily basis. Materials and Methods: A quality control procedure was designed to evaluate the functionality of the Stereo Navigator accessory to the PEM Flex PET Scanner (Naviscan PET Systems, Inc., San Diego, CA). During the procedure, 1 microCurie point source was placed in the field of view of the PEM scanner. PEM scan of the point source was performed. The software was used to select the point source as a target and guide a radioactive rod containing 0.1 microCurie/cm of Germanium‐68 toward the source. A distance of less than 5mm from the tip of the rod to the point source was considered acceptable. A second PEM image was acquired, and regions of interest were used to verify the activities of the sources. To test the validity of the procedure, failures were introduced such as incompatible hardware/software and incorrect calibration rod activity. Time to perform the procedure was recorded. Results: The procedure detects clinically‐relevant failures and can be performed by a trained user in less than 5 minutes. Conclusions: The quality control procedure for the localization accessory to the PEM scanner can be performed in clinically acceptable time.
SU‐FF‐T‐77: Analysis of Dose Distributions in Buildup Region for IMRT Beams
Authors: Li T , Gong J , Bassalow R , Chu K
Published: June 2008

Purpose: To measure the dose distribution in buildup region with a 2D ion chamber array. Measurements are compared with calculation from Eclipse and analyzed using Gamma Index method. Method and Materials: Dose distributions from 6 MV photon IMRT beams in buildup region are calculated with Eclipse TPS (Varian Medical Systems) in a phantom using sliding window technique for a head and neck case. Those beams are delivered by a Varian Clinac iX linear accelerator with 120‐leaf Millennium MLC and are measured with PTW729 ion chamber array (PTW, Inc.). All the measurements are performed at 0.5 cm depth with 96.5 cm SSD. The calculated and measured dose distributions are compared with Gamma index method using Verisoft software (PTW, Inc.). By changing the acceptance criteria in Gamma Index method from 5% dose difference, and 5 mm DTA (distance‐to‐agreement) to 20%, and 20 mm respectively, the comparison between measured and calculated dose distribution are analyzed. Results: Typical preliminary results are listed below: It can be seen for highly modulated beams, dose difference of 20% and positional difference of 20 mm can result between measurement and calculation. Conclusion: The dose distributions in the build up region measured by PTW 2D ion chamber array are compared with those calculated by Eclipse. The comparison is analyzed by Gamma Index method. Detailed measurement validation is underway with different intensity modulation levels and positional accuracy. This type of study can help us to better understand of the accuracy of dose calculations and measurement in buildup region.
Poynting’s theorem for plane waves at an interface: A scattering matrix approach
Authors: Domínguez-Rocha V. , Zagoya C. , Martínez-Mares M.
Published: June 2008

We write Poynting’s theorem in a form that allows us to introduce a natural definition of the scattering matrix S. For a dielectric-dielectric interface this balance equation leads to energy flux conservation and the unitarity property of S. For the dielectric-conductor interface the scattering matrix is no longer unitary due to the presence of losses in the conductor, and we denote it by S̃. The dissipative term in Poynting’s theorem can be interpreted as due to a single parasitic channel or excitation of the absorptive interface. We define an S matrix that includes the parasitic channel, so that S is unitary.
Relativistic aberration for accelerating observers
Authors: Beig Robert , Heinzle J. Mark
Published: June 2008

We investigate the effects of the aberration of light for a uniformly accelerating observer. The observer is initially at rest with respect to a luminous spherical object and then starts to move away with constant acceleration. Our main results are the following: (i) The observer sees an initial increase of the apparent size of the object, (ii) the apparent size of the object approaches a nonzero value as the proper time of the observer goes to infinity, and (iii) there exists a critical value of the acceleration such that the apparent size of the object is monotonically increasing when the acceleration is supercritical. Although the first effect is purely nonrelativistic, the others are the result of the relativistic aberration of light and are intimately connected with the Lorentzian geometry of Minkowksi spacetime. The examples we present illustrate that the three effects are more or less negligible in everyday life, but significant in the context of space flight.
Light cones and repulsive gravity
Authors: Preti Giovanni , de Felice Fernando
Published: June 2008

Contrary to common belief, gravitation can also be repulsive. Examples of repulsive gravity are provided by the naked singularity solutions of the Einstein equations corresponding to the negative mass Schwarzschild, the Reissner–Nordström, and the Kerr spacetimes. We show that their repulsive gravity regions can be identified by a particular behavior of the light cones when use is made of symmetry-adapted coordinate systems.
Conductors in quasistatic electric fields
Authors: Garg Anupam
Published: June 2008

The problem of determining the electric and magnetic fields in and around a conductor in a quasistatic external electric field is considered. It is shown that there are two frequency regimes corresponding to whether the ratio of the skin depth to the linear size of the conductor is large or small compared to unity. General arguments are made about the magnitudes of the fields, especially their normal and transverse components near the surface of the body. The special case of a spherical conductor is solved explicitly in order to verify the general conclusions about the nature of the fields in these two regimes. Comparison is made with behavior in an external magnetic field.
Quantum simulation of the single-particle Schrödinger equation
Authors: Benenti Giuliano , Strini Giuliano
Published: June 2008

The nature of a quantum computer is described in the concrete context of a quantum simulator of the single-particle Schrödinger equation. We show that a register of 6–10 qubits is sufficient to realize a useful quantum simulator capable of efficiently solving standard quantum mechanical problems.
Integrated approaches in physics education: A graduate level course in physics, pedagogy, and education research
Authors: Wittmann Michael C. , Thompson John R.
Published: June 2008

We describe a course designed to help future educators develop an integrated understanding of different elements of physics education research (PER), including research into student learning, content knowledge from the perspective of how it is learned, and reform-based curricula, together with evidence of their effectiveness. Course elements include equal parts of physics study through proven curricula and discussion of research results in the context of the PER literature. We provide examples of the course content and structure and representative examples of student learning in the class.
Illustrating Lyapunov’s analysis of asymptotic stability for a heavy particle affected by drag resistance
Authors: Siboni S.
Published: June 2008

The application of Lyapunov’s criterion for the asymptotic stability of equilibrium in mechanical systems is difficult in general because the natural candidate for the role of Lyapunov function, the mechanical energy, is suitable for determining simple stability but not asymptotic stability, unless the energy is modified in a way that is nontrivial, difficult to standardize, and whose physical interpretation is obscure. A simple class of mechanical systems is discussed for which the global asymptotic stability can be checked by means of simple physically reasonable Lyapunov functions. A comparison of alternative Lyapunov functions is also done when possible. The class of systems includes the motion of a heavy body moving through the atmosphere close to the Earth’s surface.
Preclinical Evaluation of 1H-Benzylindole Derivatives as Novel Human Immunodeficiency Virus Integrase Strand Transfer Inhibitors
Authors: Hombrouck Anneleen , Van Remoortel Barbara , Michiels Martine , Noppe Wim , Christ Frauke , Eneroth Anders , Sahlberg Britt Louise , Benkestock Kurt , Vrang Lotta , Johansson Nils Gunnar , Barreca Maria Letizia , De Luca Laura , Ferro Stefania , Chimirri Alba , Debyser Zeger , Witvrouw Myriam
Published: June 2008

We have identified 1H-benzylindole analogues as a novel series of human immunodeficiency virus (HIV) integrase inhibitors with antiretroviral activities against different strains of HIV type 1 (HIV-1), HIV-2, and simian immunodeficiency virus strain MAC
251
[SIV(MAC
251
)]. Molecular modeling and structure-activity relationship-based optimization resulted in the identification of CHI/1043 as the most potent congener. CHI/1043 inhibited the replication of HIV-1(III
B
) in MT-4 cells at a 50% effective concentration (EC
50
) of 0.60 μM, 70-fold below its cytotoxic concentration. Equal activities against HIV-1(NL4.3), HIV-2(ROD), HIV-2(EHO), and SIV(MAC
251
) were observed. CHI/1043 was equally active against virus strains resistant against inhibitors of reverse transcriptase or protease. Replication of both X4 and R5 strains in peripheral blood mononuclear cells was sensitive to the inhibitory effect of CHI/1043 (EC
50
, 0.30 to 0.38 μM). CHI/1043 inhibited integrase strand transfer activity in oligonucleotide-based enzymatic assays at low micromolar concentrations. Time-of-addition experiments confirmed CHI/1043 to interfere with the viral replication cycle at the time of retroviral integration. Quantitative
Alu
PCR corroborated that the anti-HIV activity is based upon the inhibition of proviral DNA integration. An HIV-1 strain selected for 70 passages in the presence of CHI/1043 was evaluated genotypically and phenotypically. The mutations T66I and Q146K were present in integrase. Cross-resistance to other integrase strand transfer inhibitors, such as L-708,906, the naphthyridine analogue L-870,810, and the clinical drugs GS/9137 and MK-0518, was observed. In adsorption, distribution, metabolism, excretion, and toxicity studies, antiviral activity was strongly reduced by protein binding, and metabolization in human liver microsomes was observed. Transport studies with Caco cells suggest a low oral bioavailability.
Staphylococcus aureus
Cell Wall Stress Stimulon Gene
-lacZ
Fusion Strains: Potential for Use in Screening for Cell Wall-Active Antimicrobials
Authors: Steidl Rebecca , Pearson Stacy , Stephenson Robert E. , Ledala Nagender , Sitthisak Sutthirat , Wilkinson Brian J. , Jayaswal Radheshyam K.
Published: June 2008

lacZ
fusion strains were constructed using the promoters of five cell wall stress stimulon genes:
pbp2
,
tcaA
,
vraSR
,
sgtB
, and
lytR
. All fusion strains were induced only in the presence of cell wall-active antibiotics, suggesting the potential of these strains for use in high-throughput screening for new cell wall-active agents.
Identification of Mutations Related to Streptomycin Resistance in Clinical Isolates of
Mycobacterium tuberculosis
and Possible Involvement of Efflux Mechanism
Authors: Spies Fernanda S. , Almeida da Silva Pedro E. , Ribeiro Marta O. , Rossetti Maria Lucia , Zaha Arnaldo
Published: June 2008

The MIC for streptomycin in the presence of efflux pump (EP) inhibitors and the sequencing of
rpsL
,
rrs
, and
gidB
genes provided evidence for the possible participation of EP in low-level streptomycin (STR) resistance of some isolates without mutations. Mutation in the
gidB
gene and an EP could act synergistically to confer low STR resistance.
Specific Roles of the
iroBCDEN
Genes in Virulence of an Avian Pathogenic
Escherichia coli
O78 Strain and in Production of Salmochelins
Authors: Caza Mélissa , Lépine François , Milot Sylvain , Dozois Charles M.
Published: June 2008

Avian pathogenic
Escherichia coli
(APEC) strains are a subset of extraintestinal pathogenic
E. coli
(ExPEC) strains associated with respiratory infections and septicemia in poultry. The
iroBCDEN
genes encode the salmochelin siderophore system present in
Salmonella enterica
and some ExPEC strains. Roles of the
iro
genes for virulence in chickens and production of salmochelins were assessed by introducing plasmids carrying different combinations of
iro
genes into an attenuated salmochelin- and aerobactin-negative mutant of O78 strain χ7122. Complementation with the
iroBCDEN
genes resulted in a regaining of virulence, whereas the absence of
iroC
,
iroDE
, or
iroN
abrogated restoration of virulence. The
iroE
gene was not required for virulence, since introduction of
iroBCDN
restored the capacity to cause lesions and colonize extraintestinal tissues. Prevalence studies indicated that
iro
sequences were associated with virulent APEC strains. Liquid chromatography-mass spectrometry analysis of supernatants of APEC χ7122 and the complemented mutants indicated that (i) for χ7122, salmochelins comprised 14 to 27% of the siderophores present in iron-limited medium or infected tissues; (ii) complementation of the mutant with the
iro
locus increased levels of glucosylated dimers (S1 and S5) and monomer (SX) compared to APEC strain χ7122; (iii) the
iroDE
genes were important for generation of S1, S5, and SX; (iv)
iroC
was required for export of salmochelin trimers and dimers; and (v)
iroB
was required for generation of salmochelins. Overall, efficient glucosylation (IroB), transport (IroC and IroN), and processing (IroD and IroE) of salmochelins are required for APEC virulence, although IroE appears to serve an ancillary role.
An Interleukin-1β (IL-1β) Single-Nucleotide Polymorphism at Position 3954 and Red Complex Periodontopathogens Independently and Additively Modulate the Levels of IL-1β in Diseased Periodontal Tissues
Authors: Ferreira Samuel B. , Trombone Ana Paula F. , Repeke Carlos E. , Cardoso Cristina R. , Martins Walter , Santos Carlos F. , Trevilatto Paula Cristina , Ávila-Campos Mario J. , Campanelli Ana Paula , Silva João S. , Garlet Gustavo P.
Published: June 2008

Inflammatory cytokines such as interleukin-1β (IL-1β) are involved in the pathogenesis of periodontal diseases. A high individual variation in the levels of IL-1β mRNA has been verified, which is possibly determined by genetic polymorphisms and/or by the presence of periodontopathogens such asPorphyromonas gingivalis, Tannerella forsythia, Treponema denticola, andAggregatibacter actinomycetemcomitans. In this study, we investigated the role of an IL-1β promoter single-nucleotide polymorphism at position 3954 [IL-1β(3954) SNP] and the presence of the periodontopathogens in the determination of the IL-1β levels in the periodontal tissues of nonsmoking chronic periodontitis (CP) patients (n= 117) and control (C) subjects (n= 175) and the possible correlations with the clinical parameters of the disease. IL-1β(3954) SNP was investigated by restriction fragment length polymorphism, while the IL-1β levels and the presence of the periodontopathogens were determined by real-time PCR. Similar frequencies of IL-1β(3954) SNP were found in the C and CP groups, in spite of a trend toward a higher incidence of T alleles in the CP group. The IL-1β(3954) SNP CT and TT genotypes, as well asP. gingivalis, T. forsythia, andT. denticola, were associated with higher IL-1β levels and with higher values of the clinical parameters of disease severity. Concomitant analyses demonstrate that IL-1β(3954) and the red complex periodontopathogens were found to independently and additively modulate the levels of IL-1β in periodontal tissues. Similarly, the concurrent presence of both factors was associated with increased scores of disease severity. IL-1β(3954) genotypes and red complex periodontopathogens, individually and additively, modulate the levels of IL-1β in the diseased tissues of nonsmoking CP patients and, consequently, are potentially involved in the determination of the disease outcome.
Sortase A Utilizes an Ancillary Protein Anchor for Efficient Cell Wall Anchoring of Pili in
Streptococcus agalactiae
Authors: Nobbs Angela H. , Rosini Roberto , Rinaudo C. Daniela , Maione Domenico , Grandi Guido , Telford John L.
Published: June 2008

Pili are putative virulence factors and promising vaccine candidates in
Streptococcus agalactiae
(group B
Streptococcus
[GBS]) infection, a leading cause of neonatal sepsis and meningitis. The genes necessary for pilus synthesis and assembly are clustered in pilus islands (PI). Each gene encodes three structural subunits (a backbone and two ancillary proteins) bearing a C-terminal LPXTG motif and two subfamily C sortases (SrtC) involved in covalent polymerization of the subunits. GBS strains also possess the conserved “housekeeping” sortase A (SrtA), but its role in pilus assembly is unclear. To address this issue, pilus expression and cell wall anchoring were analyzed in
srtA
deletion mutants. Loss of SrtA did not affect pilus polymerization. However, pilus expression on the cell surface was reduced, and pili accumulated in the culture supernatant. Furthermore, cell-associated pili could be readily released by detergent treatment, indicating that SrtA is involved in covalent anchoring of pili to the cell wall. When each of the genes comprising PI-2a was systematically deleted, only the absence of ancillary subunit GBS150 or the SrtC required for incorporation of GBS150 into pili mimicked the
srtA
mutant phenotype. Thus, from these data a model for GBS pilus assembly can be proposed in which PI sortases are responsible for polymerization of the pilus structure, while SrtA is required to covalently attach it to the cell wall, utilizing ancillary pilus subunit GBS150 as the anchor protein.
Use of Adenylate Concentrations and Adenylate Energy Charge as Indicators of Hypoxic Stress in Estuarine Fish
Authors: Vetter Russell D. , Hodson Robert E.
Published: June 2008

Normal ATP concentrations in the white muscle of 11 different estuarine fish species varied from 3.91 to 6.59 μmol/g. Concentrations of different adenylates in the white muscle were not related to a species' natural level of swimming activity. When fish were exposed to hypoxia, ATP concentrations declined as much as 72% in some species. Decreases in ATP were not reflected in stoichiometric increases in ADP or AMP but rather in a reduction in total adenylate concentration. Sensitivity to hypoxia, expressed as changes in adenylate concentrations, was related to a species' natural level of activity and habitat preference. ATP concentration, total adenylate concentration, and adenylate energy charge appear to be useful indicators of environmental stress.Key words: ATP, energy charge, hypoxia, stress assessment
Comparisons of Witch Flounder (Glyptocephalus cynoglossus) Stocks of the Newfoundland–Labrador Area, Based upon a New Multivariate Analysis Method for Meristic Characters
Authors: Bowering W. R. , Misra R. K.
Published: June 2008

Although meristic characters are recognized as a very useful basis for examining problems pertaining to differences among fish populations, in general, and fish stock separation, in particular, statistical methods used on such data have, as far as we are aware, not been very appropriate. This paper presents (i) a new multivariate statistical method developed by modifying a method that has been used on human data in the past and, (ii) a study of witch flounder (Glyptocephalus cynoglossus) meristics in the Newfoundland–Labrador area of the northwest Atlantic. Our findings indicate seven distinct populations of witch flounder throughout the area surveyed. Based on this method, our results agree remarkably well with those made by using entirely different techniques.Key words: witch flounder, meristics, multivariate, stocks, area
Respiratory Metabolism and Swimming Performance of the Squid, Loligo opalescens
Authors: O'Dor R. K.
Published: June 2008

Maximum sustainable and burst speed, standard and active metabolic rates, and metabolic scope at temperatures from 7.5 to 17.5 °C were determined for the squid, Loligo opalescens, with a Brett tunnel respirometer. A comparison with sockeye salmon (Oncorhynchus nerka) of similar size at 15 °C indicates that squid have higher standard and active rates (254 and 862 mL O2∙kg−1∙h−1), but have sustainable speeds half those of salmon (0.36 m∙s−1). This confirms the low efficiency of jet-propelled swimming, and the resultant high cost of transport (12.5 J∙kg−1∙m−1; nearly 5 times that of salmon) raises interesting questions about how and why squid make large-scale vertical and horizontal migrations and the tactics they use to compete with fish that are both their predators and prey. Burst speeds after several maximal jets do not appear to be significantly greater than the peak speed after a single jet suggesting squid must depend primarily on maneuverability and high acceleration rather than high speed. A low capacity for accumulating an oxygen debt (73 mL O2∙kg−1) confirms predictions based on biochemical evidence. This debt is approximately equal to the energy needed to rephosphorylate muscle phosphagens.Key words: squid, swimming, oxygen consumption, oxygen debt, Loligo opalescens, metabolic rate, salmon, Oncorhynchus nerka
Growth Model of Daphnia
Authors: Paloheimo J. E. , Crabtree S. J. , Taylor W. D.
Published: June 2008

Data from experiments on feeding, assimilation, and reproduction of Daphnia pulex grown in different cell concentrations of Chlamydomonas reinhardtii formed the basis for an individual growth model for D. pulex. The model predictions of both the somatic growth and reproduction agree with subsequent experimental results. Contrary to many higher organisms, the assimilation efficiency increases with increasing body size. This may be, at least in part, the reason why larger body-sized zooplankton tend to dominate in aquatic ecosystems when not controlled by predators. The uptake rate per body weight as a function of cell concentration can be described by Michaelis–Menten type equations, but not the assimilation rate. Contrast between the feeding and assimilation rates suggest that as the nutrient level increases, a higher proportion of uptake is channeled by Daphnia into the detritus/bacterial compartment.Key words: Daphnia pulex, feeding, energetics, assimilation, growth model, nutrient level