bluuebunny/crossref_metadata_2025 huggingface dataset:
A computer simulation study comparing lesion detection accuracy with digital mammography, breast tomosynthesis, and cone‐beam CT breast imaging
Authors: Gong Xing , Glick Stephen J. , Liu Bob , Vedula Aruna A. , Thacker Samta
Published: April 2006

Although conventional mammography is currently the best modality to detect early breast cancer, it is limited in that the recorded image represents the superposition of a three‐dimensional (3D) object onto a 2D plane. Recently, two promising approaches for 3D volumetric breast imaging have been proposed, breast tomosynthesis (BT) and CT breast imaging (CTBI). To investigate possible improvements in lesion detection accuracy with either breast tomosynthesis or CT breast imaging as compared to digital mammography (DM), a computer simulation study was conducted using simulated lesions embedded into a structured 3D breast model. The computer simulation realistically modeled x‐ray transport through a breast model, as well as the signal and noise propagation through a CsI based flat‐panel imager. Polyenergetic x‐ray spectra of for digital mammography, for BT, and for CTBI were modeled. For the CTBI simulation, the intensity of the x‐ray spectra for each projection view was determined so as to provide a total average glandular dose of , which is approximately equivalent to that given in conventional two‐view screening mammography. The same total dose was modeled for both the DM and BT simulations. Irregular lesions were simulated by using a stochastic growth algorithm providing lesions with an effective diameter of . Breast tissue was simulated by generating an ensemble of backgrounds with a power law spectrum, with the composition of 50% fibroglandular and 50% adipose tissue. To evaluate lesion detection accuracy, a receiver operating characteristic (ROC) study was performed with five observers reading an ensemble of images for each case. The average area under the ROC curves was 0.76 for DM, 0.93 for BT, and 0.94 for CTBI. Results indicated that for the same dose, a lesion embedded in a structured breast phantom was detected by the two volumetric breast imaging systems, BT and CTBI, with statistically significant higher confidence than with planar digital mammography, while the difference in lesion detection between BT and CTBI was not statistically significant.
Improving delivery of segments with small MU in step‐and‐shoot IMRT
Authors: Kuperman V. Y. , Lam W.‐C.
Published: April 2006

The purpose of this study is to describe four new delivery schemes for intensity‐modulated radiation therapy (IMRT). In the first two schemes the order in which segments are delivered is varied from fraction to fraction. The last two delivery schemes employ fixed order of segments. The obtained results indicate that the suggested approaches can significantly reduce the so‐called “overshoot” and “undershoot” phenomena and the associated discrepancies between planned and delivered monitor units.
Time delay study of a CT simulator in respiratory gated CT scanning
Authors: Guan Huaiqun
Published: April 2006

In respiratory‐gated radiotherapy (RGRT), if the time delay in a computed tomography (CT) simulator and that in a linear accelerator (Linac) are different, the simulation and the treatment cannot be synchronized. In this study, we presented a technique to measure the time delay of the AcQSim CT simulator (Philips Medical Systems, Cleveland, OH) using Varian's Real‐Time Positioning Management (RPM) system (Varian Medical Systems, Palo Alto, CA). A respiratory gating platform (REF 91150, Standard Imaging, Inc., Middleton, MI) was first set at the position of amplitude maximum (phase 0). Then a ball of diameter was put on the platform and set at the CT laser. A single axial scan was acquired across the center of the ball without motion. Then the motion was turned on and single axial scans gated at different phases were acquired with a very narrow gating window. The time between the phase giving a good estimate of the ball and phase 0 is the overall delay time. We found that for AcQSim CT, the overall delay for a single axial scan (with scan time) is . For multiple axial scans, the overall delay is for the first scan and for the subsequent ones. This demonstrated that the CT mechanical startup delay is . After the first axial scan, the overall delay per scan is less because CT gantry continuously spins and no mechanical delay exists. We call the overall delay without mechanical part the scanning delay, which basically equals half the scan time ( for scan time) plus the gating pulse triggering delay . The delays were also verified using metal balls of diameter set at the amplitude minimum (phase 180, initially). We note that it is the scanning delay rather than the triggering delay that should be compensated when doing motion‐synchronized radiotherapy. The current interface between the RPM system and the AcQSim CT does not compensate for this scanning delay.
Light field and crosshair quality assurance test using a simple lens system
Authors: Hadley Scott W. , Lam Kwok
Published: April 2006

We describe here a simple lens system to test the positioning of the field light source and mylar crosshair for radiation therapy linear accelerators. Ideally the light source for the field light and the crosshair should be centered on the axis of rotation of the collimator. The traditional method for testing this coincidence uses the shadow of the crosshair caused by the field light source. The shadow of the crosshair is dependent on the position of both the field light source and mylar crosshair. Geometrically it is possible for the field light source and the mylar crosshair to be off the axis of rotation of the collimator and still cause the shadow of the crosshair to be on the axis of rotation at some distance. Using a lens system the motion of the field light source and crosshair can be observed in sharp focus independently of one another as the collimator is rotated.
Imaging properties of digital magnification radiography
Authors: Boyce Sarah J. , Samei Ehsan
Published: April 2006

Flat panel detectors exhibit improved signal‐to‐noise ratio (SNR) and display capabilities compared to film. This improvement necessitates a new evaluation of optimal geometry for conventional projection imaging applications such as digital projection mammography as well as for advanced x‐ray imaging applications including cone‐beam computed tomography (CT), tomosynthesis, and mammotomography. Such an evaluation was undertaken in this study to examine the effects of x‐ray source distribution, inherent detector resolution, magnification, scatter rejection, and noise characteristics including noise aliasing. A model for x‐ray image acquisition was used to develop generic results applicable to flat panel detectors with similar x‐ray absorption characteristics. The model assumed a Gaussian distribution for the focal spot and a rectangular distribution for a pixel. A generic model for the modulated transfer function (MTF) of indirect flat panel detectors was derived by a nonlinear fit of empirical receptor data to the Burgess model for phosphor MTFs. Noise characteristics were investigated using a generic noise power spectrum (NPS) model for indirect phosphor‐based detectors. The detective quantum efficiency (DQE) was then calculated from the MTF and NPS models. The results were examined as a function of focal spot size (0.1, 0.3, and ) and pixel size (50, 100, 150, and ) for magnification ranges 1 to 3. Mammography, general radiography (also applicable to mammotomography), and chest radiography applications were explored using x‐ray energies of 28, 74, and , respectively. Nodule detection was examined using the effective point source scatter model, effective DQE, and the Hotelling efficiency. Results indicate that magnification can potentially improve the signal and noise performance of digital images. Results also show that a cross over point occurs in the spatial frequency above and below which the effects of magnification differ indicating that there are task dependent tradeoffs associated with magnification. The cross over point varies depending upon focal spot size, pixel size, x‐ray energy, and source‐to‐image‐distance (SID). For mammography, the cross over point occurs for a focal spot while a focal spot indicates that magnification does not improve image quality due to focal spot blurring. Thus, the benefit of magnification may be limited. For general radiography (as well as mammotomography), and chest radiography, the cross over point changes with SID. For a system with a focal spot, pixel size, a SID, and the applicable tissue thickness and scatter components, optimal magnification improved by approximately 1.2 times for mammography and for general radiography (and mammotomography). These results indicate that the optimal geometry can improve image quality without changing patient dose or otherwise reduce dose without compromising image quality.
Detection of breast lesion regions in ultrasound images using wavelets and order statistics
Authors: Mogatadakala Kishore V. , Donohue Kevin D. , Piccoli Catherine W. , Forsberg Flemming
Published: April 2006

Accurate detection and segmentation of suspicious regions within the complex and irregular tissues of the breast, as depicted with ultrasonic B scans, typically require human analysis and decision making. Tissue characterization methods for classifying suspicious regions often depend on identifying and then accurately segmenting these regions. Motivated by an ultimate goal to automate this critical identification and segmentation step for tissue characterization problems, this work examines ultrasonic signal characteristics between various regions of breast tissue broadly classified as normal tissue and breast lesions. This paper introduces a nonparametric model based on order statistics (OS) estimated from multiresolution (MR) decompositions of energy‐normalized subregions. Experimental results demonstrate the classification performance of the OS‐based features extracted from the tumor and normal tissue regions in multiple scans from 84 patients, which resulted in a total of 204 tumor regions (from 43 malignant and 161 benign) and 816 normal tissue regions. Performance results indicate that OS‐based features achieved an area under the receiver‐operator characteristic curve of 91% in the discrimination between breast lesions and surrounding normal tissues.
Continuous intensity map optimization (CIMO): A novel approach to leaf sequencing in step and shoot IMRT
Authors: Cao Daliang , Earl Matthew A. , Luan Shuang , Shepard David M.
Published: April 2006

A new leaf‐sequencing approach has been developed that is designed to reduce the number of required beam segments for step‐and‐shoot intensity modulated radiation therapy (IMRT). This approach to leaf sequencing is called continuous‐intensity‐map‐optimization (CIMO). Using a simulated annealing algorithm, CIMO seeks to minimize differences between the optimized and sequenced intensity maps. Two distinguishing features of the CIMO algorithm are (1) CIMO does not require that each optimized intensity map be clustered into discrete levels and (2) CIMO is not rule‐based but rather simultaneously optimizes both the aperture shapes and weights. To test the CIMO algorithm, ten IMRT patient cases were selected (four head‐and‐neck, two pancreas, two prostate, one brain, and one pelvis). For each case, the optimized intensity maps were extracted from the treatment planning system. The CIMO algorithm was applied, and the optimized aperture shapes and weights were loaded back into Pinnacle. A final dose calculation was performed using Pinnacle's convolution/superposition based dose calculation. On average, the CIMO algorithm provided a 54% reduction in the number of beam segments as compared with Pinnacle's leaf sequencer. The plans sequenced using the CIMO algorithm also provided improved target dose uniformity and a reduced discrepancy between the optimized and sequenced intensity maps. For ten clinical intensity maps, comparisons were performed between the CIMO algorithm and the power‐of‐two reduction algorithm of Xia and Verhey [Med. Phys. 25(8), 1424–1434 (1998)]. When the constraints of a Varian Millennium multileaf collimator were applied, the CIMO algorithm resulted in a 26% reduction in the number of segments. For an Elekta multileaf collimator, the CIMO algorithm resulted in a 67% reduction in the number of segments. An average leaf sequencing time of less than one minute per beam was observed.
Analytic IMRT dose calculations utilizing Monte Carlo to predict MLC fluence modulation
Authors: Mihaylov I. B. , Lerma F. A. , Wu Y. , Siebers J. V.
Published: April 2006

A hybrid dose‐computation method is designed which accurately accounts for multileaf collimator (MLC)‐induced intensity modulation in intensity modulated radiation therapy (IMRT) dose calculations. The method employs Monte Carlo (MC) modeling to determine the fluence modulation caused by the delivery of dynamic or multisegmental (step‐and‐shoot) MLC fields, and a conventional dose‐computation algorithm to estimate the delivered dose to a phantom or a patient. Thus, it determines the IMRT fluence prediction accuracy achievable by analytic methods in the limit that the analytic method includes all details of the MLC leaf transport and scatter. The hybrid method is validated and benchmarked by comparison with in‐phantom film dose measurements, as well as dose calculations from two in‐house, and two commercial treatment planning system analytic fluence estimation methods. All computation methods utilize the same dose algorithm to calculate dose to a phantom, varying only in the estimation of the MLC modulation of the incident photon energy fluence. Gamma analysis, with respect to measured two‐dimensional (2D) dose planes, is used to benchmark each algorithm's performance. The analyzed fields include static and dynamic test patterns, as well as fields from ten DMLC IMRT treatment plans (79 fields) and five SMLC treatment plans (29 fields). The test fields (fully closed MLC, picket fence, sliding windows of different size, and leaf‐tip profiles) cover the extremes of MLC usage during IMRT, while the patient fields represent realistic clinical conditions. Of the methods tested, the hybrid method most accurately reproduces measurements. For the hybrid method, 79 of 79 DMLC field calculations havefor more than 95% of the points (per field) while for SMLC fields, 27 of 29 pass the same criteria. The analytic energy fluence estimation methods show inferior pass rates, with 76 of 79 DMLC and 24 of 29 SMLC fields having more than 95% of the test points with. Paired one‐way ANOVA tests of the gamma analysis results found that the hybrid method better predicts measurements in terms of both the fraction of points withand the average gamma for bothandcriteria. These results quantify the enhancement in accuracy in IMRT dose calculations when MC is used to model the MLC field modulation.
Scatter rejection in multislit digital mammography
Authors: Åslund Magnus , Cederström Björn , Lundqvist Mats , Danielsson Mats
Published: April 2006

The scatter to primary ratio (SPR) was measured on a scanning multislit full‐field digital mammography system for different thickness of breast equivalent material and different tube voltages. Scatter within the detector was measured separately and was found to be the major source of scatter in the assembly. Measured total SPRs below 6% are reported for breast range . The performance of the multislit assembly is compared to other imaging geometries with different scatter rejection schemes by using the scatter detective quantum efficiency.
Two‐dimensional ionization chamber arrays for IMRT plan verification
Authors: Poppe Bjoern , Blechschmidt Arne , Djouguela Armand , Kollhoff Ralf , Rubach Antje , Willborn Kay C. , Harder Dietrich
Published: April 2006

In this paper we describe a concept for dosimetric treatment plan verification using two‐dimensional ionization chamber arrays. Two different versions of the 2D‐ARRAY (PTW‐Freiburg, Germany) will be presented, a matrix of chambers (chamber cross section ; the distance between chamber centers, ) and a matrix of chambers (chamber cross section ; the distance between chamber centers is ). The two‐dimensional response function of a single chamber is experimentally determined by scanning it with a slit beam. For dosimetric plan verification, the expected two‐dimensional distribution of the array signals is calculated via convolution of the planned dose distribution, obtained from the treatment planning system, with the two‐dimensional response function of a single chamber. By comparing the measured two‐dimensional distribution of the array signals with the expected one, a distribution of deviations is obtained that can be subjected to verification criteria, such as the gamma index criterion. As an example, this verification method is discussed for one sequence of an IMRT plan. The error detection capability is demonstrated in a case study. Both versions of two‐dimensional ionization chamber arrays, together with the developed treatment plan verification strategy, have been found to provide a suitable and easy‐to‐handle quality assurance instrument for IMRT.
Accurate skin dose measurements using radiochromic film in clinical applications
Authors: Devic S. , Seuntjens J. , Abdel‐Rahman W. , Evans M. , Olivares M. , Podgorsak E. B. , Vuong Té , Soares Christopher G.
Published: April 2006

Megavoltage x‐ray beams exhibit the well‐known phenomena of dose buildup within the first few millimeters of the incident phantom surface, or the skin. Results of the surface dose measurements, however, depend vastly on the measurement technique employed. Our goal in this study was to determine a correction procedure in order to obtain an accurate skin dose estimate at the clinically relevant depth based on radiochromic film measurements. To illustrate this correction, we have used as a reference point a depth of . We used the new dosimetry films (HS, XR‐T, and EBT) that have effective points of measurement at depths slightly larger than . In addition to films, we also used an Attix parallel‐plate chamber and a home‐built extrapolation chamber to cover tissue‐equivalent depths in the range from to of water‐equivalent depth. Our measurements suggest that within the first millimeter of the skin region, the PDD for a photon beam and field size of increases from 14% to 43%. For the three dosimetry film models, the beam entrance skin dose measurement corrections due to their effective point of measurement are as follows: 15% for the EBT, 15% for the HS, and 16% for the XR‐T model films. The correction factors for the exit skin dose due to the build‐down region are negligible. There is a small field size dependence for the entrance skin dose correction factor when using the EBT film model. Finally, a procedure that uses EBT model film for an accurate measurement of the skin dose in a parallel‐opposed pair photon beam arrangement is described.
Potential impact of prostate edema on the dosimetry of permanent seed implants using the new (model CS‐1) seeds
Authors: Chen Zhe , Deng Jun , Roberts Kenneth , Nath Ravinder
Published: April 2006

Our aim in this work was to study the potential dosimetric effect of prostate edema on the accuracy of conventional pre‐ and post‐implant dosimetry for prostate seed implants using the newly introduced seed, whose radioactive decay half‐life ( days) is directly comparable to the average edema resolution half‐life ( days) observed previously by Waterman et al. for implants [Int. J. Radiat. Oncol. Biol. Phys. 41, 1069–1077 (1998)]. A systematic calculation of the relative dosimetry effect of prostate edema on the implant was performed by using an analytic solution obtained previously [Int. J. Radiat. Oncol. Biol. Phys. 47, 1405–1419 (2000)]. It was found that conventional preimplant dosimetry always overestimates the true delivered dose as it ignores the temporary increase of the interseed distance caused by edema. The overestimation for implants ranged from 1.2% (for a small edema with a magnitude of 10% and a half‐life of 2 days) to approximately 45% (for larger degree edema with a magnitude of 100% and a half‐life of 25 days). The magnitude of pre‐ and post‐implant dosimetry error for implants was found to be similar to that of implants for typical edema characteristics (magnitude , and half‐life days); both of which are worse compared to implants. The preimplant dosimetry error for implants cannot be compensated effectively without knowing the edema characteristics before the seed implantation. On the other hand, the error resulted from a conventional post‐implant dosimetry can be minimized (to within ) for implants if the post‐implant dosimetry is performed at days post seed implantation. This “optimum” post‐implant dosimetry time is shorter than those determined previously for the and implants at days and weeks, respectively.
Investigation of Gamma Knife image registration errors resulting from misalignment between the patient and the imaging axis
Authors: Cernica George , Wang Zhou , Malhotra Harish , de Boer Steven , Podgorsak Matthew B.
Published: April 2006

The ability of Leksell GammaPlan to perform stereotactic space localizations with image sets where there is misalignment of the patient's head (stereotactic frame and fiducial apparatus) relative to the computed tomography (CT) scanner coordinate system was studied. Misalignment is sometimes necessary for patient comfort. Results equally apply to magnetic resonance imaging. Seven diameter CT‐visible spheres were rigidly mounted to a string tied tightly at each end to diagonally opposite posts attached to a Leksell stereotactic frame. A standard CT fiducial box was applied to the frame in the usual clinical manner. A baseline CT scan ( slice thickness) was obtained with the fiducial box perfectly aligned with the scanner axis. After localization of the image set, the coordinate of the center of each sphere was recorded. Repeat CT scans with varying fiducial box misalignments with the imaging axis were subsequently obtained. The mean difference between the base line and the respective coordinates in misaligned geometries was approximately , well within the accuracy of the image sets and the delivery of radiosurgery with the Gamma Knife.
A bench‐top megavoltage fan‐beam CT using ‐photodiode detectors. I. System description and detector characterization
Authors: Rathee S. , Tu D. , Monajemi T. T. , Rickey D. W. , Fallone B. G.
Published: April 2006

We describe the components of a bench‐top megavoltage computed tomography (MVCT) scanner that uses an 80‐element detector array consisting of scintillators coupled to photodiodes. Each crystal is . The detailed design of the detector array, timing control, and multiplexer are presented. The detectors show a linear response to dose (dose rate was varied by changing the source to detector distance) with a correlation coefficient nearly unity with the standard deviation of signal at each dose being less than 0.25%. The attenuation of a beam by solid water measured by this detector array indicates a small, yet significant spectral hardening that needs to be corrected before image reconstruction. The presampled modulation transfer function is strongly affected by the detector's large pitch and a large improvement can be obtained by reducing the detector pitch. The measured detective quantum efficiency at zero spatial frequency is 18.8% for photons which will reduce the dose to the patient in MVCT applications. The detector shows a less than a 2% reduction in response for a dose of accumulated in ; however, the lost response is recovered on the following day. A complete recovery can be assumed within the experimental uncertainty (standard deviation ); however, any smaller permanent damage could not be assessed.
A bench‐top megavoltage fan‐beam CT using ‐photodiode detectors. II. Image performance evaluation
Authors: Monajemi T. T. , Tu D. , Fallone B. G. , Rathee S.
Published: April 2006

Megavoltage computed tomography (MVCT) is a potential imaging tool for positioning and dose delivery verification during image guided radiotherapy. The problem with many MVCT detectors, however, is their low detective quantum efficiency (DQE) which leads to poor low contrast resolution (LCR) and high image noise. This makes separating the tumors from the soft tissue background difficult. This manuscript describes the imaging performance of our bench‐top MVCT scanner that uses an 80‐element detector array consisting of ‐photodiode elements with a DQE of 19% in and 26% in beams [T. T. Monajemi, S. Steciw, B. G. Fallone, and S. Rathee, “Modelling scintillator‐photodiodes as detectors for megavoltage CT,” Med. Phys. 31, 1225–1234 (2004)] at zero frequency. The imaging experiments presented were carried out mainly in a teletherapy unit, while the beam hardening characteristics of the system were also presented for a beam. During image evaluation, persistent ring artifacts, caused by air gaps at the ends of the eight‐element detector blocks, were removed by using a calibration procedure. The measured contrast of a low contrast target with a diameter was determined to be independent of dose, between 2.1 and . The measured LCR of a target with a nominal contrast of 2.8% was reduced from 2.3% to 1.2% when the contrast target diameter was reduced from , using for imaging. The signal to noise ratio of this system is shown to be proportional to the square root of dose. Most importantly, a low contrast target with a diameter of and a nominal contrast level of 1.5% is resolved with a radiation dose of in the beam. The spatial resolution in the beam is limited to one line pair per centimeter mainly due to the size of the source.
Normalized dose data for upper gastrointestinal tract contrast studies performed to infants
Authors: Damilakis John , Stratakis John , Raissaki Maria , Perisinakis Kostas , Kourbetis Nikiforos , Gourtsoyiannis Nicholas
Published: April 2006

The aim of the current study was to (a) provide normalized dose data for the estimation of the radiation dose from upper gastrointestinal tract contrast (UGIC) studies carried out to infants and (b) estimate the average patient dose and risks associated with radiation from UGIC examinations performed in our institution. Organ and effective doses, normalized to entrance skin dose (ESD) and dose area product (DAP) were estimated for UGIC procedures utilizing the Monte Carlo N‐particle (MCNP) transport code and two mathematical phantoms, one corresponding to the size of a newborn and one to the size of a 1‐year‐old child. The validity of the MCNP results was verified by comparison with dose data obtained in physical anthropomorphic phantoms simulating a newborn and a 1‐year‐old infant using thermoluminescence dosimetry (TLD). Data were also collected from 25 consecutive UGIC examinations performed to infants. Study participants were (a) 12 infants aged from 0.5 to 5.9 months (group 1) and (b) 13 infants aged from 6 to 15 months (group 2). For each examination, ESD and dose to comforters were measured using TLD. Patient effective doses were estimated using normalized dose data obtained in the simulation study. The risk for fatal cancer induction was estimated using appropriate coefficients. The results consist of tabulated dose data normalized to ESD or DAP for the estimation of patient dose. Conversion coefficients were estimated for various tube potentials and beam filtration values. The mean total fluoroscopy time was 1.26 and for groups 1 and 2, respectively. The average effective dose was for group 1 and for group 2. The risk of cancer attributable to the radiation exposure associated with a typical UGIC study was found to be up to 3 per infants undergoing an UGIC examination. The mean radiation dose absorbed by the hands of comforters was . In conclusion, estimation of radiation doses associated with UGIC studies performed to infants can be made using the normalized dose data provided in the current study. Radiation dose values associated with UGIC examinations carried out to infants are not low and should be minimized as much as possible.
Robust frameless stereotactic localization in extra‐cranial radiotherapy
Authors: Riboldi Marco , Baroni Guido , Spadea Maria Francesca , Bassanini Fabio , Tagaste Barbara , Garibaldi Cristina , Orecchia Roberto , Pedotti Antonio
Published: April 2006

In the field of extra‐cranial radiotherapy, several inaccuracies can make the application of frameless stereotactic localization techniques error‐prone. When optical tracking systems based on surface fiducials are used, inter‐ and intra‐fractional uncertainties in marker three‐dimensional (3D) detection may lead to inexact tumor position estimation, resulting in erroneous patient setup. This is due to the fact that external fiducials misdetection results in deformation effects that are poorly handled in a rigid‐body approach. In this work, the performance of two frameless stereotactic localization algorithms for 3D tumor position reconstruction in extra‐cranial radiotherapy has been specifically tested. Two strategies, unweighted versus weighted, for stereotactic tumor localization were examined by exploiting data coming from 46 patients treated for extra‐cranial lesions. Measured isocenter displacements and rotations were combined to define isocentric procedures, featuring of freedom, for correcting patient alignment (isocentric positioning correction). The sensitivity of the algorithms to uncertainties in the 3D localization of fiducials was investigated by means of 184 numerical simulations. The performance of the implemented isocentric positioning correction was compared to conventional point‐based registration. The isocentric positioning correction algorithm was tested on a clinical dataset of inter‐fractional and intra‐fractional setup errors, which was collected by means of an optical tracker on the same group of patients. The weighted strategy exhibited a lower sensitivity to fiducial localization errors in simulated misalignments than those of the unweighted strategy. Isocenter 3D displacements provided by the weighted strategy were consistently smaller than those featured by the unweighted strategy. The peak decrease in median and quartile values of isocenter 3D displacements were 1.4 and , respectively. Concerning clinical data, the weighted strategy isocentric positioning correction provided the reduction of fiducial registration errors, featuring up to 61.7% decrease in median values (versus 46.8% for the unweighted strategy) of initial displacements. The weighted strategy proved high performance in minimizing the effects of fiducial localization errors, showing a great potential in improving patient setup. The clinical data analysis revealed that the application of a robust reconstruction algorithm may provide high‐quality results in patient setup verification, by properly managing external fiducials localization errors.
AAPM TG‐43U1 formalism adaptation and Monte Carlo dosimetry simulations of multiple‐radionuclide brachytherapy sources
Authors: Nuttens V. E. , Lucas S.
Published: April 2006

This paper presents a preliminary study on multiple‐radionuclide sources for brachytherapy. An adaptation of the AAPM TG‐43U1 formalism is proposed in order to derive the dosimetry parameters of multiple‐radionuclide sources from mono‐radionuclides. The adapted formalism is applied to a bi‐radionuclide case with the help of Monte Carlo calculations (MCNPX 2.5.0). InterSource™ seed loaded with and was chosen. This combination promotes a higher dose rate than (loaded with ) and deeper tissue penetration than (loaded with ) while reducing the dose at long distance (beyond ) relative to . In conclusion, this work shows the benefits of combining different radionuclides inside the same seed and proposes an adaptation of the AAPM TG‐43U1 formalism for the implementation of multiple‐radionuclide sources in current treatment planning systems.
Deletion ofBCY1from theSaccharomyces cerevisiaeGenome Is Semidominant and Induces Autolytic Phenotypes Suitable for Improvement of Sparkling Wines
Authors: Tabera Laura , Muñoz Rosario , Gonzalez Ramon
Published: April 2006

Autolysis ofSaccharomyces cerevisiaeis the main source of molecules that contribute to the quality of sparkling wines made by the traditional method. In this work the possibility of accelerating this slow process in order to improve the quality of sparkling wines by using genetically engineered wine yeast strains was explored. The effect of partial or total deletion ofBCY1(which encodes a regulatory subunit of cAMP-dependent protein kinase A) in haploid and diploid (heterozygous and homozygous) yeast strains was studied. We proved that heterozygous strains having partial or completeBCY1deletions have a semidominant phenotype for several of the properties studied, including autolysis under simulated second-fermentation conditions, in contrast to previously published reports describing mutations inBCY1as recessive. Considering the degree of autolysis, ethanol tolerance, and technical feasibility, we propose that deletion of the 3′ end of the open reading frame of a single copy ofBCY1is a way to improve the quality of sparkling wines.
Introducing TreeClimber, a Test To Compare Microbial Community Structures
Authors: Schloss Patrick D. , Handelsman Jo
Published: April 2006

The phylogenetic and ecological complexity of microbial communities necessitates the development of new methods to determine whether two or more communities have the same structure even though it is not possible to sample the communities exhaustively. To address this need, we adapted a method used in population genetics, the parsimony test, to determine the relatedness of communities. Here we describe our implementation of the parsimony test, TreeClimber, in which we reanalyzed six previously published studies and compared the results of the analysis to those obtained using ∫-LIBSHUFF.
Assessment of the Environmental Fate of the Biological Control Agent of Fire Blight,
Pseudomonas fluorescens
EPS62e, on Apple by Culture and Real-Time PCR Methods
Authors: Pujol Marta , Badosa Esther , Manceau Charles , Montesinos Emilio
Published: April 2006

The colonization of apple blossoms and leaves by
Pseudomonas fluorescens
EPS62e was monitored in greenhouse and field trials using cultivable cell counting and real-time PCR. The real-time PCR provided a specific quantitative method for the detection of strain EPS62e. The detection level was around 10
2
cells g (fresh weight)
−1
and the standard curve was linear within a 5-log range. EPS62e actively colonized flowers reaching values from 10
7
to 10
8
cells per blossom. In apple flowers, no significant differences were observed between population levels obtained by real-time PCR and plating, suggesting that viable but nonculturable (VBNC) cells and residual nondegraded DNA were not present. In contrast, on apple leaves, where cultivable populations of EPS62e decreased with time, significant differences were observed between real-time PCR and plating. These differences indicate the presence of VBNC cells or nondegraded DNA after cell death. Therefore, the EPS62e population was under optimal conditions during the colonization of flowers but it was stressed and poorly survived on leaves. It was concluded that for monitoring this biological control agent, the combined use of cultivable cell count and real-time PCR is necessary.
Discovery of Natural Atypical Nonhemolytic
Listeria seeligeri
Isolates
Authors: Volokhov Dmitriy , George Joseph , Anderson Christine , Duvall Robert E. , Hitchins Anthony D.
Published: April 2006

We found seven
Listeria
isolates, initially identified as isolates with the Xyl
+
Rha
−
biotype of
Listeria welshimeri
by phenotypic tests, which exhibited discrepant genotypic properties in a well-validated
Listeria
species identification oligonucleotide microarray. The microarray gives results of these seven isolates being atypical
hly
-negative
L. seeligeri
isolates, not
L. welshimeri
isolates. The aberrant
L. seeligeri
isolates were
d
-xylose fermentation positive,
l
-rhamnose fermentation negative (Xyl
+
Rha
−
), and nonhemolytic on blood agar and in the CAMP test with both
Staphylococcus aureus
(S
−
reaction) and
Rhodococcus equi
(R
−
reaction). All genes of the
prfA
cluster of
L. seeligeri
, located in the
prs-ldh
region, including the
orfA2
,
orfD
,
prfA
,
orfE
,
plcA
,
hly
,
orfK
,
mpl
,
actA
,
dplcB
,
plcB
,
orfH
,
orfX
,
orfI
,
orfP
,
orfB
, and
orfA
genes, were checked by PCR and direct sequencing for evidence of their presence in the atypical isolates. The
prs-prfA
cluster-
ldh
region of the
L. seeligeri
isolates was approximately threefold shorter due to the loss of
orfD
,
prfA
,
orfE
,
plcA
,
hly
,
orfK
,
mpl
,
actA
,
dplcB
,
plcB
,
orfH
,
orfX
, and
orfI
. The genetic map order of the cluster genes of all the atypical
L. seeligeri
isolates was
prs-orfA2-orfP-orfB-orfA-ldh
, which was comparable to the similar region in
L. welshimeri
, with the exception of the presence of
orfA2
. DNA sequencing and phylogenetic analysis of 17 housekeeping genes indicated an
L. seeligeri
genomic background in all seven of the atypical
hly
-negative
L. seeligeri
isolates. Thus, the novel biotype of Xyl
+
Rha
−
Hly
−
L. seeligeri
strains can only be distinguished from Xyl
+
Rha
−
L. welshimeri
strains genotypically, not phenotypically. In contrast, the Rha
+
Xyl
+
biotype of
L. welshimeri
would not present an identification issue.
Degradation of Aroclor 1242 Dechlorination Products in Sediments by
Burkholderia xenovorans
LB400(
ohb
) and
Rhodococcus
sp. Strain RHA1(
fcb
)
Authors: Rodrigues Jorge L. M. , Kachel C. Alan , Aiello Michael R. , Quensen John F. , Maltseva Olga V. , Tsoi Tamara V. , Tiedje James M.
Published: April 2006

Burkholderia xenovorans
strain LB400, which possesses the biphenyl pathway, was engineered to contain the oxygenolytic
ortho
dehalogenation (
ohb
) operon, allowing it to grow on 2-chlorobenzoate and to completely mineralize 2-chlorobiphenyl. A two-stage anaerobic/aerobic biotreatment process for Aroclor 1242-contaminated sediment was simulated, and the degradation activities and genetic stabilities of LB400(
ohb
) and the previously constructed strain RHA1(
fcb
), capable of growth on 4-chlorobenzoate, were monitored during the aerobic phase. The population dynamics of both strains were also followed by selective plating and real-time PCR, with comparable results; populations of both recombinants increased in the contaminated sediment. Inoculation at different cell densities (10
4
or 10
6
cells g
−1
sediment) did not affect the extent of polychlorinated biphenyl (PCB) biodegradation. After 30 days, PCB removal rates for high and low inoculation densities were 57% and 54%, respectively, during the aerobic phase.
Paenibacillus curdlanolyticusStrain B-6 Xylanolytic-Cellulolytic Enzyme System That Degrades Insoluble Polysaccharides
Authors: Pason Patthra , Kyu Khin Lay , Ratanakhanokchai Khanok
Published: April 2006

A facultatively anaerobic bacterium,Paenibacillus curdlanolyticusB-6, isolated from an anaerobic digester produces an extracellular xylanolytic-cellulolytic enzyme system containing xylanase, β-xylosidase, arabinofuranosidase, acetyl esterase, mannanase, carboxymethyl cellulase (CMCase), avicelase, cellobiohydrolase, β-glucosidase, amylase, and chitinase when grown on xylan under aerobic conditions. During growth on xylan, the bacterial cells were found to adhere to xylan from the early exponential growth phase to the late stationary growth phase. Scanning electron microscopic analysis revealed the adhesion of cells to xylan. The crude enzyme preparation was found to be capable of binding to insoluble xylan and Avicel. The xylanolytic-cellulolytic enzyme system efficiently hydrolyzed insoluble xylan, Avicel, and corn hulls to soluble sugars that were exclusively xylose and glucose. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of a crude enzyme preparation exhibited at least 17 proteins, and zymograms revealed multiple xylanases and cellulases containing 12 xylanases and 9 CMCases. The cellulose-binding proteins, which are mainly in a multienzyme complex, were isolated from the crude enzyme preparation by affinity purification on cellulose. This showed nine proteins by SDS-PAGE and eight xylanases and six CMCases on zymograms. Sephacryl S-300 gel filtration showed that the cellulose-binding proteins consisted of two multienzyme complexes with molecular masses of 1,450 and 400 kDa. The results indicated that the xylanolytic-cellulolytic enzyme system of this bacterium exists as multienzyme complexes.
Characterization of the P450 Monooxygenase NysL, Responsible for C-10 Hydroxylation during Biosynthesis of the Polyene Macrolide Antibiotic Nystatin in
Streptomyces noursei
Authors: Volokhan Olga , Sletta Håvard , Ellingsen Trond E. , Zotchev Sergey B.
Published: April 2006

The
nysL
gene, encoding a putative P450 monooxygenase, was identified in the nystatin biosynthetic gene cluster of
Streptomyces noursei
. Although it has been proposed that NysL is responsible for hydroxylation of the nystatin precursor, experimental evidence for this activity was lacking. The
nysL
gene was inactivated in
S. noursei
by gene replacement, and the resulting mutant was shown to produce 10-deoxynystatin. Purification and an in vitro activity assay for 10-deoxynystatin demonstrated its antifungal activity being equal to that of nystatin. The NysL protein was expressed heterologously in
Escherichia coli
as a His-tagged protein and used in an enzyme assay with 10-deoxynystatin as a substrate. The results obtained clearly demonstrated that NysL is a hydroxylase responsible for the post-polyketide synthase modification of 10-deoxynystatin at position C-10. Kinetic studies with the purified recombinant enzyme allowed determination of

K
m

and
k
cat
and revealed no inhibition of recombinant NysL by either the substrate or the product. These studies open the possibility for in vitro evolution of NysL aimed at changing its specificity, thereby providing new opportunities for engineered biosynthesis of novel nystatin analogues hydroxylated at alternative positions of the macrolactone ring.
Symbiotic
Bradyrhizobium japonicum
Reduces N
2
O Surrounding the Soybean Root System via Nitrous Oxide Reductase
Authors: Sameshima-Saito Reiko , Chiba Kaori , Hirayama Junta , Itakura Manabu , Mitsui Hisayuki , Eda Shima , Minamisawa Kiwamu
Published: April 2006

N
2
O reductase activity in soybean nodules formed with
Bradyrhizobium japonicum
was evaluated from N
2
O uptake and conversion of
15
N-N
2
O into
15
N-N
2
. Free-living cells of USDA110 showed N
2
O reductase activity, whereas a
nosZ
mutant did not. Complementation of the
nosZ
mutant with two cosmids containing the
nosRZDFYLX
genes of
B. japonicum
USDA110 restored the N
2
O reductase activity. When detached soybean nodules formed with USDA110 were fed with
15
N-N
2
O, they rapidly emitted
15
N-N
2
outside the nodules at a ratio of 98.5% of
15
N-N
2
O uptake, but nodules inoculated with the
nosZ
mutant did not. Surprisingly, N
2
O uptake by soybean roots nodulated with USDA110 was observed even in ambient air containing a low concentration of N
2
O (0.34 ppm). These results indicate that the conversion of N
2
O to N
2
depends exclusively on the respiratory N
2
O reductase and that soybean roots nodulated with
B. japonicum
carrying the
nos
genes are able to remove very low concentrations of N
2
O.
Bioenergetic Mechanism for Nisin Resistance, Induced by the Acid Tolerance Response of
Listeria monocytogenes
Authors: Bonnet Marcelo , Rafi Mohamed M. , Chikindas Michael L. , Montville Thomas J.
Published: April 2006

This study examined the bioenergetics of
Listeria monocytogenes
, induced to an acid tolerance response (ATR). Changes in bioenergetic parameters were consistent with the increased resistance of ATR-induced (ATR
+
) cells to the antimicrobial peptide nisin. These changes may also explain the increased resistance of
L. monocytogenes
to other lethal factors. ATR
+
cells had lower transmembrane pH (ΔpH) and electric potential (Δψ) than the control (ATR
−
) cells. The decreased proton motive force (PMF) of ATR
+
cells increased their resistance to nisin, the action of which is enhanced by energized membranes. Paradoxically, the intracellular ATP levels of the PMF-depleted ATR
+
cells were ∼7-fold higher than those in ATR
−
cells. This suggested a role for the F
o
F
1
ATPase enzyme complex, which converts the energy of ATP hydrolysis to PMF. Inhibition of the F
o
F
1
ATPase enzyme complex by

N

′-

N

′-1,3-dicyclohexylcarbodiimide increased ATP levels in ATR
−
but not in ATR
+
cells, where ATPase activity was already low. Spectrometric analyses (surface-enhanced laser desorption ionization-time of flight mass spectrometry) suggested that in ATR
+
listeriae, the downregulation of the proton-translocating c subunit of the F
o
F
1
ATPase was responsible for the decreased ATPase activity, thereby sparing vital ATP. These data suggest that regulation of F
o
F
1
ATPase plays an important role in the acid tolerance response of
L. monocytogenes
and in its induced resistance to nisin.
Both
msa
Genes in
Renibacterium salmoninarum
Are Needed for Full Virulence in Bacterial Kidney Disease
Authors: Coady Alison M. , Murray Anthony L. , Elliott Diane G. , Rhodes Linda D.
Published: April 2006

Renibacterium salmoninarum
, a gram-positive diplococcobacillus that causes bacterial kidney disease among salmon and trout, has two chromosomal loci encoding the major soluble antigen (
msa
) gene. Because the MSA protein is widely suspected to be an important virulence factor, we used insertion-duplication mutagenesis to generate disruptions of either the
msa1
or
msa2
gene. Surprisingly, expression of MSA protein in broth cultures appeared unaffected. However, the virulence of either mutant in juvenile chinook salmon (
Oncorhynchus tshawytscha
) by intraperitoneal challenge was severely attenuated, suggesting that disruption of the
msa1
or
msa2
gene affected in vivo expression.
Identification of
Sinorhizobium meliloti
Early Symbiotic Genes by Use of a Positive Functional Screen
Authors: Zhang Xue-Song , Cheng Hai-Ping
Published: April 2006

The soil bacterium
Sinorhizobium meliloti
establishes nitrogen-fixing symbiosis with its leguminous host plant, alfalfa, following a series of continuous signal exchanges. The complexity of the changes of alfalfa root structures during symbiosis and the amount of
S. meliloti
genes with unknown functions raised the possibility that more
S. meliloti
genes may be required for early stages of the symbiosis. A positive functional screen of the entire
S. meliloti
genome for symbiotic genes was carried out using a modified in vivo expression technology. A group of genes and putative genes were found to be expressed in early stages of the symbiosis, and 23 of them were alfalfa root exudate inducible. These 23 genes were further separated into two groups based on their responses to apigenin, a known nodulation (
nod
) gene inducer. The group of six genes not inducible by apigenin included the
lsrA
gene, which is essential for the symbiosis, and the
dgkA
gene, which is involved in the synthesis of cyclic β-1,2-glucan required for the
S. meliloti-
alfalfa symbiosis. In the group of 17 apigenin-inducible genes, most have not been previously characterized in
S. meliloti
, and none of them belongs to the
nod
gene family. The identification of this large group of alfalfa root exudate-inducible
S. meliloti
genes suggests that the interactions in the early stages of the
S. meliloti
and alfalfa symbiosis could be complex and that further characterization of these genes will lead to a better understanding of the symbiosis.