bluuebunny/crossref_metadata_2025 huggingface dataset:
Inclusion of the treatment couch in portal dose image prediction for high precision EPID dosimetry
Authors: Ali Ali Sid Ahmed M. , Dirkx Maarten L. P. , Breuers Marcel G. J. , Heijmen Ben J. M.
Published: December 2010

Purpose:

When comparing predicted portal dose images (PDIs) to PDIs acquired by an EPID during treatment delivery, differences are often observed. These differences may be partially attributed to beam attenuation by parts of the treatment couch not taken into account in the PDI prediction. In order to improve the agreement, a model for the treatment couch was derived and included in the PDI prediction.

Methods:

A CT scan was used to model the couch top. The model for the couch top base was derived by iteratively matching the predicted and measured PDIs for gantry angles of 0°, 45°, and 90°. For PDI prediction, the modeled treatment couch was added to the CT scan of a patient or phantom by using the recorded couch positions from the record and verify system. To validate the couch model, PDI measurements were performed for a range of couch positions and gantry angles, both with and without an anatomical phantom in the beam.

Results:

After including the couch model in the PDI prediction for beams passing through the couch without phantom, the mean local dose differences between measured and predicted PDIs were reduced from up to 5.5% to less than 1.0% at each gantry angle. Similar results were obtained for measurements with a lung phantom on the couch. Although the couch model was originally derived by using a 6 MV photon beam, the results showed that it is also applicable for a 10 MV beam.

Conclusions:

A model of the treatment couch was derived and included in the PDI prediction, yielding a substantially improved agreement between measured and predicted PDIs, which makes interpretation of the observed deviations more straightforward.
Comparative study of density analysis using automated whole breast ultrasound and MRI
Authors: Moon Woo Kyung , Shen Yi‐Wei , Huang Chiun‐Sheng , Luo Sheng‐Chy , Kuzucan Aida , Chen Jeon‐Hor , Chang Ruey‐Feng
Published: December 2010

Purpose:

The purpose of this study is to compare the measurements of breast density using three‐dimensional (3‐D) automated whole breast ultrasound (ABUS) and magnetic resonance imaging (MRI).

Methods:

In this study, 3‐D ABUS and MRI breast images were obtained from 40 patients—bilaterally in 27 patients and unilaterally (due to operation in the contralateral breast) in 13 patients. To differentiate the fibroglandular and fatty tissues in ABUS and MRI images, the fuzzy C‐mean classifier was used. Calculated values for percent density and breast volume from the two modalities were compared to and correlated with linear regression analysis. Intraoperator and interoperator variations among eight cases were evaluated to verify the consistency of the density analysis.

Results:

Mean percent density and breast volume derived from ABUS ( and , respectively) and MRI images ( and ) demonstrated good correlation ( and ). Intraoperator and interoperator analyses yielded slightly larger coefficients of variation for percent density and breast volume in ABUS compared to MRI. However, the differences were not statistically significant.

Conclusions:

ABUS and MRI showed high correlation for breast density and breast volume quantification. Both modalities could provide useful breast density information to physicians.
Spatiotemporal motion estimation for respiratory‐correlated imaging of the lungs
Authors: Vandemeulebroucke Jef , Rit Simon , Kybic Jan , Clarysse Patrick , Sarrut David
Published: December 2010

Purpose: Four‐dimensional computed tomography (4D CT) can provide patient‐specific motion information for radiotherapy planning and delivery. Motion estimation in 4D CT is challenging due to the reduced image quality and the presence of artifacts. We aim to improve the robustness of deformable registration applied to respiratory‐correlated imaging of the lungs, by using a global problem formulation and pursuing a restrictive parametrization for the spatiotemporal deformation model.

Methods: A spatial transformation based on free‐form deformations was extended to the temporal domain, by explicitly modeling the trajectory using a cyclic temporal model based on B‐splines. A global registration criterion allowed to consider the entire image sequence simultaneously and enforce the temporal coherence of the deformation throughout the respiratory cycle. To ensure a parametrization capable of capturing the dynamics of respiratory motion, a prestudy was performed on the temporal dimension separately. The temporal parameters were tuned by fitting them to diaphragm motion data acquired for a large patient group. Suitable properties were retained and applied to spatiotemporal registration of 4D CT data. Registration results were validated using large sets of landmarks and compared to consecutive spatial registrations. To illustrate the benefit of the spatiotemporal approach, we also assessed the performance in the presence of motion‐induced artifacts.

Results: Cubic B‐splines gave better or similar fitting results as lower orders and were selected because of their inherently stronger regularization. The fitting and registration errors increased gradually with the temporal control point spacing, representing a trade‐off between achievable accuracy and sensitivity to noise and artifacts. A piecewise smooth trajectory model, allowing for a discontinuous change of speed at end‐inhale, was found most suitable to account for the sudden changes of motion at this breathing phase. The spatiotemporal modeling allowed a reduction of the number of parameters of 45%, while maintaining registration accuracy within 0.1 mm. The approach reduced the sensitivity to artifacts.

Conclusions: Spatiotemporal registration can provide accurate motion estimation for 4D CT and improves the robustness to artifacts.
Finite element based bladder modeling for image‐guided radiotherapy of bladder cancer
Authors: Chai Xiangfei , van Herk Marcel , van de Kamer Jeroen B. , Hulshof Maarten C. C. M. , Remeijer Peter , Lotz Heidi T. , Bel Arjan
Published: December 2010

Purpose:

A biomechanical model was constructed to give insight into pelvic organ motion as a result of bladder filling changes.

Methods:

The authors used finite element (FE) modeling to simulate bladder wall deformation caused by urine inflow. For ten volunteers, a series of MRI scans of the pelvic area was recorded at regular intervals of 10 min over 1 h. For the series of scans, the bladder volume gradually increased while the rectal volume was constant. The MR image with the bladder volume closest to 250 ml was selected as the reference in each volunteer. All pelvic structures were defined from the reference image including bladder wall, small bowel, prostate (male), uterus (female), rectum, pelvic bone, and the rest of the body. These structures were translated to FE meshes. Using appropriate material properties for all organs, deformations of these organs as a response to changing bladder pressure were computed.

Results:

The computation results showed realistic anisotropic deformation of the bladder wall: The bladder became more elongated in the cranial and anterior directions with increasing bladder volume. After fitting the volume of the computed bladder to the actual bladder volume on the test images, the computed bladder shape agreed well with the real bladder shape (overlap from 0.79 to 0.93). The average mean bladder wall prediction errors of all the volunteers were 0.31 cm average and 0.29 cm SD.

Conclusions:

In conclusion, a FE based mechanical bladder model shows promise for the prediction of the short‐term bladder shape change using only one pelvic scan and volume change of the bladder as input. The accuracy levels achieved with this method are likely mostly limited by inaccuracies in material properties and sliding tissue between organs, which has not been modeled. This model can potentially be used to improve image‐guided radiotherapy for bladder cancer patients, i.e., by prediction short‐term bladder deformation.
On Monte Carlo modeling of megavoltage photon beams: A revisited study on the sensitivity of beam parameters
Authors: Chibani Omar , Moftah Belal , Ma C.‐M. Charlie
Published: December 2010

Purpose:

To commission Monte Carlo beam models for five Varian megavoltage photon beams (4, 6, 10, 15, and 18 MV). The goal is to closely match measured dose distributions in water for a wide range of field sizes (from to ). The second objective is to reinvestigate the sensitivity of the calculated dose distributions to variations in the primary electron beam parameters.

Methods:

TheGEPTS Monte Carlo code is used for photon beam simulations and dose calculations. The linear accelerator geometric models are based on (i) manufacturer specifications, (ii) corrections made by Chibani and Ma [“On the discrepancies between Monte Carlo dose calculations and measurements for the 18 MV Varian photon beam,” Med. Phys. 34, 1206–1216 (2007)], and (iii) more recent drawings. Measurements were performed using pinpoint and Farmer ionization chambers, depending on the field size. Phase space calculations for small fields were performed with and without angle‐based photon splitting. In addition to the three commonly used primary electron beam parameters ( is the mean energy, FWHM is the energy spectrum broadening, and is the beam radius), the angular divergence of primary electrons is also considered.

Results:

The calculated and measured dose distributions agreed to within 1% local difference at any depth beyond 1 cm for different energies and for field sizes varying from to . In the penumbra regions, the distance to agreement is better than 0.5 mm, except for 15 MV (0.4–1 mm). The measured and calculated output factors agreed to within 1.2%. The 6, 10, and 18 MV beam models use , while the 4 and 15 MV beam models require and 0.6°, respectively. The parameter sensitivity study shows that varying the beam parameters around the solution can lead to 5% differences with measurements for small (e.g., ) and large (e.g., ) fields, while a perfect agreement is maintained for the field. The influence of on the central‐axis depth dose and the strong influence of on the lateral dose profiles are demonstrated.

Conclusions:

Dose distributions for very small and very large fields were proved to be more sensitive to variations in, , and in comparison with the field. Monte Carlo beam models need to be validated for a wide range of field sizes including small field sizes (e.g., ).
Sensitivity analysis of a geometric calibration method using projection matrices for digital tomosynthesis systems
Authors: Li Xinhua , Zhang Da , Liu Bob
Published: December 2010

Purpose:

To study the sensitivity of a geometric calibration method using projection matrices for digital tomosynthesis systems.

Methods:

A generic geometric calibration method for tomographic imaging systems has been presented in our previous work. The method involves a scan of a calibration phantom with multiple markers. Their locations in projection images are detected and are associated with their 3D coordinates to compute projection matrices, which can be used in subsequent image reconstruction. The accuracy of geometric calibration may be affected by errors in the input data of marker positions. The effects of errors may depend on the number of markers and the volume surrounded by them in 3D space. This work analyzed the sensitivity of the calibration method to the above factors. A 6 cm CIRS breast research phantom and a prototype breast tomosynthesis system were used for our tests. A high contrast ring and two small speck groups were reconstructed in various testing cases for comparison. To achieve quantitative assessment, a point detection mask was adopted for detecting signals and for computing changes between testing cases and the regular geometric calibration.

Results:

When 3D coordinates and 2D projections of markers were accurate, all tested numbers of markers, 6–44, provided similar high quality reconstructions of the ring and the two speck groups. Errors in marker positions resulted in image degradations and signal changes, which increased with fewer markers and smaller volume surrounded by markers in the 3D object space. Signal changes of small specks were more significant than those of the ring. Errors in marker projections produced drastic image degradations. Coplanar marker placement caused a failure in projection matrix computation.

Conclusions:

For practical geometric calibration phantom design, ample markers are desired. They need to have a large volumetric coverage in the 3D space and be far from being coplanar. Precise determination of marker projections on detector planes is crucial for accurate geometric calibration and for small object detection using the reconstructed images.
A fast double template convolution isocenter evaluation algorithm with subpixel accuracy
Authors: Winey Brian , Sharp Greg , Bussière Marc
Published: December 2010

Purpose: To design a fast Winston Lutz (fWL) algorithm for accurate analysis of radiation isocenter from images without edge detection or center of mass calculations.

Methods: An algorithm has been developed to implement the Winston Lutz test for mechanical/radiation isocenter agreement using an electronic portal imaging device (EPID). The algorithm detects the position of the radiation shadow of a tungsten ball within a stereotactic cone. The fWL algorithm employs a double convolution to independently find the position of the sphere and cone centers. Subpixel estimation is used to achieve high accuracy. Results of the algorithm were compared to (1) a human observer with template guidance and (2) an edge detection/center of mass (edCOM) algorithm. Testing was performed with high resolution (0.05mm/px, film) and low resolution (0.78mm/px, EPID) image sets.

Results: Sphere and cone center relative positions were calculated with the fWL algorithm for high resolution test images with an accuracy of compared to for the human observer, and for the edCOM algorithm. The fWL algorithm required 0.01 s per image compared to 5 s for the edCOM algorithm and 20 s for the human observer. For lower resolution images the fWL algorithm localized the centers with an accuracy of compared to for the edCOM algorithm.

Conclusions: A fast (subsecond) subpixel algorithm has been developed that can accurately determine the center locations of the ball and cone in Winston Lutz test images without edge detection or COM calculations.
Comparing performance of many‐core CPUs and GPUs for static and motion compensated reconstruction of C‐arm CT data
Authors: Hofmann Hannes G. , Keck Benjamin , Rohkohl Christopher , Hornegger Joachim
Published: December 2010

Purpose:

Interventional reconstruction of 3‐D volumetric data from C‐arm CT projections is a computationally demanding task. Hardware optimization is not an option but mandatory for interventional image processing and, in particular, for image reconstruction due to the high demands on performance. Several groups have published fast analytical 3‐D reconstruction on highly parallel hardware such as GPUs to mitigate this issue. The authors show that the performance of modern CPU‐based systems is in the same order as current GPUs for static 3‐D reconstruction and outperforms them for a recent motion compensated image reconstruction algorithm.

Methods:

This work investigates two algorithms: Static 3‐D reconstruction as well as a recent motion compensated algorithm. The evaluation was performed using a standardized reconstruction benchmark, RABBIT CT, to get comparable results and two additional clinical data sets.

Results:

The authors demonstrate for a parametric B‐spline motion estimation scheme that the derivative computation, which requires many write operations to memory, performs poorly on the GPU and can highly benefit from modern CPU architectures with large caches. Moreover, on a 32‐core Intel® Xeon® server system, the authors achieve linear scaling with the number of cores used and reconstruction times almost in the same range as current GPUs.

Conclusions:

Algorithmic innovations in the field of motion compensated image reconstruction may lead to a shift back to CPUs in the future. For analytical 3‐D reconstruction, the authors show that the gap between GPUs and CPUs became smaller. It can be performed in less than 20 s (on‐the‐fly) using a 32‐core server.
Prostate brachytherapy postimplant dosimetry: Automatic plan reconstruction of stranded implants
Authors: Chng N. , Spadinger I. , Morris W. J. , Usmani N. , Salcudean S.
Published: December 2010

Purpose:

Plan reconstruction for permanent implant prostate brachytherapy is the process of determining the correspondence between planned and implanted seeds in postimplant analysis. Plan reconstruction informs many areas of brachytherapy quality assurance, including the verification of seed segmentation, misplacement and migration assessment, implant simulations, and the dosimetry of mixed‐activity or mixed‐species implants.

Methods:

An algorithm has been developed for stranded implants which uses the interseed spacing constraints imposed by the suture to improve the accuracy of reconstruction. Seventy randomly selected clinical cases with a mean of 23.6 (range 18–30) needles and mean density of 2.0 (range 1.6–2.6) were automatically reconstructed and the accuracy compared to manual reconstructions performed using a custom 3D graphical interface.

Results:

Using the automatic algorithm, the mean accuracy of the assignment relative to manual reconstruction was found to be. Fifty‐two of the 70 cases (74%) were error‐free; of seeds in the remaining cases, were found to be attributed to the correct strand and were correctly connected to their neighbors. Any necessary manual correction using the interface is usually straightforward. For the clinical data set tested, neither the number of seeds or needles, average density, nor the presence of clusters was found to have an effect on reconstruction accuracy using this method.

Conclusions:

Routine plan reconstruction of stranded implants can be performed with a high degree of accuracy to support postimplant dosimetry and quality analyses.
Comparison of radiograph‐based texture analysis and bone mineral density with three‐dimensional microarchitecture of trabecular bone
Authors: Ranjanomennahary P. , Ghalila S. Sevestre , Malouche D , Marchadier A. , Rachidi M. , Benhamou Cl. , Chappard C.
Published: December 2010

Purpose:

Hip fracture is a serious health problem and textural methods are being developed to assess bone quality. The authors aimed to perform textural analysis at femur on high‐resolution digital radiographs compared to three‐dimensional (3D) microarchitecture comparatively to bone mineral density.

Methods:

Sixteen cadaveric femurs were imaged with an x‐ray device using a C‐MOS sensor. One 17 mm square region of interest (ROI) was selected in the femoral head (FH) and one in the great trochanter (GT). Two‐dimensional (2D) textural features from the co‐occurrence matrices were extracted. Site‐matched measurements of bone mineral density were performed. Inside each ROI, a 16 mm diameter core was extracted. Apparent density and bone volume proportion were measured from a defatted bone core using Archimedes' principle. Microcomputed tomography images of the entire length of the core were obtained (Skyscan 1072®) at of resolution and usual 3D morphometric parameters were computed on the binary volume after calibration from . Then, bone surface/bone volume, trabecular thickness, trabecular separation, and trabecular number were obtained by direct methods without model assumption and the structure model index was calculated.

Results:

In univariate analysis, the correlation coefficients between 2D textural features and 3D morphological parameters reached 0.83 at the FH and 0.79 at the GT. In multivariate canonical correlation analysis, coefficients of the first component reached 0.95 at the FH and 0.88 at the GT.

Conclusions:

Digital radiographs, widely available and economically viable, are an alternative method for evaluating bone microarchitectural structure.
Development of a facility for high‐precision irradiation of cells with carbon ions
Authors: van Goethem Marc‐Jan , Niemantsverdriet Maarten , Brandenburg Sytze , Langendijk Johannes A. , Coppes Robert P. , van Luijk Peter
Published: December 2010

Purpose:

Compared to photons, using particle radiation in radiotherapy reduces the dose and irradiated volume of normal tissues, potentially reducing side effects. The biological effect of dose deposited by particles such as carbon ions, however, differs from that of dose deposited by photons. The inaccuracy in models to estimate the biological effects of particle radiation remains the most important source of uncertainties in particle therapy. Improving this requires high‐precision studies on biological effects of particle radiation. Therefore, the authors aimed to develop a facility for reproducible and high‐precision carbon‐ion irradiation of cells in culture. The combined dose nonuniformity in the lateral and longitudinal direction should not exceed ±1.5%. Dose to the cells from particles than other carbon ions should not exceed 5%.

Methods:

A uniform lateral dose distribution was realized using a single scatter foil and quadrupole magnets. A modulator wheel was used to create a uniform longitudinal dose distribution. The choice of beam energy and the optimal design of these components was determined usingGEANT4 and SRIM Monte Carlo simulations. Verification of the uniformity of the dose distribution was performed using a scintillating screen (lateral) and a water phantom (longitudinal). The reproducibility of dose delivery between experiments was assessed by repeated measurements of the spatial dose distribution. Moreover, the reproducibility of dose‐response measurements was tested by measuring the survival of irradiated HEK293 cells in three independent experiments.

Results:

The relative contribution of dose from nuclear reaction fragments to the sample was found to be when using 90 MeV/u carbon ions. This energy still allows accurate dosimetry conforming to the IAEA Report TRS‐398, facilitating comparison to dose‐effect data obtained with other radiation qualities. A 1.3 mm long spread‐out Bragg peak with a diameter of 30 mm was created, allowing the irradiation of cell samples with the specified accuracy. Measurements of the transverse and longitudinal dose distribution showed that the dose variation over the sample volume was ±0.8% and ±0.7% in the lateral and longitudinal directions, respectively. The track‐averaged LET of and dose‐averaged LET of at the position of the sample were obtained from a GEANT4 simulation, which was validated experimentally. Three separately measured cell‐survival curves yielded nearly identical results.

Conclusions:

With the new facility, high‐precision carbon‐ion irradiations of biological samples can be performed with highly reproducible results.
Fast image reconstruction for Compton camera using stochastic origin ensemble approach
Authors: Andreyev Andriy , Sitek Arkadiusz , Celler Anna
Published: December 2010

Purpose:

Compton camera has been proposed as a potential imaging tool in astronomy, industry, homeland security, and medical diagnostics. Due to the inherent geometrical complexity of Compton camera data, image reconstruction of distributed sources can be ineffective and/or time‐consuming when using standard techniques such as filtered backprojection or maximum likelihood‐expectation maximization (ML‐EM). In this article, the authors demonstrate a fast reconstruction of Compton camera data using a novel stochastic origin ensembles (SOE) approach based on Markov chains.

Methods:

During image reconstruction, the origins of the measured events are randomly assigned to locations on conical surfaces, which are the Compton camera analogs of lines‐of‐responses in PET. Therefore, the image is defined as an ensemble of origin locations of all possible event origins. During the course of reconstruction, the origins of events are stochastically moved and the acceptance of the new event origin is determined by the predefined acceptance probability, which is proportional to the change in event density. For example, if the event density at the new location is higher than in the previous location, the new position is always accepted. After several iterations, the reconstructed distribution of origins converges to a quasistationary state which can be voxelized and displayed.

Results:

Comparison with the list‐mode ML‐EM reveals that the postfiltered SOE algorithm has similar performance in terms of image quality while clearly outperforming ML‐EM in relation to reconstruction time.

Conclusions:

In this study, the authors have implemented and tested a new image reconstruction algorithm for the Compton camera based on the stochastic origin ensembles with Markov chains. The algorithm uses list‐mode data, is parallelizable, and can be used for any Compton camera geometry. SOE algorithm clearly outperforms list‐mode ML‐EM for simple Compton camera geometry in terms of reconstruction time. The difference in computational time will be much larger when full Compton camera system model, including resolution recovery, is implemented and realistic Compton camera geometries are used. It was also shown in this article that while correctly reconstructing the relative distribution of the activity in the object, the SOE algorithm tends to underestimate the intensity values and increase variance in the images; improvements to the SOE reconstruction algorithm will be considered in future work.
Reconstruction of brachytherapy seed positions and orientations from cone‐beam CT x‐ray projections via a novel iterative forward projection matching method
Authors: Pokhrel Damodar , Murphy Martin J. , Todor Dorin A. , Weiss Elisabeth , Williamson Jeffrey F.
Published: December 2010

Purpose:

To generalize and experimentally validate a novel algorithm for reconstructing the 3D pose (position and orientation) of implanted brachytherapy seeds from a set of a few measured 2D cone‐beam CT (CBCT) x‐ray projections.

Methods:

The iterative forward projection matching (IFPM) algorithm was generalized to reconstruct the 3D pose, as well as the centroid, of brachytherapy seeds from three to ten measured 2D projections. The gIFPM algorithm finds the set of seed poses that minimizes the sum‐of‐squared‐difference of the pixel‐by‐pixel intensities between computed and measured autosegmented radiographic projections of the implant. Numerical simulations of clinically realistic brachytherapy seed configurations were performed to demonstrate the proof of principle. An in‐house machined brachytherapy phantom, which supports precise specification of seed position and orientation at known values for simulated implant geometries, was used to experimentally validate this algorithm. The phantom was scanned on an ACUITY CBCT digital simulator over a full 660 sinogram projections. Three to ten x‐ray images were selected from the full set of CBCT sinogram projections and postprocessed to create binary seed‐only images.

Results:

In the numerical simulations, seed reconstruction position and orientation errors were approximately 0.6 mm and 5°, respectively. The physical phantom measurements demonstrated an absolute positional accuracy of or less. The and angle errors were found to be and , respectively, or less when using three projections; with six projections, results were slightly better. The mean registration error was better than 1 mm/6° compared to the measured seed projections. Each test trial converged in 10–20 iterations with computation time of 12–18 min/iteration on a 1 GHz processor.

Conclusions:

This work describes a novel, accurate, and completely automatic method for reconstructing seed orientations, as well as centroids, from a small number of radiographic projections, in support of intraoperative planning and adaptive replanning. Unlike standard back‐projection methods, gIFPM avoids the need to match corresponding seed images on the projections. This algorithm also successfully reconstructs overlapping clustered and highly migrated seeds in the implant. The accuracy of better than 1 mm and 6° demonstrates that gIFPM has the potential to support 2D Task Group 43 calculations in clinical practice.
Semiautomatic method to identify the best phase for gated RT in lung region by 4D‐PET/CT acquisitions
Authors: Mancosu Pietro , Danna Massimo , Bettinardi Valentino , Aquilina Mark Anthony , Lobefalo Francesca , Cozzi Luca , Fogliata Antonella , Scorsetti Marta
Published: December 2010

Purpose: Delineating tumor motion by four‐dimensional positron emission tomography/computed tomography (4D‐PET/CT) is a crucial step for gated radiotherapy (RT). This article quantitatively evaluates semiautomatic algorithms for tumor shift estimation in the lung region due to patient respiration by 4D‐PET/CT, in order to support the selection of the best phases for gated RT, by considering the most stable phases of the breathing cycle.

Methods: Three mobile spheres and ten selected lesions were included in this study. 4D‐PET/CT data were reconstructed and classified into six/ten phases. The semiautomatic algorithms required the generation of single sets of images representative of the full target motion, used as masks for segmenting the phases. For 4D‐CT, a pre‐established HU range was used, whereas three thresholds (100%, 80%, and 40%) were evaluated for 4D‐PET. By using these segmentations, the authors estimated the lesion motion from the shifting centroids, and the phases with the least motion were also deduced including the phases with a curve slope less than . The proposed algorithms were validated by comparing the results to those generated entirely by manual contouring.

Results: In the phantom study, the mean difference between the manual contour and the semiautomatic technique was for 4D‐CT and for the 4D‐PET based on 40% threshold. In the patients' series, the mean difference was for 4D‐CT and for the 4D‐PET based on 40% threshold.

Conclusions: Estimation of lesion motion by the proposed semiautomatic algorithm can be used to evaluate tumor motion due to breathing.
A TCP model incorporating setup uncertainty and tumor cell density variation in microscopic extension to guide treatment planning
Authors: Jin Jian‐Yue , Kong Feng‐Ming , Liu Dezhi , Ren Lei , Li Haisen , Zhong Hualiang , Movsas Benjamin , Chetty Indrin J.
Published: December 2010

Purpose:

Tumor control probability (TCP) models have been proposed to evaluate and guide treatment planning. However, they are usually based on the dose volume histograms (DVHs) of the planning target volume (PTV) and may not properly reflect the substantial variation in tumor burden from the gross tumor volume (GTV) to the microscopic extension (ME) and to the margin of PTV. In this study, the authors propose a TCP model that can account for the effects of setup uncertainties and tumor cell density decay in the ME region.

Methods:

The proposed TCP model is based on the total surviving clonogenic tumor cells (CTCs) after irradiation of a known dose distribution to a region with a CTC distribution. The CTC density was considered to be homogeneous within the GTV, while decreasing exponentially in the ME region. The effect of random setup uncertainty was modeled by convolving the dose distribution with a Gaussian probability density function, represented by a standard deviation,. The effect of systematic setup uncertainty was modeled by summing each calculated TCP for all potential offsets in a Gaussian probability, represented by . The model was then applied to simplified cases to demonstrate the concept. TCP dose responses were calculated for various GTV volumes, DVH shapes, CTC density decay coefficients, probabilities of lymph node metastasis, and random and systematic errors. The slopes of the dose falloff to cover the CTC density decay in the ME region and the margins to compensate setup errors were also analyzed in generalized cases.

Results:

The sigmoid TCP dose response curve shifted to the right substantially for a larger GTV, while modestly for cold spots in DVH. A dose distribution with a uniform dose within the GTV, and a linear dose falloff in the ME region, tended to cause a minimal TCP deterioration if a proper dose falloff slope was used. When the dose falloff slope was less steep than a critical slope represented by, the , which is the prescription dose at , and , which is the TCP slope at , varied little with different dose falloff slopes. However, both and deteriorated fast when the slopes were steeper than . The random setup error tended to shift the TCP curve to the right, while the systematic error tended to compress the curve downward. For combined random and systematic errors, we demonstrated that based on the model, a margin of added to the GTV was found to cause a TCP change corresponding to 2% drop at , or 0.5 Gy shift in .

Conclusions:

This study conceptually demonstrated that a TCP model incorporating the effects of tumor cell density variation and setup uncertainty may be used to guide radiation treatment planning.
Generalized equivalent field size for nonuniform fluence maps in IMRT dose calculation
Authors: Chen Mingli , Lu Weiguo
Published: December 2010

Purpose:

The equivalent field size (EFS) method is widely used to estimate dose of nonstandard fields, such as elongated or arbitrary shaped fields, for both central axis and off axis points. However, its application is limited to fluence maps with uniform intensity. In this work, we propose a generalized EFS (GEFS) for nonuniform fluence maps and present a formula for GEFS‐based dose calculation.

Methods:

A parallel‐beam dose table (PDT) consisting of central axis dose of circular fields of various diameters at various depths is used to define scatter contributions, based on which we calculate GEFS of any given fluence map. Such obtained GEFS, together with the radiological depth and PDT, is used to determine the dose at the point of interest. We tested GEFS‐based dose calculation on a water phantom for both uniform and nonuniform fluence maps and compared the results with those by the collapsed cone convolution/superposition (CCCS) method.

Results:

For all test cases, the gamma index is less than 1 based on the 3%/1 mm criteria for more than 96% of the calculated points. Larger discrepancies mainly occur along the field edges in the buildup region.

Conclusions:

A generalized equivalent field size for nonuniform fluence maps was proposed and its application in calculating dose at any point was presented and verified through comparison with the CCCS method.
Accelerated gradient based diffuse optical tomographic image reconstruction
Authors: Biswas Samir Kumar , Rajan K. , Vasu R. M.
Published: December 2010

Purpose:

Fast reconstruction of interior optical parameter distribution using a new approach called Broyden‐based model iterative image reconstruction (BMOBIIR) and adjoint Broyden‐based MOBIIR (ABMOBIIR) of a tissue and a tissue mimicking phantom from boundary measurement data in diffuse optical tomography (DOT).

Methods:

DOT is a nonlinear and ill‐posed inverse problem. Newton‐based MOBIIR algorithm, which is generally used, requires repeated evaluation of the Jacobian which consumes bulk of the computation time for reconstruction. In this study, we propose a Broyden approach‐based accelerated scheme for Jacobian computation and it is combined with conjugate gradient scheme (CGS) for fast reconstruction. The method makes explicit use of secant and adjoint information that can be obtained from forward solution of the diffusion equation. This approach reduces the computational time many fold by approximating the system Jacobian successively through low‐rank updates.

Results:

Simulation studies have been carried out with single as well as multiple inhomogeneities. Algorithms are validated using an experimental study carried out on a pork tissue with fat acting as an inhomogeneity. The results obtained through the proposed BMOBIIR and ABMOBIIR approaches are compared with those of Newton‐based MOBIIR algorithm. The mean squared error and execution time are used as metrics for comparing the results of reconstruction.

Conclusions:

We have shown through experimental and simulation studies that Broyden‐based MOBIIR and adjoint Broyden‐based methods are capable of reconstructing single as well as multiple inhomogeneities in tissue and a tissue‐mimicking phantom. Broyden MOBIIR and adjoint Broyden MOBIIR methods are computationally simple and they result in much faster implementations because they avoid direct evaluation of Jacobian. The image reconstructions have been carried out with different initial values using Newton, Broyden, and adjoint Broyden approaches. These algorithms work well when the initial guess is close to the true solution. However, when initial guess is far away from true solution, Newton‐based MOBIIR gives better reconstructed images. The proposed methods are found to be stable with noisy measurement data.
EPID‐guided 3D dose verification of lung SBRT
Authors: Aristophanous M. , Rottmann J. , Court L. E. , Berbeco R. I.
Published: December 2010

Purpose:

To investigate the feasibility of utilizing tumor tracks from electronic portal imaging device (EPID) images taken during treatment to verify the delivered dose.

Methods:

The proposed method is based on a computation of the delivered fluence by utilizing the planned fluence and the tumor motion track for each field. A phantom study was designed to assess the feasibility of the method. The CIRS dynamic thorax phantom was utilized with a realistic soft resin tumor, modeled after a real patient tumor. The dose calculated with the proposed method was compared to direct measurements taken with 15 metal oxide semiconductor field effect transistors (MOSFETs) inserted in small fissures made in the tumor model. The phantom was irradiated with the tumor static and moved with different range of motions and setup errors. EPID images were recorded throughout all deliveries and the tumor model was tracked post‐treatment with in‐house developed software. The planned fluence for each field was convolved with the tumor motion tracks to obtain the delivered fluence. Utilizing the delivered fluence from each field, the delivered dose was calculated. The estimated delivered dose was compared to the dose directly measured with the MOSFETs. The feasibility of the proposed method was also demonstrated on a real lung cancer patient, treated with stereotactic body radiotherapy.

Results:

The calculation of delivered dose with the delivered fluence method was in good agreement with the MOSFET measurements, with average differences ranging from 0.8% to 8.3% depending on the proximity of a dose gradient. For the patient treatment, the planned and delivered dose volume histograms were compared and verified the overall good coverage of the target volume.

Conclusions:

The delivered fluence method was applied successfully on phantom and clinical data and its accuracy was evaluated. Verifying each treatment fraction may enable correction strategies that can be applied during the course of treatment to ensure the desired dose coverage.
Monte Carlo investigation of charge‐transport effects on energy resolution and detection efficiency of pixelated CZT detectors for SPECT/PET applications
Authors: Myronakis Marios E. , Darambara Dimitra G.
Published: December 2010

Purpose:

Semiconductor detectors are increasingly considered as alternatives to scintillation crystals for nuclear imaging applications such as positron emission tomography (PET) or single photon emission computed tomography (SPECT). One of the most prominent detector materials is cadmium zinc telluride (CZT), which is currently used in several application‐specific nuclear imaging systems. In this work, the charge‐transport effects in pixelated CZT detectors in relation to detector pixel size and thickness are investigated for pixels sizes from 0.4 up to 1.6 mm.

Methods:

The determination of an optimum pixel size and thickness for use with photon energies of 140 and 511 keV, suitable for SPECT and PET studies, is attempted using photon detection efficiency and energy resolution as figures of merit. The Monte Carlo method combined with detailed finite element analysis was utilized to realistically model photon interactions in the detector and the signal generation process. TheGEANT4 Application for Tomographic Emission (GATE) toolkit was used for photon irradiation and interaction simulations. The COMSOL MULTIPHYSICS® software application was used to create finite element models of the detector that included charge drift, diffusion, trapping, and generation. Data obtained from the two methods were combined to generate accurate signal induction at the detector pixels. The energy resolution was calculated as the full width at half maximum of the energy spectrum photopeak. Photon detection efficiency was also calculated. The effects of charge transport within the detector and photon escape from primary pixel of interaction were investigated; the extent of diffusion to lateral pixels was also assessed.

Results:

Charge transport and signal induction were affected by the position of a pixel in the detector. Edge and corner pixels were less susceptible to lateral diffusion than pixels located in the inner part of the detector. Higher detection efficiency and increased photon escape from primary interaction pixel were observed for thicker detectors. Energy resolution achieved better values in 0.7 and 1.0 mm pixel size for 5 mm detector thickness and 1.6 mm pixel size for 10 mm thickness.

Conclusions:

Selection of pixel size and thickness depends on the imaging application and photon energy utilized. For systems that integrate two nuclear imaging modalities (i.e., combined SPECT/PET), the pixel size should offer an appropriate balance of the effects that take place in the detector, based on the results of the current work. This allows for a system to be designed with the same detector material and the same geometrical configuration for both modalities.
Phosphate Transporter Genes as Reliable Gene Markers for the Identification and Discrimination of Arbuscular Mycorrhizal Fungi in the Genus
Glomus
Authors: Sokolski Serge , Dalpé Yolande , Piché Yves
Published: December 2010

An inorganic phosphate transporter gene sequence (852-bp section) allowed discrimination between 10
Glomus
fungal species represented by 25 strains. It was particularly valuable in differentiating between morphologically similar species with nucleotide and amino acid sequence differences higher than 3%. This gene is proposed as a reliable barcode for the
Glomeromycetes
.
Plasmid-Mediated Quinolone Resistance in
Pseudomonas putida
Isolates from Imported Shrimp
Authors: Tran Quynh T. , Nawaz Mohamed S. , Deck Joanna , Nguyen Kiet T. , Cerniglia Carl E.
Published: December 2010

Fourteen quinolone-resistant
Pseudomonas putida
isolates were recovered from imported frozen shrimp sold in the United States. Two isolates harbored plasmids with
qnrA
and
qnrB
genes. PCR and DNA sequencing of quinolone resistance-determining regions identified novel substitutions in GyrA (His139→Glu and Thr128→Ala) and GyrB (Thr442→Asn, Gly470→Ala, and Ile487→Pro) and previously reported substitutions in GyrB (Asp489→Glu) and ParC (Thr105→Pro).
Identification and Characterization of Novel and Potent Transcription Promoters of
Francisella tularensis
Authors: Zaide Galia , Grosfeld Haim , Ehrlich Sharon , Zvi Anat , Cohen Ofer , Shafferman Avigdor
Published: December 2010

Two alternative promoter trap libraries, based on the green fluorescence protein (
gfp
) reporter and on the chloramphenicol acetyltransferase (
cat
) cassette, were constructed for isolation of potent
Francisella tularensis
promoters. Of the 26,000
F. tularensis
strain LVS
gfp
library clones, only 3 exhibited visible fluorescence following UV illumination and all appeared to carry the bacterioferritin promoter (
Pbfr
). Out of a total of 2,000 chloramphenicol-resistant LVS clones isolated from the
cat
promoter library, we arbitrarily selected 40 for further analysis. Over 80% of these clones carry unique
F. tularensis
DNA sequences which appear to drive a wide range of protein expression, as determined by specific chloramphenicol acetyltransferase (CAT) Western dot blot and enzymatic assays. The DNA sequence information for the 33 unique and novel
F. tularensis
promoters reported here, along with the results of
in silico
and primer extension analyses, suggest that
F. tularensis
possesses classical
Escherichia coli
σ
70
-related promoter motifs. These motifs include the −10 (TATAAT) and −35 [TTGA(C/T)A] domains and an AT-rich region upstream from −35, reminiscent of but distinct from the
E. coli
upstream region that is termed the UP element. The most efficient promoter identified (
Pbfr
) appears to be about 10 times more potent than the
F. tularensis groEL
promoter and is probably among the strongest promoters in
F. tularensis
. The battery of promoters identified in this work will be useful, among other things, for genetic manipulation in the background of
F. tularensis
intended to gain better understanding of the mechanisms involved in pathogenesis and virulence, as well as for vaccine development studies.
Viability of
Bacillus licheniformis
and
Bacillus thuringiensis
Spores as a Model for Predicting the Fate of
Bacillus anthracis
Spores during Composting of Dead Livestock
Authors: Reuter Tim , Alexander Trevor W. , McAllister Tim A.
Published: December 2010

Safe disposal of dead livestock and contaminated manure is essential for the effective control of infectious disease outbreaks. Composting has been shown to be an effective method of disposal, but no information exists on its ability to contain diseases caused by spore-forming bacteria, such as
Bacillus anthracis
. Duplicate composters (east and west), each containing 16 dead cattle, were constructed (final capacity, 85,000 kg). Spores (10
7
CFU/g manure) of
Bacillus licheniformis
and
Bacillus thuringiensis
were mixed with autoclaved feedlot manure and placed in either sterile vials or porous nylon bags. Compost temperatures in the west composter were slightly higher than in the east composter. Viable
B. thuringiensis
spores were reduced to ≤10
2
CFU in all samples after 112 days but were isolated from bags (west composter) at ≤10
2
and at 10
5
CFU (east composter) after 230 days. In contrast,
B. licheniformis
was at ≤10
2
CFU in vials (west composter) after 112 days but remained at 10
6
CFU after 230 days (east composter). Similarly,
B. licheniformis
in bags was not detected after 230 days in the west composter but remained at 10
7
CFU in the east composter. Our study suggests that spore viability was reduced in the west composter by exposure to compost and elevated temperatures over time. Different temperature profiles may explain why spores remained viable in the east structure but were largely rendered nonviable in the west structure. Under practical conditions, variation in composting microclimates may preclude the complete inactivation of
Bacillus
spores, including those of
B. anthracis
, during composting. However, composting may still have merit as a method of biocontainment, reducing and diluting the transfer of infectious spores into the environment.