bluuebunny/crossref_metadata_2025_split huggingface dataset:
The use of high‐resolution melting analysis for genotyping Symbiodinium strains: a sensitive and fast approach
Authors: GRANADOS‐CIFUENTES CAMILA , RODRIGUEZ‐LANETTY MAURICIO 
Published: November 2010

AbstractHigh‐resolution melting (HRM) analysis is a closed‐tube, rapid and sensitive technique able to detect DNA variations. It relies on the fluorescence melting curves that are obtained from the transition of double‐stranded DNA (dsDNA) to single‐stranded DNA (ssDNA) as a result of temperature increase. In this study, we evaluated the effectiveness of HRM as a tool to rapidly and precisely genotype monotypic Symbiodinium populations using the internal transcribed spacer, region 2, ribosomal DNA (ITS2 rDNA). For this, Symbiodinium denaturing gradient gel electrophoresis (DGGE) profiles, where gel bands were excised and sequenced, were compared to HRM genotypes. Results showed that twenty cultures were correctly genotyped in <2 h using HRM analysis with a percentage of confidence >90%. Limitations of the technique were also investigated. Unlike other techniques used for genotyping Symbiodinium, such as DGGE and other fingerprint profiles, HRM is a technique of great advantage for field coral reef ecologists and physiologists as no expertise in advanced molecular methods is required.
In obese Zucker rats, lipids accumulate in the heart despite normal mitochondrial content, morphology and long‐chain fatty acid oxidation
Authors: Holloway Graham P. , Snook Laelie A. , Harris Robert J. , Glatz Jan F. C. , Luiken Joost J. F. P. , Bonen Arend 
Published: November 2010

Non‐technical summaryThe storage of fat within the heart muscle has been associated with reductions in force production, which has implications for the ability of the heart to adequately pump blood. With the assistance of membrane proteins known as transport proteins, fats from the blood can be moved into heart muscle cells, where they can either be stored or used for generating energy (within a structure called mitochondria) to pump blood. We provide evidence that in obese animals more fat accumulates within the heart as a result of their increased transport across the membranes of heart cells, not due to reductions in mitochondrial number or function. The knowledge of why fat accumulates in the heart may provide insight into novel treatments/therapies, and the current study suggests therapies focused on limiting the entry of fats into the heart may restore the ability of the heart to pump blood.
GPU‐accelerated Monte Carlo convolution/superposition implementation for dose calculation
Authors: Zhou Bo , Yu Cedric X. , Chen Danny Z. , Hu X. Sharon 
Published: November 2010

Purpose:Dose calculation is a key component in radiation treatment planning systems. Its performance and accuracy are crucial to the quality of treatment plans as emerging advanced radiation therapy technologies are exerting ever tighter constraints on dose calculation. A common practice is to choose either a deterministic method such as the convolution/superposition (CS) method for speed or a Monte Carlo (MC) method for accuracy. The goal of this work is to boost the performance of a hybrid Monte Carlo convolution/superposition (MCCS) method by devising a graphics processing unit (GPU) implementation so as to make the method practical for day‐to‐day usage.Methods:Although the MCCS algorithm combines the merits of MC fluence generation and CS fluence transport, it is still not fast enough to be used as a day‐to‐day planning tool. To alleviate the speed issue of MC algorithms, the authors adopted MCCS as their target method and implemented a GPU‐based version. In order to fully utilize the GPU computing power, the MCCS algorithm is modified to match the GPU hardware architecture. The performance of the authors' GPU‐based implementation on an Nvidia GTX260 card is compared to a multithreaded software implementation on a quad‐core system.Results:A speedup in the range of 6.7–11.4× is observed for the clinical cases used. The less than 2% statistical fluctuation also indicates that the accuracy of the authors' GPU‐based implementation is in good agreement with the results from the quad‐core CPU implementation.Conclusions:This work shows that GPU is a feasible and cost‐efficient solution compared to other alternatives such as using cluster machines or field‐programmable gate arrays for satisfying the increasing demands on computation speed and accuracy of dose calculation. But there are also inherent limitations of using GPU for accelerating MC‐type applications, which are also analyzed in detail in this article.
Ultrafast treatment plan optimization for volumetric modulated arc therapy (VMAT)
Authors: Men Chunhua , Romeijn H. Edwin , Jia Xun , Jiang Steve B. 
Published: November 2010

Purpose:To develop a novel aperture‐based algorithm for volumetric modulated arc therapy (VMAT) treatment plan optimization with high quality and high efficiency.Methods:The VMAT optimization problem is formulated as a large‐scale convex programming problem solved by a column generation approach. The authors consider a cost function consisting two terms, the first enforcing a desired dose distribution and the second guaranteeing a smooth dose rate variation between successive gantry angles. A gantry rotation is discretized into 180 beam angles and for each beam angle, only one MLC aperture is allowed. The apertures are generated one by one in a sequential way. At each iteration of the column generation method, a deliverable MLC aperture is generated for one of the unoccupied beam angles by solving a subproblem with the consideration of MLC mechanic constraints. A subsequent master problem is then solved to determine the dose rate at all currently generated apertures by minimizing the cost function. When all 180 beam angles are occupied, the optimization completes, yielding a set of deliverable apertures and associated dose rates that produce a high quality plan.Results:The algorithm was preliminarily tested on five prostate and five head‐and‐neck clinical cases, each with one full gantry rotation without any couch/collimator rotations. High quality VMAT plans have been generated for all ten cases with extremely high efficiency. It takes only 5–8 min on CPU (MATLAB code on an Intel Xeon 2.27 GHz CPU) and 18–31 s on GPU (CUDA code on an NVIDIA Tesla C1060 GPU card) to generate such plans.Conclusions:The authors have developed an aperture‐based VMAT optimization algorithm which can generate clinically deliverable high quality treatment plans at very high efficiency.
Model‐based measurements of the diameter of the internal carotid artery in CT angiography images
Authors: Gratama van Andel H. A. F. , Venema H. W. , Bol K. , Marquering H. A. , Majoie C. B. , den Heeten G. J. , Grimbergen C. A. , Streekstra G. J. 
Published: November 2010

Purpose:Computed tomography angiography (CTA) is often used to determine the degree of stenosis in patients that suffer from carotid artery occlusive disease. Accurate and precise measurements of the diameter of the stenosed internal carotid artery are required to make decisions on treatment of the patient. However, the inherent blurring of images hampers a straightforward measurement, especially for smaller vessels. The authors propose a model‐based approach to perform diameter measurements in which explicit allowance is made for the blurring of structures in the images. Three features of the authors' approach are the use of prior knowledge in the fitting of the model at the site of the stenosis, the applicability to vessels both with circular and noncircular cross‐section, and the ability to deal with additional structures close to the arteries such as calcifications.Methods:Noncircular cross‐sections of vessels were modeled with elliptic Fourier descriptors. When calcifications or other high‐intensity structures are adjacent to the lumen, both the lumen and the high‐intensity structures were modeled in order to improve the diameter estimates of the vessel. Measurements were performed in CT scans of a phantom mimicking stenosed carotids and in CTA scans of two patients with an internal carotid stenosis. In an attempt to validate the measurements in CTA images, measurements were also performed in three‐dimensional rotational angiography (3DRA) images of the same patients.Results:The validity of the approach for diameter measurements of cylindrical arteries in CTA images is evident from phantom measurements. When prior knowledge about the enhancement and the blurring parameter was used, accurate and precise diameter estimates were obtained down to a diameter of 0.4 mm. The potential of the presented approach, both with respect to the extension to noncircular cross‐sections and the modeling of adjacent calcifications, appears from the patient data. The accuracy of the size estimates in the patient images could not be unambiguously established because no gold standard was available and the quality of the 3DRA images was often suboptimal.Conclusions:The authors have shown that the inclusion ofa priori information results in accurate and precise diameter measurements of arteries with a small diameter. Furthermore, in patient data, the assumption of a circular cross‐section often appears to be too simple. The extension to noncircular cross‐sections and adjacent calcifications paves the way to realistic modeling of the carotid artery.
Evaluation of an improved algorithm for producing realistic 3D breast software phantoms: Application for mammography
Authors: Bliznakova K. , Suryanarayanan S. , Karellas A. , Pallikarakis N. 
Published: November 2010

Purpose:This work presents an improved algorithm for the generation of 3D breast software phantoms and its evaluation for mammography.Methods:The improved methodology has evolved from a previously presented 3D noncompressed breast modeling method used for the creation of breast models of different size, shape, and composition. The breast phantom is composed of breast surface, duct system and terminal ductal lobular units, Cooper's ligaments, lymphatic and blood vessel systems, pectoral muscle, skin, 3D mammographic background texture, and breast abnormalities. The key improvement is the development of a new algorithm for 3D mammographic texture generation. Simulated images of the enhanced 3D breast model without lesions were produced by simulating mammographic image acquisition and were evaluated subjectively and quantitatively. For evaluation purposes, a database with regions of interest taken from simulated and real mammograms was created. Four experienced radiologists participated in a visual subjective evaluation trial, as they judged the quality of the simulated mammograms, using the new algorithm compared to mammograms, obtained with the old modeling approach. In addition, extensive quantitative evaluation included power spectral analysis and calculation of fractal dimension, skewness, and kurtosis of simulated and real mammograms from the database.Results:The results from the subjective evaluation strongly suggest that the new methodology for mammographic breast texture creates improved breast models compared to the old approach. Calculated parameters on simulated images such as exponent deducted from the power law spectral analysis and fractal dimension are similar to those calculated on real mammograms. The results for the kurtosis and skewness are also in good coincidence with those calculated from clinical images. Comparison with similar calculations published in the literature showed good agreement in the majority of cases.Conclusions:The improved methodology generated breast models with increased realism compared to the older model as shown in evaluations of simulated images by experienced radiologists. It is anticipated that the realism will be further improved using an advanced image simulator so that simulated images may be used in feasibility studies in mammography.
Dosimetric optimization of a conical breast brachytherapy applicator for improved skin dose sparing
Authors: Yang Yun , Rivard Mark J. 
Published: November 2010

Purpose:Both the AccuBoost® D‐shaped and round applicators have been dosimetrically characterized and clinically used to treat patients with breast cancer. While the round applicators provide conformal dose coverage, under certain clinical circumstances the breast skin dose may be higher than preferred. The purpose of this study was to modify the round applicators to minimize skin dose while not substantially affecting dose uniformity within the target volume and reducing the treatment time.Methods:In order to irradiate the intended volume while sparing critical structures such as the skin, the current round applicator design has been augmented through the addition of an internal truncated cone (i.e., frustum) shield. Monte Carlo methods and clinical constraints were used to design the optimal cone applicator. With the cone applicator now defined as the entire assembly including the surrounding tungsten‐alloy shell holding the HDR source catheter, the applicator height was reduced to diminish the treatment time while minimizing skin dose. Monte Carlo simulation results were validated using both radiochromic film and ionization chamber measurements based on established techniques.Results:The optimal cone applicators diminished the maximum skin dose by 15%–32% (based on the applicator diameter and breast separation) with the tumor dose reduced by less than 3% for a constant exposure time. Furthermore, reduction in applicator height diminished the treatment time by up to 30%. Radiochromic film and ionization chamber dosimetric results in phantom agreed with Monte Carlo simulation results typically within 3%. Larger differences were outside the treatment volume in low dose regions or associated with differences between the measurement and Monte Carlo simulation environments.Conclusions:A new radiotherapy treatment device was developed and dosimetrically characterized. This set of applicators significantly reduces the skin dose and treatment time while retaining uniform target dose.
Monte Carlo simulation of the effects of anode surface roughness on x‐ray spectra
Authors: Kákonyi Róbert , Erdélyi Miklós , Szabó Gábor 
Published: November 2010

Purpose:Spectral and angular distribution of the x‐ray beam generated by medical x‐ray tubes as a function of anode surface roughness was analyzed.Methods:Different sets of profiles such as ideal flat, regular profiles, and measured profiles adopted from the literature were analyzed by means ofMCNPX Monte Carlo simulator. The geometry used was simplified to separate different physical effects. A sphere centered on the origin of the coordinate system was divided into two hemispheres filled with tungsten and a vacuum, respectively. The studied anode surfaces were placed at the center of the plane of the hemisphere. The profiles were realized by means of the general lattice structure of the MCNPX. The energy and angular distributions of the excited photons were recorded with energy and angular resolutions of 0.5 keV and 1°, respectively, by means of point detectors. The range of the studied anode surface roughness was . The emission angle dependencies of the following quantities were analyzed: Half value layer (HVL) value, intensity, and spectral photon flux.Results:The analysis of the HVL of the x‐ray beam showed that around an emission angle of 5°, the hardness of the beam was practically independent of the surface roughness. The value of this emission angle depends on the filtration. Below this critical angle, the HVL value decreases, while at a higher emission angle, the beam becomes harder with increasing surface roughness. The intensity degradation saturates with increasing roughness. The position of the maximum spectral photon flux shifts to higher emission angles as the anode surface roughness increases. The surface roughness was found to be an inadequate quantity to describe the effect of anode surface roughness on x‐ray spectra since no definite connection was found between the values of the intensity degradation and surface roughness. At 120 kVp tube voltage and at a roughness value, the effect of anode surface roughness introduces a 5% and 12% intensity degradation at a 5° and 12° emission angle, respectively. However, it has a higher impact at low tube voltages , e.g., in mammography systems where the intensity degradation could even be 25% at the “newly” polished anode surface.Conclusions:The effects of anode surface roughness on x‐ray spectra were successfully simulated by a Monte Carlo method. It was proved that the effect of the anode surface roughness could not be modeled by simple filters made from the anode material. The surface roughness was found to be an inadequate quantity to describe the effect of anode surface roughness on x‐ray spectra.
Oblique incidence for broad monoenergetic proton beams
Authors: Jette David , Yuan Jiankui , Chen Weimin 
Published: November 2010

Purpose:The depth dose of a monoenergetic broad parallel proton beam has been modeled in a number of ways, but evidently not yet for oblique incidence. The purpose of this investigation is to find an accurate analytic formula for this case, which can then be used to model the depth dose of a broad beam with an initial Gaussian angular distribution.Methods:The Bortfeld model of depth dose in a broad normally incident proton beam has been extended to the case of oblique incidence. This extension uses an empirically determined Gaussian parameter which (roughly) characterizes the off‐axis dose of a proton pencil beam. As with Bortfeld's work, the modeling is done in terms of parabolic cylinder functions. To obtain the depth dose for an initial angular distribution, the result is integrated over the angle of incidence, weighted by a Gaussian probability function. The predictions of the theory have been compared to MCNPX Monte Carlo calculations for four phantom materials (water, bone, aluminum, and copper) and for initial proton energies of 50, 100, 150, 200, and 250 MeV.Results:Comparisons of the depth dose predicted by this theory with Monte Carlo calculations have established that with very good accuracy, can be taken to be independent both of the depth and of the angle of incidence. As a function of initial proton range or of initial proton energy, has been found to obey a power law to very high accuracy. Good fits to Monte Carlo calculations have also been found for an initial Gaussian angular distribution.Conclusions:This investigation is the first step in the accurate modeling of a proton pencil beam with initial Gaussian angular distribution. It provides the longitudinal factor, with its Bragg peak buildup and sharp distal falloff. A transverse factor must still be incorporated into this theory and this will give the lateral penumbra of a collimated proton beam. Also, it will be necessary to model the dose of product particles from nuclear interactions of the proton beam. With the accurate modeling of a pencil beam, it will be possible to accurately take into account the effect of localized tissue inhomogeneities.
Three‐dimensional canine heart model for cardiac elastography
Authors: Chen Hao , Varghese Tomy 
Published: November 2010

Purpose:A three‐dimensional finite element analysis based canine heart model is introduced that would enable the assessment of cardiac function.Methods:The three‐dimensional canine heart model is based on the cardiac deformation and motion model obtained from the Cardiac Mechanics Research Group at UCSD. The canine heart model is incorporated into ultrasound simulation programs previously developed in the laboratory, enabling the generation of simulated ultrasound radiofrequency data to evaluate algorithms for cardiac elastography. The authors utilize a two‐dimensional multilevel hybrid method to estimate local displacements and strain from the simulated cardiac radiofrequency data.Results:Tissue displacements and strains estimated along both the axial and lateral directions (with respect to the ultrasound scan plane) are compared to the actual scatterer movement obtained using the canine heart model. Simulation and strain estimation algorithms combined with the three‐dimensional canine heart model provide high resolution displacement and strain curves for improved analysis of cardiac function. The use of principal component analysis along parasternal cardiac short axis views is also presented.Conclusions:A 3D cardiac deformation model is proposed for evaluating displacement tracking and strain estimation algorithms for cardiac strain imaging. Validation of the model is shown using ultrasound simulations to generate axial and lateral displacement and strain curves that are similar to the actual axial and lateral displacement and strain curves.
“SABER”: A new software tool for radiotherapy treatment plan evaluation
Authors: Zhao Bo , Joiner Michael C. , Orton Colin G. , Burmeister Jay 
Published: November 2010

Purpose:Both spatial and biological information are necessary in order to perform true optimization of a treatment plan and for predicting clinical outcome. The goal of this work is to develop an enhanced treatment plan evaluation tool which incorporates biological parameters and retains spatial dose information.Methods:A software system is developed which provides biological plan evaluation with a novel combination of features. It incorporates hyper‐radiosensitivity using the induced‐repair model and applies the new concept of dose convolution filter (DCF) to simulate dose wash‐out effects due to cell migration, bystander effect, and/or tissue motion during treatment. Further, the concept of spatial DVH (sDVH) is introduced to evaluate and potentially optimize the spatial dose distribution in the target volume. Finally, generalized equivalent uniform dose is derived from both the physical dose distribution (gEUD) and the distribution of equivalent dose in 2 Gy fractions and the software provides three separate models for calculation of tumor control probability (TCP), normal tissue complication probability (NTCP), and probability of uncomplicated tumor control . TCP, NTCP, and are provided as a function of prescribed dose and multivariable TCP, NTCP, and plots are provided to illustrate the dependence on individual parameters used to calculate these quantities. Ten plans from two clinical treatment sites are selected to test the three calculation models provided by this software.Results:By retaining both spatial and biological information about the dose distribution, the software is able to distinguish features of radiotherapy treatment plans not discernible using commercial systems. Plans that have similar DVHs may have different spatial and biological characteristics and the application of novel tools such as sDVH and DCF within the software may substantially change the apparent plan quality or predicted plan metrics such as TCP and NTCP. For the cases examined, both the calculation method and the application of DCF can change the ranking order of competing plans. The voxel‐by‐voxel TCP model makes it feasible to incorporate spatial variations of clonogen densities, radiosensitivities , and fractionation sensitivities as those data become available.Conclusions:The new software incorporates both spatial and biological information into the treatment planning process. The application of multiple methods for the incorporation of biological and spatial information has demonstrated that the order of application of biological models can change the order of plan ranking. Thus, the results of plan evaluation and optimization are dependent not only on the models used but also on the order in which they are applied. This software can help the planner choose more biologically optimal treatment plans and potentially predict treatment outcome more accurately.