bluuebunny/crossref_metadata_2025_split huggingface dataset:
A real time dose monitoring and dose reconstruction tool for patient specific VMAT QA and delivery
Authors: Tyagi Neelam , Yang Kai , Gersten David , Yan Di 
Published: November 2012

Purpose:To develop a real time dose monitoring and dose reconstruction tool to identify and quantify sources of errors during patient specific volumetric modulated arc therapy (VMAT) delivery and quality assurance.Methods:The authors develop a VMAT delivery monitor tool called linac data monitor that connects to the linac in clinical mode and records, displays, and compares real time machine parameters with the planned parameters. A new measure, called integral error, keeps a running total of leaf overshoot and undershoot errors in each leaf pair, multiplied by leaf width, and the amount of time during which the error exists in monitor unit delivery. Another tool reconstructs Pinnacle3™ format delivered plan based on the saved machine logfile and recalculates actual delivered dose in patient anatomy. Delivery characteristics of various standard fractionation and stereotactic body radiation therapy (SBRT) VMAT plans delivered on Elekta Axesse and Synergy linacs were quantified.Results:The MLC and gantry errors for all the treatment sites were 0.00 ± 0.59 mm and 0.05 ± 0.31°, indicating a good MLC gain calibration. Standard fractionation plans had a larger gantry error than SBRT plans due to frequent dose rate changes. On average, the MLC errors were negligible but larger errors of up to 6 mm and 2.5° were seen when dose rate varied frequently. Large gantry errors occurred during the acceleration and deceleration process, and correlated well with MLC errors (r = 0.858, p = 0.0004). PTV mean, minimum, and maximum dose discrepancies were 0.87 ± 0.21%, 0.99 ± 0.59%, and 1.18 ± 0.52%, respectively. The organs at risk (OAR) doses were within 2.5%, except some OARs that showed up to 5.6% discrepancy in maximum dose. Real time displayed normalized total positive integral error (normalized to the total monitor units) correlated linearly with MLC (r = 0.9279, p < 0.001) and gantry errors (r = 0.742, p = 0.005). There is a strong correlation between total integral error and PTV mean (r = 0.683, p = 0.015), minimum (r = 0.6147, p = 0.033), and maximum dose (r = 0.6038, p = 0.0376).Conclusions:Errors may exist during complex VMAT planning and delivery. Linac data monitor is capable of detecting and quantifying mechanical and dosimetric errors at various stages of planning and delivery.
Localization of deformable tumors from short‐arc projections using Bayesian estimation
Authors: Hoegele W. , Zygmanski P. , Dobler B. , Kroiss M. , Koelbl O. , Loeschel R. 
Published: November 2012

Purpose:The authors present a stochastic framework for radiotherapy patient positioning directly utilizing radiographic projections. This framework is developed to be robust against anatomical nonrigid deformations and to cope with challenging imaging scenarios, involving only a few cone beam CT projections from short arcs.Methods:Specifically, a Bayesian estimator (BE) is explicitly derived for the given scanning geometry. This estimator is compared to reference methods such as chamfer matching (CM) and the minimization of the median absolute error adapted as tools of robust image processing and statistics. In order to show the performance of the stochastic short‐arc patient positioning method, a CIRS IMRT thorax phantom study is presented with movable markers and the utilization of an Elekta Synergy® XVI system. Furthermore, a clinical prostate CBCT scan of a Varian® On‐Board Imager® system is utilized to investigate the robustness of the method for large variations of image quality (anterior‐posterior vs lateral views).Results:The results show that the BE shifts reduce the initial setup error of up to 3 cm down to 3 mm at maximum for an imaging arc as short as 10° while CM achieves residual errors of 7 mm at maximum only for arcs longer than 40°. Furthermore, the BE can compensate robustly for low image qualities using several low quality projections simultaneously.Conclusions:In conclusion, an estimation method for marker‐based patient positioning for short imaging arcs is presented and shown to be robust and accurate for deformable anatomies.
Comprehensive assessment of the slice sensitivity profiles in breast tomosynthesis and breast CT
Authors: Nosratieh Anita , Yang Kai , Aminololama‐Shakeri Shadi , Boone John M. 
Published: November 2012

Purpose:This study experimentally evaluated the slice sensitivity profile (SSP) and its relationship between acquisition angle, object size, and cone angle. The sensitivity profile metric was used to characterize a breast tomosynthesis systemˈs resolution in the z‐axis. The SSP was also measured on a prototype breast computed tomography (bCT) system.Methods:The SSP was measured using brass disks placed within adipose tissue‐equivalent breast phantoms. The digital tomosynthesis system (Selenia Dimensions, Hologic Corporation, Bedford, MA) acquires projection images over a 15° angular range and the bCT scanner acquires projection images over a 360° angular range. Angular ranges between 15° and 360° were studied by using a subset of the projection images acquired on the bCT scanner. The SSP was determined by measuring a background‐corrected mean gray scale value as a function of the z‐position (axis normal to the plane of the detector).Results:The results show that SSP improves when the angular acquisition range is increased and the SSP approaches a delta function for angles greater than 180°. Smaller objects have a narrower SSP and the SSP is not significantly dependent on the cone angle. For a 2.5, 5, 10 mm disk, the full width at half maximum of the SSP was 35, 61, 115 mm, respectively, on the tomosynthesis system (at 15°) and was 0.5 mm for all disk diameters on the bCT scanner (at 360°).Conclusions:The SSP is dependent on object size and angular acquisition range. These dependencies are overcome once the angular acquisition range is increased beyond 180°.
Speed‐of‐sound compensated photoacoustic tomography for accurate imaging
Authors: Jose Jithin , Willemink Rene G. H. , Steenbergen Wiendelt , Slump C. H. , van Leeuwen Ton G. , Manohar Srirang 
Published: November 2012

Purpose:In most photoacoustic (PA) tomographic reconstructions, variations in speed‐of‐sound (SOS) of the subject are neglected under the assumption of acoustic homogeneity. Biological tissue with spatially heterogeneous SOS cannot be accurately reconstructed under this assumption. The authors present experimental and image reconstruction methods with which 2D SOS distributions can be accurately acquired and reconstructed, and with which the SOS map can be used subsequently to reconstruct highly accurate PA tomograms.Methods:The authors begin with a 2D iterative reconstruction approach in an ultrasound transmission tomography setting, which uses ray refracted paths instead of straight ray paths to recover accurate SOS images of the subject. Subsequently, they use the SOS distribution in a new 2D iterative PA reconstruction approach, where refraction of rays originating from PA sources is accounted for in accurately retrieving the distribution of these sources. Both the SOS reconstruction and SOS‐compensated PA reconstruction methods utilize the Eikonal equation to model acoustic wavefront propagation. The equation is solved using a high accuracy fast marching method.Results:The authors validated the new reconstruction algorithms using numerical phantoms. For experiments they utilized the recently introduced PER‐PACT method which can be used to simultaneously acquire SOS and PA data from subjects.Conclusions:It is first confirmed that it is important to take SOS inhomogeneities into account in high resolution PA tomography. The iterative reconstruction algorithms, that model acoustic refractive effects, in reconstructing SOS distributions, and subsequently using these distributions to correct PA tomograms, yield artifact‐free highly accurate images. The approach of using the hybrid measurement method and the new reconstruction algorithms is successful in substantially improving the quality of PA images with a minimization of blurring and artifacts.
Consensus recommendations for incident learning database structures in radiation oncology
Authors: Ford E. C. , Fong de Los Santos L. , Pawlicki T. , Sutlief S. , Dunscombe P. 
Published: November 2012

Purpose:Incident learning plays a key role in improving quality and safety in a wide range of industries and medical disciplines. However, implementing an effective incident learning system is complex, especially in radiation oncology. One current barrier is the lack of technical standards to guide users or developers. This report, the product of an initiative by the Work Group on Prevention of Errors in Radiation Oncology of the American Association of Physicists in Medicine, provides technical recommendations for the content and structure of incident learning databases in radiation oncology.Methods:A panel of experts was assembled and tasked with developing consensus recommendations in five key areas: definitions, process maps, severity scales, causality taxonomy, and data elements. Experts included representatives from all major North American radiation oncology organizations as well as users and developers of public and in‐house reporting systems with over two decades of collective experience. Recommendations were developed that take into account existing incident learning systems as well as the requirements of outside agencies.Results:Consensus recommendations are provided for the five major topic areas. In the process mapping task, 91 common steps were identified for external beam radiation therapy and 88 in brachytherapy. A novel feature of the process maps is the identification of “safety barriers,” also known as critical control points, which are any process steps whose primary function is to prevent errors or mistakes from occurring or propagating through the radiotherapy workflow. Other recommendations include a ten‐level medical severity scale designed to reflect the observed or estimated harm to a patient, a radiation oncology‐specific root causes table to facilitate and regularize root‐cause analyses, and recommendations for data elements and structures to aid in development of electronic databases. Also presented is a list of key functional requirements of any reporting system.Conclusions:Incident learning is recognized as an invaluable tool for improving the quality and safety of treatments. The consensus recommendations in this report are intended to facilitate the implementation of such systems within individual clinics as well as on broader national and international scales.
Dedicated breast CT: Fibroglandular volume measurements in a diagnostic population
Authors: Vedantham Srinivasan , Shi Linxi , Karellas Andrew , O'Connell Avice M. 
Published: November 2012

Purpose:To determine the mean and range of volumetric glandular fraction (VGF) of the breast in a diagnostic population using a high‐resolution flat‐panel cone‐beam dedicated breast CT system. This information is important for Monte Carlo‐based estimation of normalized glandular dose coefficients and for investigating the dependence of VGF on breast dimensions, race, and pathology.Methods:Image data from a clinical trial investigating the role of dedicated breast CT that enrolled 150 women were retrospectively analyzed to determine the VGF. The study was conducted in adherence to a protocol approved by the institutional human subjects review boards and written informed consent was obtained from all study participants. All participants in the study were assigned BI‐RADS® 4 or 5 as per the American College of Radiology assessment categories after standard diagnostic work‐up and underwent dedicated breast CT exam prior to biopsy. A Gaussian‐kernel based fuzzy c‐means algorithm was used to partition the breast CT images into adipose and fibroglandular tissue after segmenting the skin. Upon determination of the accuracy of the algorithm with a phantom, it was applied to 137 breast CT volumes from 136 women. VGF was determined for each breast and the mean and range were determined. Pathology results with classification as benign, malignant, and hyperplasia were available for 132 women, and were used to investigate if the distributions of VGF varied with pathology.Results:The algorithm was accurate to within ±1.9% in determining the volume of an irregular shaped phantom. The study mean (± inter‐breast SD) for the VGF was 0.172 ± 0.142 (range: 0.012–0.719). VGF was found to be negatively correlated with age, breast dimensions (chest‐wall to nipple length, pectoralis to nipple length, and effective diameter at chest‐wall), and total breast volume, and positively correlated with fibroglandular volume. Based on pathology, pairwise statistical analysis (Mann‐Whitney test) indicated that at the 0.05 significance level, there was no significant difference in distributions of VGF without adjustment for age between malignant and nonmalignant breasts (p = 0.41). Pairwise comparisons of the distributions of VGF in increasing order of mammographic breast density indicated all comparisons were statistically significant (p < 0.002).Conclusions:This study used a different clinical prototype breast CT system than that in previous studies to image subjects from a different geographical region, and used a different algorithm for analysis of image data. The mean VGF estimated from this study is within the range reported in previous studies, indicating that the choice of 50% glandular weight fraction to represent an average breast for Monte Carlo‐based estimation of normalized glandular dose coefficients in mammography needs revising. In the study, the distributions of VGF did not differ significantly with pathology.
Organ sample generator for expected treatment dose construction and adaptive inverse planning optimization
Authors: Nie Xiaobo , Liang Jian , Yan Di 
Published: November 2012

Purpose:To create an organ sample generator (OSG) for expected treatment dose construction and adaptive inverse planning optimization. The OSG generates random samples of organs of interest from a distribution obeying the patient specific organ variation probability density function (PDF) during the course of adaptive radiotherapy.Methods:Principle component analysis (PCA) and a time‐varying least‐squares regression (LSR) method were used on patient specific geometric variations of organs of interest manifested on multiple daily volumetric images obtained during the treatment course. The construction of the OSG includes the determination of eigenvectors of the organ variation using PCA, and the determination of the corresponding coefficients using time‐varying LSR. The coefficients can be either random variables or random functions of the elapsed treatment days depending on the characteristics of organ variation as a stationary or a nonstationary random process. The LSR method with time‐varying weighting parameters was applied to the precollected daily volumetric images to determine the function form of the coefficients. Eleven h&n cancer patients with 30 daily cone beam CT images each were included in the evaluation of the OSG. The evaluation was performed using a total of 18 organs of interest, including 15 organs at risk and 3 targets.Results:Geometric variations of organs of interest during h&n cancer radiotherapy can be represented using the first 3 ∼ 4 eigenvectors. These eigenvectors were variable during treatment, and need to be updated using new daily images obtained during the treatment course. The OSG generates random samples of organs of interest from the estimated organ variation PDF of the individual. The accuracy of the estimated PDF can be improved recursively using extra daily image feedback during the treatment course. The average deviations in the estimation of the mean and standard deviation of the organ variation PDF for h&n cancer radiotherapy were less than 2 and 1 mm, respectively, for most organs after the second week of treatment. After the first three weeks of treatment, the mean discrepancy of the dose estimation accuracy was within 1% for most of organs, the corresponding standard deviation was within 2.5% for parotids, the brain stem and the cochleae, and within 1% for other organs.Conclusions:A patient specific OSG is feasible and can be used to generate random samples of organs of interest for the expected treatment dose construction and adaptive inverse planning. The accuracy of the OSG can be improved continuously and recursively during the adaptive treatment course using daily volumetric image feedback.
Endurance exercise in a rat model of metabolic syndrome
Authors: Cameron Isabelle , Alam Mohammad Ashraful , Wang Jianxiong , Brown Lindsay 
Published: November 2012

We have measured the responses to endurance exercise training on body composition and glucose regulation, as well as cardiovascular and liver structure and function in rats fed a high carbohydrate and high fat (HCHF) diet as a model of human metabolic syndrome. Male Wistar rats (9–10 weeks old) were randomly allocated into corn starch (CS) or HCHF diet groups for 16 weeks; half of each group were exercised on a treadmill for 20, 25, and then 30 min/day, 5 days/week, during the last 8 weeks of the protocol. Metabolic, cardiovascular, and liver parameters were monitored. The HCHF diet induced symptoms of metabolic syndrome, including obesity, dyslipidemia, impaired glucose tolerance, and increased systolic blood pressure associated with the development of cardiovascular remodeling and nonalcoholic steatohepatitis. Exercise in HCHF rats decreased body mass, abdominal fat pads and circumference, blood glucose concentrations, plasma lipid profiles, systolic blood pressure, left ventricular diastolic stiffness, collagen deposition and inflammatory cell infiltration in the left ventricle, improved aortic contractile and relaxation responses, and decreased liver mass and hepatic fat accumulation. This study demonstrates that endurance exercise is effective in this rat model of diet-induced metabolic syndrome in improving body composition and glucose regulation, as well as cardiovascular and liver structure and function.
ON NON-PRIMITIVE PALINDROMIC CONTEXT-FREE LANGUAGES
Authors: FAZEKAS SZILÁRD ZSOLT , LEUPOLD PETER , SHIKISHIMA-TSUJI KAYOKO 
Published: November 2012

This work continues investigations on avoidability of languages. We show that the language of primitive non-palindromes is strongly unavoidable for context-free languages that are not linear. This means that every language from this class contains infinitely many primitive non-palindromes.In the second part, we extend the defintion of palindromes. In the center of a word we admit a bounded factor that is not palindromic. For k-palindromes, the length of this factor can be up to k. For non-primitive words, k-palindromicity implies conventional palindromicity if these words are long enough. Therefore we can extend the unavoidability result to k-palindromes.
The influence of thrombophilia on the long-term survival of patients with a history of venous thromboembolism
Authors: Reitter-Pfoertner Sylvia , Waldhoer Thomas , Mayerhofer Michaela , Eigenbauer Ernst , Ay Cihan , Mannhalter Christine , Kyrle Paul Alexander , Pabinger Ingrid 
Published: November 2012

SummaryData on the long-term survival following venous thromboembolism (VTE) are rare,and the influence of thrombophilia has not been evaluated thus far. Our aim was to assess thrombophilia-parameters as predictors for long-term survival of patients with VTE. Overall, 1,905 outpatients (99 with antithrombin-, protein C or protein S deficiency, 517 with factor V Leiden, 381 with elevated factor VIII and 160 with elevated homocysteine levels, of these 202 had a combination and 961 had none of these risk factors) were included in the study between September 1, 1994 and December 31, 2007. Retrospective survival analysis showed that a total of 78 patients (4.1%) had died during the analysis period, among those four of definite or possible pulmonary embolism and four of bleeding. In multivariable analysis including age and sex an association with increased mortality was found for hyperhomocysteinemia (hazard ratio 2.0 [1.1.-3.5]) whereas this was not the case for all other investigated parameters. We conclude that the classical hereditary thrombophilia risk factors did not have an impact on the long-term survival of patients with a history of VTE. Thus our study supports the current concept that thrombophilia should not be a determinant for decision on long term anticoagulation. However, hyperhomocysteinaemia, known as a risk factor for recurrent VTE and arterial disease, might impact survival.
Characterisation of mutations and molecular studies of type 2 von Willebrand disease
Authors: Jan Rifat , Kannan Meganathan , Obser Tobias , Hassan Md Imtaiyaz , Oyen Florian , Budde Ulrich , Saxena Renu , Ahmad Firdos , Schneppenheim Reinhard 
Published: November 2012

SummaryType 2 von Willebrand disease (VWD) is characterised by qualitative defects in von Willebrand factor (VWF). Exon 28 of the VWF gene is known to be a hot spot for type 2 VWD mutations. The goal of this study was to characterise the mutations in VWF exon 28 and understand the molecular basis of phenotypes through in vitro and in silico studies. Mutation screening was performed in 56 type 2 VWD patients through direct sequencing. Expression vectors for five mutations were transiently expressed in 293-EBNA cells to understand the mutations pathology. Furthermore, in silico structure analysis was performed for 13 missense mutations.A total of 16 including eight novel mutations were detected in 23 (41%) patients. Of these, 15 were missense (including seven V1439M, A1464P, M1495L, I1509V, R1527Q, N1635I and A1647D novel ones) and one was a novel gene conversion. Expression studies and characterisation of recombinant VWF suggested the loss of VWF function for mutants P1266Q, V1439M and N1635I and gain of function for mutant R1308C. No apparent defect was seen in mutant N1231S. In silico structure analysis suggested the probable gain or loss of hydrogen/van der Waals interactions in 10 mutant proteins. In conclusion, type 2A mutations and gene conversion were found to be a common cause of type 2 VWD. Expression studies suggest the mutations N1635I for type 2A(II), P1266Q and V1439M for type 2M, R1308C for type 2B VWD and N1231S as a non-causative variant. Moreover, in silico studies of the mutants show the probable cause of respective phenotypes.