bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA Interference‐based Suppression of Phosphoenolpyruvate Carboxylase Results in Susceptibility of Rapeseed to Osmotic Stress
Authors: Chen Mei , Tang Yunlai , Zhang Jingmei , Yang Mingfeng , Xu Yinong 
Published: April 2010

Abstract The diverse functions of phosphoenolpyruvate carboxylase (PEPCase; EC 4.1.1.31) in C3 plants are not as well understood as in C4 plants. To investigate the functions of PEPCase in C3 plants, rapeseed (Brassica napus L.) PEPCase gene (referred to as BNPE15) was silenced by the RNA interference (RNAi) technique. Under normal growth conditions, no significant difference in lipid content and fatty acid composition were found between wild‐type (WT) and transgenic rapeseed plants. However, when these plants were subjected to osmotic stress induced by osmoticum polyethylene glycol (PEG‐6000), membrane permeability and membrane lipid peroxidization in roots and leaves of transgenic plants were higher than those of WT plants. It suggested that transgenic plants are more susceptible to osmotic stress than WT plants. Taken together, the results showed that the suppression of PEPCase by RNAi leads to susceptibility to osmotic stress in rapeseed, and PEPCase is involved in the response of C3 plants to environmental stress.
Constrained Kalman Filtering: Additional Results
Authors: Pizzinga Adrian 
Published: April 2010

SummaryThis paper deals with linear state space modelling subject to general linear constraints on the state vector. The discussion concentrates on four topics: the constrained Kalman filtering versus the recursive restricted least squares estimator; a new proof of the constrained Kalman filtering under a conditional expectation framework; linear constraints under a reduced state space modelling; and state vector prediction under linear constraints. The techniques proposed are illustrated in two real problems. The first problem is related to investment analysis under a dynamic factor model, whereas the second is about making constrained predictions within a GDP benchmarking estimation.
Qualitative Research in the Service of Understanding Learners and Users of Statistics
Authors: Gal Iddo , Ograjenšek Irena 
Published: April 2010

Summary This paper seeks to add to a scholarly dialogue regarding the role and value of qualitative techniques in research on learning and using statistics. The paper briefly outlines some of the core assumptions of qualitative research methods, and presents four examples to illustrate selected qualitative methods that are used by educational researchers and service organizations. The discussion emphasizes the need to integrate quantitative and qualitative approaches in research on learners and users of statistics, and suggests that such integration may be needed to study emerging web‐based communities of learners and users of statistics.
PEAS V1.0: a package for elementary analysis of SNP data
Authors: XU SHUHUA , GUPTA SANCHIT , JIN LI 
Published: April 2010

AbstractWe have developed a software package named PEAS to facilitate analyses of large data sets of single nucleotide polymorphisms (SNPs) for population genetics and molecular phylogenetics studies. PEAS reads SNP data in various formats as input and is versatile in data formatting; using PEAS, it is easy to create input files for many popular packages, such as STRUCTURE, frappe, Arlequin, Haploview, LDhat, PLINK, EIGENSOFT, PHASE, fastPHASE, MEGA and PHYLIP. In addition, PEAS fills up several analysis gaps in currently available computer programs in population genetics and molecular phylogenetics. Notably, (i) It calculates genetic distance matrices with bootstrapping for both individuals and populations from genome‐wide high‐density SNP data, and the output can be streamlined to MEGA and PHYLIP programs for further processing; (ii) It calculates genetic distances from STRUCTURE output and generates MEGA file to reconstruct component trees; (iii) It provides tools to conduct haplotype sharing analysis for phylogenetic studies based on high‐density SNP data. To our knowledge, these analyses are not available in any other computer program. PEAS for Windows is freely available for academic users from http://www.picb.ac.cn/~xushua/index.files/Download_PEAS.htm.
ANCA‐positive vasculitis associated with simvastatin/ezetimibe: expanding the spectrum of statin‐induced autoimmunity?
Authors: SEN Deepali , ROSENSTEIN Elliot D. , KRAMER Neil 
Published: April 2010

AbstractAlthough autoimmune syndromes such as systemic lupus erythematosus and dermatomyositis have been previously reported in association with statin use, vasculitis has not been well described. We present a patient with an antineutrophil cytoplasmic antibody‐positive, predominantly cutaneous vasculitis, the temporal course of which was associated with simvastatin/ezetimibe use. The patient’s serologic findings were consistent with drug‐induced disease, with high titer antimyeloperoxidase, in addition to antinuclear and anti‐Ro (SSA) antibodies. The patient demonstrated complete resolution of symptoms simply by withdrawing the drug.
The theta‐logistic is unreliable for modelling most census data
Authors: Clark Francis , Brook Barry W. , Delean Steven , Reşit Akçakaya H. , Bradshaw Corey J. A. 
Published: April 2010

Summary1.The theta‐logistic is a simple and flexible model for describing how the growth rate of a population slows as abundance increases. Starting atrm(taken as the maximum population growth rate), the growth response decreases in a convex or concave way (according to the shape parameter θ) to zero when the population reaches carrying capacity.2.We demonstrate that fitting this model to census data is not robust and explain why. The parameters θ andrmare able to play‐off against each other (providing a constant product), thus allowing both to adopt extreme and ecologically implausible values.3.We use simulated data to examine: (i) a population fluctuating around a constant carrying capacity (K); (ii) recovery of a population from 10% of carrying capacity; and (iii) a population subject to variation inK. We show that estimates of extinction risk depending on this or similar models are therefore prone to imprecision. We refute the claim that concave growth responses are shown to dominate in nature.4.As the model can also be sensitive to temporal variation in carrying capacity, we argue that the assumption of a constant carrying capacity is both problematic and presents a fruitful direction for the development of phenomenological density‐feedback models.
Refraction corrected transmission ultrasound computed tomography for application in breast imaging
Authors: Li Shengying , Jackowski Marcel , Dione Donald P. , Varslot Trond , Staib Lawrence H. , Mueller Klaus 
Published: April 2010

Purpose:We present an iterative framework for CT reconstruction from transmission ultrasound data which accurately and efficiently models the strong refraction effects that occur in our target application: Imaging the female breast.Methods:Our refractive ray tracing framework has its foundation in the fast marching method (FNMM) and it allows an accurate as well as efficient modeling of curved rays. We also describe a novel regularization scheme that yields further significant reconstruction quality improvements. A final contribution is the development of a realistic anthropomorphic digital breast phantom based on the NIH Visible Female data set.Results:Our system is able to resolve very fine details even in the presence of significant noise, and it reconstructs both sound speed and attenuation data. Excellent correspondence with a traditional, but significantly more computationally expensive wave equation solver is achieved.Conclusions:Apart from the accurate modeling of curved rays, decisive factors have also been our regularization scheme and the high‐quality interpolation filter we have used. An added benefit of our framework is that it accelerates well on GPUs where we have shown that clinical 3D reconstruction speeds on the order of minutes are possible.
Measurement and modeling of the effect of support arm backscatter on dosimetry with a Varian EPID
Authors: Rowshanfarzad Pejman , McCurdy Boyd M. C. , Sabet Mahsheed , Lee Christopher , O'Connor Daryl J. , Greer Peter B. 
Published: April 2010

Purpose:Amorphous silicon EPIDs have been used for planar dose verification in IMRT treatments for many years. The support arm used to attach some types of EPIDs to linear accelerators can introduce inaccuracies to dosimetry measurements due to the presence of metallic parts in their structures. It is demonstrated that this uncertainty may be as large as of maximum image signal for large fields. In this study, a method has been described to quantify, model and correct for the effect of backscattered radiation from the EPID support arm (E‐Arm type, Varian Medical Systems).Methods:Measurements of a support arm backscatter kernel were made using several 6 MV pencil beam irradiations at a sample of positions over the sensitive area of the EPID in standard clinical setup and repeated with the EPID removed from the support arm but at the same positions. A curve‐fit to the subtraction of EPID response obtained on and off the arm was used to define the backscatter kernel. The measured kernel was compared with a backscatter kernel obtained by Monte Carlo simulations with EGS/BEAM code. A backscatter dose prediction using the measured backscatter kernel was added to an existing EPID dose prediction model. The improvement in the agreement of the modified model predictions with EPID measurements for a number of open fields and IMRT beams were investigated by comparison to the original model results.Results:Considering all functions tested to find the best functional fit to the data points, a broad Gaussian curve proved to be the optimum fit to the backscatter data. The best fit through the Monte Carlo simulated backscatter kernel was also found to be a Gaussian curve. The maximum decrease in normalized root mean squared deviation of the measured and modeled EPID image profiles for open fields was 13.7% for a field with no decrease observed for a (the smallest) field as it was not affected by the arm backscatter. Gamma evaluation (2%, 2 mm criteria) showed the improvement in agreement between the model and measurement results when the backscatter was incorporated. The average increase in Gamma pass rate was 2% for head and neck and 1.3% for prostate IMRT fields investigated in this study.Conclusions:The application of the backscatter kernel determined in this study improved the accuracy of dosimetry using a Varian EPID with E‐arm for open fields of different sizes: Eight head and neck and seven prostate IMRT fields. Further improvement in the agreement between the modelpredictions and EPID measurements requires more sophisticated modeling of the backscatter.
Adaptive spatial calibration of a 3D ultrasound system
Authors: Hartov Alex , Paulsen Keith , Ji Songbai , Fontaine Kathryn , Furon Marie‐Laure , Borsic Andrea , Roberts David 
Published: April 2010

Purpose:The authors present a method devised to calibrate the spatial relationship between a 3D ultrasound scanhead and its tracker completely automatically and reliably. The user interaction is limited to collecting ultrasound data on which the calibration is based.Methods:The method of calibration is based on images of a fixed plane of unknown location with respect to the 3D tracking system. This approach has, for advantage, to eliminate the measurement of the plane location as a source of error. The devised method is sufficiently general and adaptable to calibrate scanheads for 2D images and 3D volume sets using the same approach. The basic algorithm for both types of scanheads is the same and can be run unattended fully automatically once the data are collected. The approach was devised by seeking the simplest and most robust solutions for each of the steps required. These are the identification of the plane intersection within the images or volumes and the optimization method used to compute a calibration transformation matrix. The authors use adaptive algorithms in these two steps to eliminate data that would otherwise prevent the convergence of the procedure, which contributes to the robustness of the method.Results:The authors have run tests amounting to 57 runs of the calibration on two a scanhead that produce 3D imaging volumes, at all the available scales. The authors evaluated the system on two criteria: Robustness and accuracy. The program converged to useful values unattended for every one of the tests (100%). Its accuracy, based on the measured location of a reference plane, was estimated to be for all tests combined.Conclusions:The system presented is robust and allows unattended computations of the calibration parameters required for freehand tracked ultrasound based on either 2D or 3D imaging systems.
Measurement of ionization chamber absorbed dose factors in megavoltage photon beams
Authors: McEwen Malcolm R. 
Published: April 2010

Purpose:Absorbed dose beam quality conversion factors ( factors) were obtained for 27 different types of ionization chamber. The aim was to obtain objective evidence on the performance of a wide range of chambers currently available, and potentially used for reference dosimetry, and to investigate the accuracy of the calculation algorithm used in the TG‐51 protocol.Methods:Measurements were made using the irradiator and Elekta Precise linac facilities at the National Research Council of Canada. The objective was to characterize the chambers over the range of energies applicable to TG‐51 and determine whether each chamber met the requirements of a reference‐class instrument. Chamber settling, leakage current, ion recombination and polarity, and waterproofing sleeve effects were investigated, and absorbed dose calibration coefficients were obtained for and 6, 10, and 25 MV photon beams. Only thimble‐type chambers were considered in this investigation and were classified into three groups: (i) Reference chambers (“standard” Farmer‐type chambers and their derivatives traditionally used for beam output calibration); (ii) scanning chambers (typically volume chambers used for beam commissioning with 3‐D scanning phantoms); and (iii) microchambers (very small volume ion chambers used for small field dosimetry).Results:As might be expected, thimble chambers showed the most predictable performance and experimental factors were obtained with a relative uncertainty of 0.1%. The performance of scanning and microchambers was somewhat variable. Some chambers showed very good behavior but others showed anomalous polarity and recombination corrections that are not fully explained at present. For the well‐behaved chambers, agreement between measured and calculated factors was within 0.4%; for some chambers, differences of more than 1% were seen that may be related to the recombination/polarity results. Use of such chambers could result in significant errors in the determination of reference dose in the clinic.Conclusions:Based on the experimental evidence obtained here, specification for a reference‐class ionization chamber could be developed that would minimize the error in using a dosimetry protocol with calculated beam quality conversion factors. The experimental data obtained here for a wide range of thimble chambers can be used when choosing suitable detectors for reference dosimetry and are intended to be used in the upcoming update/addendum to the AAPM TG‐51 dosimetry protocol.
Experimental and theoretical dosimetry of a new polymer encapsulated iodine‐125 source—SmartSeed: Dosimetric impact of fluorescence x rays
Authors: Abboud F. , Hollows M. , Scalliet P. , Vynckier S. 
Published: April 2010

Purpose: The detailed study of a new permanent iodine‐125 brachytherapy source, SmartSeed, is presented in this article. It is the first iodine seed made with biocompatible polymer and is manufactured by the IBt‐Bebig group.Methods: Three dosimetric studies have been performed: The first one used thermoluminescent detectors in a solid water phantom with NIST (National Institute of Standards and Technology, USA) calibrated seeds, and two separate studies were of Monte Carlo photon transport calculations (MCNP5 code). The TG‐43U1 protocol was applied to derive dosimetric parameters for clinical applications.Results: The radial dose function was determined at different distances ranging from 0.5 to 10 cm; and the anisotropy function at angles ranging from 0° to 350° in 10° increments. Monte Carlo calculations were performed in liquid water to obtain values for , , , and as recommended by the TG‐43U1 protocol for use in treatment planning system software. SmartSeed's biocompatible polymer capsule permits fluorescence x rays (3, 5, and 12 keV), generated by lead glass marker, to be present in the emission spectrum, influencing the dose rate constant. The impact on near field dosimetry in water from these x rays was also investigated and reported. The capsule also attenuates iodine‐125 energies much less than typical titanium encased sources, resulting in a highly isotropic source.Conclusions: SmartSeed has a dose rate constant of , a radial dose function nearly identical to the IBt‐Bebig model I25.S06 seed, and a highly isotropic dose distribution. Fluorescence x rays account for the relatively low value of , yet their variable contribution to dosimetry arising from seed dimensional uncertainties is estimated to be .
Homogenized blocked arcs for multicriteria optimization of radiotherapy: Analytical and numerical solutions
Authors: Fenwick John D. , Pardo‐Montero Juan 
Published: April 2010

Purpose:Homogenized blocked arcs are intuitively appealing as basis functions for multicriteria optimization of rotational radiotherapy. Such arcs avoid an organ‐at‐risk (OAR), spread dose out well over the rest‐of‐body (ROB), and deliver homogeneous doses to a planning target volume (PTV) using intensity modulated fluence profiles, obtainable either from closed‐form solutions or iterative numerical calculations. Here, the analytic and iterative arcs are compared.Methods:Dose‐distributions have been calculated for nondivergent beams, both including and excluding scatter, beam penumbra, and attenuation effects, which are left out of the derivation of the analytic arcs. The most straightforward analytic arc is created by truncating the well‐known Brahme, Roos, and Lax (BRL) solution, cutting its uniform dose region down from an annulus to a smaller nonconcave region lying beyond the OAR. However, the truncation leaves behind high dose hot‐spots immediately on either side of the OAR, generated by very high BRL fluence levels just beyond the OAR. These hot‐spots can be eliminated using alternative analytical solutions “C” and “L,” which, respectively, deliver constant and linearly rising fluences in the gap region between the OAR and PTV (before truncation).Results:Measured in terms of PTV dose homogeneity, ROB dose‐spread, and OAR avoidance, C solutions generate better arc dose‐distributions than L when scatter, penumbra, and attenuation are left out of the dose modeling. Including these factors, L becomes the best analytical solution. However, the iterative approach generates better dose‐distributions than any of the analytical solutions because it can account and compensate for penumbra and scatter effects. Using the analytical solutions as starting points for the iterative methodology, dose‐distributions almost as good as those obtained using the conventional iterative approach can be calculated very rapidly.Conclusions:The iterative methodology is appropriate and useful for computing homogenized blocked arcs, as it produces better dose‐distributions than the analytic approaches and their obvious extensions, and can more straightforwardly be used to generate homogenized arcs for concave OARs. However, the analytical solutions provide promising starting points for the iterative algorithm, leading to fast convergence.
Simulation of image detectors in radiology for determination of scatter‐to‐primary ratios using Monte Carlo radiation transport codeMCNP/MCNPX
Authors: Smans Kristien , Zoetelief Johannes , Verbrugge Beatrijs , Haeck Wim , Struelens Lara , Vanhavere Filip , Bosmans Hilde 
Published: April 2010

Purpose:The purpose of this study was to compare and validate three methods to simulate radiographic image detectors with the Monte Carlo softwareMCNP/MCNPXin a time efficient way.Methods:The first detector model was the standard semideterministic radiography tally, which has been used in previous image simulation studies. Next to the radiography tally two alternative stochastic detector models were developed: A perfect energy integrating detector and a detector based on the energy absorbed in the detector material. Validation of three image detector models was performed by comparing calculated scatter‐to‐primary ratios (SPRs) with the published and experimentally acquired SPR values.Results:For mammographic applications, SPRs computed with the radiography tally were up to 44% larger than the published results, while the SPRs computed with the perfect energy integrating detectors and the blur‐free absorbed energy detector model were, on the average, 0.3% (ranging from −3% to 3%) and 0.4% (ranging from −5% to 5%) lower, respectively. For general radiography applications, the radiography tally overestimated the measured SPR by as much as 46%. The SPRs calculated with the perfect energy integrating detectors were, on the average, 4.7% (ranging from −5.3% to −4%) lower than the measured SPRs, whereas for the blur‐free absorbed energy detector model, the calculated SPRs were, on the average, 1.3% (ranging from −0.1% to 2.4%) larger than the measured SPRs.Conclusions:For mammographic applications, both the perfect energy integrating detector model and the blur‐free energy absorbing detector model can be used to simulate image detectors, whereas for conventional x‐ray imaging using higher energies, the blur‐free energy absorbing detector model is the most appropriate image detector model. The radiography tally overestimates the scattered part and should therefore not be used to simulate radiographic image detectors.