bluuebunny/crossref_metadata_2025_split huggingface dataset:
GPUMCD: A new GPU‐oriented Monte Carlo dose calculation platform
Authors: Hissoiny Sami , Ozell Benoît , Bouchard Hugo , Després Philippe 
Published: February 2011

Purpose:Monte Carlo methods are considered as the gold standard for dosimetric computations in radiotherapy. Their execution time is, however, still an obstacle to the routine use of Monte Carlo packages in a clinical setting. To address this problem, a completely new, and designed from the ground up for the GPU, Monte Carlo dose calculation package for voxelized geometries is proposed:GPUMCD.Method:GPUMCDimplements a coupled photon‐electron Monte Carlo simulation for energies in the range of 0.01–20 MeV. An analog simulation of photon interactions is used and a class II condensed history method has been implemented for the simulation of electrons. A new GPU random number generator, some divergence reduction methods, as well as other optimization strategies are also described.GPUMCDwas run on a NVIDIA GTX480, while single threaded implementations of EGSnrc andDPMwere run on an Intel Core i7 860.Results:Dosimetric results obtained withGPUMCDwere compared to EGSnrc. In all but one test case, 98% or more of all significant voxels passed the gamma criteria of 2%‐2 mm. In terms of execution speed and efficiency,GPUMCDis more than 900 times faster than EGSnrc and more than 200 times faster thanDPM, a Monte Carlo package aiming fast executions. Absolute execution times of less than 0.3 s are found for the simulation of 1M electrons and 4M photons in water for monoenergetic beams of 15 MeV, including GPU‐CPU memory transfers.Conclusion:GPUMCD, a new GPU‐oriented Monte Carlo dose calculation platform, has been compared to EGSnrc andDPMin terms of dosimetric results and execution speed. Its accuracy and speed make it an interesting solution for full Monte Carlo dose calculation in radiation oncology.
Characterization of a gated fiber‐optic‐coupled detector for application in clinical electron beam dosimetry
Authors: Tanyi James A. , Nitzling Kevin D. , Lodwick Camille J. , Huston Alan L. , Justus Brian L. 
Published: February 2011

Purpose:Assessment of the fundamental dosimetric characteristics of a novel gated fiber‐optic‐coupled dosimetry system for clinical electron beam irradiation.Methods:The response of fiber‐optic‐coupled dosimetry system to clinical electron beam, with nominal energy range of 6–20 MeV, was evaluated for reproducibility, linearity, and output dependence on dose rate, dose per pulse, energy, and field size. The validity of the detector system's response was assessed in correspondence with a reference ionization chamber.Results:The fiber‐optic‐coupled dosimetry system showed little dependence to dose rate variations (coefficient of variation ±0.37%) and dose per pulse changes (with 0.54% of reference chamber measurements). The reproducibility of the system was ±0.55% for dose fractions of. Energy dependence was within ±1.67% relative to the reference ionization chamber for the 6–20 MeV nominal electron beam energy range. The system exhibited excellent linear response compared to reference ionization chamber in the dose range of 1–1000 cGy. The output factors were within ±0.54% of the corresponding reference ionization chamber measurements.Conclusions:The dosimetric properties of the gated fiber‐optic‐coupled dosimetry system compare favorably to the corresponding reference ionization chamber measurements and show considerable potential for applications in clinical electron beam radiotherapy.
Multimodal image registration using IECC as the similarity measure
Authors: Itou Takeshi , Shinohara Hiroyuki , Sakaguchi Kazuya , Hashimoto Takeyuki , Yokoi Takashi , Souma Tsutomu 
Published: February 2011

Purpose:The registration of images from positron emission tomography (PET) to those from magnetic resonance imaging (MRI) using mutual information is usually effective, but fails occasionally because of small region of overlap, low‐activity defects in the PET image, difference in spatial resolution, etc. In this article, the authors propose the pixel‐based individual entropy correlation coefficient (IECC) as a new, more accurate and more robust registration criterion.Methods:The authors compare it to the current criteria: Mutual information (MI), normalized mutual information (NMI), and the entropy correlation coefficient (ECC). The anatomical region to be registered was the head. A rigid‐body registration was used; no deformation was employed. The authors established the effectiveness of IECC by both simulated data and clinical studies using brain fluorodeoxyglucose (FDG) PET and MRI. Both a normal‐activity FDG model and a FDG model with a perfusion defect were used for the PET image. Reconstruction by both filtered backprojection and by ordered subset‐expectation maximization was investigated.Results:The mean errors and SDs of IECC were for translation and for rotation in clinical PET. Those of MI, NMI, and ECC were , , and for translations and , , and for rotations. The mean errors and SDs of IECC were for translation and for rotation in clinical PET model with a 30% perfusion defect. Those of MI, NMI, and ECC were , , and for translations and , , and for rotations. The mean errors and SDs of IECC were for translation and for rotation in clinical PET model with a 50% perfusion defect. Those of MI, NMI, and ECC were , , and for translations and , , and for rotations. The significant differences between IECC and each of the other three criteria were found for displacement misregistration in almost all parameters .Conclusions:Accuracy of the IECC criterion was higher than that of the other criteria, usually in a statistically significant way.
Localizing intracavitary brachytherapy applicators from cone‐beam CT x‐ray projections via a novel iterative forward projection matching algorithm
Authors: Pokhrel Damodar , Murphy Martin J. , Todor Dorin A. , Weiss Elisabeth , Williamson Jeffrey F. 
Published: February 2011

Purpose:To present a novel method for reconstructing the 3D pose (position and orientation) of radio‐opaque applicators of known but arbitrary shape from a small set of 2D x‐ray projections in support of intraoperative brachytherapy planning.Methods:The generalized iterative forward projection matching (gIFPM) algorithm finds the six degree‐of‐freedom pose of an arbitrary rigid object by minimizing the sum‐of‐squared‐intensity differences (SSQD) between the computed and experimentally acquired autosegmented projection of the objects. Starting with an initial estimate of the object's pose, gIFPM iteratively refines the pose parameters (3D position and three Euler angles) until the SSQD converges. The object, here specialized to a Fletcher–Weeks intracavitary brachytherapy (ICB) applicator, is represented by a fine mesh of discrete points derived from complex combinatorial geometric models of the actual applicators. Three pairs of computed and measured projection images with known imaging geometry are used. Projection images of an intrauterine tandem and colpostats were acquired from an ACUITY cone‐beam CT digital simulator. An image postprocessing step was performed to create blurred binary applicators only images. To quantify gIFPM accuracy, the reconstructed 3D pose of the applicator model was forward projected and overlaid with the measured images and empirically calculated the nearest‐neighbor applicator positional difference for each image pair.Results:In the numerical simulations, the tandem and colpostats positions and orientations were estimated with accuracies of 0.6 mm and 2°, respectively. For experimentally acquired images of actual applicators, the residual 2D registration error was less than 1.8 mm for each image pair, corresponding to about 1 mm positioning accuracy at isocenter, with a total computation time of less than 1.5 min on a 1 GHz processor.Conclusions:This work describes a novel, accurate, fast, and completely automatic method to localize radio‐opaque applicators of arbitrary shape from measured 2D x‐ray projections. The results demonstrate accuracy while compared against the measured applicator projections. No lateral film is needed. By localizing the applicator internal structure as well as radioactive sources, the effect of intra‐applicator and interapplicator attenuation can be included in the resultant dose calculations. Further validation tests using clinically acquired tandem and colpostats images will be performed for the accurate and robust applicator/sources localization in ICB patients.
CT scanner x‐ray spectrum estimation from transmission measurements
Authors: Duan Xinhui , Wang Jia , Yu Lifeng , Leng Shuai , McCollough Cynthia H. 
Published: February 2011

Purpose:In diagnostic CT imaging, multiple important applications depend on the knowledge of the x‐ray spectrum, including Monte Carlo dose calculations and dual‐energy material decomposition analysis. Due to the high photon flux involved, it is difficult to directly measure spectra from the x‐ray tube of a CT scanner. One potential method for indirect measurement involves estimating the spectrum from transmission measurements. The expectation maximization (EM) method is an accurate and robust method to solve this problem. In this article, this method was evaluated in a commercial CT scanner.Methods:Two step‐wedges (polycarbonate and aluminum) were used to produce different attenuation levels. Transmission measurements were performed on the scanner and the measured data from the scanner were exported to an external computer to calculate the spectra. The EM method was applied to solve the equations that represent the attenuation processes of polychromatic x‐ray photons. Estimated spectra were compared to the spectra simulated using a software provided by the manufacturer of the scanner. To test the accuracy of the spectra, a verification experiment was performed using a phantom containing different depths of water. The measured transmission data were compared to the transmission values calculated using the estimated spectra.Results:Spectra of 80, 100, 120, and 140 kVp from a dual‐source CT scanner were estimated. The estimated and simulated spectra were well matched. The differences of mean energies were less than 1 keV. In the verification experiment, the measured and calculated transmission values were in excellent agreement.Conclusions:Spectrum estimation using transmission data and the EM method is a quantitatively accurate and robust technique to estimate the spectrum of a CT system. This method could benefit studies relying on accurate knowledge of the x‐ray spectra from CT scanner.
Essential Metabolites of Mycobacterium tuberculosis and Their Mimics
Authors: Lamichhane Gyanu , Freundlich Joel S. , Ekins Sean , Wickramaratne Niluka , Nolan Scott T. , Bishai William R. 
Published: February 2011

ABSTRACT

An organism requires a range of biomolecules for its growth. By definition, these are essential molecules which constitute the basic metabolic requirements of an organism. A small organic molecule with chemical similarity to that of an essential metabolite may bind to the enzyme that catalyzes its production and inhibit it, likely resulting in the stasis or death of the organism. Here, we report a high-throughput approach for identifying essential metabolites of an organism using genetic and biochemical approaches and then implement computational approaches to identify metabolite mimics. We generated and genotyped 5,126
Mycobacterium tuberculosis
mutants and performed a statistical analysis to determine putative essential genes. The essential molecules of
M. tuberculosis
were classified as products of enzymes that are encoded by genes in this list. Although incomplete, as many enzymes of
M. tuberculosis
have yet to be identified and characterized, this is the first report of a large number of essential molecules of the organism. We identified essential metabolites of three distinct metabolic pathways in
M. tuberculosis
and selected molecules with chemical similarity using cheminformatics strategies that illustrate a variety of different pharmacophores. Our approach is aimed at systematic identification of essential molecules and their mimics as a blueprint for development of effective chemical probes of
M. tuberculosis
metabolism, with the ultimate goal of seeking drugs that can kill this pathogen. As an illustration of this approach, we report that compounds JFD01307SC and
l
-methionine-
S
-sulfoximine, which share chemical similarity with an essential molecule of
M. tuberculosis
, inhibited the growth of this organism at micromolar concentrations.

IMPORTANCE
The estimate that more lives may have been lost in 2009 due to tuberculosis (TB) than in any year in history is alarming. Approximately 9.2 million new cases and 1.8 million deaths due to TB were reported in 2008. The widespread prevalence of
Mycobacterium tuberculosis
strains that are resistant to drugs currently used to treat TB means that new drugs are urgently needed to treat these infections. Here, we have identified pathways for the biosynthesis of essential metabolites and associated enzymes in
M. tuberculosis
using a genetics-based approach. Small molecules that mimic these essential metabolites were identified, and some of them were shown to inhibit the growth of
M. tuberculosis
. Therefore, we illustrate an approach based on genetics to develop inhibitors that have the potential to be advanced as candidate drugs for treating TB.
The impact of diabetes on the extent of pial collaterals in acute ischemic stroke patients
Authors: Lazzaro Marc A , Chen Michael , Christoforidis Gregory A , Mohammad Yousef 
Published: February 2011

IntroductionThe threatened vascular territory in ischemic stroke is maintained by pial collateral circulation. Neovascularization varies among organ systems in diabetic patients. The effect of diabetes on the extent of pial collaterals is not well known. The pial collateral supply was compared among diabetic and non-diabetic patients presenting with acute ischemic stroke.Material and methodsDatabases from two institutions were accessed to identify all patients who presented with acute middle cerebral artery occlusion and underwent emergent cerebral angiography. Angiograms were reviewed and graded using a previously published pial collateral grading system. The collateral grading system was dichotomized into good (pial grades 1–2) and poor (pial grades 3–5). A χ2analysis was performed to compare the association between diabetes and pial collateral grade.Results104 patients were identified; 56 (54%) patients were men, mean age was 63.5 years and 22 (21%) patients had diabetes. Mean admission National Institutes of Health Stroke Scale was 15.7. In the diabetic population, 15 (68.2%) patients had good pial collaterals while seven (31.8%) patients had poor pial collaterals. In the non-diabetic population, 59 (71.9%) patients had good pial collaterals while 23 (28.0%) patients had poor pial collaterals. There was no association between diabetes and pial collateral grade (p=0.7290, Pearson χ2).ConclusionsThis series suggests there is no association between diabetes and the extent of pial collaterals in ischemic stroke patients. Further studies are warranted to understand pial collateral patterns in acute ischemic stroke patients and their impact on clinical outcomes.
Stability of measured and modelled spatial contrasts in NO2over time
Authors: Eeftens Marloes , Beelen Rob , Fischer Paul , Brunekreef Bert , Meliefste Kees , Hoek Gerard 
Published: February 2011

ObjectivesLand use regression (LUR) modelling is a popular method to estimate outdoor air pollution concentrations at the home and/or work addresses of individual subjects in epidemiological studies. Typically, such models are constructed using measurements from dedicated monitoring campaigns lasting up to 1 year. It is unknown to what extent such models can adequately predict concentrations in earlier or later time periods. We tested the stability of measured and modelled spatial contrasts in outdoor nitrogen dioxide (NO2) pollution across the Netherlands over 8 years.MethodsNO2measurements were conducted at 40 locations in the Netherlands in 1999–2000. In 2007, NO2was again measured at 144 locations, of which 35 were the same as in 1999–2000. This enabled us to compare measurements as well as model predictions between the two time periods.ResultsNO2measurements conducted in 2007 agreed well with NO2measurements taken in 1999–2000 at the same locations (R2=0.86). LUR models from 1999–2000 and 2007 explained 85% and 86% of observed spatial variance, respectively. The 2007 LUR model explained 77% of spatial variability in the 1999–2000 measurements and the 1999–2000 model explained 81% of variability in the 2007 measurements.ConclusionWe found good agreement between measured spatial contrasts in outdoor NO2in 1999–2000 and 2007. LUR models predicted spatial contrast 8 years in the past (2007 model) and 8 years in the future (1999–2000 model) well. This supports the use of LUR models in epidemiological studies with health data available for a later or earlier timepoint.
Kinematic evolution and structural styles of fold-and-thrust belts
Authors: Poblet J. , Lisle R. J. 
Published: February 2011

AbstractFold-and-thrust (FAT) belts occur worldwide and have long been the focus of research of structural geologists who have devised a variety of techniques to image, characterize and model their main structural features. This introductory chapter reviews the principal geological features of FAT belts formed in different settings, emphasizing aspects related to their kinematic evolution and structural styles. Despite great advances, challenges remain, particularly in the understanding of the spatial and temporal evolution (4D) of FAT belts and their controlling factors. These research efforts are being assisted by the growing availability to researchers of relatively new tools to collect field data, high quality 3D seismic data, and computer and laboratory modelling tools. This volume includes technical papers presented in the conference ‘International Meeting of Young Researchers in Structural Geology and Tectonics (YORSGET-08)’ held in Oviedo (Spain), together with other papers on the same theme. These papers deal with FAT belts in different parts of the world and cover a broad range of different aspects, from detailed structural analysis of single structures to regional issues, and from studies based on classical field structural geology to modelling.
Thrust tectonics of the Upper Jurassic limestones in the Pavlov Hills (Outer Western Carpathians, Czech Republic)
Authors: Poul Ivan , Melichar Rostislav , Janečka Jiří 
Published: February 2011

Abstract
The Pavlov Hills are formed by separated limestone blocks previously identified as klippen. A new flat-ramp-flat thrust model of the Pavlov Hills is formulated in this paper. The main tectonic detachment is located at the base of the limestone plate and other subsidiary detachments are located within the nodular limestone horizon and also at the base and top of the Upper Cretaceous deposits. The ramps are situated in the Klentnice Fm and Ernstbrunn Lst. The ramp angle was determined by structural evidence combined with interpretation of seismic profiles. Two parallel antiformal structures plunging to the NE are recognized within the study area. The antiformal fold axes are gently plunging to the NE so the anticlines are not ideal for 3-point hydrocarbon trap setting. These anticlines were subsequently cut by sinistral strike-slip faults perpendicular to the fold axis which resulted in the formation of a large-scale pseudo en-echelon structure in an approximate north–south direction.
The roles of complex mechanical stratigraphy and syn-kinematic sedimentation in fold development: insights from discrete-element modelling and application to the Pico del Águila anticline (External Sierras, Southern Pyrenees)
Authors: Vidal-Royo Oskar , Hardy Stuart , Muñoz Josep Anton 
Published: February 2011

Abstract
A 2D discrete-element modelling technique is used to explore the effects of complex mechanical stratigraphy and syn-kinematic sedimentation in the development of the Pico del Águila anticline (External Sierras, Southern Pyrenees). The stratigraphy (Middle Triassic–Oligocene in age) involved in this structure is characterized by a gross interlayering of competent and incompetent units, which leads to a striking variation in outcrop-scale deformation of the units observed in the field. The numerical model attempts to reproduce the stratigraphic variation seen in the field by using a mechanical stratigraphy that contains a complex interlayering of competent/incompetent units. Two experiments are presented. Model 1 tests the response of this complex mechanical stratigraphy to shortening under conditions that lead to the formation of a detachment fold. This experiment shows that folding mechanisms vary abruptly depending on the mechanical properties of the materials involved: the incompetent units are strongly internally deformed, accommodating much layer-parallel shearing; the competent units deform by rigid-body translation/rotation, localized faulting and minor internal shearing. Model 2 tests the effect of syn-kinematic sedimentation under identical boundary conditions: these sediments stabilize the fold against gravitational instabilities and cause a concentration of deformation in the core of the structure, leading to a tighter, narrower fold.
The Adaptor Protein AMOT Promotes the Proliferation of Mammary Epithelial Cells via the Prolonged Activation of the Extracellular Signal-Regulated Kinases
Authors: Ranahan William P. , Han Zhang , Smith-Kinnaman Whitney , Nabinger Sarah C. , Heller Brigitte , Herbert Britney-Shea , Chan Rebecca , Wells Clark D. 
Published: February 2011

Abstract
The asymmetric organization of epithelial cells is a basic counter to cellular proliferation. However, the mechanisms whereby pro-growth pathways are modulated by intracellular factors that control cell shape are not well understood. This study demonstrates that the adaptor protein Amot, in addition to its established role in regulating cellular asymmetry, also promotes extracellular signal-regulated kinase 1 and 2 (ERK1/2)–dependent proliferation of mammary cells. Specifically, expression of Amot80, but not a mutant lacking its polarity protein interaction domain, enhances ERK1/2-dependent proliferation of MCF7 cells. Further, expression of Amot80 induces nontransformed MCF10A cells to overgrow as disorganized cellular aggregates in Matrigel. Conversely, Amot expression is required for proliferation of breast cancer cells in specific microenvironmental contexts that require ERK1/2 signaling. Thus, Amot is proposed to coordinate the dysregulation of cell polarity with the induction of neoplastic growth in mammary cells. Cancer Res; 71(6); 2203–11. ©2011 AACR.