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https://www.readbyqxmd.com/read/28207388/segmentation-of-pathological-structures-by-landmark-assisted-deformable-models
#1
Bulat Ibragimov, Robert Korez, Bostjan Likar, Franjo Pernus, Lei Xing, Tomaz Vrtovec
Computerized segmentation of pathological structures in medical images is challenging, as, in addition to unclear image boundaries, image artifacts and traces of surgical activities, the shape of pathological structures may be very different from the shape of normal structures. Even if a sufficient number of pathological training samples are collected, statistical shape modeling cannot always capture shape features of pathological samples as they may be suppressed by shape features of a considerably larger number of healthy samples...
February 13, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28198568/compressed-sensing-mri-reconstruction-from-3d-multichannel-data-using-gpus
#2
Ching-Hua Chang, Xiangdong Yu, Jim X Ji
PURPOSE: To accelerate iterative reconstructions of compressed sensing (CS) MRI from 3D multichannel data using graphics processing units (GPUs). METHODS: The sparsity of MRI signals and parallel array receivers can reduce the data acquisition requirements. However, iterative CS reconstructions from data acquired using an array system may take a significantly long time, especially for a large number of parallel channels. This paper presents an efficient method for CS-MRI reconstruction from 3D multichannel data using GPUs...
February 15, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28191844/armsd-a-comprehensive-tool-for-structural-analysis
#3
Arne Wagner, Hans-Joerg Himmel
A new tool for structural comparison is presented that combines existing and new features into a single software package. aRMSD incorporates the functions of establishing a pair-wise correlation between the atoms of two molecular structures and the calculation of the optimal rotation matrix that minimizes the RMSD between the molecules. The complexity of the Hungarian assignation problem is reduced by decomposing molecules into different subsets based on different atom or group types allowing for an efficient and robust treatment of large molecules while tolerating different substituents...
February 13, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28176265/deformation-of-facial-model-for-complete-denture-prosthesis-using-arap-group-method-and-elastic-properties
#4
Cheng Cheng, Xiaosheng Cheng, Ning Dai, Yuchun Sun, Xiaotong Jiang, Weiwei Li
With the development of 3D printing and computer graphics technology, mouth rehabilitation has increasingly adopted digital methods. This research proposes a new method to transform the appearance of facial model after complete denture prosthesis. A feature template with few feature points is first constructed according to the facial muscle anatomy and facial deformation after complete denture prosthesis. Next, the traditional as-rigid-as-possible (ARAP) method is optimised by clustering based on facial muscles...
February 7, 2017: Medical & Biological Engineering & Computing
https://www.readbyqxmd.com/read/28168640/3d-computer-graphical-anatomy-study-of-the-femur-a-basis-for-a-new-nail-design
#5
Beat Schmutz, Stanley Kmiec, Martin E Wullschleger, Martin Altmann, Michael Schuetz
BACKGROUND: Current intramedullary nails with a radius of curvature (ROC) of 1500-2000 mm sometimes cause distal anterior cortical encroachment. Furthermore, clinical data indicate that the proximal nail end is too long for some Asian patients. The objective of our study was to develop a comprehensive 3D measurement protocol that measures both the anatomy of the canal and the proximal region. The protocol was used to obtain measurements from Caucasian and Asian (Japanese and Thai) specimens...
February 6, 2017: Archives of Orthopaedic and Trauma Surgery
https://www.readbyqxmd.com/read/28166493/a-gpu-accelerated-3d-coupled-sub-sample-estimation-algorithm-for-volumetric-breast-strain-elastography
#6
Bo Peng, Yuqi Wang, Timothy J Hall, Jingfeng Jiang
Our primary objective of this work was to extend a previously published 2D coupled sub-sample tracking algorithm for 3D speckle tracking in the framework of ultrasound breast strain elastography. In order to overcome heavy computational cost, we investigated the use of a graphic processing unit (GPU) to accelerate the 3D coupled sub-sample speckle tracking method. The performance of the proposed GPU implementation was tested using a tissue-mimicking (TM) phantom and in vivo breast ultrasound data. The performance of this 3D sub-sample tracking algorithm was compared with the conventional 3D quadratic subsample estimation algorithm...
January 31, 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/28147684/a-new-non-contact-approach-for-the-measurement-and-uniformity-evaluation-of-coating-thickness-for-sheet-metal
#7
Zixue Qiu, Tianchi Zheng, Liping Wan, Guan Lu, Jianxin Shao, Jiang Yuan
To realize the automatic measurement and uniformity evaluation of the coating thickness for sheet metal, a new non-contact detection method for coating thickness was proposed based on a double laser probe and mechanical servo system. Non-contact measurement of coating thickness can be achieved by differential measurement principle of double laser probe, and the influences of sheet metal's Z position changes and platform's vibration on the measurement results can be removed by this method. A new coating thickness evaluation algorithm by integrating the least squares principle and cubic spline interpolation was given, which can fit the discrete thickness data into visual and accurate 3D graphics; and the measurement accuracy was evaluated based on grey theory, solving the problem of low accuracy by using limited measurement data to evaluate the thickness uniformity of an entire sheet metal...
January 2017: Review of Scientific Instruments
https://www.readbyqxmd.com/read/28125221/3d-e-chem-vm-structural-cheminformatics-research-infrastructure-in-a-freely-available-virtual-machine
#8
Ross McGuire, Stefan Verhoeven, Márton Vass, Gerrit Vriend, Iwan J P de Esch, Scott J Lusher, Rob Leurs, Lars Ridder, Albert J Kooistra, Tina Ritschel, Chris de Graaf
3D-e-Chem-VM is an open source, freely available Virtual Machine ( http://3d-e-chem.github.io/3D-e-Chem-VM/ ) that integrates cheminformatics and bioinformatics tools for the analysis of protein-ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteomewide databases (e...
February 14, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28113746/fast-realistic-mri-simulations-based-on-generalized-multi-pool-exchange-tissue-model
#9
Fang Liu, Julia V Velikina, Walter F Block, Richard Kijowski, Alexey A Samsonov
We present MRiLab, a new comprehensive simulator for large-scale realistic MRI simulations on a regular PC equipped with a modern graphical processing unit (GPU). MRiLab combines realistic tissue modeling with numerical virtualization of an MRI system and scanning experiment to enable assessment of a broad range of MRI approaches including advanced quantitative MRI methods inferring microstructure on a sub-voxel level. A flexible representation of tissue microstructure is achieved in MRiLab by employing the generalized tissue model with multiple exchanging water and macromolecular proton pools rather than a system of independent proton isochromats typically used in previous simulators...
February 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28113150/spatial-interfaces-and-interactive-3d-environments-for-immersive-musical-performances
#10
Florent Berthaut, Martin Hachet
The power of interactive 3D graphics, immersive displays, and spatial interfaces is still under-explored in domains where the main target is to enhance creativity and emotional experiences. This article presents a set of work the attempts to extent the frontiers of music creation as well as the experience of audiences attending to digital performances. The goal is to connect sounds to interactive 3D graphics that musicians can interact with and the audience can observe.
September 2016: IEEE Computer Graphics and Applications
https://www.readbyqxmd.com/read/28097495/the-expression-of-hypoxia-inducible-factor-1%C3%AE-gene-is-not-affected-by-low-oxygen-conditions-in-yellow-perch-perca-flavescens-juveniles
#11
Karolina Kwasek, Simona Rimoldi, Anna Giulia Cattaneo, Timothy Parker, Konrad Dabrowski, Genciana Terova
Hypoxia can affect various fish populations, including yellow perch Perca flavescens, which is an economically and ecologically important species in Lake Erie, a freshwater system that often experiences hypoxia in the hypolimnetic part of the lake. Fish, similarly to mammals, possess molecular oxygen sensor-hypoxia-inducible factor-1 (HIF-1), a transcription factor that can affect expression of many downstream genes related to animal growth and locomotion, protein synthesis, as well as ATP and amino acid metabolism...
January 18, 2017: Fish Physiology and Biochemistry
https://www.readbyqxmd.com/read/28094984/a-generalized-grid-based-fast-multipole-method-for-integrating-helmholtz-kernels
#12
Pauli Parkkinen, Sergio A Losilla, Eelis Solala, Elias A Toivanen, Wen-Hua Xu, Dage Sundholm
A grid-based fast multipole method (GB-FMM) for optimizing three-dimensional (3D) numerical molecular orbitals in the bubbles and cube double basis has been developed and implemented. The present GB-FMM method is a generalization of our recently published GB-FMM approach for numerically calculating electrostatic potentials and two-electron interaction energies. The orbital optimization is performed by integrating the Helmholtz kernel in the double basis. The steep part of the functions in the vicinity of the nuclei is represented by one-center bubbles functions, whereas the remaining cube part is expanded on an equidistant 3D grid...
January 31, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28091811/charge-transfer-dissociation-ctd-mass-spectrometry-of-peptide-cations-study-of-charge-state-effects-and-side-chain-losses
#13
Pengfei Li, Glen P Jackson
1+, 2+, and 3+ precursors of substance P and bradykinin were subjected to helium cation irradiation in a 3D ion trap mass spectrometer. Charge exchange with the helium cations produces a variety of fragment ions, the number and type of which are dependent on the charge state of the precursor ions. For 1+ peptide precursors, fragmentation is generally restricted to C-CO backbone bonds (a and x ions), whereas for 2+ and 3+ peptide precursors, all three backbone bonds (C-CO, C-N, and N-Cα) are cleaved. The type of backbone bond cleavage is indicative of possible dissociation channels involved in CTD process, including high-energy, kinetic-based, and ETD-like pathways...
January 13, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28048632/tu-d-209-03-alignment-of-the-patient-graphic-model-using-fluoroscopic-images-for-skin-dose-mapping
#14
A Oines, A Oines, J Kilian-Meneghin, B Karthikeyan, S Rudin, D Bednarek
PURPOSE: The Dose Tracking System (DTS) was developed to provide realtime feedback of skin dose and dose rate during interventional fluoroscopic procedures. A color map on a 3D graphic of the patient represents the cumulative dose distribution on the skin. Automated image correlation algorithms are described which use the fluoroscopic procedure images to align and scale the patient graphic for more accurate dose mapping. METHODS: Currently, the DTS employs manual patient graphic selection and alignment...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048442/su-d-206-02-evaluation-of-partial-storage-of-the-system-matrix-for-cone-beam-computed-tomography-using-a-gpu-platform
#15
D Matenine, G Cote, J Mascolo-Fortin, Y Goussard, P Despres
PURPOSE: Iterative reconstruction algorithms in computed tomography (CT) require a fast method for computing the intersections between the photons' trajectories and the object, also called ray-tracing or system matrix computation. This work evaluates different ways to store the system matrix, aiming to reconstruct dense image grids in reasonable time. METHODS: We propose an optimized implementation of the Siddon's algorithm using graphics processing units (GPUs) with a novel data storage scheme...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047909/tu-fg-201-07-development-of-srs-conical-collimator-collision-prediction-software-for-radiation-treatment-safety
#16
V Gutti, A Morrow, S Kim, M Patel
PURPOSE: Stereotactic radiosurgery (SRS) treatments using conical collimators can potentially result in gantry collision with treatment table due to limited collision-clear spaces. An in-house software was developed to help the SRS treatment planner mitigate potential SRS conical collimator (Varian Medical System, Palo Alto, CA) collisions with the treatment table. This software was designed to remove treatment re-planning secondary to unexpected collisions. METHODS: A BrainLAB SRS ICT Frameless Extension used for SRS treatments in our clinic was mathematically modelled using surface points registered to the 3D co-ordinate space of the couch extension...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046657/su-f-j-72-a-clinical-usable-integrated-contouring-quality-evaluation-software-for-radiotherapy
#17
S Jiang, S Dolly, B Cai, S Mutic, H Li
PURPOSE: To introduce the Auto Contour Evaluation (ACE) software, which is the clinical usable, user friendly, efficient and all-in-one toolbox for automatically identify common contouring errors in radiotherapy treatment planning using supervised machine learning techniques. METHODS: ACE is developed with C# using Microsoft .Net framework and Windows Presentation Foundation (WPF) for elegant GUI design and smooth GUI transition animations through the integration of graphics engines and high dots per inch (DPI) settings on modern high resolution monitors...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046579/tu-d-209-02-a-backscatter-point-spread-function-for-entrance-skin-dose-determination
#18
S Vijayan, Z Xiong, A Shankar, S Rudin, D Bednarek
PURPOSE: To determine the distribution of backscattered radiation to the skin resulting from a non-uniform distribution of primary radiation through convolution with a backscatter point spread function (PSF). METHODS: A backscatter PSF is determined using Monte Carlo simulation of a 1 mm primary beam incident on a 30 × 30 cm × 20 cm thick PMMA phantom using EGSnrc software. A primary profile is similarly obtained without the phantom and the difference from the total provides the backscatter profile...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28032382/pymoldyn-identification-structure-and-properties-of-cavities-vacancies-in-condensed-matter-and-molecules
#19
Ingo Heimbach, Florian Rhiem, Fabian Beule, David Knodt, Josef Heinen, Robert O Jones
pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three...
March 5, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28027669/the-vertebroplacental-ratio-as-an-alternative-to-the-cerebroplacental-ratio-in-the-evaluation-of-the-fetus-at-the-end-of-pregnancy
#20
José Morales-Roselló, Asma Khalil, Victoria Fornes Ferrer, David Hervas-Marín, Nuria Peralta Llorens, Juan Rubio Moll, Alfredo Perales-Marín
OBJECTIVE: Low cerebroplacental ratio (CPR) near term has emerged as a marker of fetal adverse outcome. The aim of this study was to evaluate the predictive accuracy of an alternative ratio using the vertebral artery (vertebroplacental ratio or VPR) for acid-base status at birth. METHODS: This was a prospective cohort study of 1470 pregnancies undergoing an ultrasound assessment of the umbilical artery, middle cerebral artery and vertebral artery Doppler beyond 34 weeks' gestation within 14 days of delivery...
December 27, 2016: Journal of Maternal-fetal & Neonatal Medicine
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