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EM simulation

Hien D Nguyen, Geoffrey J McLachlan, Pierre Orban, Pierre Bellec, Andrew L Janke
Mixture of autoregressions (MoAR) models provide a model-based approach to the clustering of time series data. The maximum likelihood (ML) estimation of MoAR models requires evaluating products of large numbers of densities of normal random variables. In practical scenarios, these products converge to zero as the length of the time series increases, and thus the ML estimation of MoAR models becomes infeasible without the use of numerical tricks. We propose a maximum pseudolikelihood (MPL) estimation approach as an alternative to the use of numerical tricks...
January 17, 2017: Neural Computation
Jaekyun Jeon, Xin Qiao, Ivan Hung, Alok K Mitra, Ambroise Desfosses, Daniel Huang, Peter L Gor'kov, Rebecca C Craven, Richard L Kingston, Zhehong Gan, Fangqiang Zhu, Bo Chen
The orthoretroviral capsid protein (CA) assembles into polymorphic capsids, whose architecture, assembly and stability are still being investigated. The N-terminal and C-terminal domains of CA (NTD and CTD, respectively) engage in both homotypic and heterotypic interactions to create the capsid. Hexameric turrets formed by the NTD decorate the majority of the capsid surface. We report nearly-complete solid-state NMR (ssNMR) resonance assignments of Rous sarcoma virus (RSV) CA, assembled into hexamer tubes that mimic the authentic capsid...
January 17, 2017: Journal of the American Chemical Society
Lingyi Meng, Yu Zhang, ChiYung Yam
Nanometallic structures that support surface plasmons provide new ways to confine light at deep-subwavelength scales. In this paper, the effect of light scattering in nanowire array solar cells is studied by a multiscale approach combining classical electromagnetics (EM) and quantum mechanical (QM) simulations. A photovoltaic device is constructed by integrating a silicon nanowire array with a plasmonic silver nanosphere. The light scatterings by plasmonic element and nanowire array are obtained via classical EM simulations while current-voltage characteristics and optical properties of the nanowire cells are evaluated quantum mechanically...
January 11, 2017: Journal of Physical Chemistry Letters
An-Min Tang, Nian-Sheng Tang, Hongtu Zhu
The normality assumption of measurement error is a widely used distribution in joint models of longitudinal and survival data, but it may lead to unreasonable or even misleading results when longitudinal data reveal skewness feature. This paper proposes a new joint model for multivariate longitudinal and multivariate survival data by incorporating a nonparametric function into the trajectory function and hazard function and assuming that measurement errors in longitudinal measurement models follow a skew-normal distribution...
January 9, 2017: Statistics in Medicine
Zhen Li, Hee Sun Lee, Eric Darve, George Em Karniadakis
Memory effects are often introduced during coarse-graining of a complex dynamical system. In particular, a generalized Langevin equation (GLE) for the coarse-grained (CG) system arises in the context of Mori-Zwanzig formalism. Upon a pairwise decomposition, GLE can be reformulated into its pairwise version, i.e., non-Markovian dissipative particle dynamics (DPD). GLE models the dynamics of a single coarse particle, while DPD considers the dynamics of many interacting CG particles, with both CG systems governed by non-Markovian interactions...
January 7, 2017: Journal of Chemical Physics
E Mainegra-Hing, H Bouchard, F Tessier, B Walters
PURPOSE: Determine accuracy of the current implementation of electron transport under magnetic fields in EGSnrc by means of single scattering (SS) and Fano convergence tests, and establish quantitatively the electron step size restriction required to achieve a desired level of accuracy for ionization chamber dosimetry. METHODS: Condensed history (CH) dose calculations are compared to SS results for a PTW30013 ionization chamber irradiated in air by a 60Co photon beam...
June 2016: Medical Physics
J Yue, R Hobbs, G Sgouros, E Frey
PURPOSE: Ra-223 therapy of prostate cancer bone metastases is being used to treat patients routinely. However, the absorbed dose distribution at the macroscopic and microscopic scales remains elusive, due to the inability to image the small activities injected. Accurate activity quantification through imaging is essential to calculate the absorbed dose in organs and sub-units in radiopharmaceutical therapy, enabling personalized absorbed dose-based treatment planning methodologies and more effective and optimal treatments...
June 2016: Medical Physics
Q Wang, D Sengupta, G Pratx
PURPOSE: Radioluminescence microscopy, an emerging and powerful tool for high resolution beta imaging, has been applied to molecular imaging of cellular metabolism to understand tumor biology. A novel thin-film (10 µm thickness) scintillator made of Lu2 O3 : Eu has been developed to enhance the system performance. However the advances of radioluminescence imaging with Lu2 O3 scintillator compared with that using conventional scintillator have not been explored theoretically to date. To validate the advantages of the thin-film scintillator, this study uses a novel computational simulation framework to evaluate the performance of radioluminescence microscopy using both conventional and thin-film scintillators...
June 2016: Medical Physics
Baudouin Dillmann, Luc Dubois, Erick Paleczny, Julien Trébosc, Jean-Paul Amoureux, Frédérique Pourpoint, Olivier Lafon
The development of probes for Nuclear Magnetic Resonance (NMR) spectroscopy of metabolites, biomolecules or materials requires the accurate determination of the radio-frequency (RF) magnetic field strength, B1, at the position of the sample since this RF-field strength is related to the signal sensitivity and the excitation bandwidth. The Ball Shift (BS) technique is a commonly employed test bench method to measure the B1 value. Nevertheless, the influence of the RF electric field, E1, on BS is often overlooked...
December 18, 2016: Solid State Nuclear Magnetic Resonance
Christoph M Augustin, Andrew Crozier, Aurel Neic, Anton J Prassl, Elias Karabelas, Tiago Ferreira da Silva, Joao F Fernandes, Fernando Campos, Titus Kuehne, Gernot Plank
AIMS: Models of blood flow in the left ventricle (LV) and aorta are an important tool for analysing the interplay between LV deformation and flow patterns. Typically, image-based kinematic models describing endocardial motion are used as an input to blood flow simulations. While such models are suitable for analysing the hemodynamic status quo, they are limited in predicting the response to interventions that alter afterload conditions. Mechano-fluidic models using biophysically detailed electromechanical (EM) models have the potential to overcome this limitation, but are more costly to build and compute...
December 2016: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
Biswajit Gorai, Thirunavukkarasu Sivaraman
Cardiotoxins (CTXs) are single polypeptide chain consisting of 59-62 amino acids with four disulfide bridges and globular proteins of simple β-sheet folds. The CTXs are one of principal toxic components causing haemolysis and damaging various cells and belong to three-finger toxin (TFT) superfamily of snake venoms. However, there is no natural or synthetic small molecular inhibitor to the protein toxins to date. In the present study, modes of interaction of cardiotoxin 1 (CTX1) from Indian cobra (Naja naja) with heterogeneous erythrocyte membrane (EM) model system have been extensively examined by using all-atom molecular dynamics (MD) simulations in near physiological conditions and comprehensive analyses of the MD data revealed two distinct principal regions ('head groove' and 'loop groove') of the protein toxin for establishing structural interactions with the EM system...
February 2017: International Journal of Biological Macromolecules
Liang Li, Huzhang Mao, Hemant Ishwaran, Jeevanantham Rajeswaran, John Ehrlinger, Eugene H Blackstone
Atrial fibrillation (AF) is an abnormal heart rhythm characterized by rapid and irregular heartbeat, with or without perceivable symptoms. In clinical practice, the electrocardiogram (ECG) is often used for diagnosis of AF. Since the AF often arrives as recurrent episodes of varying frequency and duration and only the episodes that occur at the time of ECG can be detected, the AF is often underdiagnosed when a limited number of repeated ECGs are used. In studies evaluating the efficacy of AF ablation surgery, each patient undergoes multiple ECGs and the AF status at the time of ECG is recorded...
December 16, 2016: Biometrical Journal. Biometrische Zeitschrift
Wenjun Zheng
Dynactin, a large multiprotein complex, binds with the cytoplasmic dynein-1 motor and various adaptor proteins to allow recruitment and transportation of cellular cargoes toward the minus end of microtubules. The structure of the dynactin complex is built around an actin-like minifilament with a defined length, which has been visualized in a high-resolution structure of the dynactin filament determined by cryo-electron microscopy (cryo-EM). To understand the energetic basis of dynactin filament assembly, we used molecular dynamics simulation to probe the intersubunit interactions among the actin-like proteins, various capping proteins, and four extended regions of the dynactin shoulder...
December 29, 2016: Biochemistry
R Meena Prakash, R Shantha Selva Kumari
The Fuzzy C Means (FCM) and Expectation Maximization (EM) algorithms are the most prevalent methods for automatic segmentation of MR brain images into three classes Gray Matter (GM), White Matter (WM) and Cerebrospinal Fluid (CSF). The major difficulties associated with these conventional methods for MR brain image segmentation are the Intensity Non-uniformity (INU) and noise. In this paper, EM and FCM with spatial information and bias correction are proposed to overcome these effects. The spatial information is incorporated by convolving the posterior probability during E-Step of the EM algorithm with mean filter...
January 2017: Journal of Medical Systems
Yaofang Xu, Jiayi Wu, Chang-Cheng Yin, Youdong Mao
In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership...
2016: PloS One
Suresh Venkatesh, David Schurig
We describe and provide a systematic procedure for computationally fast propagation of arbitrary vector electromagnetic (EM) fields through an axially symmetric medium. A cylindrical harmonic field propagator is chosen for this purpose and in most cases, this is the best and the obvious choice. Firstly, we describe the cylindrical harmonic decomposition technique in terms of both scalar and vector basis for a given input excitation field. Then we formulate a generalized discrete Fourier-Hankel transform to achieve efficient vector basis decomposition...
December 12, 2016: Optics Express
Stephanie Zeil, Julio Kovacs, Willy Wriggers, Jing He
Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably...
December 12, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Lili Yang, Menggang Yu, Sujuan Gao
Joint models are statistical tools for estimating the association between time-to-event and longitudinal outcomes. One challenge to the application of joint models is its computational complexity. Common estimation methods for joint models include a two-stage method, Bayesian and maximum-likelihood methods. In this work, we consider joint models of a time-to-event outcome and multiple longitudinal processes and develop a maximum-likelihood estimation method using the expectation-maximization (EM) algorithm...
2016: Journal of Statistical Computation and Simulation
Tian Dai, Ying Guo
Network-oriented analysis of functional magnetic resonance imaging (fMRI), especially resting-state fMRI, has revealed important association between abnormal connectivity and brain disorders such as schizophrenia, major depression and Alzheimer's disease. Imaging-based brain connectivity measures have become a useful tool for investigating the pathophysiology, progression and treatment response of psychiatric disorders and neurodegenerative diseases. Recent studies have started to explore the possibility of using functional neuroimaging to help predict disease progression and guide treatment selection for individual patients...
November 30, 2016: NeuroImage
Andreas Tag, Vikrant Chauhan, Christian Huck, Bernhard Bader, Dominik Karolewski, F Maximilian Pitschi, Robert Weigel, Amelie Hagelauer
A novel approach for multiphysics modeling of bulk acoustic wave (BAW) filters is presented allowing accurate and at the same time efficient modeling of BAW filters at high power levels. The approach takes the different types of losses and their spatial distribution into account in order to provide the required input for thermal simulation. The temperature distribution determined by thermal simulation is used to modify the geometry and the layer stack of each single resonator of the filter. In this way, the required input for modeling of electromagnetic (EM) and acoustic behavior at high power level is generated...
December 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
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