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EM simulation

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
José Gardiazabal, Philipp Matthies, Jakob Vogel, Benjamin Frisch, Nassir Navab, Sibylle Ziegler, Tobias Lasser
PURPOSE: Hand- and robot-guided mini gamma cameras have been introduced for the acquisition of single-photon emission computed tomography (SPECT) images. Less cumbersome than whole-body scanners, they allow for a fast acquisition of the radioactivity distribution, for example, to differentiate cancerous from hormonally hyperactive lesions inside the thyroid. This work compares acquisition protocols and reconstruction algorithms in an attempt to identify the most suitable approach for fast acquisition and efficient image reconstruction, suitable for localization of extended sources, such as lesions inside the thyroid...
December 2016: Medical Physics
Nicolas A Karakatsanis, Charalampos Tsoumpas, Habib Zaidi
Bulk body motion may randomly occur during PET acquisitions introducing blurring, attenuation-emission mismatches and, in dynamic PET, discontinuities in the measured time activity curves between consecutive frames. Meanwhile, dynamic PET scans are longer, thus increasing the probability of bulk motion. In this study, we propose a streamlined 3D PET motion-compensated image reconstruction (3D-MCIR) framework, capable of robustly deconvolving intra-frame motion from a static or dynamic 3D sinogram. The presented 3D-MCIR methods need not partition the data into multiple gates, such as 4D MCIR algorithms, or access list-mode (LM) data, such as LM MCIR methods, both associated with increased computation or memory resources...
November 16, 2016: Computerized Medical Imaging and Graphics: the Official Journal of the Computerized Medical Imaging Society
Milad Lankarany, Jaime E Heiss, Ilan Lampl, Taro Toyoizumi
Advanced statistical methods have enabled trial-by-trial inference of the underlying excitatory and inhibitory synaptic conductances (SCs) of membrane-potential recordings. Simultaneous inference of both excitatory and inhibitory SCs sheds light on the neural circuits underlying the neural activity and advances our understanding of neural information processing. Conventional Bayesian methods can infer excitatory and inhibitory SCs based on a single trial of observed membrane potential. However, if multiple recorded trials are available, this typically leads to suboptimal estimation because they neglect common statistics (of synaptic inputs (SIs)) across trials...
2016: Frontiers in Computational Neuroscience
Yan Zhou, Pei Wang, Xianlong Wang, Ji Zhu, Peter X-K Song
The multivariate regression model is a useful tool to explore complex associations between two kinds of molecular markers, which enables the understanding of the biological pathways underlying disease etiology. For a set of correlated response variables, accounting for such dependency can increase statistical power. Motivated by integrative genomic data analyses, we propose a new methodology-sparse multivariate factor analysis regression model (smFARM), in which correlations of response variables are assumed to follow a factor analysis model with latent factors...
November 10, 2016: Genetic Epidemiology
Yatao Zhang, Shoushui Wei, Costanzo Di Maria, Chengyu Liu
The poor quality of wireless electrocardiography (ECG) recordings can lead to misdiagnosis and waste of medical resources. This study presents an interpretation of Lempel-Ziv (LZ) complexity in terms of ECG quality assessment, and verifies its performance on real ECG signals. Firstly, LZ complexities for typical signals, namely high-frequency (HF) noise, low-frequency (LF) noise, power-line (PL) noise, impulse (IM) noise, clean artificial ECG signals, and ECG signals with various types of noise added (ECG plus HF, LF, PL, and IM noise, respectively) were analyzed...
2016: Journal of Medical and Biological Engineering
Zhenqiu Liu, Gang Li
Variable selections for regression with high-dimensional big data have found many applications in bioinformatics and computational biology. One appealing approach is the L0 regularized regression which penalizes the number of nonzero features in the model directly. However, it is well known that L0 optimization is NP-hard and computationally challenging. In this paper, we propose efficient EM (L0EM) and dual L0EM (DL0EM) algorithms that directly approximate the L0 optimization problem. While L0EM is efficient with large sample size, DL0EM is efficient with high-dimensional (n ≪ m) data...
2016: Computational and Mathematical Methods in Medicine
Pei Lu, Jun Xia, Zhicheng Li, Jing Xiong, Jian Yang, Shoujun Zhou, Lei Wang, Mingyang Chen, Cheng Wang
BACKGROUND: Accurate segmentation of blood vessels plays an important role in the computer-aided diagnosis and interventional treatment of vascular diseases. The statistical method is an important component of effective vessel segmentation; however, several limitations discourage the segmentation effect, i.e., dependence of the image modality, uneven contrast media, bias field, and overlapping intensity distribution of the object and background. In addition, the mixture models of the statistical methods are constructed relaying on the characteristics of the image histograms...
November 8, 2016: Biomedical Engineering Online
Xuejin Li, He Li, Hung-Yu Chang, George Lykotrafitis, George Em Karniadakis
We review recent advances in multiscale modeling of the biomechanical characteristics of red blood cells (RBCs) in hematological diseases, and their relevance to the structure and dynamics of defective RBCs. We highlight examples of successful simulations of blood disorders including malaria and other hereditary disorders, such as sickle-cell anemia, spherocytosis and elliptocytosis.
November 4, 2016: Journal of Biomechanical Engineering
Thomas Lehmann, Peter Schlattmann
Multiple imputation has become a widely accepted technique to deal with the problem of incomplete data. Typically, imputation of missing values and the statistical analysis are performed separately. Therefore, the imputation model has to be consistent with the analysis model. If the data are analyzed with a mixture model, the parameter estimates are usually obtained iteratively. Thus, if the data are missing not at random, parameter estimation and treatment of missingness should be combined. We solve both problems by simultaneously imputing values using the data augmentation method and estimating parameters using the EM algorithm...
November 2, 2016: Biometrical Journal. Biometrische Zeitschrift
Zaixiang Tang, Yueping Shen, Xinyan Zhang, Nengjun Yi
Large-scale omics data have been increasingly used as an important resource for prognostic prediction of diseases and detection of associated genes. However, there are considerable challenges in analyzing high-dimensional molecular data, including the large number of potential molecular predictors, limited number of samples, and small effect of each predictor. We propose new Bayesian hierarchical generalized linear models, called spike-and-slab lasso GLMs, for prognostic prediction and detection of associated genes using large-scale molecular data...
October 31, 2016: Genetics
Manushka V Vaidya, Christopher M Collins, Daniel K Sodickson, Ryan Brown, Graham C Wiggins, Riccardo Lattanzi
In high field MRI, the spatial distribution of the radiofrequency magnetic ( B1) field is usually affected by the presence of the sample. For hardware design and to aid interpretation of experimental results, it is important both to anticipate and to accurately simulate the behavior of these fields. Fields generated by a radiofrequency surface coil were simulated using dyadic Green's functions, or experimentally measured over a range of frequencies inside an object whose electrical properties were varied to illustrate a variety of transmit [Formula: see text] and receive [Formula: see text] field patterns...
February 2016: Concepts in Magnetic Resonance. Part B, Magnetic Resonance Engineering
Hung-Yu Chang, Xuejin Li, He Li, George Em Karniadakis
Healthy red blood cells (RBCs) have remarkable deformability, squeezing through narrow capillaries as small as 3 microns in diameter without any damage. However, in many hematological disorders the spectrin network and lipid bilayer of diseased RBCs may be significantly altered, leading to impaired functionality including loss of deformability. We employ a two-component whole-cell multiscale model to quantify the biomechanical characteristics of the healthy and diseased RBCs, including Plasmodium falciparum-infected RBCs (Pf-RBCs) and defective RBCs in hereditary disorders, such as spherocytosis and elliptocytosis...
October 2016: PLoS Computational Biology
Leopold Kong, David E Lee, Rameshwar U Kadam, Tong Liu, Erick Giang, Travis Nieusma, Fernando Garces, Netanel Tzarum, Virgil L Woods, Andrew B Ward, Sheng Li, Ian A Wilson, Mansun Law
Hepatitis C virus (HCV) is a major cause of liver disease, affecting over 2% of the world's population. The HCV envelope glycoproteins E1 and E2 mediate viral entry, with E2 being the main target of neutralizing antibody responses. Structural investigations of E2 have produced templates for vaccine design, including the conserved CD81 receptor-binding site (CD81bs) that is a key target of broadly neutralizing antibodies (bNAbs). Unfortunately, immunization with recombinant E2 and E1E2 rarely elicits sufficient levels of bNAbs for protection...
October 24, 2016: Proceedings of the National Academy of Sciences of the United States of America
Mingge Deng, Zhen Li, Oleg Borodin, George Em Karniadakis
We develop a "charged" dissipative particle dynamics (cDPD) model for simulating mesoscopic electrokinetic phenomena governed by the stochastic Poisson-Nernst-Planck and the Navier-Stokes equations. Specifically, the transport equations of ionic species are incorporated into the DPD framework by introducing extra degrees of freedom and corresponding evolution equations associated with each DPD particle. Diffusion of ionic species driven by the ionic concentration gradient, electrostatic potential gradient, and thermal fluctuations is captured accurately via pairwise fluxes between DPD particles...
October 14, 2016: Journal of Chemical Physics
Paul McKenna, Brent Thoma, Ken Milne, Chris Bond
As part of the Canadian Journal of Emergency Medicine's (CJEM) developing social media strategy, 1 we are collaborating with the Skeptics' Guide to Emergency Medicine (SGEM) to summarize and critically appraise the current emergency medicine (EM) literature using evidence-based medicine principles. In the "Hot Off the Press" series, we select original research manuscripts published in CJEM to be featured on the SGEM website/podcast 2 and discussed by the study authors and the online EM community. A similar collaboration is underway between the SGEM and Academic Emergency Medicine...
October 26, 2016: CJEM
Huanhuan Yang, Xiangyu Cao, Fan Yang, Jun Gao, Shenheng Xu, Maokun Li, Xibi Chen, Yi Zhao, Yuejun Zheng, Sijia Li
Diverse electromagnetic (EM) responses of a programmable metasurface with a relatively large scale have been investigated, where multiple functionalities are obtained on the same surface. The unit cell in the metasurface is integrated with one PIN diode, and thus a binary coded phase is realized for a single polarization. Exploiting this anisotropic characteristic, reconfigurable polarization conversion is presented first. Then the dynamic scattering performance for two kinds of sources, i.e. a plane wave and a point source, is carefully elaborated...
October 24, 2016: Scientific Reports
Daniel R Ripoll, Ilja Khavrutskii, Anders Wallqvist, Sidhartha Chaudhury
Cryo-electron-microscopy (cryo-EM) structures of flaviviruses reveal significant variation in epitope occupancy across different monoclonal antibodies that have largely been attributed to epitope-level differences in conformation or accessibility that affect antibody binding. The consequences of these variations for macroscopic properties such as antibody binding and neutralization are the results of the law of mass action-a stochastic process of innumerable binding and unbinding events between antibodies and the multiple binding sites on the flavivirus in equilibrium-that cannot be directly imputed from structure alone...
October 18, 2016: Biophysical Journal
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