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EM simulation

Jae Yong Park, Juyoung Ham, Illhwan Lee, Jong-Lam Lee
This paper presents a method to produce subwavelength-scale (<250 nm) AgCl nanostructures on a flexible plastic film, which is indispensable for highly efficient flexible displays. Using Cl2 plasma treatment on an Ag-coated plastic film, AgCl nanostructures were produced through the reaction of Ag atoms with Cl radicals. During the reaction, the volume of AgCl expands, leading to drastically changed surface morphology from a two-dimensional (2D) flat Ag surface to a 3D subwavelength-scale AgCl nanostructure...
May 22, 2018: Nanoscale
Sojung Yi, Olivier Félix Umuhire, Doris Uwamahoro, Mindi Guptill, Giles N Cattermole
Background: There is a growing demand by medical trainees for meaningful, short-term global emergency medicine (EM) experiences. EM programs in high-income countries (HICs) have forged opportunities for their trainees to access this experience in low-and middle-income countries (LMICs). However, few programs in LMICs have created and managed such courses. As more LMICs establish EM programs, these settings are ideal for developing courses beneficial for all participants. We describe our experience of creating and implementing a short-term global EM course in Rwanda...
September 2017: Education for Health: Change in Training & Practice
Brice Hoffmann, Ahmad Elbahnsi, Pierre Lehn, Jean-Luc Décout, Fabio Pietrucci, Jean-Paul Mornon, Isabelle Callebaut
Cryo-electron microscopy (cryo-EM) has recently provided invaluable experimental data about the full-length cystic fibrosis transmembrane conductance regulator (CFTR) 3D structure. However, this experimental information deals with inactive states of the channel, either in an apo, quiescent conformation, in which nucleotide-binding domains (NBDs) are widely separated or in an ATP-bound, yet closed conformation. Here, we show that 3D structure models of the open and closed forms of the channel, now further supported by metadynamics simulations and by comparison with the cryo-EM data, could be used to gain some insights into critical features of the conformational transition toward active CFTR forms...
May 19, 2018: Cellular and Molecular Life Sciences: CMLS
Jeffrey Huang, Jiayan Wu, Christina Dai, Xianwei Zhang, Hui Ju, Yiqi Chen, Chunyuan Zhang, Fan Ye, Yi Tan, Yongbo Zong, Telong Liu
INTRODUCTION: Emergency manuals (EMs) can help healthcare providers respond to crises more efficiently. Three anesthesia EMs have been translated into Chinese. These EMs have been made publicly available as a free document downloadable in China. A year after these Chinese versions of EMs were published, we conducted a multi-institutional survey in China to assess the progress of how well EM had been adapted and used in the setting of critical events. METHODS: Our study used a multi-institutional, anonymous electronic survey...
May 16, 2018: Simulation in Healthcare: Journal of the Society for Simulation in Healthcare
Amol R Holkundkar, Gert Brodin
It is well known that when a short laser pulse propagates in an underdense plasma, it induces longitudinal plasma oscillations at the plasma frequency after the pulse, typically referred to as the wakefield. However, for plasma densities approaching the critical density, wakefield generation is suppressed, and instead the EM-pulse (electromagnetic pulse) undergoes nonlinear self-modulation. In this article we have studied the transition from the wakefield generation to formation of quasi-solitons as the plasma density is increased...
April 2018: Physical Review. E
Nan Li, Shengping Liu, Xiaoqing Hu, Chao Luo, Xiaoliang Zhang, Ye Li
Electromagnetic (EM) field simulation plays a key role in the design of magnetic resonance imaging radio frequency (RF) coils. However, the values of the components in tuning and matching circuits often need to be iterated repeatedly in the conventional simulation method in order to achieve optimal scattering parameters. This leads to a time-consuming optimization to tune and match RF coils, particularly dual-tuned coils that are comprised of multiple lumped elements. A method combining EM field simulation and circuit simulation was employed in this paper, which can dramatically improve simulation efficiency for the optimization of the values of the lumped elements and corresponding EM field distribution...
March 2018: IEEE Transactions on Magnetics
Alberto Bartesaghi, Cecilia Aguerrebere, Veronica Falconieri, Soojay Banerjee, Lesley A Earl, Xing Zhu, Nikolaus Grigorieff, Jacqueline L S Milne, Guillermo Sapiro, Xiongwu Wu, Sriram Subramaniam
The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of methods to account for local variations in defocus and beam-induced drift, and the implementation of a data-driven dose compensation scheme that significantly improves the extraction of high-resolution information recorded during exposure of the specimen to the electron beam...
April 30, 2018: Structure
Xiaoxu Wang, Quan Pan, Zhengtao Ding, Zhengya Ma
This paper proposes a novel filtering design, from a viewpoint of identification instead of the conventional nonlinear estimation schemes (NESs), to improve the performance of orbit state estimation for a space target. First, a nonlinear perturbation is viewed or modeled as an unknown input (UI) coupled with the orbit state, to avoid the intractable nonlinear perturbation integral (INPI) required by NESs. Then, a simultaneous mean and covariance correction filter (SMCCF), based on a two-stage expectation maximization (EM) framework, is proposed to simply and analytically fit or identify the first two moments (FTM) of the perturbation (viewed as UI), instead of directly computing such the INPI in NESs...
May 5, 2018: Sensors
M D Koslovsky, M D Swartz, L Leon-Novelo, W Chan, A V Wilkinson
We develop a Bayesian variable selection method for logistic regression models that can simultaneously accommodate qualitative covariates and interaction terms under various heredity constraints. We use expectation-maximization variable selection (EMVS) with a deterministic annealing variant as the platform for our method, due to its proven flexibility and efficiency. We propose a variance adjustment of the priors for the coefficients of qualitative covariates, which controls false-positive rates, and a flexible parameterization for interaction terms, which accommodates user-specified heredity constraints...
2018: Journal of Statistical Computation and Simulation
Tian Mou, Jian Huang, Finbarr O'Sullivan
The basic emission process associated with positron emission tomography (PET) imaging is Poisson in nature. Reconstructed images inherit some aspects of this-regional variability is typically proportional to the regional mean. Iterative reconstruction using expectation-maximization (EM), widely used in clinical imaging now, imposes positivity constraints that impact noise properties. This paper is motivated by the analysis of data from a physical phantom study of a PET/CT scanner in routine clinical use. Both traditional filtered back-projection (FBP) and EM reconstructions of the images are considered...
May 2018: IEEE Transactions on Medical Imaging
Abdulkadir C Yucel, Weitian Sheng, Chenming Zhou, Yang Liu, Hakan Bagci, Eric Michielssen
A fast and memory efficient three-dimensional full-wave simulator for analyzing electromagnetic (EM) wave propagation in electrically large and realistic mine tunnels/galleries loaded with conductors is proposed. The simulator relies on Muller and combined field surface integral equations (SIEs) to account for scattering from mine walls and conductors, respectively. During the iterative solution of the system of SIEs, the simulator uses a fast multipole method-fast Fourier transform (FMM-FFT) scheme to reduce CPU and memory requirements...
2018: IEEE journal on multiscale and multiphysics computational techniques
Thomas J Paul, Gerhard Schenk, Rajeev Prabhakar
Glycerophosphodiesterase (GpdQ) is a binuclear metallophosphatase that catalyzes the hydrolytic cleavage of mono-, di-, and triphosphoester bonds of a wide range of critical molecules. Upon substrate binding, this enzyme undergoes a complex transformation from an inactive mononuclear form (Em, where the metal resides in the α site) to an active binuclear center (Eb-S, with metals bound to both the α and β site) through a mononuclear, substrate-bound intermediate state (Em-S). In this study, all-atom molecular dynamics (MD) simulations have been employed to investigate structures and dynamical transformations in this process using eight different variants, i...
May 3, 2018: Journal of Physical Chemistry. B
Jodi A Hadden, Juan R Perilla, Christopher John Schlicksup, Balasubramanian Venkatakrishnan, Adam Zlotnick, Klaus Schulten
The hepatitis B virus capsid represents a promising therapeutic target. Experiments suggest the capsid must be flexible to function; however, capsid structure and dynamics have not been thoroughly characterized in the absence of icosahedral symmetry constraints. Here, all-atom molecular dynamics simulations are leveraged to investigate the capsid without symmetry bias, enabling study of capsid flexibility and its implications for biological function and cryo-EM resolution limits. Simulation results confirm flexibility and reveal a propensity for asymmetric distortion...
April 27, 2018: ELife
Laura L Perissinotti, Pablo M De Biase, Jiqing Guo, Pei-Chi Yang, Miranda C Lee, Colleen E Clancy, Henry J Duff, Sergei Y Noskov
IKr is the rapidly activating component of the delayed rectifier potassium current, the ion current largely responsible for the repolarization of the cardiac action potential. Inherited forms of long QT syndrome (LQTS) (Lees-Miller et al., 1997) in humans are linked to functional modifications in the Kv11.1 (hERG) ion channel and potentially life threatening arrhythmias. There is little doubt now that hERG-related component of IKr in the heart depends on the tetrameric (homo- or hetero-) channels formed by two alternatively processed isoforms of hERG, termed hERG1a and hERG1b...
2018: Frontiers in Physiology
Magnus Lundborg, Ali Narangifard, Christian L Wennberg, Erik Lindahl, Bertil Daneholt, Lars Norlén
In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety...
April 24, 2018: Journal of Structural Biology
He Li, Jun Yang, Trang T Chu, Renugah Naidu, Lu Lu, Rajesh Chandramohanadas, Ming Dao, George Em Karniadakis
Reticulocytes, the precursors of erythrocytes, undergo drastic alterations in cell size, shape, and deformability during maturation. Experimental evidence suggests that young reticulocytes are stiffer and less stable than their mature counterparts; however, the underlying mechanism is yet to be fully understood. Here, we develop a coarse-grained molecular-dynamics reticulocyte membrane model to elucidate how the membrane structure of reticulocytes contributes to their particular biomechanical properties and pathogenesis in blood diseases...
April 24, 2018: Biophysical Journal
Rachel G Sinkey, Jasmin Lacevic, Tea Reljic, Iztok Hozo, Kelly S Gibson, Anthony O Odibo, Benjamin Djulbegovic, Charles J Lockwood
OBJECTIVE: Optimal management of pregnancies at 39 weeks gestational age is unknown. Therefore, we sought to perform a comparative effectiveness analysis of elective induction of labor (eIOL) at 39 weeks among nulliparous women with non-anomalous singleton, vertex fetuses as compared to expectant management (EM) which included IOL for medical or obstetric indications or at 41 weeks in undelivered mothers. MATERIALS AND METHODS: A Monte Carlo micro-simulation model was constructed modeling two mutually exclusive health states: eIOL at 39 weeks, or EM with IOL for standard medical or obstetrical indications or at 41 weeks if undelivered...
2018: PloS One
Genki Terashi, Daisuke Kihara
An increasing number of protein structures are determined by cryo-electron microscopy (cryo-EM) at near atomic resolution. However, tracing the main-chains and building full-atom models from EM maps of ~4-5 Å is still not trivial and remains a time-consuming task. Here, we introduce a fully automated de novo structure modeling method, MAINMAST, which builds three-dimensional models of a protein from a near-atomic resolution EM map. The method directly traces the protein's main-chain and identifies Cα positions as tree-graph structures in the EM map...
April 24, 2018: Nature Communications
Wenchao Ma
Constructed-response items have been shown to be appropriate for cognitively diagnostic assessments because students' problem-solving procedures can be observed, providing direct evidence for making inferences about their proficiency. However, multiple strategies used by students make item scoring and psychometric analyses challenging. This study introduces the so-called two-digit scoring scheme into diagnostic assessments to record both students' partial credits and their strategies. This study also proposes a diagnostic tree model (DTM) by integrating the cognitive diagnosis models with the tree model to analyse the items scored using the two-digit rubrics...
April 23, 2018: British Journal of Mathematical and Statistical Psychology
Eric F Lock, Gen Li
We describe a probabilistic PARAFAC/CANDECOMP (CP) factorization for multiway (i.e., tensor) data that incorporates auxiliary covariates, SupCP . SupCP generalizes the supervised singular value decomposition (SupSVD) for vector-valued observations, to allow for observations that have the form of a matrix or higher-order array. Such data are increasingly encountered in biomedical research and other fields. We use a novel likelihood-based latent variable representation of the CP factorization, in which the latent variables are informed by additional covariates...
2018: Electronic Journal of Statistics
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