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EM simulation

A Hauser, J L Verhey
The present work shows a method for stable simulations via the lattice Boltzmann (LB) model for electromagnetic waves (EM) transiting homogeneous media. LB models for such media were already presented in the literature, but they suffer from numerical instability when the media transitions are sharp. We use one of these models in the limit of pure vacuum derived from Liu and Yan [Appl. Math. MODEL: 38, 1710 (2014)AMMODL0307-904X10.1016/j.apm.2013.09.009] and apply an extension that treats the effects of polarization and magnetization separately...
December 2017: Physical Review. E
Christian Donner, Manfred Opper
We consider the inverse Ising problem: the inference of network couplings from observed spin trajectories for a model with continuous time Glauber dynamics. By introducing two sets of auxiliary latent random variables we render the likelihood into a form which allows for simple iterative inference algorithms with analytical updates. The variables are (1) Poisson variables to linearize an exponential term which is typical for point process likelihoods and (2) Pólya-Gamma variables, which make the likelihood quadratic in the coupling parameters...
December 2017: Physical Review. E
Ashley C Crimmins, Ambrose H Wong, James W Bonz, Alina Tsyrulnik, Karen Jubanyik, James D Dziura, Kelly L Dodge, Leigh V Evans
INTRODUCTION: Although error disclosure is critical in promoting safety and patient-centered care, physicians are inconsistently trained in its practice, and few objective methods to assess competence exist. We used an immersive simulation scenario to determine whether providers with varying levels of clinical experience adhere to the disclosure safe practice guidelines when exposed to a serious adverse event simulation scenario. METHODS: This was a prospective cohort study with medical students, junior emergency medicine (EM) residents (PGY 1-2), senior EM residents (PGY 3-4), and attending EM physicians participating in a simulated case in which a scripted medication overdose resulted in an adverse event...
January 17, 2018: Simulation in Healthcare: Journal of the Society for Simulation in Healthcare
A Popinako, M Antonov, D Dibrova, A Chemeris, O S Sokolova
The Arp2/3 complex plays a key role in nucleating actin filaments branching. The glia maturation factor (GMF) competes with activators for interacting with the Arp2/3 complex and initiates the debranching of actin filaments. In this study, we performed a comparative analysis of interactions between GMF and the Arp2/3 complex and identified new amino acid residues involved in GMF binding to the Arp2/3 complex at two separate sites, revealed by X-ray and single particle EM techniques. Using molecular dynamics simulations we demonstrated the quantitative and qualitative changes in hydrogen bonds upon binding with GMF...
January 12, 2018: Biochemical and Biophysical Research Communications
Yasutaka Kitahama, Tamitake Itoh, Toshiaki Suzuki
To evaluate the shape of an Ag tip with regard to tip-enhanced Raman scattering (TERS) signal, the enhanced electromagnetic (EM) field and scattering spectrum, arising from surface plasmon resonance at the apex of the tip, were calculated using a finite-difference time domain (FDTD) method. In the calculated forward scattering spectra from the smooth Ag tip, the band appeared within the visible region, similar to the experimental results and calculation for a corrugated Ag cone. In the FDTD calculation of TERS, the Ag tip acting as a monopole antenna was adopted by insertion of a perfect electric conductor between the root of the tip and a top boundary surface of the calculation space...
January 5, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Atasi Chatterjee, T Bai, Frederik Edler, Christoph Tegenkamp, Kirsten Weide-Zaage, Herbert Pfnür
Electromigration (EM) as a structuring tool was investigated in Ag nanowires (width 300 nm, thickness 25 nm) and partly in notched and bow-tie Ag structures on a Si(100) substrate in ultra-high vacuum (UHV) using a 4-tip scanning tunneling microscope (STM) in combination with a scanning electron microscope (SEM). From simulations of Ag nanowires we got estimates of temperature profiles, current density profiles, EM and thermal migration (TM) mass flux distributions within the nanowire induced by critical current densities of $10^{8}$ A/cm$^2$...
January 16, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Kyeong Hwan Han, Changho Kim, Peter Talkner, George Em Karniadakis, Eok Kyun Lee
In the present study, quantitative feasibility tests of the hydrodynamic description of a two-dimensional fluid at the molecular level are performed, both with respect to length and time scales. Using high-resolution fluid velocity data obtained from extensive molecular dynamics simulations, we computed the transverse and longitudinal components of the velocity field by the Helmholtz decomposition and compared them with those obtained from the linearized Navier-Stokes (LNS) equations with time-dependent transport coefficients...
January 14, 2018: Journal of Chemical Physics
Taylor E T Hughes, David T Lodowski, Kevin W Huynh, Aysenur Yazici, John Del Rosario, Abhijeet Kapoor, Sandip Basak, Amrita Samanta, Xu Han, Sudha Chakrapani, Z Hong Zhou, Marta Filizola, Tibor Rohacs, Seungil Han, Vera Y Moiseenkova-Bell
The transient receptor potential vanilloid 5 (TRPV5) channel is a member of the transient receptor potential (TRP) channel family, which is highly selective for Ca2+, that is present primarily at the apical membrane of distal tubule epithelial cells in the kidney and plays a key role in Ca2+ reabsorption. Here we present the structure of the full-length rabbit TRPV5 channel as determined using cryo-EM in complex with its inhibitor econazole. This structure reveals that econazole resides in a hydrophobic pocket analogous to that occupied by phosphatidylinositides and vanilloids in TRPV1, thus suggesting conserved mechanisms for ligand recognition and lipid binding among TRPV channels...
January 2018: Nature Structural & Molecular Biology
Mehran Aflakparast, Mathisca C M de Gunst, Wessel N van Wieringen
Cross-sectional studies may shed light on the evolution of a disease like cancer through the comparison of patient traits among disease stages. This problem is especially challenging when a gene-gene interaction network needs to be reconstructed from omics data, and, in addition, the patients of each stage need not form a homogeneous group. Here, the problem is operationalized as the estimation of stage-wise mixtures of Gaussian graphical models (GGMs) from high-dimensional data. These mixtures are fitted by a (fused) ridge penalized EM algorithm...
January 10, 2018: Biometrical Journal. Biometrische Zeitschrift
Hao Ouyang, Karen Meyer, Prithwiraj Maitra, Susan Daly, Ryan M Svoboda, Aaron S Farberg, Darrell S Rigel
BACKGROUND: Studies show that sunscreen under real-life conditions is often not reapplied and/or applied insufficiently. This study investigated the durability of 2 current sunscreens with different SPF protection over an 8-hour period under simulated real-life conditions. METHODS: Participants (n=24) were randomized into two study groups utilizing either 2 mg/cm2 (FDA testing concentration) or 1 mg/cm2 (real-life application levels) of sunscreen. Two current SPF 15 and 70 sunscreens were applied to test spots on each participant's back...
January 1, 2018: Journal of Drugs in Dermatology: JDD
R Philip Chalmers
An efficient and accurate numerical approximation methodology useful for obtaining the observed information matrix and subsequent asymptotic covariance matrix when fitting models with the EM algorithm is presented. The numerical approximation approach is compared to existing algorithms intended for the same purpose, and the computational benefits and accuracy of this new approach are highlighted. Instructive and real-world examples are included to demonstrate the methodology concretely, properties of the estimator are discussed in detail, and a Monte Carlo simulation study is included to investigate the behaviour of a multi-parameter item response theory model using three competing finite-difference algorithms...
January 9, 2018: British Journal of Mathematical and Statistical Psychology
Yuta Yoshimoto, Zhen Li, Ikuya Kinefuchi, George Em Karniadakis
We propose a new coarse-grained (CG) molecular simulation technique based on the Mori-Zwanzig (MZ) formalism along with the iterative Boltzmann inversion (IBI). Non-Markovian dissipative particle dynamics (NMDPD) taking into account memory effects is derived in a pairwise interaction form from the MZ-guided generalized Langevin equation. It is based on the introduction of auxiliary variables that allow for the replacement of a non-Markovian equation with a Markovian one in a higher dimensional space. We demonstrate that the NMDPD model exploiting MZ-guided memory kernels can successfully reproduce the dynamic properties such as the mean square displacement and velocity autocorrelation function of a Lennard-Jones system, as long as the memory kernels are appropriately evaluated based on the Volterra integral equation using the force-velocity and velocity-velocity correlations...
December 28, 2017: Journal of Chemical Physics
Eva K Fenwick, Jyoti Khadka, Konrad Pesudovs, Gwyn Rees, Tien Y Wong, Ecosse L Lamoureux
Purpose: The purpose of this study was to assess the psychometric properties of diabetic retinopathy (DR) and diabetic macular edema (DME) quality-of-life (QoL) item banks and determine the utility of the final calibrated item banks by simulating a computerized adaptive testing (CAT) application. Methods: In this clinical, cross-sectional study, 514 participants with DR/DME (mean age ± SD, 60.4 ± 12.6 years; 64% male) answered 314 items grouped under nine QoL item pools: Visual Symptoms (SY); Ocular Comfort Symptoms (OS); Activity Limitation (AL); Mobility (MB); Emotional (EM); Health Concerns (HC); Social (SC); Convenience (CV); and Economic (EC)...
December 1, 2017: Investigative Ophthalmology & Visual Science
Mikael Peterson, Johan Gustafsson, Michael Ljungberg
BACKGROUND: Monte Carlo simulations provide accurate models of nuclear medicine imaging systems as they can properly account for the full physics of photon transport. The accuracy of the model included in the maximum-likelihood-expectation-maximization (ML-EM) reconstruction limits the overall accuracy of the reconstruction results. In this paper, we present a Monte Carlo-based ML-EM reconstruction method for pinhole single-photon emission computed tomography (SPECT) that has been incorporated into the SIMIND Monte Carlo program...
December 15, 2017: EJNMMI Physics
Jue Hou, Christina D Chambers, Ronghui Xu
We consider observational studies in pregnancy where the outcome of interest is spontaneous abortion (SAB). This at first sight is a binary 'yes' or 'no' variable, albeit there is left truncation as well as right-censoring in the data. Women who do not experience SAB by gestational week 20 are 'cured' from SAB by definition, that is, they are no longer at risk. Our data is different from the common cure data in the literature, where the cured subjects are always right-censored and not actually observed to be cured...
December 13, 2017: Lifetime Data Analysis
Stefan Zimmermann, Dietrich Klusmann, Wolfgang Hampe
BACKGROUND: The validity of selection tests is underestimated if it is determined by simply calculating the predictor-outcome correlation found in the admitted group. This correlation is usually attenuated by two factors: (1) the combination of selection variables which can compensate for each other and (2) range restriction in predictor and outcome due to the absence of outcome measures for rejected applicants. METHODS: Here we demonstrate the logic of these artifacts in a situation typical for student selection tests and compare four different methods for their correction: two formulas for the correction of direct and indirect range restriction, expectation maximization algorithm (EM) and multiple imputation by chained equations (MICE)...
December 11, 2017: BMC Medical Education
Lars V Bock, Michal H Kolář, Helmut Grubmüller
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM), the structure of the ribosome was resolved at atomic resolution in many functional and conformational states. Molecular dynamics simulations have added information on dynamics and energetics to the available structural information, thereby have bridged the gap to the kinetics obtained from single-molecule and bulk experiments...
December 1, 2017: Current Opinion in Structural Biology
Marcelo A da Silva, Eduardo S B de Oliveira, Alina A von Davier, Jorge L Bazán
The deterministic inputs, noisy, "and" gate (DINA) model is a popular cognitive diagnosis model (CDM) in psychology and psychometrics used to identify test takers' profiles with respect to a set of latent attributes or skills. In this work, we propose an estimation method for the DINA model with the No-U-Turn Sampler (NUTS) algorithm, an extension to Hamiltonian Monte Carlo (HMC) method. We conduct a simulation study in order to evaluate the parameter recovery and efficiency of this new Markov chain Monte Carlo method and to compare it with two other Bayesian methods, the Metropolis Hastings and Gibbs sampling algorithms, and with a frequentist method, using the Expectation-Maximization (EM) algorithm...
December 1, 2017: Biometrical Journal. Biometrische Zeitschrift
Yingxue Chen, Diansong Zhou, Weifeng Tang, Wangda Zhou, Nidal Al-Huniti, Eric Masson
Gefitinib is a selective inhibitor of epidermal growth factor receptor (EGFR) tyrosine kinase and is used for the treatment of non-small-cell lung cancer (NSCLC) with activating EGFR mutations. Gefitinib is metabolized by CYP2D6 and CYP3A4. This analysis compared the systemic exposure of gefitinib after oral administration in CYP2D6 ultrarapid metabolizers (UM) vs extensive metabolizers (EM). Physiologically based pharmacokinetic (PBPK) modeling was conducted using a population-based simulator. The model was calibrated using itraconazole-gefitinib clinical drug-drug interaction data and validated with gefitinib data in CYP2D6 EM vs poor metabolizers (PM)...
November 28, 2017: Journal of Clinical Pharmacology
Sudeep Pradhan, Byungjeong Song, Jaeyeon Lee, Jung-Woo Chae, Kyung Im Kim, Hyun-Moon Back, Nayoung Han, Kwang-Il Kwon, Hwi-Yeol Yun
BACKGROUND: Exploratory preclinical, as well as clinical trials, may involve a small number of patients, making it difficult to calculate and analyze the pharmacokinetic (PK) parameters, especially if the PK parameters show very high inter-individual variability (IIV). In this study, the performance of a classical first-order conditional estimation with interaction (FOCE-I) and expectation maximization (EM)-based Markov chain Monte Carlo Bayesian (BAYES) estimation methods were compared for estimating the population parameters and its distribution from data sets having a low number of subjects...
December 1, 2017: BMC Medical Research Methodology
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