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EM simulation

Hang Dou, Derek W Burrows, Matthew L Baker, Tao Ju
Although electron cryo-microscopy (cryo-EM) has recently achieved resolutions of better than 3 Å, at which point molecular modeling can be done directly from the density map, analysis and annotation of a cryo-EM density map still primarily rely on fitting atomic or homology models to the density map. In this article, we present, to our knowledge, a new method for flexible fitting of known or modeled protein structures into cryo-EM density maps. Unlike existing methods that are guided by local density gradients, our method is guided by correspondences between the α-helices in the density map and model, and does not require an initial rigid-body fitting step...
June 20, 2017: Biophysical Journal
Birgit I Witte, Johannes Berkhof, Marianne A Jonker
In screening and surveillance studies, event times are interval censored. Besides, screening tests are imperfect so that the interval at which an event takes place may be uncertain. We describe an expectation-maximization algorithm to find the nonparametric maximum likelihood estimator of the cumulative incidence function of an event based on screening test data. Our algorithm has a closed-form solution for the combined expectation and maximization step and is computationally undemanding. A simulation study indicated that the bias of the estimator tends to zero for large sample size, and its mean squared error is in general lower than the mean squared error of the estimator that assumes the screening test is perfect...
June 20, 2017: Statistics in Medicine
Huang Lihong, Bai Jianling, Yu Hao, Chen Feng
Sample size re-estimation is essential in oncology studies. However, the use of blinded sample size reassessment for survival data has been rarely reported. Based on the density function of the exponential distribution, an expectation-maximization (EM) algorithm of the hazard ratio was derived, and several simulation studies were used to verify its applications. The method had obvious variation in the hazard ratio estimates and overestimation for the relatively small hazard ratios. Our studies showed that the stability of the EM estimation results directly correlated with the sample size, the convergence of the EM algorithm was impacted by the initial values, and a balanced design produced the best estimates...
June 20, 2017: Journal of Biomedical Research
Xinyang Liu, Christina E Rice, Raj Shekhar
PURPOSE: The oblique-viewing (i.e., angled) rigid endoscope is a commonly used tool in conventional endoscopic surgeries. The relative rotation between its two moveable parts, the telescope and the camera head, creates a rotation offset between the actual and the projection of an object in the camera image. A calibration method tailored to compensate such offset is needed. METHODS: We developed a fast calibration method for oblique-viewing rigid endoscopes suitable for clinical use...
June 16, 2017: International Journal of Computer Assisted Radiology and Surgery
Si Li, Jiahan Zhang, Andrzej Krol, C Ross Schmidtlein, David Feiglin, Yuesheng Xu
PURPOSE: The authors recently developed a preconditioned alternating projection algorithm (PAPA) for solving the penalized-likelihood SPECT reconstruction problem. The proposed algorithm can solve a wide variety of non-differentiable optimization models. This work is dedicated to comparing the performance of PAPA with total variation (TV) regularization (TV-PAPA) and a novel forward-backward algorithm with nested expectation maximization (EM)-TV iteration scheme (FB-EM-TV). METHODS: Monte Carlo technique was used to simulate multiple noise realizations of the fan-beam collimated SPECT data for a piecewise constant phantom with warm background, and hot and cold spheres with uniform activities at two noise levels...
June 2017: Physica Medica: PM
Hangwen Guo, Zhen Wang, Shuai Dong, Saurabh Ghosh, Mohammad Saghayezhian, Lina Chen, Yakui Weng, Andreas Herklotz, Thomas Z Ward, Rongying Jin, Sokrates T Pantelides, Yimei Zhu, Jiandi Zhang, E W Plummer
Interfaces between materials present unique opportunities for the discovery of intriguing quantum phenomena. Here, we explore the possibility that, in the case of superlattices, if one of the layers is made ultrathin, unexpected properties can be induced between the two bracketing interfaces. We pursue this objective by combining advanced growth and characterization techniques with theoretical calculations. Using prototype La2/3Sr1/3MnO3 (LSMO)/BaTiO3 (BTO) superlattices, we observe a structural evolution in the LSMO layers as a function of thickness...
June 12, 2017: Proceedings of the National Academy of Sciences of the United States of America
Fei Gao, Rahul Kishor, Xiaohua Feng, Siyu Liu, Ran Ding, Ruochong Zhang, Yuanjin Zheng
Photoacoustic (PA) and thermoacoustic (TA) effects have been explored in many applications, such as bio-imaging, laser-induced ultrasound generator, and sensitive electromagnetic (EM) wave film sensor. In this paper, we propose a compact analytical PA/TA generation model to incorporate EM, thermal and mechanical parameters, etc. From the derived analytical model, both intuitive predictions and quantitative simulations are performed. It shows that beyond the EM absorption improvement, there are many other physical parameters that deserve careful consideration when designing contrast agents or film composites, followed by simulation study...
September 2017: Photoacoustics
Xiaoqing Yang, Di Zhang, Shiyue Wu, Yang Yin, Lanshuo Li, Kaiyuan Cao, Kama Huang
Dynamic control transmission and polarization properties of electromagnetic (EM) wave propagation is investigated using chemical reconfigurable all-dielectric metasurface. The metasurface is composed of cross-shaped periodical teflon tubes and inner filled chemical systems (i.e., mixtures and chemical reaction) in aqueous solution. By tuning the complex permittivity of chemical systems, the reconfigurable metasurface can be easily achieved. The transmission properties of different incident polarized waves (i...
June 9, 2017: Scientific Reports
Regina Tomie Ivata Bernal, Deborah Carvalho Malta, Rafael Moreira Claro, Carlos Augusto Monteiro
OBJECTIVE: To evaluate the impact on the prevalence changes of risk factors for chronic diseases, published in the Surveillance System of Risk and Protection Factors for Chronic Diseases by Telephone Survey (Vigitel), after the inclusion of data from the population only with mobile phone. METHODS: Our study used data from the 26 State capitals and Federal District of Brazil obtained by the National Survey on Health (PNS) and Vigitel, both held in 2013. In each capital, we added a subsample of 200 adults living in households with only mobile phones, extracted from PNS, to the Vigitel 2013 database, with approximately 1,900 households, named Vigitel dual frame...
June 1, 2017: Revista de Saúde Pública
Chun Yu, Weixin Yao, Kun Chen
Finite mixture regression models have been widely used for modelling mixed regression relationships arising from a clustered and thus heterogenous population. The classical normal mixture model, despite its simplicity and wide applicability, may fail in the presence of severe outliers. Using a sparse, case-specific, and scale-dependent mean-shift mixture model parameterization, we propose a robust mixture regression approach for simultaneously conducting outlier detection and robust parameter estimation. A penalized likelihood approach is adopted to induce sparsity among the mean-shift parameters so that the outliers are distinguished from the remainder of the data, and a generalized Expectation-Maximization (EM) algorithm is developed to perform stable and efficient computation...
March 2017: Canadian Journal of Statistics, Revue Canadienne de Statistique
Peizhou Liao, Glen A Satten, Yi-Juan Hu
A fundamental challenge in analyzing next-generation sequencing (NGS) data is to determine an individual's genotype accurately, as the accuracy of the inferred genotype is essential to downstream analyses. Correctly estimating the base-calling error rate is critical to accurate genotype calls. Phred scores that accompany each call can be used to decide which calls are reliable. Some genotype callers, such as GATK and SAMtools, directly calculate the base-calling error rates from phred scores or recalibrated base quality scores...
May 31, 2017: Genetic Epidemiology
Sophie Dewey, Lucas Burigo, Igor A Pshenichnov, Igor Mishustin, Marcus Bleicher
As known, in cancer therapy with ion beams the relative biological effectiveness (RBE) of ions changes in the course of their propagation in tissues. Such changes are caused not only by increasing the linear energy transfer (LET) of beam particles with the penetration depth towards the Bragg peak, but also by nuclear reactions induced by beam nuclei leading to the production of various secondary particles. Although the changes of RBE along the beam axis have been studied quite well, much less attention has been paid to the evolution of RBE in the transverse direction, perpendicular to the beam axis...
May 30, 2017: Physics in Medicine and Biology
Yu-Hang Tang, Lu Lu, He Li, Constantinos Evangelinos, Leopold Grinberg, Vipin Sachdeva, George Em Karniadakis
We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment-simulating an entire mammal red blood cell lipid bilayer and cytoskeleton as modeled by multiple millions of mesoscopic particles-using a single shared memory commodity workstation. To achieve this, we invented an adaptive spatial-searching algorithm to accelerate the computation of short-range pairwise interactions in an extremely sparse three-dimensional space. The algorithm is based on a Voronoi partitioning of the point cloud of coarse-grained particles, and is continuously updated over the course of the simulation...
May 23, 2017: Biophysical Journal
Albert Juan Ramon, Yongyi Yang, P Hendrik Pretorius, Piotr J Slomka, Karen L Johnson, Michael A King, Miles N Wernick
BACKGROUND: We investigated the extent to which the administered dose (activity) level can be reduced without sacrificing diagnostic accuracy for three reconstruction strategies for SPECT-myocardial perfusion imaging (MPI). METHODS: We optimized the parameters of the three reconstruction strategies for perfusion-defect detection over a range of simulated administered dose levels using a set of hybrid studies (derived from 190 subjects) consisting of clinical SPECT-MPI data modified to contain realistic simulated lesions...
May 23, 2017: Journal of Nuclear Cardiology: Official Publication of the American Society of Nuclear Cardiology
Suvra Pal, N Balakrishnan
In this paper, we develop likelihood inference based on the expectation maximization (EM) algorithm for the Box- Cox transformation cure rate model assuming the lifetimes to follow a Weibull distribution. A simulation study is carried out to demonstrate the performance of the proposed estimation method. Through Monte Carlo simulations, we also study the effect of model mis-specification on the estimate of cure rate. Finally, we analyze a well-known data on melanoma with the model and the inferential method developed here...
May 16, 2017: IEEE Journal of Biomedical and Health Informatics
Evan Russell, Andrew Koch Hall, Carly Hagel, Andrew Petrosoniak, Jeffrey Damon Dagnone, Daniel Howes
OBJECTIVES: Simulation-based education (SBE) is an important training strategy in emergency medicine (EM) postgraduate programs. This study sought to characterize the use of simulation in FRCPC-EM residency programs across Canada. METHODS: A national survey was administered to residents and knowledgeable program representatives (PRs) at all Canadian FRCPC-EM programs. Survey question themes included simulation program characteristics, the frequency of resident participation, the location and administration of SBE, institutional barriers, interprofessional involvement, content, assessment strategies, and attitudes about SBE...
May 17, 2017: CJEM
Joonsung Lee, Narae Choi, Jin Keun Seo, Dong-Hyun Kim
PURPOSE: Magnetic Resonance Electrical Property Tomography (MREPT) is an emerging imaging modality using measured B1 maps from Magnetic Resonance Imaging (MRI) to measure a distribution of electric conductivity and permittivity of the subject at the Larmor frequency. Conventional MREPT approachesat single transmit channel system using the Helmholtz equation rely on an assumption that conductivity and permittivity of the subject are locally homogeneous. For small tissue structures and tissue boundaries, in which the assumption of locally homogeneous conductivity and permittivity does not hold, the reconstructed conductivity values deviated from the actual values, so called "Boundary Artifacts"...
May 16, 2017: Medical Physics
Verena Müller, Panagiotis Fikatas, Safak Gül, Maximilian Noesser, Kirs Ten Fuehrer, Igor Sauer, Johann Pratschke, Ricardo Zorron
Background: Bariatric surgery is currently the most effective method to ameliorate co-morbidities as consequence of morbidly obese patients with BMI over 35 kg/m2. Endoscopic techniques have been developed to treat patients with mild obesity and ameliorate comorbidities, but endoscopic skills are needed, beside the costs of the devices. Aim: To report a new technique for internal gastric plication using an intragastric single port device in an experimental swine model...
January 2017: Arquivos Brasileiros de Cirurgia Digestiva: ABCD, Brazilian Archives of Digestive Surgery
Michael P Wallace, Erica Em Moodie, David A Stephens
Model assessment is a standard component of statistical analysis, but it has received relatively little attention within the dynamic treatment regime literature. In this paper, we focus on the dynamic-weighted ordinary least squares approach to optimal dynamic treatment regime estimation, introducing how its double-robustness property may be leveraged for model assessment, and how quasilikelihood may be used for model selection. These ideas are demonstrated through simulation studies, as well as through application to data from the sequenced treatment alternatives to relieve depression study...
January 1, 2017: Statistical Methods in Medical Research
Carmen D Tekwe, Roger S Zoh, Fuller W Bazer, Guoyao Wu, Raymond J Carroll
Objective measures of oxygen consumption and carbon dioxide production by mammals are used to predict their energy expenditure. Since energy expenditure is not directly observable, it can be viewed as a latent construct with multiple physical indirect measures such as respiratory quotient, volumetric oxygen consumption, and volumetric carbon dioxide production. Metabolic rate is defined as the rate at which metabolism occurs in the body. Metabolic rate is also not directly observable. However, heat is produced as a result of metabolic processes within the body...
May 8, 2017: Biometrics
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