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EM simulation

Weixuan Zhang, Kaiyang Cheng, Chao Wu, Yi Wang, Hongqiang Li, Xiangdong Zhang
Metamaterials, artificially structured electromagnetic (EM) materials, have enabled the realization of many unconventional EM properties not found in nature, such as negative refractive index, magnetic response, invisibility cloaking, and so on. Based on these man-made materials with novel EM properties, various devices are designed and realized. However, quantum analog devices based on metamaterials have not been achieved so far. Here, metamaterials are designed and printed to perform quantum search algorithm...
November 17, 2017: Advanced Materials
Zainab Ahdash, Andy M Lau, Robert Thomas Byrne, Katja Lammens, Alexandra Stüetzer, Henning Urlaub, Paula J Booth, Eamonn Reading, Karl-Peter Hopfner, Argyris Politis
The HerA-NurA helicase-nuclease complex cooperates with Mre11 and Rad50 to coordinate the repair of double-stranded DNA breaks. Little is known, however, about the assembly mechanism and activation of the HerA-NurA. By combining hybrid mass spectrometry with cryo-EM, computational and biochemical data, we investigate the oligomeric formation of HerA and detail the mechanism of nucleotide binding to the HerA-NurA complex from thermophilic archaea. We reveal that ATP-free HerA and HerA-DNA complexes predominantly exist in solution as a heptamer and act as a DNA loading intermediate...
November 16, 2017: Nucleic Acids Research
Anthony Chauvin, Jennifer Truchot, Aida Bafeta, Dominique Pateron, Patrick Plaisance, Youri Yordanov
The number of trials assessing Simulation-Based Medical Education (SBME) interventions has rapidly expanded. Many studies show that potential flaws in design, conduct and reporting of randomized controlled trials (RCTs) can bias their results. We conducted a methodological review of RCTs assessing a SBME in Emergency Medicine (EM) and examined their methodological characteristics. We searched MEDLINE via PubMed for RCT that assessed a simulation intervention in EM, published in 6 general and internal medicine and in the top 10 EM journals...
November 16, 2017: Internal and Emergency Medicine
Z Jiang, Z Dou, W L Song, J Xu, Z Y Wu
Objective: To compare results of different methods: in organizing HIV viral load (VL) data with missing values mechanism. Methods We used software SPSS 17.0 to simulate complete and missing data with different missing value mechanism from HIV viral loading data collected from MSM in 16 cities in China in 2013. Maximum Likelihood Methods Using the Expectation and Maximization Algorithm (EM), regressive method, mean imputation, delete method, and Markov Chain Monte Carlo (MCMC) were used to supplement missing data respectively...
November 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
Christopher McMahan, James Baurley, William Bridges, Chase Joyner, Muhamad Fitra Kacamarga, Robert Lund, Carissa Pardamean, Bens Pardamean
Genomic studies of plants often seek to identify genetic factors associated with desirable traits. The process of evaluating genetic markers one by one (i.e. a marginal analysis) may not identify important polygenic and environmental effects. Further, confounding due to growing conditions/factors and genetic similarities among plant varieties may influence conclusions. When developing new plant varieties to optimize yield or thrive in future adverse conditions (e.g. flood, drought), scientists seek a complete understanding of how the factors influence desirable traits...
November 15, 2017: Statistical Applications in Genetics and Molecular Biology
Cong Huai, Gan Li, Ruijie Yao, Yingyi Zhang, Mi Cao, Liangliang Kong, Chenqiang Jia, Hui Yuan, Hongyan Chen, Daru Lu, Qiang Huang
CRISPR-Cas9 technology has been widely used for genome engineering. Its RNA-guided endonuclease Cas9 binds specifically to target DNA and then cleaves the two DNA strands with HNH and RuvC nuclease domains. However, structural information regarding the DNA cleavage-activating state of two nuclease domains remains sparse. Here, we report a 5.2 Å cryo-EM structure of Cas9 in complex with sgRNA and target DNA. This structure reveals a conformational state of Cas9 in which the HNH domain is closest to the DNA cleavage site...
November 9, 2017: Nature Communications
Hosik Choi, Jungsoo Gim, Sungho Won, You Jin Kim, Sunghoon Kwon, Changyi Park
BACKGROUND: Undirected graphical models or Markov random fields have been a popular class of models for representing conditional dependence relationships between nodes. In particular, Markov networks help us to understand complex interactions between genes in biological processes of a cell. Local Poisson models seem to be promising in modeling positive as well as negative dependencies for count data. Furthermore, when zero counts are more frequent than are expected, excess zeros should be considered in the model...
November 6, 2017: BMC Genetics
Qianqian Wang, Yanyuan Ma, Yuanjia Wang
Some biomedical studies lead to mixture data. When a discrete covariate defining subgroup membership is missing for some of the subjects in a study, the distribution of the outcome follows a mixture distribution of the subgroup-specific distributions. Taking into account the uncertain distribution of the group membership and the covariates, we model the relation between the disease onset time and the covariates through transformation models in each sub-population, and develop a nonparametric maximum likelihood based estimation implemented through EM algorithm along with its inference procedure...
October 2017: Statistica Sinica
Abimbola O Kolawole, Hong Q Smith, Sophia A Svoboda, Madeline S Lewis, Michael B Sherman, Gillian C Lynch, B Montgomery Pettitt, Thomas J Smith, Christiane E Wobus
Ideal antiviral vaccines elicit antibodies (Abs) with broad strain recognition that bind to regions that are difficult to mutate for escape. Using 10 murine norovirus (MNV) strains and 5 human norovirus (HuNoV) virus-like particles (VLPs), we identified monoclonal antibody (MAb) 2D3, which broadly neutralized all MNV strains tested. Importantly, escape mutants corresponding to this antibody were very slow to develop and were distal to those raised against our previously studied antibody, A6.2. To understand the atomic details of 2D3 neutralization, we determined the cryo-electron microscopy (cryo-EM) structure of the 2D3/MNV1 complex...
September 2017: MSphere
Giorgio Bonmassar, Laleh Golestanirad
Micro-magnetic stimulation (μMS) is an emerging neurostimulation technology that promises to revolutionize the therapeutic stimulation of the human nervous system. μMS uses sub-millimeter sized coils that can be implemented in the central nervous system to elicit neuronal activation using magnetically induced electric currents. By their microscopic size, μMS coils can be acutely implanted in deep brain structures to deliver therapeutic stimulation with effects analogous to those achieved by state-of-the-art deep brain stimulation (DBS)...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Mikhail Kozlov, Marc Horner, Wolfgang Kainz, Leonardo M Angelone
The goal of this work is to investigate the effect of coil losses on the electromagnetic field generated in an ASTM phantom by a birdcage coil. The study was based on different numerical implementations of an RF body coil at 64 MHz, using the same 3D EM and RF circuit co-simulation procedure. The coil quality factor was evaluated with respect to losses due to power feed mismatch and to resistive losses of the coil components. The results of the study showed that the magnetic field at the coil iso-center, normalized to the square root of the whole body specific absorption rate, depends on the coil quality factor...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Hamidreza Abbaspourazad, Maryam M Shanechi
Technological advances have enabled the simultaneous recording of multiscale neural activity consisting of spikes, local field potential (LFP), and electrocorticogram (ECoG). Developing models that describe the encoding of behavior within multiscale activity is essential both for understanding neural mechanisms and for various neurotechnologies such as brain-machine interfaces (BMI). Multiscale recordings consist of signals with different statistical profiles and time-scales. While encoding models have been developed for each scale of activity alone, developing statistical models that simultaneously characterize discrete spike and continuous LFP/ECoG recordings and their various time-scales is a major challenge...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Lajmi Lakhal-Chaieb, Celia M T Greenwood, Mohamed Ouhourane, Kaiqiong Zhao, Belkacem Abdous, Karim Oualkacha
We consider the assessment of DNA methylation profiles for sequencing-derived data from a single cell type or from cell lines. We derive a kernel smoothed EM-algorithm, capable of analyzing an entire chromosome at once, and to simultaneously correct for experimental errors arising from either the pre-treatment steps or from the sequencing stage and to take into account spatial correlations between DNA methylation profiles at neighbouring CpG sites. The outcomes of our algorithm are then used to (i) call the true methylation status at each CpG site, (ii) provide accurate smoothed estimates of DNA methylation levels, and (iii) detect differentially methylated regions...
October 23, 2017: Statistical Applications in Genetics and Molecular Biology
Alireza Karbalayghareh, Ulisses Braga-Neto, Edward Russell Dougherty
This paper studies classification of gene-expression trajectories coming from two classes, healthy and mutated (cancerous) using Boolean networks with perturbation (BNps) to model the dynamics of each class at the state level. Each class has its own BNp, which is partially known based on gene pathways. We employ a Gaussian model at the observation level to show the expression values of the genes given the hidden binary states at each time point. We use expectation maximization (EM) to learn the BNps and the unknown model parameters, derive closed-form updates for the parameters, and propose a learning algorithm...
October 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Andreas Horneff, Michael Eder, Erich Hell, Johannes Ulrici, Jorg Felder, Volker Rasche, Jens Anders
Developing custom-built MR coils is a cumbersome task, in which an a priori prediction of the coils' SNR performance, their sensitivity pattern and their depth of penetration helps to greatly speed up the design process by reducing the required hardware manufacturing iterations. The simulationbased design flow presented in this paper takes the entire MR imaging process into account. That is, it includes all geometric and material properties of the coil and the phantom, the thermal noise as well as the target MR sequences...
October 17, 2017: IEEE Transactions on Medical Imaging
Gyu Rie Lee, Lim Heo, Chaok Seok
Advances in protein model refinement techniques are required as diverse sources of protein structure information are available from low-resolution experiments or informatics-based computations such as cryo-EM, NMR, homology models, or predicted residue contacts. Given semi-reliable or incomplete structural information, structure quality of a protein model has to be improved by ab initio methods such as energy-based simulation. In this study, we describe a new automatic refinement server method designed to improve locally inaccurate regions and overall structure simultaneously...
October 16, 2017: Proteins
Roxana-Mariana Beiu, Valeriu Beiu, Virgil-Florin Duma
Existing fiber optics (FOs)-based sensors, including mechanical deformation ones rely on structures embedded along the length of the FO. In this paper, we introduce and evaluate photonic crystals (PCs) embedded into FO cores acting as mechanical deformation sensors which are departing from this classical approach as the PCs are perpendicular to the length of the FO. Another noteworthy difference from classical FO-PC based sensors is that while classical ones rely on amplitude variations, the ones presented here use the phase variations of the electromagnetic components for assessing mechanical deformations...
September 18, 2017: Optics Express
Jeremy Udkoff, Lawrence F Eichenfield
INTRODUCTION: Biologic therapies have revolutionized the treatment of psoriasis; however, their use is limited by costs. Ixekizumab was more effective than etanercept in the UNCOVER trials, and the Food and Drug Administration (FDA) approved ixekizumab for treating psoriasis. Evaluating the cost-effectiveness of these therapies is crucial for medical decision making and our objective was to determine the cost-effectiveness of various ixekizumab dosing frequencies compared with etanercept...
October 1, 2017: Journal of Drugs in Dermatology: JDD
Albert Ng, Dong Si
Cryo-electron microscopy (cryo-EM) is a technique that produces three-dimensional density maps of large protein complexes. This allows for the study of the structure of these proteins. Identifying the secondary structures within proteins is vital to understanding the overall structure and function of the protein. The [Formula: see text]-barrel is one such secondary structure, commonly found in lipocalins and membrane proteins. In this article, we present a novel approach that utilizes genetic algorithms, kd-trees, and ray tracing to automatically detect and extract [Formula: see text]-barrels from cryo-EM density maps...
October 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Hongbin Zhang, Hubert Wong, Lang Wu
When modeling longitudinal data, the true values of time-varying covariates may be unknown because of detection-limit censoring or measurement error. A common approach in the literature is to empirically model the covariate process based on observed data and then predict the censored values or mismeasured values based on this empirical model. Such an empirical model can be misleading, especially for censored values since the (unobserved) censored values may behave very differently than observed values due to the underlying data-generation mechanisms or disease status...
October 16, 2017: Statistics in Medicine
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