14,033 research outputs found

    Inferring Latent States and Refining Force Estimates via Hierarchical Dirichlet Process Modeling in Single Particle Tracking Experiments

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    Optical microscopy provides rich spatio-temporal information characterizing in vivo molecular motion. However, effective forces and other parameters used to summarize molecular motion change over time in live cells due to latent state changes, e.g., changes induced by dynamic micro-environments, photobleaching, and other heterogeneity inherent in biological processes. This study focuses on techniques for analyzing Single Particle Tracking (SPT) data experiencing abrupt state changes. We demonstrate the approach on GFP tagged chromatids experiencing metaphase in yeast cells and probe the effective forces resulting from dynamic interactions that reflect the sum of a number of physical phenomena. State changes are induced by factors such as microtubule dynamics exerting force through the centromere, thermal polymer fluctuations, etc. Simulations are used to demonstrate the relevance of the approach in more general SPT data analyses. Refined force estimates are obtained by adopting and modifying a nonparametric Bayesian modeling technique, the Hierarchical Dirichlet Process Switching Linear Dynamical System (HDP-SLDS), for SPT applications. The HDP-SLDS method shows promise in systematically identifying dynamical regime changes induced by unobserved state changes when the number of underlying states is unknown in advance (a common problem in SPT applications). We expand on the relevance of the HDP-SLDS approach, review the relevant background of Hierarchical Dirichlet Processes, show how to map discrete time HDP-SLDS models to classic SPT models, and discuss limitations of the approach. In addition, we demonstrate new computational techniques for tuning hyperparameters and for checking the statistical consistency of model assumptions directly against individual experimental trajectories; the techniques circumvent the need for "ground-truth" and subjective information.Comment: 25 pages, 6 figures. Differs only typographically from PLoS One publication available freely as an open-access article at http://journals.plos.org/plosone/article?id=10.1371/journal.pone.013763

    Simulating Brain Tumor Heterogeneity with a Multiscale Agent-Based Model: Linking Molecular Signatures, Phenotypes and Expansion Rate

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    We have extended our previously developed 3D multi-scale agent-based brain tumor model to simulate cancer heterogeneity and to analyze its impact across the scales of interest. While our algorithm continues to employ an epidermal growth factor receptor (EGFR) gene-protein interaction network to determine the cells' phenotype, it now adds an explicit treatment of tumor cell adhesion related to the model's biochemical microenvironment. We simulate a simplified tumor progression pathway that leads to the emergence of five distinct glioma cell clones with different EGFR density and cell 'search precisions'. The in silico results show that microscopic tumor heterogeneity can impact the tumor system's multicellular growth patterns. Our findings further confirm that EGFR density results in the more aggressive clonal populations switching earlier from proliferation-dominated to a more migratory phenotype. Moreover, analyzing the dynamic molecular profile that triggers the phenotypic switch between proliferation and migration, our in silico oncogenomics data display spatial and temporal diversity in documenting the regional impact of tumorigenesis, and thus support the added value of multi-site and repeated assessments in vitro and in vivo. Potential implications from this in silico work for experimental and computational studies are discussed.Comment: 37 pages, 10 figure

    Efficient and realistic device modeling from atomic detail to the nanoscale

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    As semiconductor devices scale to new dimensions, the materials and designs become more dependent on atomic details. NEMO5 is a nanoelectronics modeling package designed for comprehending the critical multi-scale, multi-physics phenomena through efficient computational approaches and quantitatively modeling new generations of nanoelectronic devices as well as predicting novel device architectures and phenomena. This article seeks to provide updates on the current status of the tool and new functionality, including advances in quantum transport simulations and with materials such as metals, topological insulators, and piezoelectrics.Comment: 10 pages, 12 figure

    The Effects of Task, Task Mapping, and Layout Space on User Performance in Information-Rich Virtual Environments

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    How should abstract information be displayed in Information-Rich Virtual Environments (IRVEs)? There are a variety of techniques available, and it is important to determine which techniques help foster a user’s understanding both within and between abstract and spatial information types. Our evaluation compared two such techniques: Object Space and Display Space. Users strongly prefer Display Space over Object Space, and those who use Display Space may perform better. Display Space was faster and more accurate than Object Space for tasks comparing abstract information. Object Space was more accurate for comparisons of spatial information. These results suggest that for abstract criteria, visibility is a more important requirement than perceptual coupling by depth and association cues. They also support the value of perceptual coupling for tasks with spatial criteria
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