2,898 research outputs found

    Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster

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    Background: Reaction-diffusion systems are frequently used in systems biology to model developmental and signalling processes. In many applications, count numbers of the diffusing molecular species are very low, leading to the need to explicitly model the inherent variability using stochastic methods. Despite their importance and frequent use, parameter estimation for both deterministic and stochastic reaction-diffusion systems is still a challenging problem. Results: We present a Bayesian inference approach to solve both the parameter and state estimation problem for stochastic reaction-diffusion systems. This allows a determination of the full posterior distribution of the parameters (expected values and uncertainty). We benchmark the method by illustrating it on a simple synthetic experiment. We then test the method on real data about the diffusion of the morphogen Bicoid in Drosophila melanogaster. The results show how the precision with which parameters can be inferred varies dramatically, indicating that the ability to infer full posterior distributions on the parameters can have important experimental design consequences. Conclusions: The results obtained demonstrate the feasibility and potential advantages of applying a Bayesian approach to parameter estimation in stochastic reaction-diffusion systems. In particular, the ability to estimate credibility intervals associated with parameter estimates can be precious for experimental design. Further work, however, will be needed to ensure the method can scale up to larger problems

    Board of Dental Examiners

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    Board of Dental Examiners

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    Board of Dental Examiners

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    Locally Adaptive Frames in the Roto-Translation Group and their Applications in Medical Imaging

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    Locally adaptive differential frames (gauge frames) are a well-known effective tool in image analysis, used in differential invariants and PDE-flows. However, at complex structures such as crossings or junctions, these frames are not well-defined. Therefore, we generalize the notion of gauge frames on images to gauge frames on data representations U:RdSd1RU:\mathbb{R}^{d} \rtimes S^{d-1} \to \mathbb{R} defined on the extended space of positions and orientations, which we relate to data on the roto-translation group SE(d)SE(d), d=2,3d=2,3. This allows to define multiple frames per position, one per orientation. We compute these frames via exponential curve fits in the extended data representations in SE(d)SE(d). These curve fits minimize first or second order variational problems which are solved by spectral decomposition of, respectively, a structure tensor or Hessian of data on SE(d)SE(d). We include these gauge frames in differential invariants and crossing preserving PDE-flows acting on extended data representation UU and we show their advantage compared to the standard left-invariant frame on SE(d)SE(d). Applications include crossing-preserving filtering and improved segmentations of the vascular tree in retinal images, and new 3D extensions of coherence-enhancing diffusion via invertible orientation scores

    Numerical Approaches for Linear Left-invariant Diffusions on SE(2), their Comparison to Exact Solutions, and their Applications in Retinal Imaging

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    Left-invariant PDE-evolutions on the roto-translation group SE(2)SE(2) (and their resolvent equations) have been widely studied in the fields of cortical modeling and image analysis. They include hypo-elliptic diffusion (for contour enhancement) proposed by Citti & Sarti, and Petitot, and they include the direction process (for contour completion) proposed by Mumford. This paper presents a thorough study and comparison of the many numerical approaches, which, remarkably, is missing in the literature. Existing numerical approaches can be classified into 3 categories: Finite difference methods, Fourier based methods (equivalent to SE(2)SE(2)-Fourier methods), and stochastic methods (Monte Carlo simulations). There are also 3 types of exact solutions to the PDE-evolutions that were derived explicitly (in the spatial Fourier domain) in previous works by Duits and van Almsick in 2005. Here we provide an overview of these 3 types of exact solutions and explain how they relate to each of the 3 numerical approaches. We compute relative errors of all numerical approaches to the exact solutions, and the Fourier based methods show us the best performance with smallest relative errors. We also provide an improvement of Mathematica algorithms for evaluating Mathieu-functions, crucial in implementations of the exact solutions. Furthermore, we include an asymptotical analysis of the singularities within the kernels and we propose a probabilistic extension of underlying stochastic processes that overcomes the singular behavior in the origin of time-integrated kernels. Finally, we show retinal imaging applications of combining left-invariant PDE-evolutions with invertible orientation scores.Comment: A final and corrected version of the manuscript is Published in Numerical Mathematics: Theory, Methods and Applications (NM-TMA), vol. (9), p.1-50, 201

    California Coastal Commission

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    Home, head direction stability, and grid cell distortion

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    The home is a unique location in the life of humans and animals. In rats, home presents itself as a multicompartmental space that involves integrating navigation through subspaces. Here we embedded the laboratory rat’s home cage in the arena, while recording neurons in the animal’s parasubiculum and medial entorhinal cortex, two brain areas encoding the animal’s location and head direction. We found that head direction signals were unaffected by home cage presence or translocation. Head direction cells remain globally stable and have similar properties inside and outside the embedded home. We did not observe egocentric bearing encoding of the home cage. However, grid cells were distorted in the presence of the home cage. While they did not globally remap, single firing fields were translocated toward the home. These effects appeared to be geometrical in nature rather than a home-specific distortion and were not dependent on explicit behavioral use of the home cage during a hoarding task. Our work suggests that medial entorhinal cortex and parasubiculum do not remap after embedding the home, but local changes in grid cell activity overrepresent the embedded space location and might contribute to navigation in complex environments

    Absolute frequency measurements of 85Rb nF7/2 Rydberg states using purely optical detection

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    A three-step laser excitation scheme is used to make absolute frequency measurements of highly excited nF7/2 Rydberg states in 85Rb for principal quantum numbers n=33-100. This work demonstrates the first absolute frequency measurements of rubidium Rydberg levels using a purely optical detection scheme. The Rydberg states are excited in a heated Rb vapour cell and Doppler free signals are detected via purely optical means. All of the frequency measurements are made using a wavemeter which is calibrated against a GPS disciplined self-referenced optical frequency comb. We find that the measured levels have a very high frequency stability, and are especially robust to electric fields. The apparatus has allowed measurements of the states to an accuracy of 8.0MHz. The new measurements are analysed by extracting the modified Rydberg-Ritz series parameters.Comment: 12 pages, 5 figures, submitted to New. J. Phy
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