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Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows
(2021)
Amoeboid cell motility is essential for a wide range of biological processes including wound healing, embryonic morphogenesis, and cancer metastasis. It relies on complex dynamical patterns of cell shape changes that pose long-standing challenges to mathematical modeling and raise a need for automated and reproducible approaches to extract quantitative morphological features from image sequences. Here, we introduce a theoretical framework and a computational method for obtaining smooth representations of the spatiotemporal contour dynamics from stacks of segmented microscopy images. Based on a Gaussian process regression we propose a one-parameter family of regularized contour flows that allows us to continuously track reference points (virtual markers) between successive cell contours. We use this approach to define a coordinate system on the moving cell boundary and to represent different local geometric quantities in this frame of reference. In particular, we introduce the local marker dispersion as a measure to identify localized membrane expansions and provide a fully automated way to extract the properties of such expansions, including their area and growth time. The methods are available as an open-source software package called AmoePy, a Python-based toolbox for analyzing amoeboid cell motility (based on time-lapse microscopy data), including a graphical user interface and detailed documentation. Due to the mathematical rigor of our framework, we envision it to be of use for the development of novel cell motility models. We mainly use experimental data of the social amoeba Dictyostelium discoideum to illustrate and validate our approach. <br /> Author summary Amoeboid motion is a crawling-like cell migration that plays an important key role in multiple biological processes such as wound healing and cancer metastasis. This type of cell motility results from expanding and simultaneously contracting parts of the cell membrane. From fluorescence images, we obtain a sequence of points, representing the cell membrane, for each time step. By using regression analysis on these sequences, we derive smooth representations, so-called contours, of the membrane. Since the number of measurements is discrete and often limited, the question is raised of how to link consecutive contours with each other. In this work, we present a novel mathematical framework in which these links are described by regularized flows allowing a certain degree of concentration or stretching of neighboring reference points on the same contour. This stretching rate, the so-called local dispersion, is used to identify expansions and contractions of the cell membrane providing a fully automated way of extracting properties of these cell shape changes. We applied our methods to time-lapse microscopy data of the social amoeba Dictyostelium discoideum.
We present a supervised learning method to learn the propagator map of a dynamical system from partial and noisy observations. In our computationally cheap and easy-to-implement framework, a neural network consisting of random feature maps is trained sequentially by incoming observations within a data assimilation procedure. By employing Takens's embedding theorem, the network is trained on delay coordinates. We show that the combination of random feature maps and data assimilation, called RAFDA, outperforms standard random feature maps for which the dynamics is learned using batch data.
The superposition operation S-n,S-A, n >= 1, n is an element of N, maps to each (n + 1)-tuple of n-ary operations on a set A an n-ary operation on A and satisfies the so-called superassociative law, a generalization of the associative law. The corresponding algebraic structures are Menger algebras of rank n. A partial algebra of type (n + 1) which satisfies the superassociative law as weak identity is said to be a partial Menger algebra of rank n. As a generalization of linear terms we define r-terms as terms where each variable occurs at most r-times. It will be proved that n-ary r-terms form partial Menger algebras of rank n. In this paper, some algebraic properties of partial Menger algebras such as generating systems, homomorphic images and freeness are investigated. As generalization of hypersubstitutions and linear hypersubstitutions we consider r-hypersubstitutions.U
The Rarita-Schwinger operator is the twisted Dirac operator restricted to 3/2-spinors. Rarita-Schwinger fields are solutions of this operator which are in addition divergence-free. This is an overdetermined problem and solutions are rare; it is even more unexpected for there to be large dimensional spaces of solutions. In this paper we prove the existence of a sequence of compact manifolds in any given dimension greater than or equal to 4 for which the dimension of the space of Rarita-Schwinger fields tends to infinity. These manifolds are either simply connected Kahler-Einstein spin with negative Einstein constant, or products of such spaces with flat tori. Moreover, we construct Calabi-Yau manifolds of even complex dimension with more linearly independent Rarita-Schwinger fields than flat tori of the same dimension.
We study superharmonic functions for Schrodinger operators on general weighted graphs. Specifically, we prove two decompositions which both go under the name Riesz decomposition in the literature. The first one decomposes a superharmonic function into a harmonic and a potential part. The second one decomposes a superharmonic function into a sum of superharmonic functions with certain upper bounds given by prescribed superharmonic functions. As application we show a Brelot type theorem.
We adapt the Faddeev-LeVerrier algorithm for the computation of characteristic polynomials to the computation of the Pfaffian of a skew-symmetric matrix. This yields a very simple, easy to implement and parallelize algorithm of computational cost O(n(beta+1)) where nis the size of the matrix and O(n(beta)) is the cost of multiplying n x n-matrices, beta is an element of [2, 2.37286). We compare its performance to that of other algorithms and show how it can be used to compute the Euler form of a Riemannian manifold using computer algebra.
Sequential data assimilation of the stochastic SEIR epidemic model for regional COVID-19 dynamics
(2021)
Newly emerging pandemics like COVID-19 call for predictive models to implement precisely tuned responses to limit their deep impact on society. Standard epidemic models provide a theoretically well-founded dynamical description of disease incidence. For COVID-19 with infectiousness peaking before and at symptom onset, the SEIR model explains the hidden build-up of exposed individuals which creates challenges for containment strategies. However, spatial heterogeneity raises questions about the adequacy of modeling epidemic outbreaks on the level of a whole country. Here, we show that by applying sequential data assimilation to the stochastic SEIR epidemic model, we can capture the dynamic behavior of outbreaks on a regional level. Regional modeling, with relatively low numbers of infected and demographic noise, accounts for both spatial heterogeneity and stochasticity. Based on adapted models, short-term predictions can be achieved. Thus, with the help of these sequential data assimilation methods, more realistic epidemic models are within reach.
In the semiclassical limit (h) over bar -> 0, we analyze a class of self-adjoint Schrodinger operators H-(h) over bar = (h) over bar L-2 + (h) over barW + V center dot id(E) acting on sections of a vector bundle E over an oriented Riemannian manifold M where L is a Laplace type operator, W is an endomorphism field and the potential energy V has non-degenerate minima at a finite number of points m(1),... m(r) is an element of M, called potential wells. Using quasimodes of WKB-type near m(j) for eigenfunctions associated with the low lying eigenvalues of H-(h) over bar, we analyze the tunneling effect, i.e. the splitting between low lying eigenvalues, which e.g. arises in certain symmetric configurations. Technically, we treat the coupling between different potential wells by an interaction matrix and we consider the case of a single minimal geodesic (with respect to the associated Agmon metric) connecting two potential wells and the case of a submanifold of minimal geodesics of dimension l + 1. This dimension l determines the polynomial prefactor for exponentially small eigenvalue splitting.
In this short survey article, we showcase a number of non-trivial geometric problems that have recently been resolved by marrying methods from functional calculus and real-variable harmonic analysis. We give a brief description of these methods as well as their interplay. This is a succinct survey that hopes to inspire geometers and analysts alike to study these methods so that they can be further developed to be potentially applied to a broader range of questions.
Lie group method in combination with Magnus expansion is utilized to develop a universal method applicable to solving a Sturm–Liouville Problem (SLP) of any order with arbitrary boundary conditions. It is shown that the method has ability to solve direct regular and some singular SLPs of even orders (tested up to order eight), with a mix of boundary conditions (including non-separable and finite singular endpoints), accurately and efficiently.
The present technique is successfully applied to overcome the difficulties in finding suitable sets of eigenvalues so that the inverse SLP problem can be effectively solved.
Next, a concrete implementation to the inverse Sturm–Liouville problem
algorithm proposed by Barcilon (1974) is provided. Furthermore, computational feasibility and applicability of this algorithm to solve inverse Sturm–Liouville problems of order n=2,4 is verified successfully. It is observed that the method is successful even in the presence of significant noise, provided that the assumptions of the algorithm are satisfied.
In conclusion, this work provides methods that can be adapted successfully for solving a direct (regular/singular) or inverse SLP of an arbitrary order with arbitrary boundary conditions.