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Register a new userAccounting for Randomness in Measurement and Sampling in Study of Cancer Cell Population Dynamics
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Studying the development of malignant tumours, it is important to know and predict the proportions of different cell types in tissue samples. Knowing the expected temporal evolution of the proportion of normal tissue cells, compared to stem-like and non-stem like cancer cells, gives an indication about the progression of the disease and indicates the expected response to interventions with drugs. Such processes have been modeled using Markov processes. An essential step for the simulation of such models is then the determination of state transition probabilities. We here consider the experimentally more realistic scenario in which the measurement of cell population sizes is noisy, leading to a particular hidden Markov model. In this context, randomness in measurement is related to noisy measurements, which are used for the estimation of the transition probability matrix. Randomness in sampling, on the other hand, is here related to the error in estimating the state probability from small cell populations. Using aggregated data of fluorescence-activated cell sorting (FACS) measurement, we develop a minimum mean square error estimator (MMSE) and maximum likelihood (ML) estimator and formulate two problems to find the minimum number of required samples and measurements to guarantee the accuracy of predicted population sizes using a transition probability matrix estimated from noisy data. We analyze the properties of two estimators for different noise distributions and prove an optimal solution for Gaussian distributions with the MMSE. Our numerical results show, that for noisy measurements the convergence mechanism of transition probabilities and steady states differ widely from the real values if one uses the standard deterministic approach in which measurements are assumed to be noise free.
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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.
In this paper we develop mathematical models for collective cell motility. Initially we develop a model using a linear diffusion-advection type equation and fit the parameters to data from cell motility assays. This approach is helpful in classifying the results of cell motility assay experiments. In particular, this model can determine degrees of directed versus undirected collective cell motility. Next we develop a model using a nonlinear diffusion term that is able capture in a unified way directed and undirected collective cell motility. Finally we apply the nonlinear diffusion approach to a problem in tumor cell invasion, noting that neither chemotaxis or haptotaxis are present in the system under consideration in this article.
Complete understanding of the mechanisms regulating the proliferation and differentiation that takes place during human immune CD8+ T cell responses is still lacking. Human clinical data is usually limited to blood cell counts, yet the initiation of these responses occurs in the draining lymph nodes; antigen-specific effector and memory CD8+ T cells generated in the lymph nodes migrate to those tissues where they are required. We use approximate Bayesian computation with deterministic mathematical models of CD8+ T cell populations (naive, central memory, effector memory and effector) and yellow fever virus vaccine data to infer the dynamics of these CD8+ T cell populations in three spatial compartments: draining lymph nodes, circulation and skin. We have made use of the literature to obtain rates of division and death for human CD8+ T cell population subsets and thymic export rates. Under the decreasing potential hypothesis for differentiation during an immune response, we find that, as the number of T cell clonotypes driven to an immune response increases, there is a reduction in the number of divisions required to differentiate from a naive to an effector CD8+ T cell, supporting the division of labour hypothesis observed in murine studies. We have also considered the reverse differentiation scenario, the increasing potential hypothesis. The decreasing potential model is better supported by the yellow fever virus vaccine data.
The conventional cancer stem cell (CSC) theory indicates a hierarchy of CSCs and non-stem cancer cells (NSCCs), that is, CSCs can differentiate into NSCCs but not vice versa. However, an alternative paradigm of CSC theory with reversible cell plasticity among cancer cells has received much attention very recently. Here we present a generalized multi-phenotypic cancer model by integrating cell plasticity with the conventional hierarchical structure of cancer cells. We prove that under very weak assumption, the nonlinear dynamics of multi-phenotypic proportions in our model has only one stable steady state and no stable limit cycle. This result theoretically explains the phenotypic equilibrium phenomena reported in various cancer cell lines. Furthermore, according to the transient analysis of our model, it is found that cancer cell plasticity plays an essential role in maintaining the phenotypic diversity in cancer especially during the transient dynamics. Two biological examples with experimental data show that the phenotypic
Following antigen stimulation, the net outcomes of a T cell response are shaped by integrated signals from both positive co-stimulatory and negative regulatory molecules. Recently, the blockade of negative regulatory molecules (i.e. immune checkpoint signals) demonstrates therapeutic effects in treatment of human cancer, but only in a fraction of cancer patients. Since this therapy is aimed to enhance T cell responses to cancers, here we devised a conceptual model by integrating both positive and negative signals in addition to antigen stimulation. A digital range of adjustment of each signal is formulated in our model for prediction of a final T cell response. This model allows us to evaluate strategies in order to enhance antitumor T cell responses. Our model provides a rational combination strategy for maximizing the therapeutic effects of cancer immunotherapy.
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