An optimal transportation approach for assessing almost stochastic order

When stochastic dominance $F\leq_{st}G$ does not hold, we can improve agreement to stochastic order by suitably trimming both distributions. In this work we consider the $L_2-$Wasserstein distance, $\mathcal W_2$, to stochastic order of these trimmed versions. Our characterization for that distance naturally leads to consider a $\mathcal W_2$-based index of disagreement with stochastic order, $\varepsilon_{\mathcal W_2}(F,G)$. We provide asymptotic results allowing to test $H_0: \varepsilon_{\mathcal W_2}(F,G)\geq \varepsilon_0$ vs $H_a: \varepsilon_{\mathcal W_2}(F,G)<\varepsilon_0$, that, under rejection, would give statistical guarantee of almost stochastic dominance. We include a simulation study showing a good performance of the index under the normal model

Non-linear effects on Turing patterns: time oscillations and chaos.

We show that a model reaction-diffusion system with two species in a monostable regime and over a large region of parameter space, produces Turing patterns coexisting with a limit cycle which cannot be discerned from the linear analysis. As a consequence, Turing patterns oscillate in time, a phenomenon which is expected to occur only in a three morphogen system. When varying a single parameter, a series of bifurcations lead to period doubling, quasi-periodic and chaotic oscillations without modifying the underlying Turing pattern. A Ruelle-Takens-Newhouse route to chaos is identified. We also examined the Turing conditions for obtaining a diffusion driven instability and discovered that the patterns obtained are not necessarily stationary for certain values of the diffusion coefficients. All this results demonstrates the limitations of the linear analysis for reaction-diffusion systems

Quantification of the morphological characteristics of hESC colonies

The maintenance of the undifferentiated state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells and colonies for propagation is typically performed by eye, in terms of the displayed morphological features, such as prominent/abundant nucleoli and a colony with a tightly packed appearance and a well-defined edge. Using image analysis and computational tools, we precisely quantify these properties using phase-contrast images of hESC colonies of different sizes (0.1–1.1 mm2) during days 2, 3 and 4 after plating. Our analyses reveal noticeable differences in their structure influenced directly by the colony area A. Large colonies (A > 0.6 mm2) have cells with smaller nuclei and a short intercellular distance when compared with small colonies (A  0.6 mm2) due to the proliferation of the cells in the bulk. This increases the colony density and the number of nearest neighbours. We also detect the self-organisation of cells in the colonies where newly divided (smallest) cells cluster together in patches, separated from larger cells at the final stages of the cell cycle. This might influence directly cell-to-cell interactions and the community effects within the colonies since the segregation induced by size differences allows the interchange of neighbours as the cells proliferate and the colony grows. Our findings are relevant to efforts to determine the quality of hESC colonies and establish colony characteristics database

Modeling the skin pattern of fishes

Complicated patterns showing various spatial scales have been obtained in the past by coupling Turing systems in such a way that the scales of the independent systems resonate. This produces superimposed patterns with different length scales. Here we propose a model consisting of two identical reaction-diffusion systems coupled together in such a way that one of them produces a simple Turing pattern of spots or stripes, and the other traveling wave fronts that eventually become stationary. The basic idea is to assume that one of the systems becomes fixed after some time and serves as a source of morphogens for the other system. This mechanism produces patterns very similar to the pigmentation patterns observed in different species of stingrays and other fishes. The biological mechanisms that support the realization of this model are discussed

Bifurcations and Slow-Fast Analysis in a Cardiac Cell Model for Investigation of Early Afterdepolarizations

In this study, we teased out the dynamical mechanisms underlying the generation of arrhythmogenic early afterdepolarizations (EADs) in a three-variable model of a mammalian ventricular cell. Based on recently published studies, we consider a 1-fast, 2-slow variable decomposition of the system describing the cellular action potential. We use sweeping techniques, such as the spike-counting method, and bifurcation and continuation methods to identify parametric regions with EADs. We show the existence of isolas of periodic orbits organizing the different EAD patterns and we provide a preliminary classification of our fast-slow decomposition according to the involved dynamical phenomena. This investigation represents a basis for further studies into the organization of EAD patterns in the parameter space and the involved bifurcations

Using the Sound Card as a Timer

Experiments in mechanics can often be timed by the sounds they produce. In such cases, digital audio recordings provide a simple way of measuring time intervals with an accuracy comparable to that of photogate timers. We illustrate this with an experiment in the physics of sports: to measure the speed of a hard-kicked soccer ball.Comment: 3 pages, 4 figures, Late

Quantification of the morphological characteristics of hESC colonies

The maintenance of the pluripotent state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells and colonies for propagation is typically performed by eye, in terms of the displayed morphological features, such as prominent/abundant nucleoli and a colony with a tightly packed appearance and a well-defined edge. Using image analysis and computational tools, we precisely quantify these properties using phase-contrast images of hESC colonies of different sizes (0.1 -- 1.1$\, \text{mm}^2$) during days 2, 3 and 4 after plating. Our analyses reveal noticeable differences in their structure influenced directly by the colony area $A$. Large colonies ($A > 0.6 \, \text{mm}^2$) have cells with smaller nuclei and a short intercellular distance when compared with small colonies ($A < 0.2 \, \text{mm}^2$). The gaps between the cells, which are present in small and medium sized colonies with $A \le 0.6 \, \text{mm}^2$, disappear in large colonies ($A > 0.6 \, \text{mm}^2$) due to the proliferation of the cells in the bulk. This increases the colony density and the number of nearest neighbours. We also detect the self-organisation of cells in the colonies where newly divided (smallest) cells cluster together in patches, separated from larger cells at the final stages of the cell cycle. This might influence directly cell-to-cell interactions and the community effects within the colonies since the segregation induced by size differences allows the interchange of neighbours as the cells proliferate and the colony grows. Our findings are relevant to efforts to determine the quality of hESC colonies and establish colony characteristics database