Ratio control in a cascade model of cell differentiation

We propose a kind of reaction-diffusion equations for cell differentiation, which exhibits the Turing instability. If the diffusivity of some variables is set to be infinity, we get coupled competitive reaction-diffusion equations with a global feedback term. The size ratio of each cell type is controlled by a system parameter in the model. Finally, we extend the model to a cascade model of cell differentiation. A hierarchical spatial structure appears as a result of the cell differentiation. The size ratio of each cell type is also controlled by the system parameter.Comment: 13 pages, 7 figure

Morphogen Transport in Epithelia

We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case of transcytosis where morphogens undergo repeated rounds of internalization into cells and recycling. Based on a description on the cellular scale, we derive effective nonlinear transport equations in one and two dimensions which are valid on larger scales. We derive analytic expressions for the concentration dependence of the effective diffusion coefficient and the effective degradation rate. We discuss the effects of a directional bias on morphogen transport and those of the coupling of the morphogen and receptor kinetics. Furthermore, we discuss general properties of cellular transport processes such as the robustness of gradients and relate our results to recent experiments on the morphogen Decapentaplegic (Dpp) that acts in the fruit fly Drosophila

HOLISMOKES -- IV. Efficient mass modeling of strong lenses through deep learning

Modelling the mass distributions of strong gravitational lenses is often necessary to use them as astrophysical and cosmological probes. With the high number of lens systems ($>10^5$) expected from upcoming surveys, it is timely to explore efficient modeling approaches beyond traditional MCMC techniques that are time consuming. We train a CNN on images of galaxy-scale lenses to predict the parameters of the SIE mass model ($x,y,e_x,e_y$, and $\theta_E$). To train the network, we simulate images based on real observations from the HSC Survey for the lens galaxies and from the HUDF as lensed galaxies. We tested different network architectures, the effect of different data sets, and using different input distributions of $\theta_E$. We find that the CNN performs well and obtain with the network trained with a uniform distribution of $\theta_E$ $>0.5"$ the following median values with $1\sigma$ scatter: $\Delta x=(0.00^{+0.30}_{-0.30})"$, $\Delta y=(0.00^{+0.30}_{-0.29})"$, $\Delta \theta_E=(0.07^{+0.29}_{-0.12})"$, $\Delta e_x = -0.01^{+0.08}_{-0.09}$ and $\Delta e_y = 0.00^{+0.08}_{-0.09}$. The bias in $\theta_E$ is driven by systems with small $\theta_E$. Therefore, when we further predict the multiple lensed image positions and time delays based on the network output, we apply the network to the sample limited to $\theta_E>0.8"$. In this case, the offset between the predicted and input lensed image positions is $(0.00_{-0.29}^{+0.29})"$ and $(0.00_{-0.31}^{+0.32})"$ for $x$ and $y$, respectively. For the fractional difference between the predicted and true time delay, we obtain $0.04_{-0.05}^{+0.27}$. Our CNN is able to predict the SIE parameters in fractions of a second on a single CPU and with the output we can predict the image positions and time delays in an automated way, such that we are able to process efficiently the huge amount of expected lens detections in the near future.Comment: 17 pages, 14 Figure

HOLISMOKES -- IX. Neural network inference of strong-lens parameters and uncertainties from ground-based images

Modeling of strong gravitational lenses is a necessity for further applications in astrophysics and cosmology. Especially with the large number of detections in current and upcoming surveys such as the Rubin Legacy Survey of Space and Time (LSST), it is timely to investigate in automated and fast analysis techniques beyond the traditional and time consuming Markov chain Monte Carlo sampling methods. Building upon our convolutional neural network (CNN) presented in Schuldt et al. (2021b), we present here another CNN, specifically a residual neural network (ResNet), that predicts the five mass parameters of a Singular Isothermal Ellipsoid (SIE) profile (lens center $x$ and $y$, ellipticity $e_x$ and $e_y$, Einstein radius $\theta_E$) and the external shear ($\gamma_{ext,1}$, $\gamma_{ext,2}$) from ground-based imaging data. In contrast to our CNN, this ResNet further predicts a 1$\sigma$ uncertainty for each parameter. To train our network, we use our improved pipeline from Schuldt et al. (2021b) to simulate lens images using real images of galaxies from the Hyper Suprime-Cam Survey (HSC) and from the Hubble Ultra Deep Field as lens galaxies and background sources, respectively. We find overall very good recoveries for the SIE parameters, while differences remain in predicting the external shear. From our tests, most likely the low image resolution is the limiting factor for predicting the external shear. Given the run time of milli-seconds per system, our network is perfectly suited to predict the next appearing image and time delays of lensed transients in time. Therefore, we also present the performance of the network on these quantities in comparison to our simulations. Our ResNet is able to predict the SIE and shear parameter values in fractions of a second on a single CPU such that we are able to process efficiently the huge amount of expected galaxy-scale lenses in the near future.Comment: 16 pages, including 11 figures, accepted for publication by A&

Mode transitions in a model reaction-diffusion system driven by domain growth and noise

Pattern formation in many biological systems takes place during growth of the underlying domain. We study a specific example of a reaction–diffusion (Turing) model in which peak splitting, driven by domain growth, generates a sequence of patterns. We have previously shown that the pattern sequences which are presented when the domain growth rate is sufficiently rapid exhibit a mode-doubling phenomenon. Such pattern sequences afford reliable selection of certain final patterns, thus addressing the robustness problem inherent of the Turing mechanism. At slower domain growth rates this regular mode doubling breaks down in the presence of small perturbations to the dynamics. In this paper we examine the breaking down of the mode doubling sequence and consider the implications of this behaviour in increasing the range of reliably selectable final patterns

Noise-induced inhibitory suppression of malfunction neural oscillators

Motivated by the aim to find new medical strategies to suppress undesirable neural synchronization we study the control of oscillations in a system of inhibitory coupled noisy oscillators. Using dynamical properties of inhibition, we find regimes when the malfunction oscillations can be suppressed but the information signal of a certain frequency can be transmitted through the system. The mechanism of this phenomenon is a resonant interplay of noise and the transmission signal provided by certain value of inhibitory coupling. Analyzing a system of three or four oscillators representing neural clusters, we show that this suppression can be effectively controlled by coupling and noise amplitudes.Comment: 10 pages, 14 figure

HOLISMOKES -- II. Identifying galaxy-scale strong gravitational lenses in Pan-STARRS using convolutional neural networks

We present a systematic search for wide-separation (Einstein radius >1.5"), galaxy-scale strong lenses in the 30 000 sq.deg of the Pan-STARRS 3pi survey on the Northern sky. With long time delays of a few days to weeks, such systems are particularly well suited for catching strongly lensed supernovae with spatially-resolved multiple images and open new perspectives on early-phase supernova spectroscopy and cosmography. We produce a set of realistic simulations by painting lensed COSMOS sources on Pan-STARRS image cutouts of lens luminous red galaxies with known redshift and velocity dispersion from SDSS. First of all, we compute the photometry of mock lenses in gri bands and apply a simple catalog-level neural network to identify a sample of 1050207 galaxies with similar colors and magnitudes as the mocks. Secondly, we train a convolutional neural network (CNN) on Pan-STARRS gri image cutouts to classify this sample and obtain sets of 105760 and 12382 lens candidates with scores pCNN>0.5 and >0.9, respectively. Extensive tests show that CNN performances rely heavily on the design of lens simulations and choice of negative examples for training, but little on the network architecture. Finally, we visually inspect all galaxies with pCNN>0.9 to assemble a final set of 330 high-quality newly-discovered lens candidates while recovering 23 published systems. For a subset, SDSS spectroscopy on the lens central regions proves our method correctly identifies lens LRGs at z~0.1-0.7. Five spectra also show robust signatures of high-redshift background sources and Pan-STARRS imaging confirms one of them as a quadruply-imaged red source at z_s = 1.185 strongly lensed by a foreground LRG at z_d = 0.3155. In the future, we expect that the efficient and automated two-step classification method presented in this paper will be applicable to the deeper gri stacks from the LSST with minor adjustments.Comment: 18 pages and 11 figures (plus appendix), submitted to A&