Numerical Methods for Two-Dimensional Stem Cell Tissue Growth.

Growth of developing and regenerative biological tissues of different cell types is usually driven by stem cells and their local environment. Here, we present a computational framework for continuum tissue growth models consisting of stem cells, cell lineages, and diffusive molecules that regulate proliferation and differentiation through feedback. To deal with the moving boundaries of the models in both open geometries and closed geometries (through polar coordinates) in two dimensions, we transform the dynamic domains and governing equations to fixed domains, followed by solving for the transformation functions to track the interface explicitly. Clustering grid points in local regions for better efficiency and accuracy can be achieved by appropriate choices of the transformation. The equations resulting from the incompressibility of the tissue is approximated by high-order finite difference schemes and is solved using the multigrid algorithms. The numerical tests demonstrate an overall spatiotemporal second-order accuracy of the methods and their capability in capturing large deformations of the tissue boundaries. The methods are applied to two biological systems: stratified epithelia for studying the effects of two different types of stem cell niches and the scaling of a morphogen gradient with the size of the Drosophila imaginal wing disc during growth. Direct simulations of both systems suggest that that the computational framework is robust and accurate, and it can incorporate various biological processes critical to stem cell dynamics and tissue growth

The case for absolute ligand discrimination : modeling information processing and decision by immune T cells

Some cells have to take decision based on the quality of surroundings ligands, almost irrespective of their quantity, a problem we name "absolute discrimination". An example of absolute discrimination is recognition of not-self by immune T Cells. We show how the problem of absolute discrimination can be solved by a process called "adaptive sorting". We review several implementations of adaptive sorting, as well as its generic properties such as antagonism. We show how kinetic proofreading with negative feedback implements an approximate version of adaptive sorting in the immune context. Finally, we revisit the decision problem at the cell population level, showing how phenotypic variability and feedbacks between population and single cells are crucial for proper decision

Supply chain management of blood products: a literature review.

This paper presents a review of the literature on inventory and supply chain management of blood products. First, we identify different perspectives on approaches to classifying the existing material. Each perspective is presented as a table in which the classification is displayed. The classification choices are exemplified through the citation of key references or by expounding the features of the perspective. The main contribution of this review is to facilitate the tracing of published work in relevant fields of interest, as well as identifying trends and indicating which areas should be subject to future research.OR in health services; Supply chain management; Inventory; Blood products; Literature review;

Infections with extracellular trypanosomes require control by efficient innate immune mechanisms and can result in the destruction of the mammalian humoral immune system

Salivarian trypanosomes are extracellular parasites that affect humans, livestock, and game animals around the world. Through co-evolution with the mammalian immune system, trypanosomes have developed defense mechanisms that allow them to thrive in blood, lymphoid vessels, and tissue environments such as the brain, the fat tissue, and testes. Trypanosomes have developed ways to circumvent antibody-mediated killing and block the activation of the lytic arm of the complement pathway. Hence, this makes the innate immune control of the infection a crucial part of the host-parasite interaction, determining infection susceptibility, and parasitemia control. Indeed, trypanosomes use a combination of several independent mechanisms to avoid clearance by the humoral immune system. First, perpetuated antigenic variation of the surface coat allows to escape antibody-mediated elimination. Secondly, when antibodies bind to the coat, they are efficiently transported toward the endocytosis pathway, where they are removed from the coat proteins. Finally, trypanosomes engage in the active destruction of the mammalian humoral immune response. This provides them with a rescue solution in case antigenic variation does not confer total immunological invisibility. Both antigenic variation and B cell destruction pose significant hurdles for the development of anti-trypanosome vaccine strategies. However, developing total immune escape capacity and unlimited growth capabilities within a mammalian host is not beneficial for any parasite, as it will result in the accelerated death of the host itself. Hence, trypanosomes have acquired a system of quorum sensing that results in density-dependent population growth arrest in order to prevent overpopulating the host. The same system could possibly sense the infection-associated host tissue damage resulting from inflammatory innate immune responses, in which case the quorum sensing serves to prevent excessive immunopathology and as such also promotes host survival. In order to put these concepts together, this review summarizes current knowledge on the interaction between trypanosomes and the mammalian innate immune system, the mechanisms involved in population growth regulation, antigenic variation and the immuno-destructive effect of trypanosomes on the humoral immune system. Vaccine trials and a discussion on the role of innate immune modulation in these trials are discussed at the end

Mathematical description of bacterial traveling pulses

The Keller-Segel system has been widely proposed as a model for bacterial waves driven by chemotactic processes. Current experiments on {\em E. coli} have shown precise structure of traveling pulses. We present here an alternative mathematical description of traveling pulses at a macroscopic scale. This modeling task is complemented with numerical simulations in accordance with the experimental observations. Our model is derived from an accurate kinetic description of the mesoscopic run-and-tumble process performed by bacteria. This model can account for recent experimental observations with {\em E. coli}. Qualitative agreements include the asymmetry of the pulse and transition in the collective behaviour (clustered motion versus dispersion). In addition we can capture quantitatively the main characteristics of the pulse such as the speed and the relative size of tails. This work opens several experimental and theoretical perspectives. Coefficients at the macroscopic level are derived from considerations at the cellular scale. For instance the stiffness of the signal integration process turns out to have a strong effect on collective motion. Furthermore the bottom-up scaling allows to perform preliminary mathematical analysis and write efficient numerical schemes. This model is intended as a predictive tool for the investigation of bacterial collective motion

A high-order spectral deferred correction strategy for low Mach number flow with complex chemistry

We present a fourth-order finite-volume algorithm in space and time for low Mach number reacting flow with detailed kinetics and transport. Our temporal integration scheme is based on a multi-implicit spectral deferred correction (MISDC) strategy that iteratively couples advection, diffusion, and reactions evolving subject to a constraint. Our new approach overcomes a stability limitation of our previous second-order method encountered when trying to incorporate higher-order polynomial representations of the solution in time to increase accuracy. We have developed a new iterative scheme that naturally fits within our MISDC framework that allows us to simultaneously conserve mass and energy while satisfying on the equation of state. We analyse the conditions for which the iterative schemes are guaranteed to converge to the fixed point solution. We present numerical examples illustrating the performance of the new method on premixed hydrogen, methane, and dimethyl ether flames.Comment: 27 pages, 5 figure