Related papers: Control of human immune response function by T-cel…
Organisms have evolved immune systems that can counter pathogenic threats. The adaptive immune system in vertebrates consists of a diverse repertoire of immune receptors that can dynamically reorganize to specifically target the…
Time-integrated state observables, which quantify the fraction of time spent by the system in a specific pool of states, are important in many fields, such as chemical sensing or the theory of fluorescence spectroscopy. We derive exact…
Myriad experiments have identified an important role for $\rm CD8^+$ T cell response mechanisms in determining recovery from influenza A virus infection. Animal models of influenza infection further implicate multiple elements of the immune…
Feedback loops are essential for regulating cell proliferation and maintaining the delicate balance between cell division and cell death. Thanks to the exact solution of a few simple models of cell growth it is by now clear that stochastic…
The rate at which individual bacterial cells grow depends on the concentrations of cellular components such as ribosomes and proteins. These concentrations continuously fluctuate over time and are inherited from mother to daughter cells,…
When an infectious disease propagates throughout society, the incidence function may rise at first due to an increase in pathogenicity and then decrease due to inhibitory effects until it reaches saturation. Effective vaccination and…
The initial mass function (IMF) succinctly characterizes a stellar population, provides a statistical measure of the end result of the star-formation process, and informs our under- standing of the structure and dynamical evolution of…
The progression of a cell population where each individual is characterized by the value of an internal variable varying with time (e.g. size, weight, and protein concentration) is typically modeled by a Population Balance Equation, a first…
The dynamics of adaptation is difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from number fluctuations, called genetic drift, arising in the small number of particularly fit…
The clonal expansion of T cells during an infection is tightly regulated to ensure an appropriate immune response against invading pathogens. Although experiments have mapped the trajectory from expansion to contraction, the interplay…
High-throughput sequencing of B- and T-cell receptors makes it possible to track immune repertoires across time, in different tissues, and in acute and chronic diseases or in healthy individuals. However, quantitative comparison between…
The tumor microenvironment (TME) plays a critical role in cancer cell proliferation, invasion, and resistance to therapy. A principal component of the TME is the tumor immune microenvironment (TIME), which includes various immune cells such…
The immune system recognizes a myriad of invading pathogens and their toxic products. It does so with a finite repertoire of antibodies and T cell receptors. We here describe theories that quantify the immune system dynamics. We describe…
The efficient recognition of pathogens by the adaptive immune system relies on the diversity of receptors displayed at the surface of immune cells. T-cell receptor diversity results from an initial random DNA editing process, called VDJ…
We investigate the relationship of resting-state fMRI functional connectivity estimated over long periods of time with time-varying functional connectivity estimated over shorter time intervals. We show that using Pearson's correlation to…
For most stochastic dynamical systems, variables which are tightly regulated tend to respond slowly to external changes. This idea is often discussed for applicable systems, within a linear response regime, through the Fluctuation…
When confronted with an undesired cell population, such as bacterial infections or tumors, we seek the most effective treatment, designed to eliminate the population as rapidly as possible. A common practice is to monitor the cells…
We consider a general class of Markovian models describing the growth in a randomly fluctuating environment of a clonal biological population having several phenotypes related by stochastic switching. Phenotypes differ e.g. by the level of…
Tumor-immune interactions are shaped by both antigenic heterogeneity and stochastic perturbations in the tumor microenvironment, yet the mathematical mechanisms underlying immune phase transitions remain poorly understood. We propose a…
A cornerstone of the classical view of tolerance is the elimination of self-reactive T cells during negative selection in the thymus. However, high-throughput T-cell receptor sequencing data has so far failed to detect substantial…