High Levels of Extracellular Potassium Can Delay Myxoma Virus Replication by Preventing Release of Virions from the Endosomes.

Potassium (K+) is one of the most abundant cations in the human body. Under normal conditions, the vast majority of K+ is found within cells, and the extracellular [K+] is tightly regulated to within 3.0 to 5.0 mM. However, it has recently been shown that high levels of localized necrosis can increase the extracellular concentration of K+ to above 50 mM. This raises the possibility that elevated extracellular K+ might influence a variety of biological processes that occur within regions of necrotic tissue. For example, K+ has been shown to play a central role in the replication cycles of numerous viral families, and in cases of lytic infection, localized regions containing large numbers of necrotic cells can be formed. Here, we show that the replication of the model poxvirus myxoma virus (MYXV) is delayed by elevated levels of extracellular K+. These increased K+ concentrations alter the cellular endocytic pathway, leading to increased phagocytosis but a loss of endosomal/lysosomal segregation. This slows the release of myxoma virus particles from the endosomes, resulting in delays in genome synthesis and infectious particle formation as well as reduced viral spread. Additionally, mathematical modeling predicts that the extracellular K+ concentrations required to impact myxoma virus replication can be reached in viral lesions under a variety of conditions. Taken together, these data suggest that the extracellular [K+] plays a role in determining the outcomes of myxoma infection and that this effect could be physiologically relevant during pathogenic infection. IMPORTANCE Intracellular K+ homeostasis has been shown to play a major role in the replication of numerous viral families. However, the potential impact of altered extracellular K+ concentrations is less well understood. Our work demonstrates that increased concentrations of extracellular K+ can delay the replication cycle of the model poxvirus MYXV by inhibiting virion release from the endosomes. Additionally, mathematical modeling predicts that the levels of extracellular K+ required to impact MYXV replication can likely be reached during pathogenic infection. These results suggest that localized viral infection can alter K+ homeostasis and that these alterations might directly affect viral pathogenesis.

Stochastic dynamics of human papillomavirus delineates cervical cancer progression.

Starting from a deterministic model, we propose and study a stochastic model for human papillomavirus infection and cervical cancer progression. Our analysis shows that the chronic infection state as random variables which have the ergodic invariant probability measure is necessary for progression from infected cell population to cervical cancer cells. It is shown that small progression rate from infected cells to precancerous cells and small microenvironmental noises associated with the progression rate and viral infection help to establish such chronic infection states. It implicates that large environmental noises associated with viral infection and the progression rate in vivo can reduce chronic infection. We further show that there will be a cervical cancer if the noise associated with precancerous cell growth is large enough. In addition, comparable numerical studies for the deterministic model and stochastic model, together with Hopf bifurcations in both deterministic and stochastic systems, highlight our analytical results.

Deterministic and stochastic modeling for PDGF-driven gliomas reveals a classification of gliomas.

Motivated by our study of infiltrating dynamics of immune cells into tumors, we propose a stochastic model in terms of Ito stochastic differential equations to study how two parameters, the chemoattractant production rate and the chemotactic coefficient, influence immune cell migration and how these parameters distinguish two types of gliomas. We conduct a detailed analysis of the stochastic model and its deterministic counterpart. The deterministic model can differentiate two types of gliomas according to the range of the chemoattractant production rate as two equilibrium solutions, while the stochastic model also can differentiate two types of gliomas according to the ranges of the chemoattractant production rate and chemotactic coefficient with thresholds as one non-zero ergodic invariant measure and one weak persistent state when the noise intensities are small. When the noise intensities are large comparing with the chemotactic coefficient, there is only one type of glioma that corresponds to a non-zero ergodic invariant measure. Using our experimental data, numerical simulations are carried out to demonstrate properties of our models, and we give medical interpretations and implications for our analytical results and numerical simulations. This study also confirms some of our results about IDH gliomas.

Spatial Model for Oncolytic Virotherapy with Lytic Cycle Delay.

We formulate a mathematical model of functional partial differential equations for oncolytic virotherapy which incorporates virus diffusivity, tumor cell diffusion, and the viral lytic cycle based on a basic oncolytic virus dynamics model. We conduct a detailed analysis for the dynamics of the model and carry out numerical simulations to demonstrate our analytic results. Particularly, we establish the positive invariant domain for the [Formula: see text] limit set of the system and show that the model has three spatially homogenous equilibriums solutions. We prove that the spatially uniform virus-free steady state is globally asymptotically stable for any viral lytic period delay and diffusion coefficients of tumor cells and viruses when the viral burst size is smaller than a critical value. We obtain the conditions, for example the ratio of virus diffusion coefficient to that of tumor cells is greater than a value and the viral lytic cycle, is greater than a critical value, under which the spatially uniform positive steady state is locally asymptotically stable. We also obtain conditions under which the system undergoes Hopf bifurcations, and stable periodic solutions occur. We point out medical implications of our results which are difficult to obtain from models without combining diffusive properties of viruses and tumor cells with viral lytic cycles.

ASYMPTOTIC BEHAVIOR OF THE STOCHASTIC KELLER-SEGEL EQUATIONS.

This paper deals with the asymptotic behavior of the solutions of the non-autonomous one-dimensional stochastic Keller-Segel equations defined in a bounded interval with Neumann boundary conditions. We prove the existence and uniqueness of tempered pullback random attractors under certain conditions. We also establish the convergence of the solutions as well as the pullback random attractors of the stochastic equations as the intensity of noise approaches zero.

Mathematical and Computational Modeling for Tumor Virotherapy with Mediated Immunity.

We propose a new mathematical modeling framework based on partial differential equations to study tumor virotherapy with mediated immunity. The model incorporates both innate and adaptive immune responses and represents the complex interaction among tumor cells, oncolytic viruses, and immune systems on a domain with a moving boundary. Using carefully designed computational methods, we conduct extensive numerical simulation to the model. The results allow us to examine tumor development under a wide range of settings and provide insight into several important aspects of the virotherapy, including the dependence of the efficacy on a few key parameters and the delay in the adaptive immunity. Our findings also suggest possible ways to improve the virotherapy for tumor treatment.

Minimal Model of Plankton Systems Revisited with Spatial Diffusion and Maturation Delay.

This study revisits the minimal model for a plankton ecosystem proposed by Scheffer with spatial diffusion of plankton and the delay of the maturation period of herbivorous zooplankton. It deepens our understanding of effects of the nutrients and the predation of fish upon zooplankton on the dynamical patterns of the plankton system and also presents new phenomena induced by the delay with spatial diffusion. When the nutrient level is sufficient low, the zooplankton population collapses and the phytoplankton population reaches its carrying capacity. Mathematically, the global stability of the boundary equilibrium is proved. As the nutrient level increases, the system switches to coexistent equilibria or oscillations depending on the maturation period of zooplankton and the predation rate of fish on herbivorous zooplankton. Under an eutrophic condition, there is a unique coexistent homogeneous equilibrium, and the equilibrium density of phytoplankton increases, while the equilibrium density of herbivorous zooplankton decreases as the fish predation rate on herbivorous zooplankton is increasing. The study shows that the system will never collapses under the eutrophic condition unless the fish predation rate approaches infinite. The study also finds a functional bifurcation relation between the delay parameter of the maturation period of herbivorous zooplankton and the fish predation rate on herbivorous zooplankton that, above a critical value of the fish predation rate, the system stays at the coexistent equilibrium, and below that value, the system switches its dynamical patterns among stable and unstable equilibria and oscillations. The oscillations emerge from Hopf bifurcations, and a detailed mathematical analysis about the Hopf bifurcations is carried out to give relevant ecological predications.

Fairy circles and temporal periodic patterns in the delayed plant-sulfide feedback model.

Incorporating the self-regulatory mechanism with time delay to a plant-sulfide feedback system for intertidal salt marshes, we proposed and studied a functional reaction-diffusion model. We analyzed the stability of the positive steady state of the system, and derived the sufficient conditions for the occurrence of Hopf bifurcations. By deriving the normal form on the center manifold, we obtained the formulas determining the properties of the Hopf bifurcations. Our analysis showed that there is a critical value of time delay. When the time delay is greater than the critical value, the system will show asymptotical temporal periodic patterns while the system will display asymptotical spatial homogeneous patterns when the time delay is smaller than the critical value. Our numerical study showed that there are transient fairy circles for any time delay while there are different types of fairy circles and rings in the system. Our results enhance the concept that transient fairy circle patterns in intertidal salt marshes can infer the underlying ecological mechanisms and provide a measure of ecological resilience when the self-regulatory mechanism with time delay is considered.

A stochastic framework for evaluating CAR T cell therapy efficacy and variability.

Based on a deterministic and stochastic process hybrid model, we use white noises to account for patient variabilities in treatment outcomes, use a hyperparameter to represent patient heterogeneity in a cohort, and construct a stochastic model in terms of Ito stochastic differential equations for testing the efficacy of three different treatment protocols in CAR T cell therapy. The stochastic model has three ergodic invariant measures which correspond to three unstable equilibrium solutions of the deterministic system, while the ergodic invariant measures are attractors under some conditions for tumor growth. As the stable dynamics of the stochastic system reflects long-term outcomes of the therapy, the transient dynamics provide chances of cure in short-term. Two stopping times, the time to cure and time to progress, allow us to conduct numerical simulations with three different protocols of CAR T cell treatment through the transient dynamics of the stochastic model. The probability distributions of the time to cure and time to progress present outcome details of different protocols, which are significant for current clinical study of CAR T cell therapy.

Mathematical model for IL-2-based cancer immunotherapy.

A basic mathematical model for IL-2-based cancer immunotherapy is proposed and studied. Our analysis shows that the outcome of therapy is mainly determined by three parameters, the relative death rate of CD4+ T cells, the relative death rate of CD8+ T cells, and the dose of IL-2 treatment. Minimal equilibrium tumor size can be reached with a large dose of IL-2 in the case that CD4+ T cells die out. However, in cases where CD4+ and CD8+ T cells persist, the final tumor size is independent of the IL-2 dose and is given by the relative death rate of CD4+ T cells. Two groups of in silico clinical trials show some short-term behaviors of IL-2 treatment. IL-2 administration can slow the proliferation of CD4+ T cells, while high doses for a short period of time over several days transiently increase the population of CD8+ T cells during treatment before it recedes to its equilibrium. IL-2 administration for a short period of time over many days suppresses the tumor population for a longer time before approaching its steady-state levels. This implies that intermittent administration of IL-2 may be a good strategy for controlling tumor size.

Mathematical model for two germline stem cells competing for niche occupancy.

In the Drosophila germline stem cell ovary niche, two stem cells compete with each other for niche occupancy to maintain stem cell quality by ensuring that differentiated stem cells are rapidly pushed out the niche and replenished by normal ones (Jin et al. in Cell Stem Cell 2:39-49, 2008). To gain a deeper understanding of this biological phenomenon, we have derived a mathematical model for explaining the physical interactions between two stem cells. The model is a system of two nonlinear first order and one second order differential equations coupled with E-cadherins expression levels. The model can explain the dynamics of the competition process of two germline stem cells and may help to reveal missing information obtained from experimental results. The model predicts several qualitative features in the competition process, which may help to design rational experiments for a better understanding of the stem cell competition process.

Hopf bifurcation without parameters in deterministic and stochastic modeling of cancer virotherapy, part II.

In part II, we analyze our stochastic model which incorporates microenvironmental noises and uncertainties related to immune responses. Outcomes of the therapy in our model are largely determined by the infectivity constant, the infection value, and stochastic relative immune clearance rates. The infection value is a universal critical value for immune-free ergodic invariant probability measures and persistence in all cases. Asymptotic behaviors of the stochastic model are similar to those of its deterministic counterpart. Our stochastic model displays an interesting dynamical behavior, stochastic Hopf bifurcation without parameters, which is a new phenomenon. We perform numerical study to demonstrate how stochastic Hopf bifurcation without parameters occurs. In addition, we give biological implications about our analytical results in stochastic setting versus deterministic setting.

DYNAMICS OF CHOLERA EPIDEMIC MODELS IN FLUCTUATING ENVIRONMENTS.

Based on our deterministic models for cholera epidemics, we propose a stochastic model for cholera epidemics to incorporate environmental fluctuations which is a nonlinear system of Itô stochastic differential equations. We conduct an asymptotical analysis of dynamical behaviors for the model. The basic stochastic reproduction value R s is defined in terms of the basic reproduction number R 0 for the corresponding deterministic model and noise intensities. The basic stochastic reproduction value determines the dynamical patterns of the stochastic model. When R s < 1 , the cholera infection will extinct within finite periods of time almost surely. When R s > 1 , the cholera infection will persist most of time, and there exists a unique stationary ergodic distribution to which all solutions of the stochastic model will approach almost surely as noise intensities are bounded. When the basic reproduction number R 0 for the corresponding deterministic model is greater than 1, and the noise intensities are large enough such that R s < 1 , the cholera infection is suppressed by environmental noises. We carry out numerical simulations to illustrate our analysis, and to compare with the corresponding deterministic model. Biological implications are pointed out.

Basic stochastic model for tumor virotherapy.

The complexity of oncolytic virotherapy arises from many factors. In this study, we incorporate environmental noise and stochastic effects to our basic deterministic model and propose a stochastic model for viral therapy in terms of Ito stochastic differential equations. We conduct a detailed analysis of the model using boundary methods. We find two combined parameters, one describes possibilities of eradicating tumors and one is an increasing function of the viral burst size, which serve as thresholds to classify asymptotical dynamics of the model solution paths. We show there are three ergodic invariant probability measures which correspond to equilibrium states of the deterministic model, and extra possibility to eradicate tumor due to strong variance of tumor growth rate and medium viral burst size. Numerical analysis demonstrates several typical solution paths with biological explanations. In addition, we provide some medical interpretations and implications.

Asymptomatic transmission shifts epidemic dynamics.

Asymptomatic transmission of infectious diseases has been recognized recently in several epidemics or pandemics. There is a great need to incorporate asymptomatic transmissions into traditional modeling of infectious diseases and to study how asymptomatic transmissions shift epidemic dynamics. In this work, we propose a compartmental model with asymptomatic transmissions for waterborne infectious diseases. We conduct a detailed analysis and numerical study with shigellosis data. Two parameters, the proportion $p$ of asymptomatic infected individuals and the proportion $k$ of asymptomatic infectious individuals who can asymptomatically transmit diseases, play major rules in the epidemic dynamics. The basic reproduction number $\mathscr{R}_{0}$ is a decreasing function of parameter $p$ when parameter $k$ is smaller than a critical value while $\mathscr{R}_{0}$ is an increasing function of $p$ when $k$ is greater than the critical value. $\mathscr{R}_{0}$ is an increasing function of $k$ for any value of $p$. When $\mathscr{R}_{0}$ passes through 1 as $p$ or $k$ varies, the dynamics of epidemics is shifted. If asymptomatic transmissions are not counted, $\mathscr{R}_{0}$ will be underestimated while the final size may be overestimated or underestimated. Our study provides a theoretical example for investigating other asymptomatic transmissions and useful information for public health measurements in waterborne infectious diseases.

Mathematical modeling of PDGF-driven glioma reveals the dynamics of immune cells infiltrating into tumors.

BACKGROUND: Tumor-infiltrated immune cells compose a significant component of many cancers. They have been observed to have contradictory impacts on tumors. Although the primary reasons for these observations remain elusive, it is important to understand how immune cells infiltrating into tumors is regulated. Recently our group conducted a series of experimental studies, which showed that muIDH1 gliomas have a significant global reduction of immune cells and suggested that the longer survival time of mice with CIMP gliomas may be due to the IDH mutation and its effect on reducing of the tumor-infiltrated immune cells. However, to comprehend how IDH1 mutants regulate infiltration of immune cells into gliomas and how they affect the aggressiveness of gliomas, it is necessary to integrate our experimental data into a dynamical system to acquire a much deeper understanding of subtle regulation of immune cell infiltration. METHODS: The method is integration of mathematical modeling and experiments. According to mass conservation laws and assumption that immune cells migrate into the tumor site along a chemotactic gradient field, a mathematical model is formulated. Parameters are estimated from our experiments. Numerical methods are developed to solve the problem. Numerical predictions are compared with experimental results. RESULTS: Our analysis shows that the net rate of increase of immune cells infiltrated into the tumor is approximately proportional to the 4/5 power of the chemoattractant production rate, and it is an increasing function of time while the percentage of immune cells infiltrated into the tumor is a decreasing function of time. Our model predicts that wtIDH1 mice will survive longer if the immune cells are blocked by reducing chemotactic coefficient. For more aggressive gliomas, our model shows that there is little difference in their survivals between wtIDH1 and muIDH1 tumors, and the percentage of immune cells infiltrated into the tumor is much lower. These predictions are verified by our experimental results. In addition, wtIDH1 and muIDH1 can be quantitatively distinguished by their chemoattractant production rates, and the chemotactic coefficient determines possibilities of immune cells migration along chemoattractant gradient fields. CONCLUSIONS: The chemoattractant gradient field produced by tumor cells may facilitate immune cells migration to the tumor cite. The chemoattractant production rate may be utilized to classify wtIDH1 and muIDH1 tumors. The dynamics of immune cells infiltrating into tumors is largely determined by tumor cell chemoattractant production rate and chemotactic coefficient.

Stochastic growth pattern of untreated human glioblastomas predicts the survival time for patients.

Glioblastomas are highly malignant brain tumors. Knowledge of growth rates and growth patterns is useful for understanding tumor biology and planning treatment logistics. Based on untreated human glioblastoma data collected in Trondheim, Norway, we first fit the average growth to a Gompertz curve, then find a best fitted white noise term for the growth rate variance. Combining these two fits, we obtain a new type of Gompertz diffusion dynamics, which is a stochastic differential equation (SDE). Newly collected untreated human glioblastoma data in Seattle, US, re-verify our model. Instead of growth curves predicted by deterministic models, our SDE model predicts a band with a center curve as the tumor size average and its width as the tumor size variance over time. Given the glioblastoma size in a patient, our model can predict the patient survival time with a prescribed probability. The survival time is approximately a normal random variable with simple formulas for its mean and variance in terms of tumor sizes. Our model can be applied to studies of tumor treatments. As a demonstration, we numerically investigate different protocols of surgical resection using our model and provide possible theoretical strategies.

Modeling the effects of resection, radiation and chemotherapy in glioblastoma.

The standard treatment for newly diagnosed glioblastoma multiforme is surgical resection followed by radiotherapy and chemotherapy. Most studies on these treatments are retrospective clinical data analysis. To integrate these studies, a mathematical model is developed. The model predicts the survival time of patients who undergo resection, radiation, and chemotherapy with different protocols.

The mutation process in colored coalescent theory.

The mutation process is introduced into the colored coalescent theory. The mutation process can be viewed as an independent Poisson process running on the colored genealogical random tree generated by the colored coalescent process, with the edge lengths of the random tree serving as the time scale for the mutation process. Moving backward along the colored genealogical tree, the color of vertices may change in two ways, when two vertices coalesce, or when a mutation happens. The rule that governs the coalescent change of color involves a parameter x; the rule that governs the mutation involves a parameter micro. Explicit computations of the expectation of the coalescent time (the first hitting time), and the coalescent probabilities (the first hitting probabilities) are carried out. For example, our calculation shows that when x = 1/2, for a sample of n colored individuals, the expected time for the colored coalescent process with the mutation process superimposed to first reach a black MRCA or a white MRCA, respectively, is 3 -- 2/n with probability 1/2 for any value of the parameter micro. On the other hand, the expected time for the colored coalescent process with mutation to first reach a MRCA, either black or white, is 2 -- 2/n for any values of the parameters micro and x, which is the same as that for the standard Kingman coalescent process.

Backward Hopf bifurcation in a mathematical model for oncolytic virotherapy with the infection delay and innate immune effects.

In this paper, we consider a system of delay differential equations that models the oncolytic virotherapy on solid tumours with the delay of viral infection in the presence of the innate immune response. We conduct qualitative and numerical analysis, and provide possible medical implications for our results. The system has four equilibrium solutions. Fixed point analysis indicates that increasing the burst size and infection rate of the viruses has positive contribution to the therapy. However, increasing the immune killing infection rate, the immune stimulation rate, or the immune killing virus rate may lead the treatment failed. The viral infection time delay induces backward Hopf bifurcations, which means that the therapy may fail before time delay increases passing through a Hopf bifurcation. The parameter analysis also shows how saddle-node and Hopf bifurcations occur as viral burst size and other parameters vary, which yields further insights into the dynamics of the virotherapy.