The Effect of Movement Behavior on Population Density in Patchy Landscapes

A stochastic multi-host model for West Nile virus transmission

When initially introduced into a susceptible population, a disease may die out or result in a major outbreak. We present a Continuous-Time Markov Chain model for enzootic WNV transmission between two avian host species and a single vector, and use multitype branching process theory to determine the probability of disease extinction based upon the type of infected individual initially introducing the disease into the population - an exposed vector, infectious vector, or infectious host of either species. We explore how the likelihood of disease extinction depends on the ability of each host species to transmit WNV, vector biting rates on host species, and the relative abundance of host species, as well as vector abundance. Theoretical predictions are compared to the outcome of stochastic simulations. We find the community composition of hosts and vectors, as well as the means of disease introduction, can greatly affect the probability of disease extinction.

Cancer mutationscape: revealing the link between modular restructuring and intervention efficacy among mutations

There is increasing evidence that biological systems are modular in both structure and function. Complex biological signaling networks such as gene regulatory networks (GRNs) are proving to be composed of subcategories that are interconnected and hierarchically ranked. These networks contain highly dynamic processes that ultimately dictate cellular function over time, as well as influence phenotypic fate transitions. In this work, we use a stochastic multicellular signaling network of pancreatic cancer (PC) to show that the variance in topological rankings of the most phenotypically influential modules implies a strong relationship between structure and function. We further show that induction of mutations alters the modular structure, which analogously influences the aggression and controllability of the disease in silico. We finally present evidence that the impact and location of mutations with respect to PC modular structure directly corresponds to the efficacy of single agent treatments in silico, because topologically deep mutations require deep targets for control.

Differentiating spillover: an examination of cross-habitat movement in ecology spillover in ecology

Organisms that immigrate into a recipient habitat generate a movement pattern that affects local population dynamics and the environment. Spillover is the pattern of unidirectional movement from a donor habitat to a different, adjacent recipient habitat. However, ecological definitions are often generalized to include any cross-habitat movement, which limits within- and cross-discipline collaboration. To assess spillover nomenclature, we reviewed 337 studies within the agriculture, disease, fisheries and habitat fragmentation disciplines. Each study's definition of spillover and the methods used were analysed. We identified four descriptors (movement, habitat type and arrangement, and effect) used that differentiate spillover from other cross-habitat movement patterns (dispersal, foray loops and edge movement). Studies often define spillover as movement (45%) but rarely measure it as such (4%), particularly in disease and habitat fragmentation disciplines. Consequently, 98% of studies could not distinguish linear from returning movement out of a donor habitat, which can overestimate movement distance. Overall, few studies (12%) included methods that matched their own definition, revealing a distinct mismatch. Because theory shows that long-term impacts of the different movement patterns can vary, differentiating spillover from other movement patterns is necessary for effective long-term and inter-disciplinary management of organisms that use heterogeneous landscapes.

Phenotype Control techniques for Boolean gene regulatory networks

Modeling cell signal transduction pathways via Boolean networks (BNs) has become an established method for analyzing intracellular communications over the last few decades. What's more, BNs provide a course-grained approach, not only to understanding molecular communications, but also for targeting pathway components that alter the long-term outcomes of the system. This has come to be known as phenotype control theory. In this review we study the interplay of various approaches for controlling gene regulatory networks such as: algebraic methods, control kernel, feedback vertex set, and stable motifs. The study will also include comparative discussion between the methods, using an established cancer model of T-Cell Large Granular Lymphocyte Leukemia. Further, we explore possible options for making the control search more efficient using reduction and modularity. Finally, we will include challenges presented such as the complexity and the availability of software for implementing each of these control techniques.

Picking winners in cell-cell collisions: Wetting, speed, and contact

Groups of eukaryotic cells can coordinate their crawling motion to follow cues more effectively, stay together, or invade new areas. This collective cell migration depends on cell-cell interactions, which are often studied by colliding pairs of cells together. Can the outcome of these collisions be predicted? Recent experiments on trains of colliding epithelial cells suggest that cells with a smaller contact angle to the surface or larger speeds are more likely to maintain their direction ("win") upon collision. When should we expect shape or speed to correlate with the outcome of a collision? To investigate this question, we build a model for two-cell collisions within the phase field framework, which allows for cell shape changes. We can reproduce the observation that cells with high speed and small contact angles are more likely to win with two different assumptions for how cells interact: (1) velocity aligning, in which we hypothesize that cells sense their own velocity and align to it over a finite timescale, and (2) front-front contact repolarization, where cells polarize away from cell-cell contact, akin to contact inhibition of locomotion. Surprisingly, though we simulate collisions between cells with widely varying properties, in each case, the probability of a cell winning is completely captured by a single summary variable: its relative speed (in the velocity-aligning model) or its relative contact angle (in the contact repolarization model). Both models are currently consistent with reported experimental results, but they can be distinguished by varying cell contact angle and speed through orthogonal perturbations.

Modern perspectives on near-equilibrium analysis of Turing systems

In the nearly seven decades since the publication of Alan Turing's work on morphogenesis, enormous progress has been made in understanding both the mathematical and biological aspects of his proposed reaction-diffusion theory. Some of these developments were nascent in Turing's paper, and others have been due to new insights from modern mathematical techniques, advances in numerical simulations and extensive biological experiments. Despite such progress, there are still important gaps between theory and experiment, with many examples of biological patterning where the underlying mechanisms are still unclear. Here, we review modern developments in the mathematical theory pioneered by Turing, showing how his approach has been generalized to a range of settings beyond the classical two-species reaction-diffusion framework, including evolving and complex manifolds, systems heterogeneous in space and time, and more general reaction-transport equations. While substantial progress has been made in understanding these more complicated models, there are many remaining challenges that we highlight throughout. We focus on the mathematical theory, and in particular linear stability analysis of 'trivial' base states. We emphasize important open questions in developing this theory further, and discuss obstacles in using these techniques to understand biological reality. This article is part of the theme issue 'Recent progress and open frontiers in Turing's theory of morphogenesis'.

Modeling the importance of temporary hospital beds on the dynamics of emerged infectious disease

To explore the impact of available and temporarily arranged hospital beds on the prevention and control of an infectious disease, an epidemic model is proposed and investigated. The stability analysis of the associated equilibria is carried out, and a threshold quantity basic reproduction number ( R₀) that governs the disease dynamics is derived and observed whether it depends both on available and temporarily arranged hospital beds. We have used the center manifold theory to derive the normal form and have shown that the proposed model undergoes different types of bifurcations including transcritical (backward and forward), Bogdanov-Takens, and Hopf-bifurcation. Bautin bifurcation is obtained at which the first Lyapunov coefficient vanishes. We have taken advantage of Sotomayor's theorem to establish the saddle-node bifurcation. Numerical simulations are performed to support the theoretical findings.

Mathematical modeling of intervention and low medical resource availability with delays: Applications to COVID-19 outbreaks in Spain and Italy

Infectious diseases have been one of the major causes of human mortality, and mathematical models have been playing significant roles in understanding the spread mechanism and controlling contagious diseases. In this paper, we propose a delayed SEIR epidemic model with intervention strategies and recovery under the low availability of resources. Non-delayed and delayed models both possess two equilibria: the disease-free equilibrium and the endemic equilibrium. When the basic reproduction number $ R_0 = 1 $, the non-delayed system undergoes a transcritical bifurcation. For the delayed system, we incorporate two important time delays: $ \tau_1 $ represents the latent period of the intervention strategies, and $ \tau_2 $ represents the period for curing the infected individuals. Time delays change the system dynamics via Hopf-bifurcation and oscillations. The direction and stability of delay induced Hopf-bifurcation are established using normal form theory and center manifold theorem. Furthermore, we rigorously prove that local Hopf bifurcation implies global Hopf bifurcation. Stability switching curves and crossing directions are analyzed on the two delay parameter plane, which allows both delays varying simultaneously. Numerical results demonstrate that by increasing the intervention strength, the infection level decays; by increasing the limitation of treatment, the infection level increases. Our quantitative observations can be useful for exploring the relative importance of intervention and medical resources. As a timing application, we parameterize the model for COVID-19 in Spain and Italy. With strict intervention policies, the infection numbers would have been greatly reduced in the early phase of COVID-19 in Spain and Italy. We also show that reducing the time delays in intervention and recovery would have decreased the total number of cases in the early phase of COVID-19 in Spain and Italy. Our work highlights the necessity to consider the time delays in intervention and recovery in an epidemic model.

A Mathematical Study of the Influence of Hypoxia and Acidity on the Evolutionary Dynamics of Cancer

Hypoxia and acidity act as environmental stressors promoting selection for cancer cells with a more aggressive phenotype. As a result, a deeper theoretical understanding of the spatio-temporal processes that drive the adaptation of tumour cells to hypoxic and acidic microenvironments may open up new avenues of research in oncology and cancer treatment. We present a mathematical model to study the influence of hypoxia and acidity on the evolutionary dynamics of cancer cells in vascularised tumours. The model is formulated as a system of partial integro-differential equations that describe the phenotypic evolution of cancer cells in response to dynamic variations in the spatial distribution of three abiotic factors that are key players in tumour metabolism: oxygen, glucose and lactate. The results of numerical simulations of a calibrated version of the model based on real data recapitulate the eco-evolutionary spatial dynamics of tumour cells and their adaptation to hypoxic and acidic microenvironments. Moreover, such results demonstrate how nonlinear interactions between tumour cells and abiotic factors can lead to the formation of environmental gradients which select for cells with phenotypic characteristics that vary with distance from intra-tumour blood vessels, thus promoting the emergence of intra-tumour phenotypic heterogeneity. Finally, our theoretical findings reconcile the conclusions of earlier studies by showing that the order in which resistance to hypoxia and resistance to acidity arise in tumours depend on the ways in which oxygen and lactate act as environmental stressors in the evolutionary dynamics of cancer cells.

Addressing the COVID-19 transmission in inner Brazil by a mathematical model

In 2020, the world experienced its very first pandemic of the globalized era. A novel coronavirus, SARS-CoV-2, is the causative agent of severe pneumonia and has rapidly spread through many nations, crashing health systems and leading a large number of people to death. In Brazil, the emergence of local epidemics in major metropolitan areas has always been a concern. In a vast and heterogeneous country, with regional disparities and climate diversity, several factors can modulate the dynamics of COVID-19. What should be the scenario for inner Brazil, and what can we do to control infection transmission in each of these locations? Here, a mathematical model is proposed to simulate disease transmission among individuals in several scenarios, differing by abiotic factors, social-economic factors, and effectiveness of mitigation strategies. The disease control relies on keeping all individuals’ social distancing and detecting, followed by isolating, infected ones. The model reinforces social distancing as the most efficient method to control disease transmission. Moreover, it also shows that improving the detection and isolation of infected individuals can loosen this mitigation strategy. Finally, the effectiveness of control may be different across the country, and understanding it can help set up public health strategies.

Impact of cattle on joint dynamics and disease burden of Japanese encephalitis and leptospirosis

Japanese encephalitis (JE) is a mosquito-borne neglected tropical disease. JE is mostly found in rural areas where people usually keep cattle at home for their needs. Cattle in households reduce JE virus infections since they distract vectors and act as a dead-end host for the virus. However, the presence of cattle introduces risk of leptospirosis infections in humans. Leptospirosis is a bacterial disease that spreads through direct or indirect contact of urine of the infected cattle. Thus, cattle have both positive and negative impacts on human disease burden. This study uses a mathematical model to study the joint dynamics of these two diseases in the presence of cattle and to identify the net impact of cattle on the annual disease burden in JE-prevalent areas. Analysis indicates that the presence of cattle helps to reduce the overall disease burden in JE-prevalent areas. However, this reduction is dominated by the vector's feeding pattern. To the best of our knowledge, this is the first study to examine the joint dynamics of JE and leptospirosis.

Fitness value of information with delayed phenotype switching: Optimal performance with imperfect sensing

The ability of organisms to accurately sense their environment and respond accordingly is critical for evolutionary success. However, exactly how the sensory ability influences fitness is a topic of active research, while the necessity of a time delay between when unreliable environmental cues are sensed and when organisms can mount a response has yet to be explored at any length. Accounting for this delay in phenotype response in models of population growth, we find that a critical error probability can exist under certain environmental conditions: An organism with a sensory system with any error probability less than the critical value can achieve the same long-term growth rate as an organism with a perfect sensing system. We also observe a tradeoff between the evolutionary value of sensory information and robustness to error, mediated by the rate at which the phenotype distribution relaxes to steady state. The existence of the critical error probability could have several important evolutionary consequences, primarily that sensory systems operating at the nonzero critical error probability may be evolutionarily optimal.

Leveraging Computational Modeling to Understand Infectious Diseases

Purpose of Review

Computational and mathematical modeling have become a critical part of understanding in-host infectious disease dynamics and predicting effective treatments. In this review, we discuss recent findings pertaining to the biological mechanisms underlying infectious diseases, including etiology, pathogenesis, and the cellular interactions with infectious agents. We present advances in modeling techniques that have led to fundamental disease discoveries and impacted clinical translation.

Recent Findings

Combining mechanistic models and machine learning algorithms has led to improvements in the treatment of Shigella and tuberculosis through the development of novel compounds. Modeling of the epidemic dynamics of malaria at the within-host and between-host level has afforded the development of more effective vaccination and antimalarial therapies. Similarly, in-host and host-host models have supported the development of new HIV treatment modalities and an improved understanding of the immune involvement in influenza. In addition, large-scale transmission models of SARS-CoV-2 have furthered the understanding of coronavirus disease and allowed for rapid policy implementations on travel restrictions and contract tracing apps.

Summary

Computational modeling is now more than ever at the forefront of infectious disease research due to the COVID-19 pandemic. This review highlights how infectious diseases can be better understood by connecting scientists from medicine and molecular biology with those in computer science and applied mathematics.