Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses.

Macrophages initiate inflammatory responses via the transcription factor NFκB. The temporal pattern of NFκB activity determines which genes are expressed and thus, the type of response that ensues. Here, we examined how information about the stimulus is encoded in the dynamics of NFκB activity. We generated an mVenus-RelA reporter mouse line to enable high-throughput live-cell analysis of primary macrophages responding to host- and pathogen-derived stimuli. An information-theoretic workflow identified six dynamical features-termed signaling codons-that convey stimulus information to the nucleus. In particular, oscillatory trajectories were a hallmark of responses to cytokine but not pathogen-derived stimuli. Single-cell imaging and RNA sequencing of macrophages from a mouse model of Sjögren's syndrome revealed inappropriate responses to stimuli, suggestive of confusion of two NFκB signaling codons. Thus, the dynamics of NFκB signaling classify immune threats through six signaling codons, and signal confusion based on defective codon deployment may underlie the etiology of some inflammatory diseases.

New results on bifurcation for fractional-order octonion-valued neural networks involving delays.

This work chiefly explores fractional-order octonion-valued neural networks involving delays. We decompose the considered fractional-order delayed octonion-valued neural networks into equivalent real-valued systems via Cayley-Dickson construction. By virtue of Lipschitz condition, we prove that the solution of the considered fractional-order delayed octonion-valued neural networks exists and is unique. By constructing a fairish function, we confirm that the solution of the involved fractional-order delayed octonion-valued neural networks is bounded. Applying the stability theory and basic bifurcation knowledge of fractional order differential equations, we set up a sufficient condition remaining the stability behaviour and the appearance of Hopf bifurcation for the addressed fractional-order delayed octonion-valued neural networks. To illustrate the justifiability of the derived theoretical results clearly, we give the related simulation results to support these facts. Simultaneously, the bifurcation plots are also displayed. The established theoretical results in this work have important guiding significance in devising and improving neural networks.

Evolution of Cooperation in Spatio-Temporal Evolutionary Games with Public Goods Feedback.

In biology, evolutionary game-theoretical models often arise in which players' strategies impact the state of the environment, driving feedback between strategy and the surroundings. In this case, cooperative interactions can be applied to studying ecological systems, animal or microorganism populations, and cells producing or actively extracting a growth resource from their environment. We consider the framework of eco-evolutionary game theory with replicator dynamics and growth-limiting public goods extracted by population members from some external source. It is known that the two sub-populations of cooperators and defectors can develop spatio-temporal patterns that enable long-term coexistence in the shared environment. To investigate this phenomenon and unveil the mechanisms that sustain cooperation, we analyze two eco-evolutionary models: a well-mixed environment and a heterogeneous model with spatial diffusion. In the latter, we integrate spatial diffusion into replicator dynamics. Our findings reveal rich strategy dynamics, including bistability and bifurcations, in the temporal system and spatial stability, as well as Turing instability, Turing-Hopf bifurcations, and chaos in the diffusion system. The results indicate that effective mechanisms to promote cooperation include increasing the player density, decreasing the relative timescale, controlling the density of initial cooperators, improving the diffusion rate of the public goods, lowering the diffusion rate of the cooperators, and enhancing the payoffs to the cooperators. We provide the conditions for the existence, stability, and occurrence of bifurcations in both systems. Our analysis can be applied to dynamic phenomena in fields as diverse as human decision-making, microorganism growth factors secretion, and group hunting.

Oscillations in a Spatial Oncolytic Virus Model.

Virotherapy treatment is a new and promising target therapy that selectively attacks cancer cells without harming normal cells. Mathematical models of oncolytic viruses have shown predator-prey like oscillatory patterns as result of an underlying Hopf bifurcation. In a spatial context, these oscillations can lead to different spatio-temporal phenomena such as hollow-ring patterns, target patterns, and dispersed patterns. In this paper we continue the systematic analysis of these spatial oscillations and discuss their relevance in the clinical context. We consider a bifurcation analysis of a spatially explicit reaction-diffusion model to find the above mentioned spatio-temporal virus infection patterns. The desired pattern for tumor eradication is the hollow ring pattern and we find exact conditions for its occurrence. Moreover, we derive the minimal speed of travelling invasion waves for the cancer and for the oncolytic virus. Our numerical simulations in 2-D reveal complex spatial interactions of the virus infection and a new phenomenon of a periodic peak splitting. An effect that we cannot explain with our current methods.

In distributive phosphorylation catalytic constants enable non-trivial dynamics.

Ordered distributive double phosphorylation is a recurrent motif in intracellular signaling and control. It is either sequential (where the site phosphorylated last is dephosphorylated first) or cyclic (where the site phosphorylated first is dephosphorylated first). Sequential distributive double phosphorylation has been extensively studied and an inequality involving only the catalytic constants of kinase and phosphatase is known to be sufficient for multistationarity. As multistationarity is necessary for bistability it has been argued that these constants enable bistability. Here we show for cyclic distributive double phosphorylation that if its catalytic constants satisfy an analogous inequality, then Hopf bifurcations and hence sustained oscillations can occur. Hence we argue that in distributive double phosphorylation (sequential or distributive) the catalytic constants enable non-trivial dynamics. In fact, if the rate constant values in a network of cyclic distributive double phosphorylation satisfy this inequality, then a network of sequential distributive double phosphorylation with the same rate constant values will show multistationarity-albeit for different values of the total concentrations. For cyclic distributive double phosphorylation we further describe a procedure to generate rate constant values where Hopf bifurcations and hence sustained oscillations can occur. This may, for example, allow for an efficient sampling of oscillatory regions in parameter space. Our analysis is greatly simplified by the fact that it is possible to reduce the network of cyclic distributive double phosphorylation to what we call a network with a single extreme ray. We summarize key properties of these networks.

Dynamics and bifurcations in a model of chronic myeloid leukemia with optimal immune response windows.

Chronic Myeloid Leukemia is a blood cancer for which standard therapy with Tyrosine-Kinase Inhibitors is successful in the majority of patients. After discontinuation of treatment half of the well-responding patients either present undetectable levels of tumor cells for a long time or exhibit sustained fluctuations of tumor load oscillating at very low levels. Motivated by the consequent question of whether the observed kinetics reflect periodic oscillations emerging from tumor-immune interactions, in this work, we analyze a system of ordinary differential equations describing the immune response to CML where both the functional response against leukemia and the immune recruitment exhibit optimal activation windows. Besides investigating the stability of the equilibrium points, we provide rigorous proofs that the model exhibits at least two types of bifurcations: a transcritical bifurcation around the tumor-free equilibrium point and a Hopf bifurcation around a biologically plausible equilibrium point, providing an affirmative answer to our initial question. Focusing our attention on the Hopf bifurcation, we examine the emergence of limit cycles and analyze their stability through the calculation of Lyapunov coefficients. Then we illustrate our theoretical results with numerical simulations based on clinically relevant parameters. Besides the mathematical interest, our results suggest that the fluctuating levels of low tumor load observed in CML patients may be a consequence of periodic orbits arising from predator-prey-like interactions.

Effects of whaling and krill fishing on the whale-krill predation dynamics: bifurcations in a harvested predator-prey model with Holling type I functional response.

In the Antarctic, the whale population had been reduced dramatically due to the unregulated whaling. It was expected that Antarctic krill, the main prey of whales, would grow significantly as a consequence and exploratory krill fishing was practiced in some areas. However, it was found that there has been a substantial decline in abundance of krill since the end of whaling, which is the phenomenon of krill paradox. In this paper, to study the krill-whale interaction we revisit a harvested predator-prey model with Holling I functional response. We find that the model admits at most two positive equilibria. When the two positive equilibria are located in the region { ( N , P ) | 0 ≤ N < 2 N c , P ≥ 0 } , the model exhibits degenerate Bogdanov-Takens bifurcation with codimension up to 3 and Hopf bifurcation with codimension up to 2 by rigorous bifurcation analysis. When the two positive equilibria are located in the region { ( N , P ) | N > 2 N c , P ≥ 0 } , the model has no complex bifurcation phenomenon. When there is one positive equilibrium on each side of N = 2 N c , the model undergoes Hopf bifurcation with codimension up to 2. Moreover, numerical simulation reveals that the model not only can exhibit the krill paradox phenomenon but also has three limit cycles, with the outmost one crosses the line N = 2 N c under some specific parameter conditions.

Mutations make pandemics worse or better: modeling SARS-CoV-2 variants and imperfect vaccination.

COVID-19 is a respiratory disease triggered by an RNA virus inclined to mutations. Since December 2020, variants of COVID-19 (especially Delta and Omicron) continuously appeared with different characteristics that influenced death and transmissibility emerged around the world. To address the novel dynamics of the disease, we propose and analyze a dynamical model of two strains, namely native and mutant, transmission dynamics with mutation and imperfect vaccination. It is also assumed that the recuperated individuals from the native strain can be infected with mutant strain through the direct contact with individual or contaminated surfaces or aerosols. We compute the basic reproduction number, R 0 , which is the maximum of the basic reproduction numbers of native and mutant strains. We prove the nonexistence of backward bifurcation using the center manifold theory, and global stability of disease-free equilibrium when R 0 < 1 , that is, vaccine is effective enough to eliminate the native and mutant strains even if it cannot provide full protection. Hopf bifurcation appears when the endemic equilibrium loses its stability. An intermediate mutation rate ν 1 leads to oscillations. When ν 1 increases over a threshold, the system regains its stability and exhibits an interesting dynamics called endemic bubble. An analytical expression for vaccine-induced herd immunity is derived. The epidemiological implication of the herd immunity threshold is that the disease may effectively be eradicated if the minimum herd immunity threshold is attained in the community. Furthermore, the model is parameterized using the Indian data of the cumulative number of confirmed cases and deaths of COVID-19 from March 1 to September 27 in 2021, using MCMC method. The cumulative cases and deaths can be reduced by increasing the vaccine efficacies to both native and mutant strains. We observe that by considering the vaccine efficacy against native strain as 90%, both cumulative cases and deaths would be reduced by 0.40%. It is concluded that increasing immunity against mutant strain is more influential than the vaccine efficacy against it in controlling the total cases. Our study demonstrates that the COVID-19 pandemic may be worse due to the occurrence of oscillations for certain mutation rates (i.e., outbreaks will occur repeatedly) but better due to stability at a lower infection level with a larger mutation rate. We perform sensitivity analysis using the Latin Hypercube Sampling methodology and partial rank correlation coefficients to illustrate the impact of parameters on the basic reproduction number, the number of cumulative cases and deaths, which ultimately sheds light on disease mitigation.

Hopf bifurcation in an age-structured predator-prey system with Beddington-DeAngelis functional response and constant harvesting.

In this paper, an age-structured predator-prey system with Beddington-DeAngelis (B-D) type functional response, prey refuge and harvesting is investigated, where the predator fertility function f(a) and the maturation function ß ( a ) are assumed to be piecewise functions related to their maturation period τ . Firstly, we rewrite the original system as a non-densely defined abstract Cauchy problem and show the existence of solutions. In particular, we discuss the existence and uniqueness of a positive equilibrium of the system. Secondly, we consider the maturation period τ as a bifurcation parameter and show the existence of Hopf bifurcation at the positive equilibrium by applying the integrated semigroup theory and Hopf bifurcation theorem. Moreover, the direction of Hopf bifurcation and the stability of bifurcating periodic solutions are studied by applying the center manifold theorem and normal form theory. Finally, some numerical simulations are given to illustrate of the theoretical results and a brief discussion is presented.

The impact of harvesting on the evolutionary dynamics of prey species in a prey-predator systems.

Matsuda and Abrams (Theor Popul Biol 45(1):76-91, 1994) initiated the exploration of self-extinction in species through evolution, focusing on the advantageous position of mutants near the extinction boundary in a prey-predator system with evolving foraging traits. Previous models lacked theoretical investigation into the long-term effects of harvesting. In our model, we introduce constant-effort prey and predator harvesting, along with individual logistic growth of predators. The model reveals two distinct evolutionary outcomes: (i) Evolutionary suicide, marked by a saddle-node bifurcation, where prey extinction results from the invasion of a lower forager mutant; and (ii) Evolutionary reversal, characterized by a subcritical Hopf bifurcation, leading to cyclic prey evolution. Employing an innovative approach based on Gröbner basis computation, we identify various bifurcation manifolds, including fold, transcritical, cusp, Hopf, and Bogdanov-Takens bifurcations. These contrasting scenarios emerge from variations in harvesting parameters while keeping other factors constant, rendering the model an intriguing subject of study.

Improved Mathematical Models of Parkinson's Disease with Hopf Bifurcation and Huntington's Disease with Chaos.

Using delay differential equations to study mathematical models of Parkinson's disease and Huntington's disease is important to show how important it is for synchronization between basal ganglia loops to work together. We used the delay circuit RLC (resistor, inductor, capacitor) model to show how the direct pathway and the indirect pathway in the basal ganglia excite and inhibit the motor cortex, respectively. A term has been added to the mathematical model without time delay in the case of the hyperdirect pathway. It is proposed to add a non-linear term to adjust the synchronization. We studied Hopf bifurcation conditions for the proposed models. The desynchronization of response times between the direct pathway and the indirect pathway leads to different symptoms of Parkinson's disease. Tremor appears when the response time in the indirect pathway increases at rest. The simulation confirmed that tremor occurs and the motor cortex is in an inhibited state. The direct pathway can increase the time delay in the dopaminergic pathway, which significantly increases the activity of the motor cortex. The hyperdirect pathway regulates the activity of the motor cortex. The simulation showed bradykinesia occurs when we switch from one movement to another that is less exciting for the motor cortex. A decrease of GABA in the striatum or delayed excitation of the substantia nigra from the subthalamus may be a major cause of Parkinson's disease. An increase in the response time delay in one of the pathways results in the chaotic movement characteristic of Huntington's disease.

Are physiological oscillations physiological?

Despite widespread and striking examples of physiological oscillations, their functional role is often unclear. Even glycolysis, the paradigm example of oscillatory biochemistry, has seen questions about its oscillatory function. Here, we take a systems approach to argue that oscillations play critical physiological roles, such as enabling systems to avoid desensitization, to avoid chronically high and therefore toxic levels of chemicals, and to become more resistant to noise. Oscillation also enables complex physiological systems to reconcile incompatible conditions such as oxidation and reduction, by cycling between them, and to synchronize the oscillations of many small units into one large effect. In pancreatic ß-cells, glycolytic oscillations synchronize with calcium and mitochondrial oscillations to drive pulsatile insulin release, critical for liver regulation of glucose. In addition, oscillation can keep biological time, essential for embryonic development in promoting cell diversity and pattern formation. The functional importance of oscillatory processes requires a re-thinking of the traditional doctrine of homeostasis, holding that physiological quantities are maintained at constant equilibrium values, a view that has largely failed in the clinic. A more dynamic approach will initiate a paradigm shift in our view of health and disease. A deeper look into the mechanisms that create, sustain and abolish oscillatory processes requires the language of nonlinear dynamics, well beyond the linearization techniques of equilibrium control theory. Nonlinear dynamics enables us to identify oscillatory ('pacemaking') mechanisms at the cellular, tissue and system levels.

Waves of infection emerging from coupled social and epidemiological dynamics.

The coronavirus (SARS-CoV-2) exhibited waves of infection in 2020 and 2021 in Japan. The number of infected had multiple distinct peaks at intervals of several months. One possible process causing these waves of infection is people switching their activities in response to the prevalence of infection. In this paper, we present a simple model for the coupling of social and epidemiological dynamics. The assumptions are as follows. Each person switches between active and restrained states. Active people move more often to crowded areas, interact with each other, and suffer a higher rate of infection than people in the restrained state. The rate of transition from restrained to active states is enhanced by the fraction of currently active people (conformity), whereas the rate of backward transition is enhanced by the abundance of infected people (risk avoidance). The model may show transient or sustained oscillations, initial-condition dependence, and various bifurcations. The infection is maintained at a low level if the recovery rate is between the maximum and minimum levels of the force of infection. In addition, waves of infection may emerge instead of converging to the stationary abundance of infected people if both conformity and risk avoidance of people are strong.

Critical observation of WHO recommended multidrug therapy on the disease leprosy through mathematical study.

Leprosy is a skin disease and it is characterized by a disorder of the peripheral nervous system which occurs due to the infection of Schwann cells. In this research article, we have formulated a four-dimensional ODE-based mathematical model which consists of the densities of healthy Schwann cells, infected Schwann cells, M. leprae bacteria, and the concentration of multidrug therapy (MDT). This work primarily aims on exploring the dynamical changes and interrelations of the system cell populations during the disease progression. Also, evaluating a critical value of the drug efficacy rate of MDT remains our key focus in this article so that a safe drug dose regimen for leprosy can be framed more effectively and realistically. We have examined the stability scenario of different equilibria and the occurrence of Hopf-bifurcation for the densities of our system cell populations with respect to the drug efficacy rate of MDT to gain insight on the precise impact of the efficiency rate on both the infected Schwann cell and the bacterial populations. Also, a necessary transversality condition for the occurrence of the bifurcation has been established. Our analytical and numerical investigations in this research work precisely explores that the process of demyelination, nerve regeneration, and infection of the healthy Schwann cells are the three most crucial factors in the leprosy pathogenesis and to control the M. leprae-induced infection of Schwann cells successfully, a more flexible version of MDT regime with efficacy rate varying in the range η∈(0.025,0.059) for 100-120 days in PB cases and 300 days in MB cases obtained in this research article should be applied. All of our analytical outcomes have been verified through numerical simulations and compared with some existing clinical findings.

Treatment of melanoma with dendritic cell vaccines and immune checkpoint inhibitors: A mathematical modeling study.

Dendritic cell (DC) vaccines and immune checkpoint inhibitors (ICIs) play critical roles in shaping the immune responses of tumor cells (TCs) and are widely used in cancer immunotherapies. Quantitatively evaluating the effectiveness of these therapies are essential for the optimization of treatment strategies. Here, based on the combined therapy of melanoma with DC vaccines and ICIs, we formulated a mathematical model to investigate the dynamic interactions between TCs and the immune system and understand the underlying mechanisms of immunotherapy. First, we obtained a threshold parameter for the growth of TCs, which is given by the ratio of spontaneous proliferation to immune inhibition. Next, we proved the existence and locally asymptotic stability of steady states of tumor-free, tumor-dominant, and tumor-immune coexistent equilibria, and identified the existence of Hopf bifurcation of the proposed model. Furthermore, global sensitivity analysis showed that the growth of TCs strongly correlates with the injection rate of DC vaccines, the activation rate of CTLs, and the killing rate of TCs. Finally, we tested the efficacy of multiple monotherapies and combined therapies with model simulations. Our results indicate that DC vaccines can decelerate the growth of TCs, and ICIs can inhibit the growth of TCs. Besides, both therapies can prolong the lifetime of patients, and the combined therapy of DC vaccines and ICIs can effectively eradicate TCs.

Bistability at the onset of neuronal oscillations.

The Hodgkin-Huxley (HH) model and squid axon (bathed in reduced Ca2+) fire repetitively for steady current injection. Moreover, for a current-range just suprathreshold, repetitive firing coexists with a stable steady state. Neuronal excitability, as such, shows bistability and hysteresis providing the opportunity for the system to perform as switchable between firing and non-firing states with transient input and providing the backbone as a dynamical mechanism for bursting oscillations. Some conditions for bistability can be derived by intricate analysis (bifurcation theory) and characterized by simulation, but conditions for emergence and robustness of such bistability do not typically follow from intuition. Here, we demonstrate with a semi-quantitative two-variable, V-w, reduction of the HH model features that promote/reduce bistability. Visualization of flow and trajectories in the V-w phase plane provides an intuitive grasp for bistability. The geometry of action potential recovery involves a late phase during which the dynamic negative feedback of [Formula: see text] inactivation and [Formula: see text] activation over/undershoot, respectively, their resting values, thereby leading to hyperexcitabilty and an intrinsically generated opportunity to by-pass the spiral-like stable rest state and initiate the next spike upstroke. We illustrate control of bistability and dependence of the degree of hysteresis on recovery timescales and gating properties. Our dynamical dissection reveals the strongly attracting depolarized phase of the spike, enabling approximations like the resetting feature of adapting integrate-and-fire models. We extend our insights and show that the Morris-Lecar model can also exhibit robust bistability.

Temporary Cross-Immunity as a Plausible Driver of Asynchronous Cycles of Dengue Serotypes.

Many infectious diseases exist as multiple variants, with interactions between variants potentially driving epidemiological dynamics. These diseases include dengue, which infects hundreds of millions of people every year and exhibits complex multi-serotype dynamics. Antibodies produced in response to primary infection by one of the four dengue serotypes can produce a period of temporary cross-immunity (TCI) to infection by other serotypes. After this period, the remaining antibodies can facilitate the entry of heterologous serotypes into target cells, thus enhancing severity of secondary infection by a heterologous serotype. This represents antibody-dependent enhancement (ADE). In this study, we analyze an epidemiological model to provide novel insights into the importance of TCI and ADE in producing cyclic outbreaks of dengue serotypes. Our analyses reveal that without TCI, such cyclic outbreaks are synchronous across serotypes and only occur when ADE produces high transmission rates. In contrast, the presence of TCI allows asynchronous cycles of serotypes by inducing a time lag between recovery from primary infection by one serotype and secondary infection by another, with such cycles able to occur without ADE. Our results suggest that TCI is a fundamental driver of asynchronous cycles of dengue serotypes and possibly other multi-variant diseases.

Rich dynamics of a bidirectionally linked immuno-epidemiological model for cholera.

Cholera is an environmentally driven disease where the human hosts both ingest the pathogen from polluted environment and shed the pathogen to the environment, generating a two-way feedback cycle. In this paper, we propose a bidirectionally linked immuno-epidemiological model to study the interaction of within- and between-host cholera dynamics. We conduct a rigorous analysis for this multiscale model, with a focus on the stability and bifurcation properties of each feasible equilibrium. We find that the parameter that represents the bidirectional connection is a key factor in shaping the rich dynamics of the system, including the occurrence of the backward bifurcation and Hopf bifurcation. Numerical results illustrate a practical application of our model and add new insight into the prevention and intervention of cholera epidemics.

Substrate inhibition can produce coexistence and limit cycles in the chemostat model with allelopathy.

In this work, we consider a model of two microbial species in a chemostat in which one of the competitors can produce a toxin (allelopathic agent) against the other competitor, and is itself inhibited by the substrate. The existence and stability conditions of all steady states of the reduced model in the plane are determined according to the operating parameters. With Michaelis-Menten or Monod growth functions, it is well known that the model can have a unique positive equilibrium which is unstable as long as it exists. By including both monotone and non-monotone growth functions (which is the case when there is substrate inhibition), it is shown that a new positive equilibrium point exists which can be stable according to the operating parameters of the system. This general model exhibits a rich behavior with the coexistence of two microbial species, the multi-stability, the occurrence of stable limit cycles through super-critical Hopf bifurcations and the saddle-node bifurcation of limit cycles. Moreover, the operating diagram describes some asymptotic behavior of this model by varying the operating parameters and illustrates the effect of the inhibition on the emergence of the coexistence region of the species.

Dynamical analysis of a glucose-insulin regulatory system with insulin-degrading enzyme and multiple delays.

This paper investigates the dynamics of a glucose-insulin regulatory system model that incorporates: (1) insulin-degrading enzyme in the insulin equation; and (2) discrete time delays respectively in the insulin production term, hepatic glucose production term, and the insulin-degrading enzyme. We provide rigorous results of our model including the asymptotic stability of the equilibrium solution and the existence of Hopf bifurcation. We show that analytically and numerically at a certain value the time delays driven stability or instability occurs when the corresponding model has an interior equilibrium. Moreover, we illustrate the oscillatory regulation and insulin secretion via numerical simulations, which show that the model dynamics exhibit physiological observations and more information by allowing parameters to vary. Our results may provide useful biological insights into diabetes for the glucose-insulin regulatory system model.