Modeling delay of age at natural menopause with planned tissue cryopreservation and autologous transplantation.

BACKGROUND: Ovarian tissue cryopreservation has been proven to preserve fertility against gonadotoxic treatments. It has not been clear how this procedure would perform if planned for slowing ovarian aging. OBJECTIVE: This study aimed to determine the feasibility of cryopreserving ovarian tissue to extend reproductive life span and delay menopause by autotransplantation near menopause. STUDY DESIGN: Based on the existing biological data on follicle loss rates, a stochastic model of primordial follicle wastage was developed to determine the years of delay in menopause (denoted by D) by ovarian tissue cryopreservation and transplantation near menopause. Our model accounted for (1) age at ovarian tissue harvest (21-40 years), (2) the amount of ovarian cortex harvested, (3) transplantation of harvested tissues in single vs multiple procedures (fractionation), and (4) posttransplant follicle survival (40% [conservative] vs 80% [improved] vs 100% [ideal or hypothetical]). RESULTS: Our model predicted that, for most women aged <40 years, ovarian tissue cryopreservation and transplantation would result in a significant delay in menopause. The advantage is greater if the follicle loss after transplant can be minimized. As an example, the delay in menopause (D) for a woman with a median ovarian reserve who cryopreserves 25% of her ovarian cortex at the age of 25 years and for whom 40% of follicles survive after transplantation would be approximately 11.8 years, but this extends to 15.5 years if the survival is 80%. As another novel finding, spreading the same amount of tissue to repetitive transplants significantly extends the benefit. For example, for the same 25-year-old woman with a median ovarian reserve, 25% cortex removal, and 40% follicle survival, fractionating the transplants to 3 or 6 procedures would result in the corresponding delay in menopause (D) of 23 or 31 years. The same conditions (3 or 6 procedures) would delay menopause as much as 47 years if posttransplant follicle survival is improved to 80% with modern approaches. An interactive Web tool was created to test all variables and the feasibility of ovarian tissue freezing and transplantation to delay ovarian aging (here). CONCLUSION: Our model predicts that with harvesting at earlier adult ages and better transplant techniques, a significant menopause postponement and, potentially, fertile life span extension can be achieved by ovarian tissue cryopreservation and transplantation in healthy women.

Understanding and Quantifying Network Robustness to Stochastic Inputs.

A variety of biomedical systems are modeled by networks of deterministic differential equations with stochastic inputs. In some cases, the network output is remarkably constant despite a randomly fluctuating input. In the context of biochemistry and cell biology, chemical reaction networks and multistage processes with this property are called robust. Similarly, the notion of a forgiving drug in pharmacology is a medication that maintains therapeutic effect despite lapses in patient adherence to the prescribed regimen. What makes a network robust to stochastic noise? This question is challenging due to the many network parameters (size, topology, rate constants) and many types of noisy inputs. In this paper, we propose a summary statistic to describe the robustness of a network of linear differential equations (i.e. a first-order mass-action system). This statistic is the variance of a certain random walk passage time on the network. This statistic can be quickly computed on a modern computer, even for complex networks with thousands of nodes. Furthermore, we use this statistic to prove theorems about how certain network motifs increase robustness. Importantly, our analysis provides intuition for why a network is or is not robust to noise. We illustrate our results on thousands of randomly generated networks with a variety of stochastic inputs.

How drug onset rate and duration of action affect drug forgiveness.

Medication nonadherence is one of the largest problems in healthcare today, particularly for patients undergoing long-term pharmacotherapy. To combat nonadherence, it is often recommended to prescribe so-called "forgiving" drugs, which maintain their effect despite lapses in patient adherence. Nevertheless, drug forgiveness is difficult to quantify and compare between different drugs. In this paper, we construct and analyze a stochastic pharmacokinetic/pharmacodynamic (PK/PD) model to quantify and understand drug forgiveness. The model parameterizes a medication merely by an effective rate of onset of effect when the medication is taken (on-rate) and an effective rate of loss of effect when a dose is missed (off-rate). Patient dosing is modeled by a stochastic process that allows for correlations in missed doses. We analyze this "on/off" model and derive explicit formulas that show how treatment efficacy depends on drug parameters and patient adherence. As a case study, we compare the effects of nonadherence on the efficacy of various antihypertensive medications. Our analysis shows how different drugs can have identical efficacies under perfect adherence, but vastly different efficacies for adherence patterns typical of actual patients. We further demonstrate that complex PK/PD models can indeed be parameterized in terms of effective on-rates and off-rates. Finally, we have created an online app to allow pharmacometricians to explore the implications of our model and analysis.

Why is there an "oversupply" of human ovarian follicles?†.

Women are born with hundreds of thousands to over a million primordial ovarian follicles (PFs) in their ovarian reserve. However, only a few hundred PFs will ever ovulate and produce a mature egg. Why are hundreds of thousands of PFs endowed around the time of birth when far fewer follicles are required for ongoing ovarian endocrine function and only a few hundred will survive to ovulate? Recent experimental, bioinformatics, and mathematical analyses support the hypothesis that PF growth activation (PFGA) is inherently stochastic. In this paper, we propose that the oversupply of PFs at birth enables a simple stochastic PFGA mechanism to yield a steady supply of growing follicles that lasts for several decades. Assuming stochastic PFGA, we apply extreme value theory to histological PF count data to show that the supply of growing follicles is remarkably robust to a variety of perturbations and that the timing of ovarian function cessation (age of natural menopause) is surprisingly tightly controlled. Though stochasticity is often viewed as an obstacle in physiology and PF oversupply has been called "wasteful," this analysis suggests that stochastic PFGA and PF oversupply function together to ensure robust and reliable female reproductive aging.

Boundary homogenization for patchy surfaces trapping patchy particles.

Trapping diffusive particles at surfaces is a key step in many systems in chemical and biological physics. Trapping often occurs via reactive patches on the surface and/or the particle. The theory of boundary homogenization has been used in many prior works to estimate the effective trapping rate for such a system in the case that either (i) the surface is patchy and the particle is uniformly reactive or (ii) the particle is patchy and the surface is uniformly reactive. In this paper, we estimate the trapping rate for the case that the surface and the particle are both patchy. In particular, the particle diffuses translationally and rotationally and reacts with the surface when a patch on the particle contacts a patch on the surface. We first formulate a stochastic model and derive a five-dimensional partial differential equation describing the reaction time. We then use matched asymptotic analysis to derive the effective trapping rate, assuming that the patches are roughly evenly distributed and occupy a small fraction of the surface and the particle. This trapping rate involves the electrostatic capacitance of a four-dimensional duocylinder, which we compute using a kinetic Monte Carlo algorithm. We further use Brownian local time theory to derive a simple heuristic estimate of the trapping rate and show that it is remarkably close to the asymptotic estimate. Finally, we develop a kinetic Monte Carlo algorithm to simulate the full stochastic system and then use these simulations to confirm the accuracy of our trapping rate estimates and homogenization theory.

Slowest first passage times, redundancy, and menopause timing.

Biological events are often initiated when a random "searcher" finds a "target," which is called a first passage time (FPT). In some biological systems involving multiple searchers, an important timescale is the time it takes the slowest searcher(s) to find a target. For example, of the hundreds of thousands of primordial follicles in a woman's ovarian reserve, it is the slowest to leave that trigger the onset of menopause. Such slowest FPTs may also contribute to the reliability of cell signaling pathways and influence the ability of a cell to locate an external stimulus. In this paper, we use extreme value theory and asymptotic analysis to obtain rigorous approximations to the full probability distribution and moments of slowest FPTs. Though the results are proven in the limit of many searchers, numerical simulations reveal that the approximations are accurate for any number of searchers in typical scenarios of interest. We apply these general mathematical results to models of ovarian aging and menopause timing, which reveals the role of slowest FPTs for understanding redundancy in biological systems. We also apply the theory to several popular models of stochastic search, including search by diffusive, subdiffusive, and mortal searchers.

Inferences from FRAP data are model dependent: A subdiffusive analysis.

Fluorescence recovery after photobleaching (FRAP) is a widely used biological experiment to study the kinetics of molecules that react and move randomly. Since the development of FRAP in the 1970s, many reaction-diffusion models have been used to interpret FRAP data. However, intracellular molecules are widely observed to move by anomalous subdiffusion instead of normal diffusion. In this article, we extend a popular reaction-diffusion model of FRAP to the case of subdiffusion modeled by a fractional diffusion equation. By analyzing this reaction-subdiffusion model, we show that FRAP data are consistent with both diffusive and subdiffusive motion in many scenarios. We illustrate this general result by fitting our model to FRAP data from glucocorticoid receptors in a cell nucleus. We further show that the assumed model of molecular motion (normal diffusion or subdiffusion) strongly impacts the biological parameter values inferred from a given experimentally observed FRAP curve. We additionally analyze our model in three simplified parameter regimes and discuss parameter identifiability for varying subdiffusion exponents.

Spiracular fluttering decouples oxygen uptake and water loss: a stochastic PDE model of respiratory water loss in insects.

In insect respiration, oxygen from the air diffuses through a branching system of air-filled tubes to the cells of the body and carbon dioxide produced in cellular respiration diffuses out. The tracheal system has a very large surface area, so water loss is a potential threat and the question of how insects regulate oxygen uptake and water loss has been an important issue in insect physiology for the past century. The tracheal system starts at spiracles on the surface of the body that insects can open and close, and three phases are observed experimentally, open or closed for relatively long periods of time and opening and closing rapidly, which is called fluttering. In previous work we have shown that during this flutter phase, no matter how small the percentage of time that the spiracles are open, the insect can absorb almost as much oxygen as if the spiracle were always open, if the insect flutters fast enough. This left open the question of water loss during the flutter phase, which is the question addressed in this paper. We formulate a stochastic diffusion-convection model for the concentration of water vapor in the tracheae. Mathematical analysis of the model yields an explicit formula for water loss as a function of six non-dimensional parameters and we use experimental data from various insects to show that, for parameters in the physiological ranges, water loss during the flutter phase is approximately proportional to the percentage of time open. This means that the insect can solve the oxygen uptake versus water loss problem by choosing to have their spiracles open a small percentage of time during the flutter phase and fluttering rapidly.

Should patients skip late doses of medication? A pharmacokinetic perspective.

Missed doses, late doses, and other dosing irregularities are major barriers to effective pharmacotherapy, especially for the treatment of chronic conditions. What should a patient do if they did not take their last dose at the prescribed time? Should they take it late or skip it? In this paper, we investigate the pharmacokinetic effects of taking a late dose. We consider a single compartment model with linear absorption and elimination for a patient instructed to take doses at regular time intervals. We suppose that the patient forgets to take a dose and then realizes some time later and must decide what remedial steps to take. Using mathematical analysis, we derive several metrics which quantify the effects of taking the dose late. The metrics involve the difference between the drug concentration time courses for the case that the dose is taken late and the case that the dose is taken on time. In particular, the metrics are the integral of the absolute difference over all time, the maximum of the difference, and the maximum of the integral of the difference over any single dosing interval. We apply these general mathematical formulas to levothyroxine, atorvastatin, and immediate release and extended release formulations of lamotrigine. We further show how population variability can be immediately incorporated into these results. Finally, we use this analysis to propose general principles and strategies for dealing with dosing irregularities.

A pharmacokinetic and pharmacodynamic analysis of drug forgiveness.

Nonadherence to medication is a major public health problem. To combat nonadherence, some clinicians have suggested using "forgiving" drugs, which maintain efficacy in spite of delayed or missed doses. What pharmacokinetic (PK) and pharmacodynamic (PD) factors make a drug forgiving? In this paper, we address this question by analyzing a linear PK/PD model for a patient with imperfect adherence. We assume that the drug effect is far from maximal and consider direct effect, effect compartment (biophase), and indirect response PD models. We prove that the average drug effect relative to the clinically desired effect is simply the fraction of prescribed doses actually taken by the patient. Hence, under these assumptions, drug forgiveness cannot be defined in terms of the average effect. We argue that forgiveness should instead be understood in terms of effect fluctuations. We prove that the rates of PK absorption, PK elimination, and PD elimination are exactly equivalent for determining effect fluctuations. We prove all the aforementioned results for any pattern of nonadherence, including late doses, missed doses, drug holidays, extra doses, etc. To obtain quantitative estimates of effect fluctuations, we consider a simple statistical pattern of nonadherence and analytically calculate the coefficient of variation of effect. We further show how effect fluctuations can be reduced by taking an extra "make up" dose following a missed dose if any one of the aforementioned PK/PD rates is sufficiently slow. We illustrate some of our results for a nonlinear indirect response model of metformin.

Revising Berg-Purcell for finite receptor kinetics.

From nutrient uptake to chemoreception to synaptic transmission, many systems in cell biology depend on molecules diffusing and binding to membrane receptors. Mathematical analysis of such systems often neglects the fact that receptors process molecules at finite kinetic rates. A key example is the celebrated formula of Berg and Purcell for the rate that cell surface receptors capture extracellular molecules. Indeed, this influential result is only valid if receptors transport molecules through the cell wall at a rate much faster than molecules arrive at receptors. From a mathematical perspective, ignoring receptor kinetics is convenient because it makes the diffusing molecules independent. In contrast, including receptor kinetics introduces correlations between the diffusing molecules because, for example, bound receptors may be temporarily blocked from binding additional molecules. In this work, we present a modeling framework for coupling bulk diffusion to surface receptors with finite kinetic rates. The framework uses boundary homogenization to couple the diffusion equation to nonlinear ordinary differential equations on the boundary. We use this framework to derive an explicit formula for the cellular uptake rate and show that the analysis of Berg and Purcell significantly overestimates uptake in some typical biophysical scenarios. We confirm our analysis by numerical simulations of a many-particle stochastic system.

Designing Drug Regimens that Mitigate Nonadherence.

Medication adherence is a well-known problem for pharmaceutical treatment of chronic diseases. Understanding how nonadherence affects treatment efficacy is made difficult by the ethics of clinical trials that force patients to skip doses of the medication being tested, the unpredictable timing of missed doses by actual patients, and the many competing variables that can either mitigate or magnify the deleterious effects of nonadherence, such as pharmacokinetic absorption and elimination rates, dosing intervals, dose sizes, and adherence rates. In this paper, we formulate and analyze a mathematical model of the drug concentration in an imperfectly adherent patient. Our model takes the form of the standard single compartment pharmacokinetic model with first-order absorption and elimination, except that the patient takes medication only at a given proportion of the prescribed dosing times. Doses are missed randomly, and we use stochastic analysis to study the resulting random drug level in the body. We then use our mathematical results to propose principles for designing drug regimens that are robust to nonadherence. In particular, we quantify the resilience of extended release drugs to nonadherence, which is quite significant in some circumstances, and we show the benefit of taking a double dose following a missed dose if the drug absorption or elimination rate is slow compared to the dosing interval. We further use our results to compare some antiepileptic and antipsychotic drug regimens.

What should patients do if they miss a dose of medication? A theoretical approach.

Medication adherence is a major problem for patients with chronic diseases that require long term pharmacotherapy. Many unanswered questions surround adherence, including how adherence rates translate into treatment efficacy and how missed doses of medication should be handled. To address these questions, we formulate and analyze a mathematical model of the drug concentration in a patient with imperfect adherence. We find exact formulas for drug concentration statistics, including the mean, the coefficient of variation, and the deviation from perfect adherence. We determine how adherence rates translate into drug concentrations, and how this depends on the drug half-life, the dosing interval, and how missed doses are handled. While clinical recommendations require extensive validation and should depend on drug and patient specifics, as a general principle our theory suggests that nonadherence is best mitigated by taking double doses following missed doses if the drug has a long half-life. This conclusion contradicts some existing recommendations that cite long drug half-lives as the reason to avoid a double dose after a missed dose. Furthermore, we show that a patient who takes double doses after missed doses can have at most only slightly more drug in their body than a perfectly adherent patient if the drug half-life is long. We also investigate other ways of handling missed doses, including taking an extra fractional dose following a missed dose. We discuss our results in the context of hypothyroid patients taking levothyroxine.

Receptor Organization Determines the Limits of Single-Cell Source Location Detection.

Many types of cells require the ability to pinpoint the location of an external stimulus from the arrival of diffusing signaling molecules at cell-surface receptors. How does the organization (number and spatial configuration) of these receptors shape the limit of a cell's ability to infer the source location? In the idealized scenario of a spherical cell, we apply asymptotic analysis to compute splitting probabilities between individual receptors and formulate an information-theoretic framework to quantify the role of receptor organization. Clustered configurations of receptors provide an advantage in detecting sources aligned with the clusters, suggesting a possible multiscale mechanism for single-cell source inference.

Distribution of extreme first passage times of diffusion.

Many events in biology are triggered when a diffusing searcher finds a target, which is called a first passage time (FPT). The overwhelming majority of FPT studies have analyzed the time it takes a single searcher to find a target. However, the more relevant timescale in many biological systems is the time it takes the fastest searcher(s) out of many searchers to find a target, which is called an extreme FPT. In this paper, we apply extreme value theory to find a tractable approximation for the full probability distribution of extreme FPTs of diffusion. This approximation can be easily applied in many diverse scenarios, as it depends on only a few properties of the short time behavior of the survival probability of a single FPT. We find this distribution by proving that a careful rescaling of extreme FPTs converges in distribution as the number of searchers grows. This limiting distribution is a type of Gumbel distribution and involves the LambertW function. This analysis yields new explicit formulas for approximations of statistics of extreme FPTs (mean, variance, moments, etc.) which are highly accurate and are accompanied by rigorous error estimates.

Receptor recharge time drastically reduces the number of captured particles.

Many diverse biological systems are described by randomly moving particles that can be captured by traps in their environment. Examples include neurotransmitters diffusing in the synaptic cleft before binding to receptors and prey roaming an environment before capture by predators. In most cases, the traps cannot capture particles continuously. Rather, each trap must wait a transitory "recharge" time after capturing a particle before additional captures. This recharge time is often overlooked. In the case of instant recharge, the average number of particles captured before they escape grows linearly in the total number of particles. In stark contrast, we prove that for any nonzero recharge time, the average number of captured particles grows at most logarithmically in the total particle number. This is a fundamental effect of recharge, as it holds under very general assumptions on particle motion and spatial domain. Furthermore, we characterize the parameter regime in which a given recharge time will dramatically affect a system, allowing researchers to easily verify if they need to account for recharge in their specific system. Finally, we consider a few examples, including a neural system in which recharge reduces neurotransmitter bindings by several orders of magnitude.

Rebinding in biochemical reactions on membranes.

The behavior of many biochemical processes depends crucially on molecules rapidly rebinding after dissociating. In the case of multisite protein modification, the importance of rebinding has been demonstrated both experimentally and through several recent computational studies involving stochastic spatial simulations. As rebinding stems from spatio-temporal correlations, theorists have resorted to models that explicitly include space to properly account for the effects of rebinding. However, for reactions in three space dimensions it was recently shown that well-mixed ordinary differential equation (ODE) models can incorporate rebinding by adding connections to the reaction network. The rate constants for these new connections involve the probability that a pair of molecules rapidly rebinds after dissociation. In order to study biochemical reactions on membranes, in this paper we derive an explicit formula for this rebinding probability for reactions in two space dimensions. We show that ODE models can use the formula to replicate detailed stochastic spatial simulations, and that the formula can predict ultrasensitivity for reactions involving multisite modification of membrane-bound proteins. Further, we compute a new concentration-dependent rebinding probability for reactions in three space dimensions. Our analysis predicts that rebinding plays a much larger role in reactions on membranes compared to reactions in cytoplasm.

Including Rebinding Reactions in Well-Mixed Models of Distributive Biochemical Reactions.

The behavior of biochemical reactions requiring repeated enzymatic substrate modification depends critically on whether the enzymes act processively or distributively. Whereas processive enzymes bind only once to a substrate before carrying out a sequence of modifications, distributive enzymes release the substrate after each modification and thus require repeated bindings. Recent experimental and computational studies have revealed that distributive enzymes can act processively due to rapid rebindings (so-called quasi-processivity). In this study, we derive an analytical estimate of the probability of rapid rebinding and show that well-mixed ordinary differential equation models can use this probability to quantitatively replicate the behavior of spatial models. Importantly, rebinding requires that connections be added to the well-mixed reaction network; merely modifying rate constants is insufficient. We then use these well-mixed models to suggest experiments to 1) detect quasi-processivity and 2) test the theory. Finally, we show that rapid rebindings drastically alter the reaction's Michaelis-Menten rate equations.

Mathematical modeling of the effects of glutathione on arsenic methylation.

BACKGROUND: Arsenic is a major environmental toxin that is detoxified in the liver by biochemical mechanisms that are still under study. In the traditional metabolic pathway, arsenic undergoes two methylation reactions, each followed by a reduction, after which it is exported and released in the urine. Recent experiments show that glutathione plays an important role in arsenic detoxification and an alternative biochemical pathway has been proposed in which arsenic is first conjugated by glutathione after which the conjugates are methylated. In addition, in rats arsenic-glutathione conjugates can be exported into the plasma and removed by the liver in the bile. METHODS: We have developed a mathematical model for arsenic biochemistry that includes three mechanisms by which glutathione affects arsenic methylation: glutathione increases the speed of the reduction steps; glutathione affects the activity of arsenic methyltranferase; glutathione sequesters inorganic arsenic and its methylated downstream products. The model is based as much as possible on the known biochemistry of arsenic methylation derived from cellular and experimental studies. RESULTS: We show that the model predicts and helps explain recent experimental data on the effects of glutathione on arsenic methylation. We explain why the experimental data imply that monomethyl arsonic acid inhibits the second methylation step. The model predicts time course data from recent experimental studies. We explain why increasing glutathione when it is low increases arsenic methylation and that at very high concentrations increasing glutathione decreases methylation. We explain why the possible temporal variation of the glutathione concentration affects the interpretation of experimental studies that last hours. CONCLUSIONS: The mathematical model aids in the interpretation of data from recent experimental studies and shows that the Challenger pathway of arsenic methylation, supplemented by the glutathione effects described above, is sufficient to understand and predict recent experimental data. More experimental studies are needed to explicate the detailed mechanisms of action of glutathione on arsenic methylation. Recent experimental work on the effects of glutathione on arsenic methylation and our modeling study suggest that supplements that increase hepatic glutathione production should be considered as strategies to reduce adverse health effects in affected populations.

Cover times of many random walkers on a discrete network.

The speed of an exhaustive search can be measured by a cover time, which is defined as the time it takes a random searcher to visit every state in some target set. Cover times have been studied in both the physics and probability literatures, with most prior works focusing on a single searcher. In this paper, we prove an explicit formula for all the moments of the cover time for many searchers on an arbitrary discrete network. Our results show that such cover times depend only on properties of the network along the shortest paths to the most distant parts of the target. This mere local dependence contrasts with the well-known result that cover times for single searchers depend on global properties of the network. We illustrate our rigorous results by stochastic simulations.