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Id | Title * | Authors * | Abstract * | Picture * | Thematic fields * | Recommender▲ | Reviewers | Submission date | |
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27 Jul 2021
![]() Estimating dates of origin and end of COVID-19 epidemicsThomas Bénéteau, Baptiste Elie, Mircea T. Sofonea, Samuel Alizon https://doi.org/10.1101/2021.01.19.21250080The importance of model assumptions in estimating the dynamics of the COVID-19 epidemicRecommended by Valery Forbes based on reviews by Bastien Boussau and 1 anonymous reviewerIn “Estimating dates of origin and end of COVID-19 epidemics”, Bénéteau et al. develop and apply a mathematical modeling approach to estimate the date of the origin of the SARS-CoV-2 epidemic in France. They also assess how long strict control measures need to last to ensure that the prevalence of the virus remains below key public health thresholds. This problem is challenging because the numbers of infected individuals in both tails of the epidemic are low, which can lead to errors when deterministic models are used. To achieve their goals, the authors developed a discrete stochastic model. The model is non-Markovian, meaning that individual infection histories influence the dynamics. The model also accounts for heterogeneity in the timing between infection and transmission and includes stochasticity as well as consideration of superspreader events. By comparing the outputs of their model with several alternative models, Bénéteau et al. were able to assess the importance of stochasticity, individual heterogeneity, and non-Markovian effects on the estimates of the dates of origin and end of the epidemic, using France as a test case. Some limitations of the study, which the authors acknowledge, are that the time from infection to death remains largely unknown, a lack of data on the heterogeneity of transmission among individuals, and the assumption that only a single infected individual caused the epidemic. Despite the acknowledged limitations of the work, the results suggest that cases may be detected long before the detection of an epidemic wave. Also, the approach may be helpful for informing public health decisions such as the necessary duration of strict lockdowns and for assessing the risks of epidemic rebound as restrictions are lifted. In particular, the authors found that estimates of the end of the epidemic following lockdowns are more sensitive to the assumptions of the models used than estimates of its beginning. In summary, this model adds to a valuable suite of tools to support decision-making in response to disease epidemics. References Bénéteau T, Elie B, Sofonea MT, Alizon S (2021) Estimating dates of origin and end of COVID-19 epidemics. medRxiv, 2021.01.19.21250080, ver. 3 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://doi.org/10.1101/2021.01.19.21250080 | Estimating dates of origin and end of COVID-19 epidemics | Thomas Bénéteau, Baptiste Elie, Mircea T. Sofonea, Samuel Alizon | <p style="text-align: justify;">Estimating the date at which an epidemic started in a country and the date at which it can end depending on interventions intensity are important to guide public health responses. Both are potentially shaped by simi... | ![]() | Epidemiology, Probability and statistics, Stochastic dynamics | Valery Forbes | 2021-02-23 16:37:32 | View | |
07 Sep 2021
![]() The origin of the allometric scaling of lung ventilation in mammalsFrédérique Noël, Cyril Karamaoun, Jerome A. Dempsey, Benjamin Mauroy https://doi.org/10.48550/arXiv.2005.12362How mammals adapt their breath to body activity – and how this depends on body sizeRecommended by Wolfram LiebermeisterHow fast and how deep do animals breathe, and how does this depend on how active they are? To answer this question, one needs to dig deeply into how breathing works and what biophysical processes it involves. And one needs to think about body size. It is impressive how nature adapts the same body plan – e.g. the skeletal structure of mammals – to various shapes and sizes. From mice to whales, also the functioning of most organs remains the same; they are just differently scaled. Scaling does not just mean “making bigger or smaller”. As already noted by Galilei, body shapes change as they are adapted to body dimensions, and the same holds for physiological variables. Many such variables, for instance, heartbeat rates, follow scaling laws of the form y~x^a, where x denotes body mass and the exponent a is typically a multiple of ¼ [1]. These unusual exponents – instead of multiples of ⅓, which would be expected from simple geometrical scaling – are why these laws are called “allometric”. Kleiber’s law for metabolic rates, with a scaling exponent of ¾, is a classic example [2]. As shown by G. West, allometric laws can be explained through a few simple steps [1]. In his models, he focused on network-like organs such as the vascular system and assumed that these systems show a self-similar structure, with a fixed minimal unit (for instance, capillaries) but varying numbers of hierarchy levels depending on body size. To determine the flow through such networks, he employed biophysical models and optimality principles (for instance, assuming that oxygen must be transported at a minimal mechanical effort), and showed that the solutions – and the physiological variables – respect the known scaling relations. The paper “The origin of the allometric scaling of lung ventilation in mammals“ by Noël et al. [3], applies this thinking to the depth and rate of breathing in mammals. Scaling laws describing breathing in resting animals have been known since the 1950s [4], with exponents of 1 (for tidal volume) and -¼ (for breathing frequency). Equipped with a detailed biophysical model, Noël et al. revisit this question, extending these laws to other metabolic regimes. Their starting point is a model of the human lung, developed previously by two of the authors [5], which assumes that we meet our oxygen demand with minimal lung movements. To state this as an optimization problem, the model combines two submodels: a mechanical model describing the energetic effort of ventilation and a highly detailed model of convection and diffusion in self-similar lung geometries. Breathing depths and rates are computed by numerical optimization, and to obtain results for mammals of any size many of the model parameters are described by known scaling laws. As expected, the depth of breathing (measured by tidal volume) scales almost proportionally with body mass and increases with metabolic demand, while the breathing rate decreases with body mass, with an exponent of about -¼. However, the laws for the breathing rate hold only for basal activity; at higher metabolic rates, which are modeled here for the first time, the exponent deviates strongly from this value, in line with empirical data. Why is this paper important? The authors present a highly complex model of lung physiology that integrates a wide range of biophysical details and passes a difficult test: the successful prediction of unexplained scaling exponents. These scaling relations may help us transfer insights from animal models to humans and in reverse: data for breathing during exercise, which are easy to measure in humans, can be extrapolated to other species. Aside from the scaling laws, the model also reveals physiological mechanisms. In the larger lung branches, oxygen is transported mainly by air movement (convection), while in smaller branches air flow is slow and oxygen moves by diffusion. The transition between these regimes can occur at different depths in the lung: as the authors state, “the localization of this transition determines how ventilation should be controlled to minimize its energetic cost at any metabolic regime”. In the model, the optimal location for the transition depends on oxygen demand [5, 6]: the transition occurs deeper in the lung in exercise regimes than at rest, allowing for more oxygen to be taken up. However, the effects of this shift depend on body size: while small mammals generally use the entire exchange surface of their lungs, large mammals keep a reserve for higher activities, which becomes accessible as their transition zone moves at high metabolic rates. Hence, scaling can entail qualitative differences between species! Altogether, the paper shows how the dynamics of ventilation depend on lung morphology. But this may also play out in the other direction: if energy-efficient ventilation depends on body activity, and therefore on ecological niches, a niche may put evolutionary pressures on lung geometry. Hence, by understanding how deep and fast animals breathe, we may also learn about how behavior, physiology, and anatomy co-evolve. References [1] West GB, Brown JH, Enquist BJ (1997) A General Model for the Origin of Allometric Scaling Laws in Biology. Science 276 (5309), 122–126. https://doi.org/10.1126/science.276.5309.122 [2] Kleiber M (1947) Body size and metabolic rate. Physiological Reviews, 27, 511–541. https://doi.org/10.1152/physrev.1947.27.4.511 [3] Noël F., Karamaoun C., Dempsey J. A. and Mauroy B. (2021) The origin of the allometric scaling of lung's ventilation in mammals. arXiv, 2005.12362, ver. 6 peer-reviewed and recommended by Peer community in Mathematical and Computational Biology. https://arxiv.org/abs/2005.12362 [4] Otis AB, Fenn WO, Rahn H (1950) Mechanics of Breathing in Man. Journal of Applied Physiology, 2, 592–607. https://doi.org/10.1152/jappl.1950.2.11.592 [5] Noël F, Mauroy B (2019) Interplay Between Optimal Ventilation and Gas Transport in a Model of the Human Lung. Frontiers in Physiology, 10, 488. https://doi.org/10.3389/fphys.2019.00488 [6] Sapoval B, Filoche M, Weibel ER (2002) Smaller is better—but not too small: A physical scale for the design of the mammalian pulmonary acinus. Proceedings of the National Academy of Sciences, 99, 10411–10416. https://doi.org/10.1073/pnas.122352499 | The origin of the allometric scaling of lung ventilation in mammals | Frédérique Noël, Cyril Karamaoun, Jerome A. Dempsey, Benjamin Mauroy | <p>A model of optimal control of ventilation has recently been developed for humans. This model highlights the importance of the localization of the transition between a convective and a diffusive transport of respiratory gas. This localization de... | ![]() | Biophysics, Evolutionary Biology, Physiology | Wolfram Liebermeister | 2020-08-28 15:18:03 | View | |
07 Dec 2021
![]() The emergence of a birth-dependent mutation rate in asexuals: causes and consequencesFlorian Patout, Raphaël Forien, Matthieu Alfaro, Julien Papaïx, Lionel Roques https://doi.org/10.1101/2021.06.11.448026A new perspective in modeling mutation rate for phenotypically structured populationsRecommended by Yuan Lou based on reviews by Hirohisa Kishino and 1 anonymous reviewerIn standard mutation-selection models for describing the dynamics of phenotypically structured populations, it is often assumed that the mutation rate is constant across the phenotypes. In particular, this assumption leads to a constant diffusion coefficient for diffusion approximation models (Perthame, 2007 and references therein). Patout et al (2021) study the dependence of the mutation rate on the birth rate, by introducing some diffusion approximations at the population level, derived from the large population limit of a stochastic, individual-based model. The reaction-diffusion model in this article is of the “cross-diffusion” type: The form of “cross-diffusion” also appeared in ecological literature as a type of biased movement behaviors for organisms (Shigesada et al., 1979). The key underlying assumption for “cross-diffusion” is that the transition probability at the individual level depends solely upon the condition at the departure point. Patout et al (2021) envision that a higher birth rate yields more mutations per unit of time. One of their motivations is that during cancer development, the mutation rates of cancer cells at the population level could be correlated with reproduction success. The reaction-diffusion approximation model derived in this article illustrates several interesting phenomena: For the time evolution situation, their model predicts different solution trajectories under various assumptions on the fitness function, e.g. the trajectory could initially move towards the birth optimum but eventually end up at the survival optimum. Their model also predicts that the mean fitness could be flat for some period of time, which might provide another alternative to explain observed data. At the steady-state level, their model suggests that the populations are more concentrated around the survival optimum, which agrees with the evolution of the time-dependent solution trajectories. Perhaps one of the most interesting contributions of the study of Patout et al (2021) is to give us a new perspective to model the mutation rate in phenotypically structured populations and subsequently, and to help us better understand the connection between mutation and selection. More broadly, this article offers some new insights into the evolutionary dynamics of phenotypically structured populations, along with potential implications in empirical studies. References Perthame B (2007) Transport Equations in Biology Frontiers in Mathematics. Birkhäuser, Basel. https://doi.org/10.1007/978-3-7643-7842-4_2 Patout F, Forien R, Alfaro M, Papaïx J, Roques L (2021) The emergence of a birth-dependent mutation rate in asexuals: causes and consequences. bioRxiv, 2021.06.11.448026, ver. 3 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://doi.org/10.1101/2021.06.11.448026 Shigesada N, Kawasaki K, Teramoto E (1979) Spatial segregation of interacting species. Journal of Theoretical Biology, 79, 83–99. https://doi.org/10.1016/0022-5193(79)90258-3 | The emergence of a birth-dependent mutation rate in asexuals: causes and consequences | Florian Patout, Raphaël Forien, Matthieu Alfaro, Julien Papaïx, Lionel Roques | <p style="text-align: justify;">In unicellular organisms such as bacteria and in most viruses, mutations mainly occur during reproduction. Thus, genotypes with a high birth rate should have a higher mutation rate. However, standard models of asexu... | ![]() | Dynamical systems, Evolutionary Biology, Probability and statistics, Stochastic dynamics | Yuan Lou | Anonymous, Hirohisa Kishino | 2021-06-12 13:59:45 | View |
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