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WENDY: Covariance dynamics based gene regulatory network inference 利用协方差动态推断基因调控网络。
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2024-08-20 DOI: 10.1016/j.mbs.2024.109284
Yue Wang , Peng Zheng , Yu-Chen Cheng , Zikun Wang , Aleksandr Aravkin
Determining gene regulatory network (GRN) structure is a central problem in biology, with a variety of inference methods available for different types of data. For a widely prevalent and challenging use case, namely single-cell gene expression data measured after intervention at multiple time points with unknown joint distributions, there is only one known specifically developed method, which does not fully utilize the rich information contained in this data type. We develop an inference method for the GRN in this case, netWork infErence by covariaNce DYnamics, dubbed WENDY. The core idea of WENDY is to model the dynamics of the covariance matrix, and solve this dynamics as an optimization problem to determine the regulatory relationships. To evaluate its effectiveness, we compare WENDY with other inference methods using synthetic data and experimental data. Our results demonstrate that WENDY performs well across different data sets.
确定基因调控网络(GRN)结构是生物学的核心问题,针对不同类型的数据有多种推断方法。对于一个广泛流行且具有挑战性的使用案例,即在多个时间点进行干预后测量的、具有未知联合分布的单细胞基因表达数据,目前只有一种已知的专门开发的方法,该方法没有充分利用这种数据类型所包含的丰富信息。在这种情况下,我们开发了一种针对 GRN 的推断方法,即 covariaNce DYnamics 的网络推断(netWork infErence by covariaNce DYnamics),称为 WENDY。WENDY 的核心思想是对协方差矩阵的动态进行建模,并将这种动态作为一个优化问题来解决,从而确定调控关系。为了评估其有效性,我们使用合成数据和实验数据将 WENDY 与其他推断方法进行了比较。我们的结果表明,WENDY 在不同的数据集上都表现出色。
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引用次数: 0
Insights of infected Schwann cells extinction and inherited randomness in a stochastic model of leprosy 麻风病随机模型中受感染许旺细胞消亡和遗传随机性的启示。
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2024-08-17 DOI: 10.1016/j.mbs.2024.109281
Salil Ghosh , Sourav Rana , Satyajit Mukherjee , Priti Kumar Roy

Investigating disease progression, transmission of infection and impacts of Multidrug Therapy (MDT) to inhibit demyelination in leprosy involves a certain amount of difficulty in terms of the in-built uncertain complicated and complex intracellular cell dynamical interactions. To tackle this scenario and to elucidate a more realistic, rationalistic approach of examining the infection mechanism and associated drug therapeutic interventions, we propose a four-dimensional ordinary differential equation-based model. Stochastic processes has been employed on this deterministic system by formulating the Kolmogorov forward equation introducing a transition state and the quasi-stationary distribution, exact distribution analysis have been investigated which allow us to estimate an expected time to extinction of the infected Schwann cells into the human body more prominently. Additionally, to explore the impact of uncertainty in the key intracellular factors, the stochastic system is investigated incorporating random perturbations and environmental noises in the disease dissemination, proliferation and reinfection rates. Rigorous numerical simulations validating the analytical outcomes provide us significant novel insights on the progression of leprosy and unravelling the existing major treatment complexities. Analytical experiments along with the simulations utilizing Monte-Carlo method and Euler–Maruyama scheme involving stochasticity predicts that the bacterial density is underestimated due to the recurrence of infection and suggests that maintaining a drug-efficacy rate in the range 0.60.8 would be substantially efficacious in eradicating leprosy.

研究麻风病的疾病进展、感染传播和多药疗法(MDT)对抑制麻风病脱髓鞘的影响,因细胞内动态相互作用的内在不确定性和复杂性而存在一定难度。为了解决这一问题,并阐明一种更现实、更合理的方法来研究感染机制和相关的药物治疗干预措施,我们提出了一个基于四维常微分方程的模型。我们在这一确定性系统上采用了随机过程,通过建立引入过渡状态和准稳态分布的科尔莫哥罗夫正向方程,研究了精确分布分析,从而更准确地估算出受感染的许旺细胞在人体内消亡的预期时间。此外,为了探索细胞内关键因素的不确定性所产生的影响,我们对随机系统进行了研究,在疾病传播、增殖和再感染率中加入了随机扰动和环境噪声。严谨的数值模拟验证了分析结果,为我们提供了关于麻风病进展的重要新见解,并揭开了现有主要治疗方法的复杂性。分析实验以及利用蒙特卡洛法和涉及随机性的欧拉-马鲁山方案进行的模拟预测,由于感染的复发,细菌密度被低估了,这表明将药物有效率保持在 0.6-0.8 的范围内对根除麻风病有很大的疗效。
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引用次数: 0
Presence and infestation waves of hematophagous arthropod species 噬血节肢动物物种的存在和侵袭波。
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2024-08-17 DOI: 10.1016/j.mbs.2024.109282
M. Adrian Acuña-Zegarra, Mayra R. Tocto-Erazo, Claudio C. García-Mendoza, Daniel Olmos-Liceaga

The invasion of hematophagous arthropod species in human settlements represents a threat, not only to the economy but also to the health system in general. Recent examples of this phenomenon were seen in Paris and Mexico City, evidencing the importance of understanding these dynamics. In this work, we present a reaction–diffusion model to describe the invasion dynamics of hematophagous arthropod species. The proposed model considers a denso-dependent growth rate and parameters related to the control of the invasive species. Our results illustrate the existence of two invasion levels (presence and infestation) within a region, depending on control parameter values. We also prove analytically the existence of the presence and infestation waves and show different theoretical types of invasion waves that result from varying control parameters. In addition, we present a condition threshold that determines whether or not an infestation occurs. Finally, we illustrate some results when considering the case of bedbugs and brown dog ticks as invasion species.

人类住区中噬血节肢动物物种的入侵不仅对经济构成威胁,也对整个卫生系统构成威胁。最近在巴黎和墨西哥城都出现了这种现象,这证明了了解这些动态的重要性。在这项工作中,我们提出了一个反应-扩散模型来描述噬血节肢动物物种的入侵动态。所提出的模型考虑了依赖于虫体的生长率以及与入侵物种控制相关的参数。我们的结果表明,根据控制参数值的不同,在一个区域内存在两种入侵水平(存在和侵扰)。我们还用分析方法证明了存在波和侵扰波的存在,并展示了不同控制参数导致的不同理论类型的入侵波。此外,我们还提出了一个决定是否发生侵扰的条件阈值。最后,我们以臭虫和棕狗虱作为入侵物种为例,说明了一些结果。
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引用次数: 0
Derivation and dynamics of discrete population models with distributed delay in reproduction 具有分布式繁殖延迟的离散种群模型的推导和动力学。
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2024-08-13 DOI: 10.1016/j.mbs.2024.109279
Sabrina H. Streipert , Gail S.K. Wolkowicz

We introduce a class of discrete single species models with distributed delay in the reproductive process and a cohort dependent survival function that accounts for survival pressure during that delay period. These delay recurrences track the mature population for species in which individuals reach maturity after at least τ and at most τ+τM breeding cycles. Under realistic model assumptions, we prove the existence of a critical delay threshold, τ˜c. For given delay kernel length τM, if each individual takes at least τ˜c time units to reach maturity, then the population is predicted to go extinct. We show that the positive equilibrium is decreasing in both τ and τM. In the case of a constant reproductive rate, we provide an equation to determine τ˜c for fixed τM, and similarly, provide a lower bound on the kernel length, τ˜M for fixed τ such that the population goes extinct if τMτ˜M. We compare these critical thresholds for different maturation distributions and show that if all else is the same, to avoid extinction it is best if all individuals in the population have the shortest delay possible. We apply the model derivation to a Beverton–Holt model and discuss its global dynamics. For this model with kernels that share the same mean delay, we show that populations with the largest variance in the time required to reach maturity have higher population levels and lower chances of extinction.

我们引入了一类离散的单一物种模型,该模型在繁殖过程中具有分布式延迟,并具有与群落相关的生存函数,该函数考虑了延迟期间的生存压力。对于个体至少经过 τ 个繁殖周期、最多经过 τ+τM 个繁殖周期才达到成熟的物种,这些延迟复现会跟踪其成熟种群。在现实的模型假设下,我们证明了临界延迟阈值τ˜c的存在。对于给定的延迟核长度τM,如果每个个体至少需要τ˜c个时间单位才能达到成熟,那么预测种群将灭绝。我们证明,正平衡在 τ 和 τM 中都是递减的。在繁殖率恒定的情况下,我们提供了一个方程来确定固定τM 时的τ˜c,同样,我们也提供了固定τ 时内核长度τ˜M 的下限,这样,如果τM≥τ˜M,种群就会灭绝。我们对不同成熟度分布的临界阈值进行了比较,结果表明,如果其他条件相同,要避免种群灭绝,种群中所有个体的延迟时间最好尽可能短。我们将模型推导应用于贝弗顿-霍尔特模型,并讨论其全局动态。对于这个具有相同平均延迟的核模型,我们表明,达到成熟所需时间方差最大的种群具有较高的种群水平和较低的灭绝几率。
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引用次数: 0
Finding Hopf bifurcation islands and identifying thresholds for success or failure in oncolytic viral therapy 寻找霍普夫分叉岛,确定溶瘤病毒疗法的成败阈值。
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2024-08-08 DOI: 10.1016/j.mbs.2024.109275
Sana Jahedi , Lin Wang , James A. Yorke , James Watmough

We model interactions between cancer cells and viruses during oncolytic viral therapy. One of our primary goals is to identify parameter regions that yield treatment failure or success. We show that the tumor size under therapy at a particular time is less than the size without therapy. Our analysis demonstrates two thresholds for the horizontal transmission rate: a “failure threshold” below which treatment fails, and a “success threshold” above which infection prevalence reaches 100% and the tumor shrinks to its smallest size. Moreover, we explain how changes in the virulence of the virus alter the success threshold and the minimum tumor size. Our study suggests that the optimal virulence of an oncolytic virus depends on the timescale of virus dynamics. We identify a threshold for the virulence of the virus and show how this threshold depends on the timescale of virus dynamics. Our results suggest that when the timescale of virus dynamics is fast, administering a more virulent virus leads to a greater reduction in the tumor size. Conversely, when the viral timescale is slow, higher virulence can induce oscillations with high amplitude in the tumor size. Furthermore, we introduce the concept of a “Hopf bifurcation Island” in the parameter space, an idea that has applications far beyond the results of this paper and is applicable to many mathematical models. We elucidate what a Hopf bifurcation Island is, and we prove that small Islands can imply very slowly growing oscillatory solutions.

我们为溶瘤病毒治疗过程中癌细胞与病毒之间的相互作用建模。我们的主要目标之一是确定导致治疗失败或成功的参数区域。我们表明,在特定时间接受治疗的肿瘤大小小于未接受治疗的肿瘤大小。我们的分析表明了水平传播率的两个阈值:一个是 "失败阈值",低于该阈值治疗失败;另一个是 "成功阈值",高于该阈值感染率达到 100%,肿瘤缩小到最小尺寸。此外,我们还解释了病毒毒力的变化如何改变成功阈值和最小肿瘤大小。我们的研究表明,溶瘤病毒的最佳毒力取决于病毒动态的时间尺度。我们确定了病毒毒力的阈值,并展示了这一阈值如何取决于病毒动态的时间尺度。我们的研究结果表明,当病毒动态的时间尺度较快时,施用毒性更强的病毒会使肿瘤体积缩小更多。相反,当病毒的时间尺度较慢时,较高的毒力会引起肿瘤大小的高振幅振荡。此外,我们还引入了参数空间中 "霍普夫分岔岛 "的概念,这一概念的应用范围远远超出了本文的结果,而且适用于许多数学模型。我们阐明了什么是霍普夫分岔岛,并证明了小分岔岛可能意味着增长非常缓慢的振荡解。
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引用次数: 0
Breakdown of Boltzmann-type models for the alignment of self-propelled rods 自走杆排列的波尔兹曼型模型分解。
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2024-08-08 DOI: 10.1016/j.mbs.2024.109266
Patrick Murphy , Misha Perepelitsa , Ilya Timofeyev , Matan Lieber-Kotz , Brandon Islas , Oleg A. Igoshin

Studies in the collective motility of organisms use a range of analytical approaches to formulate continuous kinetic models of collective dynamics from rules or equations describing agent interactions. However, the derivation of these kinetic models often relies on Boltzmann’s “molecular chaos” hypothesis, which assumes that correlations between individuals are short-lived. While this assumption is often the simplest way to derive tractable models, it is often not valid in practice due to the high levels of cooperation and self-organization present in biological systems. In this work, we illustrated this point by considering a general Boltzmann-type kinetic model for the alignment of self-propelled rods where rod reorientation occurs upon binary collisions. We examine the accuracy of the kinetic model by comparing numerical solutions of the continuous equations to an agent-based model that implements the underlying rules governing microscopic alignment. Even for the simplest case considered, our comparison demonstrates that the kinetic model fails to replicate the discrete dynamics due to the formation of rod clusters that violate statistical independence. Additionally, we show that introducing noise to limit cluster formation helps improve the agreement between the analytical model and agent simulations but does not restore the agreement completely. These results highlight the need to both develop and disseminate improved moment-closure methods for modeling biological and active matter systems.

对生物体集体运动的研究采用了一系列分析方法,从描述个体相互作用的规则或方程出发,建立集体动力学的连续动力学模型。然而,这些动力学模型的推导通常依赖于玻尔兹曼的 "分子混沌 "假设,即假设个体之间的相关性是短暂的。虽然这一假设通常是推导可控模型的最简单方法,但由于生物系统中存在高度的合作和自组织,这一假设在实践中往往并不成立。在这项工作中,我们通过考虑自走棒排列的一般玻尔兹曼型动力学模型来说明这一点。我们通过比较连续方程的数值解与基于代理的模型(该模型实现了微观配准的基本规则),检验了动力学模型的准确性。即使是在最简单的情况下,我们的比较也表明,动力学模型无法复制离散动力学,原因是杆簇的形成违反了统计独立性。此外,我们还表明,引入噪声来限制簇的形成有助于改善分析模型与代理模拟之间的一致性,但并不能完全恢复一致性。这些结果凸显了开发和推广用于生物和活性物质系统建模的改进型矩封闭方法的必要性。
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引用次数: 0
Effect of homophily on coupled behavior-disease dynamics near a tipping point 同质性对临界点附近行为-疾病动态耦合的影响
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2024-08-02 DOI: 10.1016/j.mbs.2024.109264
Zitao He, Chris T. Bauch

Understanding the interplay between social activities and disease dynamics is crucial for effective public health interventions. Recent studies using coupled behavior-disease models assumed homogeneous populations. However, heterogeneity in population, such as different social groups, cannot be ignored. In this study, we divided the population into social media users and non-users, and investigated the impact of homophily (the tendency for individuals to associate with others similar to themselves) and online events on disease dynamics. Our results reveal that homophily hinders the adoption of vaccinating strategies, hastening the approach to a tipping point after which the population converges to an endemic equilibrium with no vaccine uptake. Furthermore, we find that online events can significantly influence disease dynamics, with early discussions on social media platforms serving as an early warning signal of potential disease outbreaks. Our model provides insights into the mechanisms underlying these phenomena and underscores the importance of considering homophily in disease modeling and public health strategies.

了解社会活动与疾病动态之间的相互作用对于有效的公共卫生干预措施至关重要。近期使用行为-疾病耦合模型的研究假定人群是同质的。然而,不同社会群体等人群的异质性不容忽视。在本研究中,我们将人群分为社交媒体用户和非用户,并调查了同质性(个人与与自己相似的人交往的倾向)和在线事件对疾病动态的影响。我们的研究结果表明,同质性阻碍了疫苗接种策略的采用,加速了临界点的接近,而在临界点之后,人群会趋于无疫苗接种的地方病平衡状态。此外,我们还发现,在线事件会对疾病动态产生重大影响,社交媒体平台上的早期讨论可作为潜在疾病爆发的预警信号。我们的模型深入揭示了这些现象的内在机制,并强调了在疾病建模和公共卫生策略中考虑同质性的重要性。
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引用次数: 0
Control of schistosomiasis by the selective competitive and predatory intervention of intermediate hosts: A mathematical modeling approach 通过中间宿主的选择性竞争和捕食性干预控制血吸虫病:数学建模方法。
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2024-07-31 DOI: 10.1016/j.mbs.2024.109263
Zadoki Tabo , Livingstone Luboobi , Philipp Kraft , Lutz Breuer , Christian Albrecht

Schistosomiasis, a freshwater-borne neglected tropical disease, disproportionately affects impoverished communities mainly in the tropical regions. Transmission involves humans and intermediate host (IH) snails. This manuscript introduces a mathematical model to probe schistosomiasis dynamics and the role of non-host snail competitors and predators as biological control agents for IH snails. The numerical analyses include investigations into steady-state conditions and reproduction numbers associated with uncontrolled scenarios, as well as scenarios involving non-host snail competitors and/or predators. Sensitivity analysis reveals that increasing snail mortality rates is a key to reducing the IH snail population and control of the transmission. Results show that specific snail competitors and/or predators with strong competition/predation abilities reduce IH snails and the subsequent infectious cercaria populations, reduce the transmission, and possibly eradicate the disease, while those with weaker abilities allow disease persistence. Hence our findings advocate for the effectiveness of snail competitors with suitable competitive pressures and/or predators with appropriate predatory abilities as nature-based solutions for combating schistosomiasis, all while preserving IH snail biodiversity. However, if these strategies are implemented at insignificant levels, IH snails can dominate, and disease persistence may pose challenges. Thus, experimental screening of potential (native) snail competitors and/or predators is crucial to assess the likely behavior of biological agents and determine the optimal biological control measures for IH snails.

血吸虫病是一种淡水传播的被忽视的热带疾病,主要影响热带地区的贫困社区。传播涉及人类和中间宿主(IH)钉螺。本手稿介绍了一种数学模型,用于探究血吸虫病的动态以及作为中间宿主钉螺生物控制剂的非宿主钉螺竞争者和捕食者的作用。数值分析包括研究与不受控情况相关的稳态条件和繁殖数量,以及涉及非宿主钉螺竞争者和/或捕食者的情况。敏感性分析表明,提高蜗牛死亡率是减少 IH 蜗牛数量和控制传播的关键。结果表明,具有较强竞争/捕食能力的特定蜗牛竞争者和/或捕食者能减少 IH 蜗牛及其感染的蛔虫数量,降低传播率,并可能根除疾病,而能力较弱的竞争者和/或捕食者则会使疾病持续存在。因此,我们的研究结果表明,具有适当竞争压力的钉螺竞争者和/或具有适当捕食能力的捕食者是防治血吸虫病的有效自然解决方案,同时还能保护IH钉螺的生物多样性。然而,如果这些策略的实施水平不高,IH钉螺可能会占据主导地位,疾病的持续存在可能会带来挑战。因此,对潜在的(本地)钉螺竞争者和/或捕食者进行实验筛选,对于评估生物制剂的可能行为和确定针对 IH 钉螺的最佳生物控制措施至关重要。
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引用次数: 0
How to correctly fit an SIR model to data from an SEIR model? 如何根据 SEIR 模型的数据正确拟合 SIR 模型?
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2024-07-30 DOI: 10.1016/j.mbs.2024.109265
Wasiur R. KhudaBukhsh , Grzegorz A. Rempała

In epidemiology, realistic disease dynamics often require Susceptible-Exposed-Infected-Recovered (SEIR)-like models because they account for incubation periods before individuals become infectious. However, for the sake of analytical tractability, simpler Susceptible-Infected-Recovered (SIR) models are commonly used, despite their lack of biological realism. Bridging these models is crucial for accurately estimating parameters and fitting models to observed data, particularly in population-level studies of infectious diseases.

This paper investigates stochastic versions of the SEIR and SIR frameworks and demonstrates that the SEIR model can be effectively approximated by a SIR model with time-dependent infection and recovery rates. The validity of this approximation is supported by the derivation of a large-population Functional Law of Large Numbers (FLLN) limit and a finite-population concentration inequality.

To apply this approximation in practice, the paper introduces a parameter inference methodology based on the Dynamic Survival Analysis (DSA) survival analysis framework. This method enables the fitting of the SIR model to data simulated from the more complex SEIR dynamics, as illustrated through simulated experiments.

在流行病学中,现实的疾病动力学通常需要类似于 "易感-暴露-感染-恢复"(SEIR)的模型,因为这些模型考虑了个体感染前的潜伏期。然而,为了分析的可操作性,人们通常使用更简单的易感-感染-恢复(SIR)模型,尽管这些模型缺乏生物真实性。衔接这些模型对于准确估计参数和将模型与观测数据拟合至关重要,尤其是在传染病的群体水平研究中。本文研究了 SEIR 和 SIR 框架的随机版本,并证明 SEIR 模型可以有效地近似于具有随时间变化的感染率和恢复率的 SIR 模型。大群体大数函数定律(FLLN)极限和有限群体浓度不等式的推导支持了这种近似的有效性。为了在实践中应用这一近似值,本文介绍了一种基于动态生存分析(DSA)生存分析框架的参数推断方法。通过模拟实验说明,该方法可将 SIR 模型与更复杂的 SEIR 动态模拟数据进行拟合。
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引用次数: 0
Assessment of bidirectional impact of stigmatization induced self-medication on COVID-19 and malaria transmissions using mathematical modeling: Nigeria as a case study 利用数学建模评估污名化引起的自我药疗对 COVID-19 和疟疾传播的双向影响:以尼日利亚为例。
IF 1.9 4区 数学 Q2 BIOLOGY Pub Date : 2024-07-24 DOI: 10.1016/j.mbs.2024.109249
Wisdom S. Avusuglo , Qing Han , Woldegebriel Assefa Woldegerima , Ali Asgary , Jianhong Wu , James Orbinski , Nicola Bragazzi , Ali Ahmadi , Jude Dzevela Kong

The continual social and economic impact of infectious diseases on nations has maintained sustained attention on their control and treatment, of which self-medication has been one of the means employed by some individuals. Self-medication complicates the attempt of their control and treatment as it conflicts with some of the measures implemented by health authorities. Added to these complications is the stigmatization of individuals with some diseases in some jurisdictions. This study investigates the co-infection of COVID-19 and malaria and its related deaths and further highlights how self-medication and stigmatization add to the complexities of the fight against these two diseases using Nigeria as a study case. Using a mathematical model on COVID-19 and malaria co-infection, we address the question: to what degree does the impact of the interaction between COVID-19 and malaria amplify infections and deaths induced by both diseases via self-medication and stigmatization? We demonstrate that COVID-19 related self-medication due to misdiagnoses contributes substantially to the prevalence of disease. The control reproduction numbers for these diseases and quantification of model parameters uncertainties and sensitivities are presented.

传染病对各国社会和经济的持续影响使人们持续关注传染病的控制和治疗,其中自我药疗是一些人采用的手段之一。自我药疗与卫生当局实施的某些措施相冲突,使控制和治疗工作变得更加复杂。除了这些复杂情况之外,在某些地区,患有某些疾病的人还会受到鄙视。本研究以尼日利亚为研究案例,调查了 COVID-19 和疟疾的合并感染及其相关死亡情况,并进一步强调了自我药疗和污名化是如何增加这两种疾病防治工作的复杂性的。利用 COVID-19 和疟疾合并感染的数学模型,我们解决了这样一个问题:COVID-19 和疟疾之间的相互作用在多大程度上通过自我药疗和污名化放大了这两种疾病引起的感染和死亡?我们证明,因误诊而导致的与 COVID-19 相关的自行用药在很大程度上加剧了疾病的流行。本文介绍了这些疾病的控制繁殖数量以及模型参数不确定性和敏感性的量化。
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