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基于个体模型的传染病检测–追踪–隔离防控措施评估

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疾病监测 2024年第4期39卷 497-504页

作者：邓月雷锦志天津工业大学软件学院天津300387 天津工业大学数学科学学院天津工业大学应用数学中心天津300387

目的通过建立计算模型研究检测–追踪–隔离措施对于疫情传播动力学的影响,以评价不同防控措施的效果。方法基于个体模型和动态密切接触网络模拟疫情传播动力学。在模型模拟中根据个体间接触网络的动态变化,对传染病确诊者的密切接触者... 详细信息

目的通过建立计算模型研究检测–追踪–隔离措施对于疫情传播动力学的影响,以评价不同防控措施的效果。方法基于个体模型和动态密切接触网络模拟疫情传播动力学。在模型模拟中根据个体间接触网络的动态变化,对传染病确诊者的密切接触者(密接)、次密切接触者(次密接)和涉疫场所暴露者进行追踪,对不同个体实施隔离或检测等不同的管控措施。通过模型计算模拟局部区域发生疫情以后的疫情演变过程,并估计累计感染人数和每日新增感染人数的变化。结果当没有采取防控措施时,疫情发生后感染人数快速指数增长,7 d左右达到每日新增感染人数的峰值。当实施检测–追踪–隔离措施后,感染规模和每日新增病例数均显著降低,但是仍需要比较强有力的防控措施以达到疫情的防控目标。结论通过定量模型计算表明中国所采取的检测–追踪–隔离措施对于应对疫情的局部暴发是有效的。

关键词：动态接触网络口罩佩戴概率疫苗个体模型

Modelling COVID-19 epidemic with confirmed cases-driven contact tracing quarantine

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Infectious Disease Modelling 2023年第2期8卷 415-426页

作者： Fei Wu Xiyin Liang jinzhi lei School of Mathematical Sciences Tiangong UniversityTianjin300387China School of Mathematical Sciences Center for Applied MathematicsTiangong UniversityTianjin300387China

The pandemic of novel coronavirus disease 2019(COVID-19)has been a severe threat to public *** policy of close contract tracing quarantine is an effective strategy in controlling the COVID-19 epidemic *** this paper,we developed a mathematical model of the COVID-19 epidemic with confirmed case-driven contact tracing quarantine,and applied the model to evaluate the effectiveness of the policy of contact tracing and *** model is established based on the combination of the compartmental model and individual-based model simulations,which results in a closed-form delay differential equation *** proposed model includes a novel form of quarantine functions to represent the number of quarantine individuals following the confirmed cases every day and provides analytic expressions to study the effects of changing the quarantine *** proposed model can be applied to epidemic dynamics during the period of community spread and when the policy of confirmed cases-driven contact tracing quarantine is *** applied the model to study the effectiveness of contact tracing and *** proposed delay differential equation model can describe the average epidemic dynamics of the stochastic-individual-based model,however,it is not enough to describe the diverse response due to the stochastic *** on model simulations,we found that the policy of contact tracing and quarantine can obviously reduce the epidemic size,however,may not be enough to achieve zero-infectious in a short time,a combination of close contact quarantine and social contact restriction is required to achieve ***,the effect of reducing epidemic size is insensitive to the period of quarantine,there are no significant changes in the epidemic dynamics when the quarantine days vary from 7 to 21 days.

关键词： COVID-19 Contact tracing quarantine Individual-based modeling Delay-differential equation model

Evolutionary dynamics of cancer:From epigenetic regulation to cell population dynamics——mathematical model framework, applications,and open problems

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Science China Mathematics 2020年第3期63卷 411-424页

作者： jinzhi lei Zhou Pei-Yuan Center for Applied Mathematics Tsinghua University School of Mathematical Sciences Tiangong University

Predictive modeling of the evolutionary dynamics of cancer is a challenging issue in computational cancer biology. In this paper, we propose a general mathematical model framework for the evolutionary dynamics of cancer, including plasticity and heterogeneity in cancer cells. Cancer is a group of diseases involving abnormal cell growth, during which abnormal regulation of stem cell regeneration is essential for the dynamics of cancer development. In general, the dynamics of stem cell regeneration can be simplified as a G0 phase cell cycle model, which leads to a delay differentiation equation. When cell heterogeneity and plasticity are considered, we establish a differential-integral equation based on the random transition of epigenetic states of stem cells during cell division. The proposed model highlights cell heterogeneity and plasticity;connects the heterogeneity with cell-to-cell variance in cellular behaviors(for example, proliferation, apoptosis, and differentiation/senescence);and can be extended to include gene mutation-induced tumor development. Hybrid computational models are developed based on the mathematical model framework and are applied to the processes of inflammationinduced tumorigenesis and tumor relapse after chimeric antigen receptor(CAR)-T cell therapy. Finally, we propose several mathematical problems related to the proposed differential-integral equation. Solutions to these problems are crucial for understanding the evolutionary dynamics of cancer.

关键词： stem cell regeneration differential-integral equation cancer development computational cancer biology open problems

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异质性干细胞增殖过程中的熵变化

生物信息学 2024年第1期22卷 58-69页

作者：张义定雷锦志天津工业大学计算机科学与技术学院天津300387 天津工业大学数学科学学院应用数学中心天津300387

干细胞在多细胞生物体内广泛存在,其增殖过程在生命体的生长、发育、衰老、组织修复过程中起着重要作用。正常组织中的细胞增殖过程受到严格的控制,干细胞的异常增殖与恶性肿瘤、肥胖症、再生障碍性贫血等疾病有密切关系。生命体内异质... 详细信息

干细胞在多细胞生物体内广泛存在,其增殖过程在生命体的生长、发育、衰老、组织修复过程中起着重要作用。正常组织中的细胞增殖过程受到严格的控制,干细胞的异常增殖与恶性肿瘤、肥胖症、再生障碍性贫血等疾病有密切关系。生命体内异质性细胞的增殖过程是复杂的动力系统行为,干细胞异常增殖过程伴随细胞的可塑性变化和细胞间相互作用的再平衡过程,如何对这一过程进行定量描述是重要的研究课题。本文构建包含细胞的增殖分化指标和异常增殖性指标异质性的干细胞增殖模型,通过所建立的模型研究由于微环境变化引起的细胞异常增殖过程的熵变化,建立不同增殖条件下的系统熵变化与宏观动力学和系统参数之间的关系。结果表明,在细胞微环境变化引起异常增殖和恢复的过程中,系统的熵与细胞数量之间存在对应关系,而与微环境变化的路径无关。此外,熵对细胞数量的依赖关系在异常增殖和恢复阶段表现出不同的行为,显示了生物过程的微观不可逆性。本文从物理学的角度对细胞异常增殖过程中熵变化与细胞数量变化的动力学给出定量刻画,为定量描述异质性干细胞增殖过程给出新的研究思路。

关键词：干细胞增殖熵肿瘤演变动力学细胞异质性

Effectiveness of non-pharmaceutical interventions against local transmission of COVID-19: An individual-based modelling study

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Infectious Disease Modelling 2021年第1期6卷 848-858页

作者： Chuang Xu Yongzhen Pei Shengqiang Liu jinzhi lei School of Computer Science and Technology Tiangong UniversityTianjin300387China School of Mathematical Sciences Center for Applied MathematicsTiangong UniversityTianjin300387China

The outbreak of the novel coronavirus disease 2019(COVID-19),caused by the novel severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),has caused global transmission,and been spread all over the *** those regions that are currently free of infected cases,it is an urgent issue to prevent and control the local outbreak of COVID-19 when there are sporadic *** evaluate the effects of non-pharmaceutical interventions against local transmission of COVID-19,and to forecast the epidemic dynamics after local outbreak of diseases under different control measures,we developed an individual-based model(IBM)to simulate the transmission dynamics of COVID-19 from a microscopic perspective of individual-to-individual contacts to heterogenous among *** on the model,we simulated the effects of different levels of non-pharmaceutical interventions in controlling disease transmission after the appearance of sporadic *** shown that isolation of infected cases and quarantine of close contacts alone would not eliminate the local transmission of COVID-19,and there is a risk of a second wave *** the second-layer close contacts can obviously reduce the size of ***,to effectively eliminate the daily new infections in a short time,it is necessary to reduce the individual-to-individual *** provides a numerical representation for the local transmission of infectious diseases,and extends the compartmental models to include individual heterogeneity and the close contacts *** study suggests that combinations of self-isolation,quarantine of close contacts,and social distancing would be necessary to block the local transmission of COVID-19.

关键词： COVID-19 SARS-CoV-2 Individual-based model Stochastic simulation Non-pharmaceutical intervention

Regulation by competition:a hidden layer of gene regulatory network

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Frontiers of Electrical and Electronic Engineering in China 2019年第2期7卷 110-121页

作者： lei Wei Ye Yuan Tao Hu Shuailin Li Tianrun Cheng jinzhi lei Zhen Xie Michael Q.Zhang Xiaowo Wang Ministry of Education Key Laboratory of Bioinformatics Center for Synthetic and Systems BiologyDepartment of AutomationTsinghua UniversityBeijing 100084China Beijing National Research Center for Information Science and Technology Beijing 100084China School of Life Sciences Tsinghua UniversityBeijing 100084China Zhou Pei-Yuan Center for Applied Mathematics Tsinghua UniversityBeijing 100084China Department of Basic Medical Sciences School of MedicineTsinghua UniversityBeijing 100084China Department of Biological Sciences Center for Systems BiologyThe University of TexasRichardsonTX 75080-3021USA

Background:Molecular competition brings about trade-offs of shared limited resources among the cellular components,and thus introduces a hidden layer of regulatory mechanism by connecting components even without direct physical *** molecular competition scenarios have been observed recently,but there is still a lack of systematic quantitative understanding to reveal the essence of molecular ***:Here,by abstracting the analogous competition mechanism behind diverse molecular systems,we built a unified coarse-grained competition motif model to systematically integrate experimental evidences in these processes and analyzed general properties shared behind them from steady-state behavior to dynamic ***:We could predict in what molecular environments competition would reveal threshold behavior or display a negative linear *** quantified how competition can shape regulator-target dose-response curve,modulate dynamic response speed,control target expression noise,and introduce correlated fluctuations between ***:This work uncovered the complexity and generality of molecular competition effect as a hidden layer of gene regulatory network,and therefore provided a unified insight and a theoretical framework to understand and employ competition in both natural and synthetic systems.

关键词： systems biology computational modeling molecular competition regulation synthetic biology network motif

Mathematical model of adult stem cell regeneration with cross-talk between genetic and epigenetic regulation

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Mathematical model of adult stem cell regeneration with cros...

Metarelation2vec:A Metapath-Free Scalable Representation Learning Model for Heterogeneous Networks

第二届全国神经动力学学术会议

作者： lei jinzhi Tsinghua University Zhou Pei-Yuan Center for Applied Mathematics

Adult stem cells,which exist throughout the body,multiply by cell division to replenish dying cells or to promote regeneration to repair damaged *** perform these functions during the lifetime of organs or tissues,stem cells need to maintain their populations in a faithful distribution of their epigenetic states,which are susceptible to stochastic fluctuations during each cell division,unexpected injury,and potential genetic mutations that occur during many cell ***,it remains unclear how the three processes of differentiation,proliferation and apoptosis in regulating stem cells collectively manage these challenging ***,without considering any molecular details,we propose a genetic optimal control model for adult stem-cell regeneration that includes the three fundamental processes,along with cell division and adaptation based on differential fitnesses of *** the model,stem cells with a distribution of epigenetic states are required to maximize expected performance after each cell *** analytical estimates and direct numerical simulations,we show that heterogeneous proliferation that depends on the epigenetic states of stem cells can improve the maintenance of stem-cell distributions to create balanced populations.A control strategy during each cell division is derived from the model,leading to a feedback mechanism involving heterogeneous proliferation that can accelerate regeneration with less fluctuation in the stem cell *** mutation is allowed,apoptosis evolves to maximize the performance during homeostasis after multiple cell *** overall modeling results highlight the importance of crosstalk between genetic and epigenetic regulation and the performance objectives during homeostasis in shaping a desirable heterogeneous distribution of stem cells in terms of epigenetic *** work is in collaboration with Simon *** from Princeton University and Qing Nie from UC Irvine,and has been publ

关键词： fitness function optimization robustness dynamic programming

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Tsinghua Science and Technology 2024年第2期29卷 553-575页

作者： lei Chen Yuan Li Yong lei Xingye Deng School of Information and Electrical Engineering Hunan University of Science and TechnologyXiangtan 411201China School of Computer Science and Engineering Hunan University of Science and TechnologyXiangtan 411201China

Metapaths with specific complex semantics are critical to learning diverse semantic and structural information of heterogeneous networks(HNs)for most of the existing representation learning ***,any metapaths consisting of multiple,simple metarelations must be driven by domain *** sensitive,expensive,and limited metapaths severely reduce the flexibility and scalability of the existing models.A metapath-free,scalable representation learning model,called Metarelation2vec,is proposed for HNs with biased joint learning of all metarelations in a bid to address this ***,a metarelation-aware,biased walk strategy is first designed to obtain better training samples by using autogenerating cooperation probabilities for all metarelations rather than using expert-given ***,grouped nodes by the type,a common and shallow skip-gram model is used to separately learn structural proximity for each node ***,grouped links by the type,a novel and shallow model is used to separately learn the semantic proximity for each link ***,supervised by the cooperation probabilities of all meta-words,the biased training samples are thrown into the shallow models to jointly learn the structural and semantic information in the HNs,ensuring the accuracy and scalability of the *** experimental results on three tasks and four open datasets demonstrate the advantages of our proposed model.

关键词： metarelation random walk heterogeneous network metapath representation learning

Structural energy storage composites based on modified carbon fiber electrode with metal-organic frame enhancing layered double hydroxide

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Nano Research 2024年第3期17卷 1552-1563页

作者： Jinrui Ye Zhongbao Wang Qin lei lei Sun Jinfeng Gu School of Aerospace Engineering Beijing Institute of TechnologyBeijing 100081China Tangshan Research Institute Beijing Institute of TechnologyTangshan 063000China School of Materials Science and Engineering Shenyang Jianzhu UniversityShenyang 110168China Department of Stomatology PLA Strategic Support Force Characteristic Medical CenterBeijing 100101China Beijing Electromechanical Engineering Research Institute Beijing 100074China

Structural energy storage composites present advantages in simultaneously achieving structural strength and electrochemical *** of carbon fiber electrodes and resin structural electrolytes in energy storage composite poses challenges in maintaining good mechanical and electrochemical properties at reasonable cost and ***,we report a simple method to fabricate structural supercapacitor using carbon fiber electrodes(modified by Ni-layered double hydroxide(Ni-LDH)and in-situ growth of Co-metal-organic framework(Co-MOF)in a two-step process denoted as Co-MOF/Ni-LDH@CF)and bicontinuous-phase epoxy resin-based structural ***-MOF/Ni-LDH@CF as electrode material exhibits improved specific capacity(42.45 F·g^(-1))and cycle performance(93.3%capacity retention after 1000 cycles)in a three-electrode *** bicontinuous-phase epoxy resin-based structural electrolyte exhibits an ionic conductivity of 3.27×10^(-4) S·cm^(-1).The fabricated Co-MOF/Ni-LDH@CF/SPE-50 structural supercapacitor has an energy density of 3.21 Wh·kg^(-1) at a power density of 42.25 W·kg^(-1),whilst maintaining tensile strength and modulus of 334.6 MPa and 25.2 *** results show practical potential of employing modified commercial carbon fiber electrodes and epoxy resin-based structural electrolytes in structural energy storage applications.

关键词： carbon fiber electrode structural electrolyte structural energy storage composites supercapacitor