scholarly journals A 3D Agent-Based Model of Lung Fibrosis

Symmetry ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 90
Author(s):  
Nicolò Cogno ◽  
Roman Bauer ◽  
Marco Durante

Understanding the pathophysiology of lung fibrosis is of paramount importance to elaborate targeted and effective therapies. As it onsets, the randomly accumulating extracellular matrix (ECM) breaks the symmetry of the branching lung structure. Interestingly, similar pathways have been reported for both idiopathic pulmonary fibrosis and radiation-induced lung fibrosis (RILF). Individuals suffering from the disease, the worldwide incidence of which is growing, have poor prognosis and a short mean survival time. In this context, mathematical and computational models have the potential to shed light on key underlying pathological mechanisms, shorten the time needed for clinical trials, parallelize hypotheses testing, and improve personalized drug development. Agent-based modeling (ABM) has proven to be a reliable and versatile simulation tool, whose features make it a good candidate for recapitulating emergent behaviors in heterogeneous systems, such as those found at multiple scales in the human body. In this paper, we detail the implementation of a 3D agent-based model of lung fibrosis using a novel simulation platform, namely, BioDynaMo, and prove that it can qualitatively and quantitatively reproduce published results. Furthermore, we provide additional insights on late-fibrosis patterns through ECM density distribution histograms. The model recapitulates key intercellular mechanisms, while cell numbers and types are embodied by alveolar segments that act as agents and are spatially arranged by a custom algorithm. Finally, our model may hold potential for future applications in the context of lung disorders, ranging from RILF (by implementing radiation-induced cell damage mechanisms) to COVID-19 and inflammatory diseases (such as asthma or chronic obstructive pulmonary disease).

2018 ◽  
Vol 10 (1) ◽  
Author(s):  
Sultanah Alshammari ◽  
Armin Mikler

ObjectiveTo develop a computational model to assess the risk of epidemics in global mass gatherings and evaluate the impact of various measures of prevention and control of infectious diseases.IntroductionGlobal Mass gatherings (MGs) such as Olympic Games, FIFA World Cup, and Hajj (Muslim pilgrimage to Makkah), attract millions of people from different countries. The gathering of a large population in a proximity facilitates transmission of infectious diseases [1]. Attendees arrive from different geographical areas with diverse disease history and immune responses. The associated travel patterns with global events can contribute to a further disease spread affecting a large number of people within a short period and lead to a potential pandemic. Global MGs pose serious health threats and challenges to the hosting countries and home countries of the participants [2]. Advanced planning and disease surveillance systems are required to control health risks in these events. The success of computational models in different areas of public health and epidemiology motivates using these models in MGs to study transmission of infectious diseases and assess the risk of epidemics. Computational models enable simulation and analysis of different disease transmission scenarios in global MGs. Epidemic models can be used to evaluate the impact of various measures of prevention and control of infectious diseases.MethodsThe annual event of the Hajj is selected to illustrate the main aspects of the proposed model and to address the associated challenges. Every year, more than two million pilgrims from over 186 countries arrive in Makkah to perform Hajj with the majority arriving by air. Foreign pilgrims can stay at one of the holy cities of Makkah and Madinah up to 30-35 days prior the starting date of the Hajj. The long duration of the arrival phase of the Hajj allows a potential epidemic to proceed in the population of international pilgrims. Stochastic SEIR (Susceptible−Exposed−Infected−Recovered) agent-based model is developed to simulate the disease transmission among pilgrims. The agent-based model is used to simulate pilgrims and their interactions during the various phases of the Hajj. Each agent represents a pilgrim and maintains a record of demographic data (gender, country of origin, age), health data (infectivity, susceptibility, number of days being exposed or infected), event related data (location, arrival date and time), and precautionary or health-related behaviors.Each pilgrim can be either healthy but susceptible to a disease, exposed who are infected but cannot transmit the infection, or infectious (asymptomatic or symptomatic) who are infected and can transmit the disease to other susceptibles. Exposed individuals transfer to the infectious compartment after 1/α days, and infectious individuals will recover and gain immunity to that disease after 1/γ days. Where α is the latent period and γ is the infectious period. Moving susceptible individuals to exposed compartment depends on a successful disease transmission given a contact with an infectious individual. The disease transmission rate is determined by the contact rate and thetransmission probability per contact. Contact rate and mixing patterns are defined by probabilistic weights based on the features of infectious pilgrims and the duration and setting of the stage where contacts are taking place. The initial infections are seeded in the population using two scenarios (Figure 1) to measure the effects of changing, the timing for introducing a disease into the population and the likelihood that a particular flight will arrive with one or more infected individuals.ResultsThe results showed that the number of initial infections is influenced by increasing the value of λ and selecting starting date within peak arrival days. When starting from the first day, the average size of the initial infectious ranges from 0.05% to 1% of the total arriving pilgrims. Using the SEIR agent-based model, a simulation of the H1N1 Influenza epidemic was completed for the 35-days arrival stage of the Hajj. The epidemic is initiated with one infectious pilgrim per flight resulting in infected 0.5% of the total arriving pilgrims. As pilgrims spend few hours at the airport, the results obtained from running the epidemic model showed only new cases of susceptible individuals entering the exposed state in a range of 0.20% to 0.35% of total susceptibles. The number of new cases is reduced by almost the same rate of the number of infectious individuals following precautionary behaviors.ConclusionsA data-driven stochastic SEIR agent-based model is developed to simulate disease spread at global mass gatherings. The proposed model can provide initial indicators of infectious disease epidemic at these events and evaluate the possible effects of intervention measures and health-related behaviors. The proposed model can be generalized to model the spread of various diseases in different mass gatherings, as it allows different factors to vary and entered as parameters.References1. Memish ZA, Stephens GM, Steffen R, Ahmed QA. Emergence of medicine for mass gatherings: lessons from the Hajj. The Lancet infectious diseases. 2012 Jan 31;12(1):56-65.2. Chowell G, Nishiura H, Viboud C. Modeling rapidly disseminating infectious disease during mass gatherings. BMC medicine. 2012 Dec 7;10(1):159.


Author(s):  
A.L. Rivera ◽  
◽  
A.S. Ramos-Bernal ◽  
A. Negrón-Mendoza ◽  
◽  
...  

2021 ◽  
Author(s):  
Augusto Cabrera-Becerril ◽  
Pedro Miramontes ◽  
Raúl Peralta

AbstractWe introduce an agent-based model to simulate the epidemiological dynamics of COVID-19. Most computational models proposed to study this epidemic do no take into account human mobility. We present a direct simulation model where mobility plays a key role and propose as well four quarantine strategies. The results show that the no-quarantine strategy does lead to a high peak of contagions with no rebound. Quarantined strategies, for their part, show a re-emergence of the epidemic with smaller and softer peaks.


Author(s):  
Jonatan Gomez ◽  
Jeisson Prieto ◽  
Elizabeth Leon ◽  
Arles Rodríguez

AbstractThe transmission dynamics of the coronavirus - COVID-19-have challenged humankind at almost every level. Currently, research groups around the globe are trying to figure out such transmission dynamics using different scientific and technological approaches. One of those is by using mathematical and computational models like the compartmental model or the agent-based models. In this paper, a general agent-based model, called INFEKTA, that combines the transmission dynamics of an infectious disease with agents (individuals) that can move on a complex network of accessible places defined over a Euclidean space representing a real town or city is proposed. The applicability of INFEKTA is shown by modeling the transmission dynamics of the COVID-19 in Bogotá city, the capital of Colombia.


SIMULATION ◽  
2017 ◽  
Vol 93 (8) ◽  
pp. 641-657 ◽  
Author(s):  
Fateme Pourhasanzade ◽  
S.H Sabzpoushan ◽  
Ali Mohammad Alizadeh ◽  
Ebrahim Esmati

Mathematical and computational models are of great help to study and predict phenomena associated with cancer growth and development. These models may lead to introduce new therapies or improve current treatments by discovering facts that may not be easily discovered in clinical experiments. Here, a new two-dimensional (2D) stochastic agent-based model is presented for the spatiotemporal study of avascular tumor growth based on the effect of the immune system. The simple decision-making rules of updating the states of each agent depend not only on its intrinsic properties but also on its environment. Tumor cells can interact with both normal and immune cells in their Moore neighborhood. The effect of hypoxia has been checked off by considering non-mutant proliferative tumor cells beside mutant ones. The recruitment of immune cells after facing a mass of tumor is also considered. Results of the simulations are presented before and after the appearance of immune cells in the studied tissue. The growth fraction and necrotic fraction are used as output parameters along with a 2D graphical growth presentation. Finally, the effect of input parameters on the output parameters generated by the model is discussed. The model is then validated by an in vivo study published in medical articles. The results show a multi-spherical tumor growth before the immune system strongly involved in competition with tumor cells. Besides, considering the immune system in the model shows more compatibility with biological facts. The effect of the microenvironment on the proliferation of cancer and immune cells is also studied.


2018 ◽  
Author(s):  
Fabrizio Cleri

AbstractComputational models aiming at the spatio-temporal description of cancer evolution are a suitable framework for testing biological hypotheses from experimental data, and generating new ones. Building on our recent work [J Theor Biol 389, 146-158 (2016)] we develop a 3D agent-based model, capable of tracking hundreds of thousands of interacting cells, over time scales ranging from seconds to years. Cell dynamics is driven by a Monte Carlo solver, incorporating partial differential equations to describe chemical pathways and the activation/repression of “genes”, leading to the up- or down-regulation of specific cell markers. Each cell-agent of different kind (stem, cancer, stromal etc.) runs through its cycle, undergoes division, can exit to a dormant, senescent, necrotic state, or apoptosis, according to the inputs from their systemic network. The basic network at this stage describes glucose/oxygen/ATP cycling, and can be readily extended to cancer-cell specific markers. Eventual accumulation of chemical/radiation damage to each cell’s DNA is described by a Markov chain of internal states, and by a damage-repair network, whose evolution is linked to the cell systemic network. Aimed at a direct comparison with experiments of tumorsphere growth from stem cells, the present model will allow to quantitatively study the role of transcription factors involved in the reprogramming and variable radio-resistance of simulated cancer-stem cells, evolving in a realistic computer simulation of a growing multicellular tumorsphere.


2019 ◽  
Author(s):  
Christopher McComb ◽  
Kathryn Jablokow ◽  
Samuel Lapp

The performance of a design team is influenced by each team member's unique cognitive style - i.e., their preferred manner of managing structure as they solve problems, make decisions, and seek to bring about change. Cognitive style plays an important role in how teams of engineers design and collaborate, but the interactions of cognitive style with team organization and processes have not been well studied. The limitations of small-scale behavioral experiments have led researchers to develop computational models for simulating teamwork; however, none have modeled the effects of individuals' cognitive styles. This paper presents KABOOM (KAI Agent-Based Organizational Optimization Model), the first agent-based model of teamwork to incorporate cognitive style. In KABOOM, heterogeneous agents imitate the diverse problem-solving styles described by Kirton's Adaption-Innovation construct, which places each individual somewhere along the spectrum of cognitive style preference. Using the model, we investigate the interacting effects of a team's communication patterns, specialization, and cognitive style composition on design performance. By simulating cognitive style in the context of team problem solving, KABOOM lays the groundwork for the development of team simulations that reflect humans' diverse problem-solving styles.


PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0245787
Author(s):  
Jonatan Gomez ◽  
Jeisson Prieto ◽  
Elizabeth Leon ◽  
Arles Rodríguez

The transmission dynamics of the coronavirus—COVID-19—have challenged humankind at almost every level. Currently, research groups around the globe are trying to figure out such transmission dynamics under special conditions such as separation policies enforced by governments. Mathematical and computational models, like the compartmental model or the agent-based model, are being used for this purpose. This paper proposes an agent-based model, called INFEKTA, for simulating the transmission of infectious diseases, not only the COVID-19, under social distancing policies. INFEKTA combines the transmission dynamic of a specific disease, (according to parameters found in the literature) with demographic information (population density, age, and genre of individuals) of geopolitical regions of the real town or city under study. Agents (virtual persons) can move, according to its mobility routines and the enforced social distancing policy, on a complex network of accessible places defined over an Euclidean space representing the town or city. The transmission dynamics of the COVID-19 under different social distancing policies in Bogotá city, the capital of Colombia, is simulated using INFEKTA with one million virtual persons. A sensitivity analysis of the impact of social distancing policies indicates that it is possible to establish a ‘medium’ (i.e., close 40% of the places) social distancing policy to achieve a significant reduction in the disease transmission.


Author(s):  
A L Rivera ◽  
◽  
S Ramos-Beltran ◽  
A Paredes-Arriaga ◽  
A Negron-Mendoza ◽  
...  

2019 ◽  
Vol 5 ◽  
Author(s):  
Samuel Lapp ◽  
Kathryn Jablokow ◽  
Christopher McComb

The performance of a design team is influenced by each team member’s unique cognitive style – i.e., their preferred manner of managing structure as they solve problems, make decisions, and seek to bring about change. Cognitive style plays an important role in how teams of engineers design and collaborate, but the interactions of cognitive style with team organization and processes have not been well studied. The limitations of small-scale behavioral experiments have led researchers to develop computational models for simulating teamwork; however, none have modeled the effects of individuals’ cognitive styles. This paper presents the Kirton Adaption–Innovation Inventory agent-based organizational optimization model (KABOOM), the first agent-based model of teamwork to incorporate cognitive style. In KABOOM, heterogeneous agents imitate the diverse problem-solving styles described by the Kirton Adaption-Innovation construct, which places each individual somewhere along the spectrum of cognitive style preference. Using the model, we investigate the interacting effects of a team’s communication patterns, specialization, and cognitive style composition on design performance. By simulating cognitive style in the context of team problem solving, KABOOM lays the groundwork for the development of team simulations that reflect humans’ diverse problem-solving styles.


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