Polymicrobial infections, caused by a community of multiple micro-organisms, are often associated with increased infection severity and poorer patient outcomes. The design of improved antimicrobial treatment strategies for PMIs can be supported by an understanding of their ecological and evolutionary dynamics. Bacterial species present in polymicrobial infections can produce virulence factors to inhibit host immune responses, such as neutrophil recruitment and phagocytosis. The presence of virulence factors can indirectly affect other bacterial species acting as a type of host-mediated interspecies interaction. The aim of this study was to assess how bacterial virulence factors targeting neutrophil function influence ecology and treatment outcomes of PMIs. An agent-based model was constructed which describes a dual-species bacterial population in the presence of neutrophils and a bacteriostatic drug. Our analysis has revealed unforeseen dynamics of the interplay of multiple virulence factors acting as interspecies interaction. We found that the distribution of two phagocytosis-inhibiting virulence factors amongst species can impact whether they have a mutually protective effect for both species. The addition of a virulence factor inhibiting neutrophil recruitment was found to reduce the protective effect of phagocytosis-inhibiting virulence factors. Furthermore we demonstrate the importance of virulence strength of a species relative to other virulent species to determine the fate of a species. We conclude that virulence factors are an important driver of population dynamics in polymicrobial infections, and may be a relevant therapeutic target for treatment of polymicrobial infections.

Previous studies conducted in the municipality of Sibaté (Colombia) have revealed alarming findings regarding asbestos exposure in the region, as it is the site of the country\'s first mesothelioma cluster. Non-occupational asbestos exposure events were identified in this population, and the young age of the mesothelioma cases at the time of diagnosis suggests that asbestos exposure occurred during their childhood. The creation of landfilled zones in the 1980s and 1990s, utilizing friable asbestos among other disposed materials, may have been a significant asbestos exposure event contributing to the elevated number of mesothelioma cases. The objective of this study was to model various historical exposure scenarios related to the creation and interaction of the population with asbestos-contaminated landfilled zones, in light of the absence of asbestos monitoring in the region. The models utilized a multi-agent simulation process, focusing on a 10-year period (1986-1995). Various relevant variables were incorporated into the modeling process, including, for example, the number of children playing in the landfilled zones and the percentage of children carrying asbestos fibers on their clothes to their homes. A range of values for input data for the models were utilized, spanning from very conservative numbers to exposure-promoting values. The average number of exposed individuals estimated over 750 simulation runs, considering all scenarios, was 571, with a range between 31 and 3800 exposed individuals. The use of multi-agent simulation models can assist the understanding of past asbestos exposure events, especially when there is a lack of environmental surveillance data.

Mate choice requires navigating an exploration-exploitation trade-off. Successful mate choice requires choosing partners who have preferred qualities; but time spent determining one partner\'s qualities could have been spent exploring for potentially superior alternatives. Here I argue that this dilemma can be modeled in a reinforcement learning framework as a multi-armed bandit problem. Moreover, using agent-based models and a sample of k = 522 real-world romantic dyads, I show that a reciprocity-weighted Thompson sampling algorithm performs well both in guiding mate search in noisy search environments and in reproducing the mate choices of real-world participants. These results provide a formal model of the understudied psychology of human mate search. They additionally offer implications for our understanding of person perception and mate choice.

An increasing amount of research is incorporating the concept of Digital twin (DT) in biomedical and health care applications. This scoping review aims to summarize existing research and identify gaps in the development and use of DTs in the health care domain. The focus of this study lies on summarizing: the different types of DTs, the techniques employed in DT development, the DT applications in health care, and the data resources used for creating DTs. We identified fifty studies, which mainly focused on creating organ- (n=15) and patient-specific twins (n=30). The research predominantly centers on cardiology, endocrinology, orthopedics, and infectious diseases. Only a few studies used real-world datasets for developing their DTs. However, there remain unresolved questions and promising directions that require further exploration. This review provides valuable reference material and insights for researchers on DTs in health care and highlights gaps and unmet needs in this field.

Per- and polyfluoroalkyl substances (PFAS), ubiquitous in a myriad of consumer and industrial products, and depending on the doses of exposure represent a hazard to both environmental and public health, owing to their persistent, mobile, and bio accumulative properties. These substances exhibit long half-lives in humans and can induce potential immunotoxic effects at low exposure levels, sparking growing concerns. While the European Food Safety Authority (EFSA) has assessed the risk to human health related to the presence of PFAS in food, in which a reduced antibody response to vaccination in infants was considered as the most critical human health effect, a comprehensive grasp of the molecular mechanisms spearheading PFAS-induced immunotoxicity is yet to be attained. Leveraging modern computational tools, including the Agent-Based Model (ABM) Universal Immune System Simulator (UISS) and Physiologically Based Kinetic (PBK) models, a deeper insight into the complex mechanisms of PFAS was sought. The adapted UISS serves as a vital tool in chemical risk assessments, simulating the host immune system\'s reactions to diverse stimuli and monitoring biological entities within specific adverse health contexts. In tandem, PBK models unravelling PFAS\' biokinetics within the body i.e. absorption, distribution, metabolism, and elimination, facilitating the development of time-concentration profiles from birth to 75 years at varied dosage levels, thereby enhancing UISS-TOX\'s predictive abilities. The integrated use of these computational frameworks shows promises in leveraging new scientific evidence to support risk assessments of PFAS. This innovative approach not only allowed to bridge existing data gaps but also unveiled complex mechanisms and the identification of unanticipated dynamics, potentially guiding more informed risk assessments, regulatory decisions, and associated risk mitigations measures for the future.

Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the intracellular level such as signaling, and at the extracellular level where cells communicate and coordinate with other cells. They aim to understand the impact of genetic or environmental deregulation observed in complex diseases, describe the interplay between a pathological tissue and the immune system, and suggest strategies to revert the diseased phenotypes. The construction of these multiscale models remains a very complex task, including the choice of the components to consider, the level of details of the processes to simulate, or the fitting of the parameters to the data. One additional difficulty is the expert knowledge needed to program these models in languages such as C++ or Python, which may discourage the participation of non-experts. Simplifying this process through structured description formalisms - coupled with a graphical interface - is crucial in making modeling more accessible to the broader scientific community, as well as streamlining the process for advanced users. This article introduces three examples of multiscale models which rely on the framework PhysiBoSS, an add-on of PhysiCell that includes intracellular descriptions as continuous time Boolean models to the agent-based approach. The article demonstrates how to easily construct such models, relying on PhysiCell Studio, the PhysiCell Graphical User Interface. A step-by-step tutorial is provided as a Supplementary Material and all models are provided at: https://physiboss.github.io/tutorial/.

To model complex systems, individual-based models (IBMs), sometimes called \"agent-based models\" (ABMs), describe a simplification of the system through an adequate representation of the elements. IBMs simulate the actions and interaction of discrete individuals/agents within a system in order to discover the pattern of behavior that comes from these interactions. Examples of individuals/agents in biological systems are individual immune cells and bacteria that act independently with their own unique attributes defined by behavioral rules. In IBMs, each of these agents resides in a spatial environment and interactions are guided by predefined rules. These rules are often simple and can be easily implemented. It is expected that following the interaction guided by these rules we will have a better understanding of agent-agent interaction as well as agent-environment interaction. Stochasticity described by probability distributions must be accounted for. Events that seldom occur such as the accumulation of rare mutations can be easily modeled.Thus, IBMs are able to track the behavior of each individual/agent within the model while also obtaining information on the results of their collective behaviors. The influence of impact of one agent with another can be captured, thus allowing a full representation of both direct and indirect causation on the aggregate results. This means that important new insights can be gained and hypotheses tested.

Purpose. To estimate the impact on mortality of nonpharmaceutical interventions (NPIs) implemented early in the COVID-19 pandemic. Methods. We implemented an agent-based modified SEIR model of COVID-19, calibrated to match death numbers reported in Pennsylvania from January 2020 to April 2021 and including representations of NPIs implemented in Pennsylvania. To investigate the impact of these strategies, we ran the calibrated model with no interventions and with varying combinations, timings, and levels of interventions. Results. The model closely replicated death outcomes data for Pennsylvania. Without NPIs, deaths in the early months of the pandemic were estimated to be much higher (67,718 deaths compared to actual 6,969). Voluntary interventions alone were relatively ineffective at decreasing mortality. Delaying implementation of interventions led to higher deaths (∼9,000 more deaths with just a 1-week delay). School closure was insufficient as a single intervention but was an important part of a combined intervention strategy. Conclusions. NPIs were effective at reducing deaths early in the COVID-19 pandemic. Agent-based models can incorporate substantial detail on infectious disease spread and the impact of mitigations. Policy Implications. The model supports the importance and effectiveness of NPIs to decrease morbidity from respiratory pathogens. This is particularly important for emerging pathogens for which no vaccines or treatments exist, but such strategies are applicable to a variety of respiratory pathogens.
UNASSIGNED: Nonpharmaceutical interventions were used extensively during the early period of the COVID-19 pandemic, but their use has remained controversial.Agent-based modeling of the impact of these mitigation strategies early in the COVID-19 pandemic supports the effectiveness of nonpharmaceutical interventions at decreasing mortality.Since such interventions are not specific to a particular pathogen, they can be used to protect against any respiratory pathogen, known or emerging. They can be applied rapidly when conditions warrant.

Water scarcity poses a significant challenge to sustainable development, necessitating innovative approaches to manage limited resources efficiently. Effective water resource management involves not just the conservation and distribution of freshwater supplies but also the strategic reuse of treated wastewater (TWW). This study proposes a novel approach for the optimal allocation of treated wastewater among three key sectors (user agents): agriculture, industry, and urban green space. Recognizing the intricate interplays among these sectors, System Dynamics (SD) and Agent-Based Modeling (ABM) were integrated in a Complex Adaptive System (CAS) to capture the interactions and feedback mechanisms inherent within treated wastewater allocation systems. The Non-dominated Sorting Genetic Algorithm II (NSGA-II) serves as the optimization tool, enabling the identification of optimal allocation strategies across various management scenarios over a 25-year simulation period. Our research navigates the complexities of long-term resource management, accounting for each sector\'s evolving its objectives and guidelines along the whole system objectives and strategies. The outcomes demonstrate how treated wastewater can be effectively distributed to support economic and social equity -as the system objectives-while supporting agricultural and industrial growth and enhancing efficiency and social well-being -reflecting individual agent objectives-within the CAS framework. The research explores four distinct management scenarios, each prioritizing different sectors to address water resource management challenges. Notably, all four scenarios align with the strategies required by the ruler (government), providing strategic guidance to water resource managers for decision-making. The simulation results reveal a scenario where all sectors\' demands are met, with Scenario 4 emerging as the most effective. Scenario 4 aligned with the objectives and guidelines of each sector, demonstrating significant improvements in the CY (Agriculture agent index; increased from 0.2 to 0.68), IGI (Industry agent index; increased from 1 to 1.63), and GAI (Urban Green Space agent index; increased from 1 to 1.23) indices over the 25-year simulation period. By providing a strategic blueprint for policymakers and stakeholders, this study contributes significantly to the discourse on sustainable water resource management, presenting a replicable model for similar contexts globally, where judicious allocation of treated wastewater is paramount for achieving harmony between human activity and ecological preservation.

While inhomogeneous diffusivity has been identified as a ubiquitous feature of the cellular interior, its implications for particle mobility and concentration at different length scales remain largely unexplored. In this work, we use agent-based simulations of diffusion to investigate how heterogeneous diffusivity affects the movement and concentration of diffusing particles. We propose that a nonequilibrium mode of membrane-less compartmentalization arising from the convergence of diffusive trajectories into low-diffusive sinks, which we call \'diffusive lensing,\' is relevant for living systems. Our work highlights the phenomenon of diffusive lensing as a potentially key driver of mesoscale dynamics in the cytoplasm, with possible far-reaching implications for biochemical processes.