BACKGROUND: Alzheimer's disease is one of the most common mental illnesses. It is posited that more than 25% of the population is affected by some mental disease during their lifetime. Treatment of each patient draws resources from the economy concerned. Therefore, it is important to quantify the potential economic impact. METHODS: Agent-based, system dynamics and numerical approaches to dynamic modeling of the population of the European Union and its patients with Alzheimer's disease are presented in this article. Simulations, their characteristics, and the results from different modeling tools are compared. RESULTS: The results of these approaches are compared with EU population growth predictions from the statistical office of the EU by Eurostat. The methodology of a creation of the models is described and all three modeling approaches are compared. The suitability of each modeling approach for the population modeling is discussed. CONCLUSION: In this case study, all three approaches gave us the results corresponding with the EU population prediction. Moreover, we were able to predict the number of patients with AD and, based on the modeling method, we were also able to monitor different characteristics of the population.

• Klíčová slova
• Alzheimer’s disease, agent-based model, numerical model, population modeling, population prediction, system dynamics.,
• MeSH
• Alzheimerova nemoc diagnóza   epidemiologie   MeSH
• biologické modely MeSH
• lidé MeSH
• systémová analýza * MeSH
• teoretické modely * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

A mathematical model of myocardial perfusion based on the lattice Boltzmann method (LBM) is proposed and its applicability is investigated in both healthy and diseased cases. The myocardium is conceptualized as a porous material in which the transport and mass transfer of a contrast agent in blood flow is studied. The results of myocardial perfusion obtained using LBM in 1D and 2D are confronted with previously reported results in the literature and the results obtained using the mixed-hybrid finite element method. Since LBM is not suitable for simulating flow in heterogeneous porous media, a simplified and computationally efficient 1D-analog approach to 2D diseased case is proposed and its applicability discussed.

• Klíčová slova
• advection–diffusion problem, contrast agent transport, lattice Boltzmann method, magnetic resonance imaging, mixed‐hybrid finite element method, myocardial perfusion,
• MeSH
• analýza metodou konečných prvků * MeSH
• kontrastní látky MeSH
• koronární cirkulace fyziologie   MeSH
• lidé MeSH
• modely kardiovaskulární * MeSH
• počítačová simulace MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• kontrastní látky MeSH

Agent-based evacuation modeling represents an effective tool for making predictions about evacuation aspects of buildings such as evacuation times, congestions, and maximum safe building capacity. Collection of real behavioral data for calibrating agent-based evacuation models is time-consuming, costly, and completely impossible in the case of buildings in the design phase, where predictions about evacuation behavior are especially needed. In recent years evacuation experiments conducted in virtual reality (VR) have been frequently proposed in the literature as an effective tool for collecting data about human behavior. However, empirical studies which would assess validity of VR-based data for such purposes are still rare and considerably lacking in the agent-based evacuation modeling domain. This study explores opportunities that the VR behavioral data may bring for refining outputs of agent evacuation models. To this end, this study employed multiple input settings of agent-based evacuation models (ABEMs), including those based on the data gathered from the VR evacuation experiment that mapped out evacuation behaviors of individuals within the building. Calibration and evaluation of models was based on empirical data gathered from an original evacuation exercise conducted in a real building (N = 35) and its virtual twin (N = 38). This study found that the resulting predictions of single agent models using data collected in the VR environment after proposed corrections have the potential to better predict real-world evacuation behavior while offering desirable variance in the data outputs necessary for practical applications.

• Klíčová slova
• Agent modeling, Evacuation behavior, Evacuation time, Indoor navigation, Pathfinder, Virtual reality,
• Publikační typ
• časopisecké články MeSH

Agent-based models (ABMs) are one of the main sources of evidence for decisions regarding mitigation and suppression measures against the spread of SARS-CoV-2. These models have not been previously included in the hierarchy of evidence put forth by the evidence-based medicine movement, which prioritizes those research methods that deliver results less susceptible to the risk of confounding. We point out the need to assess the quality of evidence delivered by ABMs and ask the question of what is the risk that assumptions entertained in ABMs do not include all the key factors and make model predictions susceptible to the problem of confounding.

• Klíčová slova
• Agent-based models, EBM, SARS-CoV-2,
• MeSH
• COVID-19 epidemiologie   MeSH
• lidé MeSH
• pandemie * MeSH
• SARS-CoV-2 fyziologie   MeSH
• systémová analýza * MeSH
• teoretické modely MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Eco-industrial parks (EIPs) are of increasing importance for implementing industrial ecology strategies and are facing increasing challenges in terms of environmental pollution and resource scarcity. As a complex adaptive system, an EIP involves multiple sectors and faces various disturbances that influence its evolutionary trajectories. This study adopts an agent-based model to simulate the material flows and industrial symbiosis process in the EIP, considering the initiative of each company and the ever-changing environment. The proposed EIP model emphasises the heterogeneity of companies and attempts to reflect multiple and dynamic factors that have received less attention in previous studies. This model contains two types of agents, companies and the external environment. A company agent makes decisions and interacts with other agents following its own behaviour rules, while the external environment agent functions to coordinate the material flows and exert influence on the companies. The model has been verified and validated by simulating a 20-year-period development of an empirical EIP in China. The simulation results are assessed by three indicators: eco-connectance, eco-efficiency, and industrial symbiosis indicator. Results showed that during the growing phase, the eco-connectance increased from 0.02 to 0.1 for the non-disturbance situation. The eco-efficiency and industrial symbiosis indicator also realised 78.5% and 74.8% of their total increments. The outcome of this research provides insights for the design of the strategies to improve the industrial symbiosis performance and is of high potential to facilitate EIPs in promoting eco-transformation and sustainable development.

• Klíčová slova
• Agent-based model, Eco-industrial park, Eco-transformation, Industrial ecology, Industrial symbiosis, Simulation,
• MeSH
• ekologie MeSH
• ekosystém * MeSH
• počítačová simulace MeSH
• průmysl MeSH
• zachování přírodních zdrojů * metody   MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Čína MeSH

BACKGROUND: Our purpose is to assess epidemiological agent-based models-or ABMs-of the SARS-CoV-2 pandemic methodologically. The rapid spread of the outbreak requires fast-paced decision-making regarding mitigation measures. However, the evidence for the efficacy of non-pharmaceutical interventions such as imposed social distancing and school or workplace closures is scarce: few observational studies use quasi-experimental research designs, and conducting randomized controlled trials seems infeasible. Additionally, evidence from the previous coronavirus outbreaks of SARS and MERS lacks external validity, given the significant differences in contagiousness of those pathogens relative to SARS-CoV-2. To address the pressing policy questions that have emerged as a result of COVID-19, epidemiologists have produced numerous models that range from simple compartmental models to highly advanced agent-based models. These models have been criticized for involving simplifications and lacking empirical support for their assumptions. METHODS: To address these voices and methodologically appraise epidemiological ABMs, we consider AceMod (the model of the COVID-19 epidemic in Australia) as a case study of the modelling practice. RESULTS: Our example shows that, although epidemiological ABMs involve simplifications of various sorts, the key characteristics of social interactions and the spread of SARS-CoV-2 are represented sufficiently accurately. This is the case because these modellers treat empirical results as inputs for constructing modelling assumptions and rules that the agents follow; and they use calibration to assert the adequacy to benchmark variables. CONCLUSIONS: Given this, we claim that the best epidemiological ABMs are models of actual mechanisms and deliver both mechanistic and difference-making evidence. Consequently, they may also adequately describe the effects of possible interventions. Finally, we discuss the limitations of ABMs and put forward policy recommendations.

• Klíčová slova
• SARS-CoV-2, agent-based modelling, causal inference, difference-making evidence, mechanism, mechanistic evidence,
• MeSH
• Betacoronavirus MeSH
• COVID-19 MeSH
• koronavirové infekce epidemiologie   MeSH
• lidé MeSH
• pandemie MeSH
• SARS-CoV-2 MeSH
• statistické modely * MeSH
• systémová analýza * MeSH
• virová pneumonie epidemiologie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Pharmacophore modeling is a widely used strategy for finding new hit molecules. Since not all protein targets have available 3D structures, ligand-based approaches are still useful. Currently, there are just a few free ligand-based pharmacophore modeling tools, and these have a lot of restrictions, e.g., using a template molecule for alignment. We developed a new approach to 3D pharmacophore representation and matching which does not require pharmacophore alignment. This representation can be used to quickly find identical pharmacophores in a given set. Based on this representation, a 3D pharmacophore ligand-based modeling approach to search for pharmacophores which preferably match active compounds and do not match inactive ones was developed. The approach searches for 3D pharmacophore models starting from 2D structures of available active and inactive compounds. The implemented approach was successfully applied for several retrospective studies. The results were compared to a 2D similarity search, demonstrating some of the advantages of the developed 3D pharmacophore models. Also, the generated 3D pharmacophore models were able to match the 3D poses of known ligands from their protein-ligand complexes, confirming the validity of the models. The developed approach is available as an open-source software tool: http://www.qsar4u.com/pages/pmapper.php and https://github.com/meddwl/psearch.

• Klíčová slova
• 3D pharmacophore hash, 3D pharmacophore signatures, ligand-based modeling, pharmacophore modeling,
• MeSH
• antagonisté adenosinového receptoru A2 chemie   MeSH
• cholinesterasové inhibitory chemie   MeSH
• inhibitory cytochromu P450 CYP3A chemie   MeSH
• ligandy MeSH
• molekulární modely * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antagonisté adenosinového receptoru A2 MeSH
• cholinesterasové inhibitory MeSH
• inhibitory cytochromu P450 CYP3A MeSH
• ligandy MeSH

This work focuses on mathematical modeling of removal of organic dyes from textile industry waste waters by a white-rot fungus Irpex lacteus in a trickle-bed bioreactor. We developed a mathematical model of biomass and decolorization process dynamics. The model comprises mass balances of glucose and the dye in a fungal biofilm and a liquid film. The biofilm is modeled using a spatially two-dimensional domain. The liquid film is considered as homogeneous in the direction normal to the biofilm surface. The biomass growth, decay and the erosion of the biofilm are taken into account. Using experimental data, we identified values of key model parameters: the dye degradation rate constant, biofilm corrugation factor and liquid velocity. Considering the dye degradation rate constant 1×10⁻⁵ kg m⁻³ s⁻¹, we found optimal values of the corrugation factor 0.853 and 0.59 and values of the liquid velocity 5.23×10⁻³ m s⁻¹ and 6.2×10⁻³ m s⁻¹ at initial dye concentrations 0.09433 kg m⁻³ and 0.05284 kg m⁻³, respectively. A good agreement between the simulated and experimental data using estimated values of the model parameters was achieved. The model can be used to simulate the performance of laboratory scale trickle-bed bioreactor operated in a batch regime or to estimate values of principal parameters of the bioreactor system.

• MeSH
• barva MeSH
• barvicí látky MeSH
• biodegradace MeSH
• biofilmy MeSH
• biomasa MeSH
• bioreaktory * MeSH
• časové faktory MeSH
• kinetika MeSH
• odpad tekutý - odstraňování přístrojové vybavení   MeSH
• počítačová simulace MeSH
• teoretické modely * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• barvicí látky MeSH

The A-series is the most recent generation of chemical warfare nerve agents (CWA) which act directly on the inhibition of the human acetylcholinesterase (HssAChE) enzyme. These compounds lack accurate experimental data on their physicochemical properties, and there is no evidence that traditional antidotes effectively reactivate HssAChE inhibited by them. In the search for potential antidotes, we employed virtual screening, molecular docking, and molecular dynamics (MD) simulations for the theoretical assessment of the performance of a library of Mannich phenols as potential reactivators of HssAChE inhibited by the Novichok agents A-230, A-232, and A-234, in comparison with the commercial oximes pralidoxime (2-PAM), asoxime (HI-6), trimedoxime (TMB-4), and obidoxime. Following the near-attack conformation (NAC) approach, our results suggest that the compounds assessed would face difficulties in triggering the proposed nucleophilic in-line displacement mechanism. Despite this, it was observed that certain Mannich phenols presented similar or superior results to those obtained by reference oximes against A-232 and A-234 model, suggesting that these compounds can adopt more favourable conformations. Additional binding energy calculations confirmed the stability of the model/ligands complexes and the reactivating potential observed in the molecular docking and MD studies. Our findings indicate that the Mannich phenols could be alternative antidotes and that their efficacy should be evaluated experimentally against the A-series CWA.

• Klíčová slova
• Molecular modeling, Near-attack conformation, Nerve agents, Non-oximes, Novichok,
• MeSH
• acetylcholinesterasa metabolismus   MeSH
• antidota farmakologie   MeSH
• chemické bojové látky * farmakologie   MeSH
• cholinesterasové inhibitory farmakologie   chemie   MeSH
• lidé MeSH
• nervová bojová látka * MeSH
• oximy farmakologie   chemie   MeSH
• pyridinové sloučeniny farmakologie   MeSH
• reaktivátory cholinesterasy * farmakologie   MeSH
• simulace molekulového dockingu MeSH
• trimedoxim chemie   farmakologie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• acetylcholinesterasa MeSH
• antidota MeSH
• chemické bojové látky * MeSH
• cholinesterasové inhibitory MeSH
• nervová bojová látka * MeSH
• oximy MeSH
• pralidoxime MeSH Prohlížeč
• pyridinové sloučeniny MeSH
• reaktivátory cholinesterasy * MeSH
• trimedoxim MeSH

UNLABELLED: This systematic review provides a comprehensive overview of tsunami evacuation models. The review covers scientific studies from the last decade (2012-2021) and is explicitly focused on models using an agent-based approach. The PRISMA methodology was used to analyze 171 selected papers, resulting in over 53 studies included in the detailed full-text analysis. This review is divided into two main parts: (1) a descriptive analysis of the presented models (focused on the modeling tools, validation, and software platform used, etc.), and (2) model analysis (e.g., model purpose, types of agents, input and output data, and modeled area). Special attention was given to the features of these models specifically associated with an agent-based approach. The results lead to the conclusion that the research domain of agent-based tsunami evacuation models is quite narrow and specialized, with a high degree of variability in the model attributes and properties. At the same time, the application of agent-specific methodologies, protocols, organizational paradigms, or standards is sparse. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11069-022-05643-x.

• Klíčová slova
• Agent-based model, Crowd motion, Evacuation, Natural hazard, Simulation, Tsunami,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH