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"Agent based model"

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https://www.readbyqxmd.com/read/29351300/empirical-validation-of-an-agent-based-model-of-wood-markets-in-switzerland
#1
Stefan Holm, Lorenz M Hilty, Renato Lemm, Oliver Thees
We present an agent-based model of wood markets and show our efforts to validate this model using empirical data from different sources, including interviews, workshops, experiments, and official statistics. Own surveys closed gaps where data was not available. Our approach to model validation used a variety of techniques, including the replication of historical production amounts, prices, and survey results, as well as a historical case study of a large sawmill entering the market and becoming insolvent only a few years later...
2018: PloS One
https://www.readbyqxmd.com/read/29351290/land-use-change-in-oil-palm-dominated-tropical-landscapes-an-agent-based-model-to-explore-ecological-and-socio-economic-trade-offs
#2
Claudia Dislich, Elisabeth Hettig, Jan Salecker, Johannes Heinonen, Jann Lay, Katrin M Meyer, Kerstin Wiegand, Suria Tarigan
Land-use changes have dramatically transformed tropical landscapes. We describe an ecological-economic land-use change model as an integrated, exploratory tool used to analyze how tropical land-use change affects ecological and socio-economic functions. The model analysis seeks to determine what kind of landscape mosaic can improve the ensemble of ecosystem functioning, biodiversity, and economic benefit based on the synergies and trade-offs that we have to account for. More specifically, (1) how do specific ecosystem functions, such as carbon storage, and economic functions, such as household consumption, relate to each other? (2) How do external factors, such as the output prices of crops, affect these relationships? (3) How do these relationships change when production inefficiency differs between smallholder farmers and learning is incorporated? We initialize the ecological-economic model with artificially generated land-use maps parameterized to our study region...
2018: PloS One
https://www.readbyqxmd.com/read/29349218/comparing-methods-of-targeting-obesity-interventions-in-populations-an-agent-based-simulation
#3
Rahmatollah Beheshti, Mehdi Jalalpour, Thomas A Glass
Social networks as well as neighborhood environments have been shown to effect obesity-related behaviors including energy intake and physical activity. Accordingly, harnessing social networks to improve targeting of obesity interventions may be promising to the extent this leads to social multiplier effects and wider diffusion of intervention impact on populations. However, the literature evaluating network-based interventions has been inconsistent. Computational methods like agent-based models (ABM) provide researchers with tools to experiment in a simulated environment...
December 2017: SSM—Population Health
https://www.readbyqxmd.com/read/29347735/spreading-of-nonmotile-bacteria-on-a-hard-agar-plate-comparison-between-agent-based-and-stochastic-simulations
#4
Navdeep Rana, Pushpita Ghosh, Prasad Perlekar
We study spreading of a nonmotile bacteria colony on a hard agar plate by using agent-based and continuum models. We show that the spreading dynamics depends on the initial nutrient concentration, the motility, and the inherent demographic noise. Population fluctuations are inherent in an agent-based model, whereas for the continuum model we model them by using a stochastic Langevin equation. We show that the intrinsic population fluctuations coupled with nonlinear diffusivity lead to a transition from a diffusion limited aggregation type of morphology to an Eden-like morphology on decreasing the initial nutrient concentration...
November 2017: Physical Review. E
https://www.readbyqxmd.com/read/29340526/simulating-the-behavior-of-patients-who-leave-a-public-hospital-emergency-department-without-being-seen-by-a-physician-a-cellular-automaton-and-agent-based-framework
#5
Milad Yousefi, Moslem Yousefi, F S Fogliatto, R P M Ferreira, J H Kim
The objective of this study was to develop an agent based modeling (ABM) framework to simulate the behavior of patients who leave a public hospital emergency department (ED) without being seen (LWBS). In doing so, the study complements computer modeling and cellular automata (CA) techniques to simulate the behavior of patients in an ED. After verifying and validating the model by comparing it with data from a real case study, the significance of four preventive policies including increasing number of triage nurses, fast-track treatment, increasing the waiting room capacity and reducing treatment time were investigated by utilizing ordinary least squares regression...
January 11, 2018: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/29330536/carbon-limitation-drives-gc-content-evolution-of-a-marine-bacterium-in-an-individual-based-genome-scale-model
#6
Ferdi L Hellweger, Yongjie Huang, Haiwei Luo
An important unanswered question in evolutionary genomics is the source of considerable variation of genomic base composition (GC content) even among organisms that share one habitat. Evolution toward GC-poor genomes has been considered a major adaptive pathway in the oligotrophic ocean, but GC-rich bacteria are also prevalent and highly successful in this environment. We quantify the contribution of multiple factors to the change of genomic GC content of Ruegeria pomeroyi DSS-3, a representative and GC-rich member in the globally abundant Roseobacter clade, using an agent-based model...
January 12, 2018: ISME Journal
https://www.readbyqxmd.com/read/29328870/agent-based-modeling-in-public-health-current-applications-and-future-directions
#7
Melissa Tracy, Magdalena Cerdá, Katherine M Keyes
Agent-based modeling is a computational approach in which agents with a specified set of characteristics interact with each other and with their environment according to predefined rules. We review key areas in public health where agent-based modeling has been adopted, including both communicable and noncommunicable disease, health behaviors, and social epidemiology. Wealso describe the main strengths and limitations of this approach for questions with public health relevance. Finally, we describe both methodologic and substantive future directions that we believe will enhance the value of agent-based modeling for public health...
January 12, 2018: Annual Review of Public Health
https://www.readbyqxmd.com/read/29321537/computational-investigation-of-environment-noise-interaction-in-single-cell-organisms-the-merit-of-expression-stochasticity-depends-on-the-quality-of-environmental-fluctuations
#8
Anja Lück, Lukas Klimmasch, Peter Großmann, Sebastian Germerodt, Christoph Kaleta
Organisms need to adapt to changing environments and they do so by using a broad spectrum of strategies. These strategies include finding the right balance between expressing genes before or when they are needed, and adjusting the degree of noise inherent in gene expression. We investigated the interplay between different nutritional environments and the inhabiting organisms' metabolic and genetic adaptations by applying an evolutionary algorithm to an agent-based model of a concise bacterial metabolism. Our results show that constant environments and rapidly fluctuating environments produce similar adaptations in the organisms, making the predictability of the environment a major factor in determining optimal adaptation...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320541/agent-based-modeling-of-the-interaction-between-cd8-t-cells-and-beta-cells-in-type-1-diabetes
#9
Mustafa Cagdas Ozturk, Qian Xu, Ali Cinar
We propose an agent-based model for the simulation of the autoimmune response in T1D. The model incorporates cell behavior from various rules derived from the current literature and is implemented on a high-performance computing system, which enables the simulation of a significant portion of the islets in the mouse pancreas. Simulation results indicate that the model is able to capture the trends that emerge during the progression of the autoimmunity. The multi-scale nature of the model enables definition of rules or equations that govern cellular or sub-cellular level phenomena and observation of the outcomes at the tissue scale...
2018: PloS One
https://www.readbyqxmd.com/read/29315715/a-mathematical-model-for-pathogen-cross-contamination-dynamics-during-the-postharvest-processing-of-leafy-greens
#10
Amir Mokhtari, David Oryang, Yuhuan Chen, Regis Pouillot, Jane Van Doren
We developed a probabilistic mathematical model for the postharvest processing of leafy greens focusing on Escherichia coli O157:H7 contamination of fresh-cut romaine lettuce as the case study. Our model can (i) support the investigation of cross-contamination scenarios, and (ii) evaluate and compare different risk mitigation options. We used an agent-based modeling framework to predict the pathogen prevalence and levels in bags of fresh-cut lettuce and quantify spread of E. coli O157:H7 from contaminated lettuce to surface areas of processing equipment...
January 8, 2018: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/29314670/eliminating-hepatitis-c-virus-as-a-public-health-threat-among-hiv-positive-men-who-have-sex-with-men-a-multi-modelling-approach-to-understand-differences-in-sexual-risk-behaviour
#11
Nick Scott, Mark Stoové, David P Wilson, Olivia Keiser, Carol El-Hayek, Joseph Doyle, Margaret Hellard
INTRODUCTION: Outbreaks of hepatitis C virus (HCV) infections among HIV-positive men who have sex with men (MSM) have been observed globally. Using a multi-modelling approach we estimate the time and number of direct-acting antiviral treatment courses required to achieve an 80% reduction in HCV prevalence among HIV-positive MSM in the state of Victoria, Australia. METHODS: Three models of HCV transmission, testing and treatment among MSM were compared: a dynamic compartmental model; an agent-based model (ABM) parametrized to local surveillance and behavioural data ("ABM1"); and an ABM with a more heterogeneous population ("ABM2") to determine the influence of extreme variations in sexual risk behaviour...
January 2018: Journal of the International AIDS Society
https://www.readbyqxmd.com/read/29297294/combining-agent-based-models-and-virtual-screening-techniques-to-predict-the-best-citrus-derived-vaccine-adjuvants-against-human-papilloma-virus
#12
Marzio Pennisi, Giulia Russo, Silvia Ravalli, Francesco Pappalardo
BACKGROUND: Human papillomavirus infection is a global social burden that, every year, leads to thousands new diagnosis of cancer. The introduction of a protocol of immunization, with Gardasil and Cervarix vaccines, has radically changed the way this infection easily spreads among people. Even though vaccination is only preventive and not therapeutic, it is a strong tool capable to avoid the consequences that this pathogen could cause. Gardasil vaccine is not free from side effects and the duration of immunity is not always well determined...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29277001/a-computational-approach-to-unraveling-tlr-signaling-in-murine-mammary-carcinoma
#13
Chun Wai Liew, Tiffany Phuong, Carli B Jones, Samantha Evans, Justin Hoot, Kendall Weedling, Damarcus Ingram, Stacy Nganga, Robert A Kurt
We developed an agent-based model to simulate a signaling cascade which allowed us to focus on the behavior of each class of agents independently of the other classes except when they were in physical contact. A critical piece was the ratio of the populations of agents that interact with one another, not their absolute values. This ratio reflects the effects of the density of each agent in the biological cascade as well as their size and velocity. Although the system can be used for any signaling cascade in any cell type, to validate the system we modeled Toll-like receptor (TLR) signaling in two very different types of cells; tumor cells and white blood cells...
December 18, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29259320/phototaxis-as-a-collective-phenomenon-in-cyanobacterial-colonies
#14
P Varuni, Shakti N Menon, Gautam I Menon
Cyanobacteria are a diverse group of photosynthetic bacteria that exhibit phototaxis, or motion in response to light. Cyanobacteria such as Synechocystis sp. secrete a mixture of complex polysaccharides that facilitate cell motion, while their type 4 pili allow them to physically attach to each other. Even though cells can respond individually to light, colonies are observed to move collectively towards the light source in dense finger-like projections. We present an agent-based model for cyanobacterial phototaxis that accounts for slime deposition as well as for direct physical links between bacteria, mediated through their type 4 pili...
December 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29259083/extracellular-dna-and-type-iv-pilus-expression-regulate-the-structure-and-kinetics-of-biofilm-formation-by-nontypeable-haemophilus-influenzae
#15
Jayajit Das, Elaine Mokrzan, Vinal Lakhani, Lucia Rosas, Joseph A Jurcisek, William C Ray, Lauren O Bakaletz
Biofilms formed in the middle ear by nontypeable Haemophilus influenzae (NTHI) are central to the chronicity, recurrence, and refractive nature of otitis media (OM). However, mechanisms that underlie the emergence of specific NTHI biofilm structures are unclear. We combined computational analysis tools and in silico modeling rooted in statistical physics with confocal imaging of NTHI biofilms formed in vitro during static culture in order to identify mechanisms that give rise to distinguishing morphological features...
December 19, 2017: MBio
https://www.readbyqxmd.com/read/29250071/dimensionality-of-motion-and-binding-valency-govern-receptor-ligand-kinetics-as-revealed-by-agent-based-modeling
#16
Teresa Lehnert, Marc Thilo Figge
Mathematical modeling and computer simulations have become an integral part of modern biological research. The strength of theoretical approaches is in the simplification of complex biological systems. We here consider the general problem of receptor-ligand binding in the context of antibody-antigen binding. On the one hand, we establish a quantitative mapping between macroscopic binding rates of a deterministic differential equation model and their microscopic equivalents as obtained from simulating the spatiotemporal binding kinetics by stochastic agent-based models...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29249555/simulating-the-impact-of-sugar-sweetened-beverage-warning-labels-in-three-cities
#17
Bruce Y Lee, Marie C Ferguson, Daniel L Hertenstein, Atif Adam, Eli Zenkov, Peggy I Wang, Michelle S Wong, Joel Gittelsohn, Yeeli Mui, Shawn T Brown
INTRODUCTION: A number of locations have been considering sugar-sweetened beverage point-of-purchase warning label policies to help address rising adolescent overweight and obesity prevalence. METHODS: To explore the impact of such policies, in 2016 detailed agent-based models of Baltimore, Philadelphia, and San Francisco were developed, representing their populations, school locations, and food sources, using data from various sources collected between 2005 and 2014...
December 6, 2017: American Journal of Preventive Medicine
https://www.readbyqxmd.com/read/29240712/developing-an-agent-based-drug-model-to-investigate-the-synergistic-effects-of-drug-combinations
#18
Hongjie Gao, Zuojing Yin, Zhiwei Cao, Le Zhang
The growth and survival of cancer cells are greatly related to their surrounding microenvironment. To understand the regulation under the impact of anti-cancer drugs and their synergistic effects, we have developed a multiscale agent-based model that can investigate the synergistic effects of drug combinations with three innovations. First, it explores the synergistic effects of drug combinations in a huge dose combinational space at the cell line level. Second, it can simulate the interaction between cells and their microenvironment...
December 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29239482/using-agent-based-modeling-to-study-multiple-risk-factors-and-multiple-health-outcomes-at-multiple-levels
#19
Yong Yang
Most health studies focus on one health outcome and examine the influence of one or multiple risk factors. However, in reality, various pathways, interactions, and associations exist not only between risk factors and health outcomes but also among the risk factors and among health outcomes. The advance of system science methods, Big Data, and accumulated knowledge allows us to examine how multiple risk factors influence multiple health outcomes at multiple levels (termed a 3M study). Using the study of neighborhood environment and health as an example, I elaborate on the significance of 3M studies...
November 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/29229960/how-costly-punishment-diversity-and-density-of-connectivity-influence-cooperation-in-a-biological-network
#20
Ivan C Ezeigbo
It has been an old unsolved puzzle to evolutionary theorists on which mechanisms would increase large-scale cooperation in human societies. Thus, how such mechanisms operate in a biological network is still not well understood. This study addresses these questions with empirical evidence from agent-based models designed to understand these network interactions. Repeated Prisoner's Dilemma games were designed to study how costly punishment, diversity, and density of connectivity interact to influence cooperation in a biological network...
December 11, 2017: Scientific Reports
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