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"Agent-based modeling"

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https://www.readbyqxmd.com/read/29330536/carbon-limitation-drives-gc-content-evolution-of-a-marine-bacterium-in-an-individual-based-genome-scale-model
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/29223196/application-of-psychological-theories-in-agent-based-modeling-the-case-of-the-theory-of-planned-behavior
#16
Andrea Scalco, Andrea Ceschi, Riccardo Sartori
It is likely that computer simulations will assume a greater role in the next future to investigate and understand reality (Rand & Rust, 2011). Particularly, agent-based models (ABMs) represent a method of investigation of social phenomena that blend the knowledge of social sciences with the advantages of virtual simulations. Within this context, the development of algorithms able to recreate the reasoning engine of autonomous virtual agents represents one of the most fragile aspects and it is indeed crucial to establish such models on well-supported psychological theoretical frameworks...
January 2018: Nonlinear Dynamics, Psychology, and Life Sciences
https://www.readbyqxmd.com/read/29208733/opinion-building-a-better-past-with-the-help-of-agent-based-modeling
#17
J Daniel Rogers, Wendy H Cegielski
No abstract text is available yet for this article.
December 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29200605/agent-based-modeling-of-china-s-rural-urban-migration-and-social-network-structure
#18
Zhaohao Fu, Lingxin Hao
We analyze China's rural-urban migration and endogenous social network structures using agent-based modeling. The agents from census micro data are located in their rural origin with an empirical-estimated prior propensity to move. The population-scale social network is a hybrid one, combining observed family ties and locations of the origin with a parameter space calibrated from census, survey and aggregate data and sampled using a stepwise Latin Hypercube Sampling method. At monthly intervals, some agents migrate and these migratory acts change the social network by turning within-nonmigrant connections to between-migrant-nonmigrant connections, turning local connections to nonlocal connections, and adding among-migrant connections...
January 15, 2018: Physica A
https://www.readbyqxmd.com/read/29197990/modeling-mechanical-inhomogeneities-in-small-populations-of-proliferating-monolayers-and-spheroids
#19
Emma Lejeune, Christian Linder
Understanding the mechanical behavior of multicellular monolayers and spheroids is fundamental to tissue culture, organism development, and the early stages of tumor growth. Proliferating cells in monolayers and spheroids experience mechanical forces as they grow and divide and local inhomogeneities in the mechanical microenvironment can cause individual cells within the multicellular system to grow and divide at different rates. This differential growth, combined with cell division and reorganization, leads to residual stress...
December 2, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/29197512/understanding-interactions-between-populations-individual-based-modelling-and-quantification-using-pair-correlation-functions
#20
S Dini, B J Binder, J E F Green
Understanding the underlying mechanisms that produce the huge variety of swarming and aggregation patterns in animals and cells is fundamental in ecology, developmental biology, and regenerative medicine, to name but a few examples. Depending upon the nature of the interactions between individuals (cells or animals), a variety of different large-scale spatial patterns can be observed in their distribution; examples include cell aggregates, stripes of different coloured skin cells, etc. For the case where all individuals are of the same type (i...
November 29, 2017: Journal of Theoretical Biology
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