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https://www.readbyqxmd.com/read/27910875/an-integrated-modelling-framework-from-cells-to-organism-based-on-a-cohort-of-digital-embryos
#1
Paul Villoutreix, Julien Delile, Barbara Rizzi, Louise Duloquin, Thierry Savy, Paul Bourgine, René Doursat, Nadine Peyriéras
We conducted a quantitative comparison of developing sea urchin embryos based on the analysis of five digital specimens obtained by automatic processing of in toto 3D+ time image data. These measurements served the reconstruction of a prototypical cell lineage tree able to predict the spatiotemporal cellular organisation of a normal sea urchin blastula. The reconstruction was achieved by designing and tuning a multi-level probabilistic model that reproduced embryo-level dynamics from a small number of statistical parameters characterising cell proliferation, cell surface area and cell volume evolution along the cell lineage...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27908025/geometry-of-behavioral-spaces-a-computational-approach-to-analysis-and-understanding-of-agent-based-models-and-agent-behaviors
#2
Martin Cenek, Spencer K Dahl
Systems with non-linear dynamics frequently exhibit emergent system behavior, which is important to find and specify rigorously to understand the nature of the modeled phenomena. Through this analysis, it is possible to characterize phenomena such as how systems assemble or dissipate and what behaviors lead to specific final system configurations. Agent Based Modeling (ABM) is one of the modeling techniques used to study the interaction dynamics between a system's agents and its environment. Although the methodology of ABM construction is well understood and practiced, there are no computational, statistically rigorous, comprehensive tools to evaluate an ABM's execution...
November 2016: Chaos
https://www.readbyqxmd.com/read/27903820/agent-based-modelling-in-synthetic-biology
#3
REVIEW
Thomas E Gorochowski
Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27893160/integrating-household-risk-mitigation-behavior-in-flood-risk-analysis-an-agent-based-model-approach
#4
Toon Haer, W J Wouter Botzen, Hans de Moel, Jeroen C J H Aerts
Recent studies showed that climate change and socioeconomic trends are expected to increase flood risks in many regions. However, in these studies, human behavior is commonly assumed to be constant, which neglects interaction and feedback loops between human and environmental systems. This neglect of human adaptation leads to a misrepresentation of flood risk. This article presents an agent-based model that incorporates human decision making in flood risk analysis. In particular, household investments in loss-reducing measures are examined under three economic decision models: (1) expected utility theory, which is the traditional economic model of rational agents; (2) prospect theory, which takes account of bounded rationality; and (3) a prospect theory model, which accounts for changing risk perceptions and social interactions through a process of Bayesian updating...
November 28, 2016: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/27890575/3d-hybrid-modelling-of-vascular-network-formation
#5
Holger Perfahl, Barry D Hughes, Tomás Alarcón, Philip K Maini, Mark C Lloyd, Matthias Reuss, Helen M Byrne
We develop an off-lattice, agent-based model to describe vasculogenesis, the de novo formation of blood vessels from endothelial progenitor cells during development. The endothelial cells that comprise our vessel network are viewed as linearly elastic spheres that move in response to the forces they experience. We distinguish two types of endothelial cells: vessel elements are contained within the network and tip cells are located at the ends of vessels. Tip cells move in response to mechanical forces caused by interactions with neighbouring vessel elements and the local tissue environment, chemotactic forces and a persistence force which accounts for their tendency to continue moving in the same direction...
November 24, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27879109/altruistic-aging-the-evolutionary-dynamics-balancing-longevity-and-evolvability
#6
Minette Herrera, Aaron Miller, Joel Nishimura
Altruism is typically associated with traits or behaviors that benefit the population as a whole, but are costly to the individual. We propose that, when the environment is rapidly changing, senescence (age-related deterioration) can be altruistic. According to numerical simulations of an agent-based model, while long-lived individuals can outcompete their short lived peers, populations composed of long-lived individuals are more likely to go extinct during periods of rapid environmental change. Moreover, as in many situations where other cooperative behavior arises, senescence can be stabilized in a structured population...
April 1, 2017: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/27875546/evaluation-of-control-strategies-for-porcine-reproductive-and-respiratory-syndrome-prrs-in-swine-breeding-herds-using-a-discrete-event-agent-based-model
#7
Andréia Gonçalves Arruda, Robert Friendship, Jane Carpenter, Amy Greer, Zvonimir Poljak
The objective of this study was to develop a discrete event agent-based stochastic model to explore the likelihood of the occurrence of porcine reproductive and respiratory syndrome (PRRS) outbreaks in swine herds with different PRRS control measures in place. The control measures evaluated included vaccination with a modified-live attenuated vaccine and live-virus inoculation of gilts, and both were compared to a baseline scenario where no control measures were in place. A typical North American 1,000-sow farrow-to-wean swine herd was used as a model, with production and disease parameters estimated from the literature and expert opinion...
2016: PloS One
https://www.readbyqxmd.com/read/27866921/models-of-evolution-and-evolutionary-game-theory-a-comment-on-evolutionary-game-theory-using-agent-based-models-by-christoph-adami-jory-schossau-arend-hintze
#8
https://www.readbyqxmd.com/read/27853586/the-dynamics-of-emotions-in-online-interaction
#9
David Garcia, Arvid Kappas, Dennis Küster, Frank Schweitzer
We study the changes in emotional states induced by reading and participating in online discussions, empirically testing a computational model of online emotional interaction. Using principles of dynamical systems, we quantify changes in valence and arousal through subjective reports, as recorded in three independent studies including 207 participants (110 female). In the context of online discussions, the dynamics of valence and arousal is composed of two forces: an internal relaxation towards baseline values independent of the emotional charge of the discussion and a driving force of emotional states that depends on the content of the discussion...
August 2016: Royal Society Open Science
https://www.readbyqxmd.com/read/27851808/an-observation-driven-agent-based-modeling-and-analysis-framework-for-c-elegans-embryogenesis
#10
Zi Wang, Benjamin J Ramsey, Dali Wang, Kwai Wong, Husheng Li, Eric Wang, Zhirong Bao
With cutting-edge live microscopy and image analysis, biologists can now systematically track individual cells in complex tissues and quantify cellular behavior over extended time windows. Computational approaches that utilize the systematic and quantitative data are needed to understand how cells interact in vivo to give rise to the different cell types and 3D morphology of tissues. An agent-based, minimum descriptive modeling and analysis framework is presented in this paper to study C. elegans embryogenesis...
2016: PloS One
https://www.readbyqxmd.com/read/27843714/planning-horizon-affects-prophylactic-decision-making-and-epidemic-dynamics
#11
Luis G Nardin, Craig R Miller, Benjamin J Ridenhour, Stephen M Krone, Paul Joyce, Bert O Baumgaertner
The spread of infectious diseases can be impacted by human behavior, and behavioral decisions often depend implicitly on a planning horizon-the time in the future over which options are weighed. We investigate the effects of planning horizons on epidemic dynamics. We developed an epidemiological agent-based model (along with an ODE analog) to explore the decision-making of self-interested individuals on adopting prophylactic behavior. The decision-making process incorporates prophylaxis efficacy and disease prevalence with the individuals' payoffs and planning horizon...
2016: PeerJ
https://www.readbyqxmd.com/read/27842507/recalibrating-disease-parameters-for-increasing-realism-in-modeling-epidemics-in-closed-settings
#12
Livio Bioglio, Mathieu Génois, Christian L Vestergaard, Chiara Poletto, Alain Barrat, Vittoria Colizza
BACKGROUND: The homogeneous mixing assumption is widely adopted in epidemic modelling for its parsimony and represents the building block of more complex approaches, including very detailed agent-based models. The latter assume homogeneous mixing within schools, workplaces and households, mostly for the lack of detailed information on human contact behaviour within these settings. The recent data availability on high-resolution face-to-face interactions makes it now possible to assess the goodness of this simplified scheme in reproducing relevant aspects of the infection dynamics...
November 14, 2016: BMC Infectious Diseases
https://www.readbyqxmd.com/read/27836518/optimization-of-municipal-solid-waste-transportation-by-integrating-gis-analysis-equation-based-and-agent-based-model
#13
Khanh Nguyen-Trong, Anh Nguyen-Thi-Ngoc, Doanh Nguyen-Ngoc, Van Dinh-Thi-Hai
The amount of municipal solid waste (MSW) has been increasing steadily over the last decade by reason of population rising and waste generation rate. In most of the urban areas, disposal sites are usually located outside of the urban areas due to the scarcity of land. There is no fixed route map for transportation. The current waste collection and transportation are already overloaded arising from the lack of facilities and insufficient resources. In this paper, a model for optimizing municipal solid waste collection will be proposed...
November 8, 2016: Waste Management
https://www.readbyqxmd.com/read/27835679/the-hunt-opinion-model-an-agent-based-approach-to-recurring-fashion-cycles
#14
Rafał Apriasz, Tyll Krueger, Grzegorz Marcjasz, Katarzyna Sznajd-Weron
We study a simple agent-based model of the recurring fashion cycles in the society that consists of two interacting communities: "snobs" and "followers" (or "opinion hunters", hence the name of the model). Followers conform to all other individuals, whereas snobs conform only to their own group and anticonform to the other. The model allows to examine the role of the social structure, i.e. the influence of the number of inter-links between the two communities, as well as the role of the stability of links. The latter is accomplished by considering two versions of the same model-quenched (parameterized by fraction L of fixed inter-links) and annealed (parameterized by probability p that a given inter-link exists)...
2016: PloS One
https://www.readbyqxmd.com/read/27826879/optimization-and-control-of-agent-based-models-in-biology-a-perspective
#15
G An, B G Fitzpatrick, S Christley, P Federico, A Kanarek, R Miller Neilan, M Oremland, R Salinas, R Laubenbacher, S Lenhart
Agent-based models (ABMs) have become an increasingly important mode of inquiry for the life sciences. They are particularly valuable for systems that are not understood well enough to build an equation-based model. These advantages, however, are counterbalanced by the difficulty of analyzing and using ABMs, due to the lack of the type of mathematical tools available for more traditional models, which leaves simulation as the primary approach. As models become large, simulation becomes challenging. This paper proposes a novel approach to two mathematical aspects of ABMs, optimization and control, and it presents a few first steps outlining how one might carry out this approach...
November 8, 2016: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/27826877/antimicrobial-stewardship-and-environmental-decontamination-for-the-control-of-clostridium-difficile-transmission-in-healthcare-settings
#16
Jason Bintz, Suzanne Lenhart, Cristina Lanzas
We implement an agent-based model for Clostridium difficile transmission in hospitals that accounts for several processes and individual factors including environmental and antibiotic heterogeneity in order to evaluate the efficacy of various control measures aimed at reducing environmental contamination and mitigating the effects of antibiotic use on transmission. In particular, we account for local contamination levels that contribute to the probability of colonization and we account for both the number and type of antibiotic treatments given to patients...
November 8, 2016: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/27811328/agent-based-modeling-case-study-in-cleavage-furrow-models
#17
Alex Mogilner, Angelika Manhart
The number of studies in cell biology in which quantitative models accompany experiments has been growing steadily. Roughly, mathematical and computational techniques of these models can be classified as "differential equation based" (DE) or "agent based" (AB). Recently AB models have started to outnumber DE models, but understanding of AB philosophy and methodology is much less widespread than familiarity with DE techniques. Here we use the history of modeling a fundamental biological problem-positioning of the cleavage furrow in dividing cells-to explain how and why DE and AB models are used...
November 7, 2016: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27806061/experimental-evaluation-of-suitability-of-selected-multi-criteria-decision-making-methods-for-large-scale-agent-based-simulations
#18
Petr Tučník, Vladimír Bureš
Multi-criteria decision-making (MCDM) can be formally implemented by various methods. This study compares suitability of four selected MCDM methods, namely WPM, TOPSIS, VIKOR, and PROMETHEE, for future applications in agent-based computational economic (ACE) models of larger scale (i.e., over 10 000 agents in one geographical region). These four MCDM methods were selected according to their appropriateness for computational processing in ACE applications. Tests of the selected methods were conducted on four hardware configurations...
2016: PloS One
https://www.readbyqxmd.com/read/27806049/containing-ebola-at-the-source-with-ring-vaccination
#19
Stefano Merler, Marco Ajelli, Laura Fumanelli, Stefano Parlamento, Ana Pastore Y Piontti, Natalie E Dean, Giovanni Putoto, Dante Carraro, Ira M Longini, M Elizabeth Halloran, Alessandro Vespignani
Interim results from the Guinea Ebola ring vaccination trial suggest high efficacy of the rVSV-ZEBOV vaccine. These findings open the door to the use of ring vaccination strategies in which the contacts and contacts of contacts of each index case are promptly vaccinated to contain future Ebola virus disease outbreaks. To provide a numerical estimate of the effectiveness of ring vaccination strategies we introduce a spatially explicit agent-based model to simulate Ebola outbreaks in the Pujehun district, Sierra Leone, structurally similar to previous modelling approaches...
November 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27805000/regulation-of-rna-binding-proteins-affinity-to-export-receptors-enables-the-nuclear-basket-proteins-to-distinguish-and-retain-aberrant-mrnas
#20
M Soheilypour, M R K Mofrad
Export of messenger ribonucleic acids (mRNAs) into the cytoplasm is a fundamental step in gene regulation processes, which is meticulously quality controlled by highly efficient mechanisms in eukaryotic cells. Yet, it remains unclear how the aberrant mRNAs are recognized and retained inside the nucleus. Using a new modelling approach for complex systems, namely the agent-based modelling (ABM) approach, we develop a minimal model of the mRNA quality control (QC) mechanism. Our results demonstrate that regulation of the affinity of RNA-binding proteins (RBPs) to export receptors along with the weak interaction between the nuclear basket protein (Mlp1 or Tpr) and RBPs are the minimum requirements to distinguish and retain aberrant mRNAs...
November 2, 2016: Scientific Reports
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