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"Agent-based modeling"

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https://www.readbyqxmd.com/read/28931635/a-computational-multiscale-agent-based-model-for-simulating-spatio-temporal-tumour-immune-response-to-pd1-and-pdl1-inhibition
#1
Chang Gong, Oleg Milberg, Bing Wang, Paolo Vicini, Rajesh Narwal, Lorin Roskos, Aleksander S Popel
When the immune system responds to tumour development, patterns of immune infiltrates emerge, highlighted by the expression of immune checkpoint-related molecules such as PDL1 on the surface of cancer cells. Such spatial heterogeneity carries information on intrinsic characteristics of the tumour lesion for individual patients, and thus is a potential source for biomarkers for anti-tumour therapeutics. We developed a systems biology multiscale agent-based model to capture the interactions between immune cells and cancer cells, and analysed the emergent global behaviour during tumour development and immunotherapy...
September 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28926374/reducing-urban-violence-a-contrast-of-public-health-and-criminal-justice-approaches
#2
Magdalena Cerdá, Melissa Tracy, Katherine M Keyes
BACKGROUND: Cities are investing millions in Cure Violence, a public health approach to reduce urban violence by targeting at-risk youth and redirecting conflict to non-violent responses. The impact of such a program compared to criminal justice responses is unknown because experiments directly comparing criminal justice and public health approaches to violence prevention are infeasible with observational data. We simulated experiments to test the influence of two interventions on violence: a) Cure Violence; and b) directed police patrol in violence hot spots...
September 18, 2017: Epidemiology
https://www.readbyqxmd.com/read/28922513/purpose-processes-partnerships-and-products-4ps-to-advance-participatory-socio-environmental-modeling
#3
Steven Gray, Alexey Voinov, Michael Paolisso, Rebecca Jordan, Todd BenDor, Pierre Bommel, Pierre Glynn, Beatrice Hedelin, Klaus Hubacek, Josh Introne, Nagesh Kolagani, Bethany Laursen, Christina Prell, Laura Schmitt-Olabisi, Alison Singer, Eleanor Sterling, Moira Zellner
Including stakeholders in environmental model building and analysis is an increasingly popular approach to understanding ecological change. This is because stakeholders often hold valuable knowledge about socio-environmental dynamics and collaborative forms of modeling produce important boundary objects used to collectively reason about environmental problems. Although the number of participatory modeling (PM) case studies and the number of researchers adopting these approaches has grown in recent years, the lack of standardized reporting and limited reproducibility have prevented PM's establishment and advancement as a cohesive field of study...
September 18, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28915909/differential-signal-sensitivities-can-contribute-to-the-stability-of-multispecies-bacterial-communities
#4
János Juhász, Dóra Bihary, Attila Jády, Sándor Pongor, Balázs Ligeti
BACKGROUND: Bacterial species present in multispecies microbial communities often react to the same chemical signal but at vastly different concentrations. The existence of different response thresholds with respect to the same signal molecule has been well documented in quorum sensing which is one of the best studied inter-cellular signalling mechanisms in bacteria. The biological significance of this phenomenon is still poorly understood, and cannot be easily studied in nature or in laboratory models...
September 15, 2017: Biology Direct
https://www.readbyqxmd.com/read/28879013/the-dual-impact-of-ecology-and-management-on-social-incentives-in-marine-common-pool-resource-systems
#5
E S Klein, M R Barbier, J R Watson
Understanding how and when cooperative human behaviour forms in common-pool resource systems is critical to illuminating social-ecological systems and designing governance institutions that promote sustainable resource use. Before assessing the full complexity of social dynamics, it is essential to understand, concretely and mechanistically, how resource dynamics and human actions interact to create incentives and pay-offs for social behaviours. Here, we investigated how such incentives for information sharing are affected by spatial dynamics and management in a common-pool resource system...
August 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28878985/task-allocation-and-site-fidelity-jointly-influence-foraging-regulation-in-honeybee-colonies
#6
Thiago Mosqueiro, Chelsea Cook, Ramon Huerta, Jürgen Gadau, Brian Smith, Noa Pinter-Wollman
Variation in behaviour among group members often impacts collective outcomes. Individuals may vary both in the task that they perform and in the persistence with which they perform each task. Although both the distribution of individuals among tasks and differences among individuals in behavioural persistence can each impact collective behaviour, we do not know if and how they jointly affect collective outcomes. Here, we use a detailed computational model to examine the joint impact of colony-level distribution among tasks and behavioural persistence of individuals, specifically their fidelity to particular resource sites, on the collective trade-off between exploring for new resources and exploiting familiar ones...
August 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28870154/projecting-prevalence-costs-and-evaluating-simulated-interventions-for-diabetic-end-stage-renal-disease-in-a-canadian-population-of-aboriginal-and-non-aboriginal-people-an-agent-based-approach
#7
Amy Gao, Nathaniel D Osgood, Ying Jiang, Roland F Dyck
BACKGROUND: Diabetes-related end stage renal disease (DM-ESRD) is a devastating consequence of the type 2 diabetes epidemic, both of which disproportionately affect Indigenous peoples. Projecting case numbers and costs into future decades would help to predict resource requirements, and simulating hypothetical interventions could guide the choice of best practices to mitigate current trends. METHODS: An agent based model (ABM) was built to forecast First Nations and non-First Nations cases of DM-ESRD in Saskatchewan from 1980 to 2025 and to simulate two hypothetical interventions...
September 4, 2017: BMC Nephrology
https://www.readbyqxmd.com/read/28865334/agent-based-modeling-as-a-tool-for-program-design-and-evaluation
#8
Jennifer A Lawlor, Sara McGirr
Recently, systems thinking and systems science approaches have gained popularity in the field of evaluation; however, there has been relatively little exploration of how evaluators could use quantitative tools to assist in the implementation of systems approaches therein. The purpose of this paper is to explore potential uses of one such quantitative tool, agent-based modeling, in evaluation practice. To this end, we define agent-based modeling and offer potential uses for it in typical evaluation activities, including: engaging stakeholders, selecting an intervention, modeling program theory, setting performance targets, and interpreting evaluation results...
August 30, 2017: Evaluation and Program Planning
https://www.readbyqxmd.com/read/28838064/a-comparison-of-agent-based-models-and-the-parametric-g-formula-for-causal-inference
#9
COMPARATIVE STUDY
Eleanor J Murray, James M Robins, George R Seage, Kenneth A Freedberg, Miguel A Hernán
Decision-making requires choosing from treatments on the basis of correctly estimated outcome distributions under each treatment. In the absence of randomized trials, 2 possible approaches are the parametric g-formula and agent-based models (ABMs). The g-formula has been used exclusively to estimate effects in the population from which data were collected, whereas ABMs are commonly used to estimate effects in multiple populations, necessitating stronger assumptions. Here, we describe potential biases that arise when ABM assumptions do not hold...
July 15, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28830527/development-of-a-dynamic-framework-to-explain-population-patterns-of-leisure-time-physical-activity-through-agent-based-modeling
#10
Leandro M T Garcia, Ana V Diez Roux, André C R Martins, Yong Yang, Alex A Florindo
Despite the increasing body of evidences on the factors influencing leisure-time physical activity, our understanding of the mechanisms and interactions that lead to the formation and evolution of population patterns is still limited. Moreover, most frameworks in this field fail to capture dynamic processes. Our aim was to create a dynamic conceptual model depicting the interaction between key psychological attributes of individuals and main aspects of the built and social environments in which they live. This conceptual model will inform and support the development of an agent-based model aimed to explore how population patterns of LTPA in adults may emerge from the dynamic interplay between psychological traits and built and social environments...
August 22, 2017: International Journal of Behavioral Nutrition and Physical Activity
https://www.readbyqxmd.com/read/28823079/mechanobiological-model-of-arterial-growth-and-remodeling
#11
Maziyar Keshavarzian, Clark A Meyer, Heather N Hayenga
A coupled agent-based model (ABM) and finite element analysis (FEA) computational framework is developed to study the interplay of bio-chemo-mechanical factors in blood vessels and their role in maintaining homeostasis. The agent-based model implements the power of REPAST Simphony libraries and adapts its environment for biological simulations. Coupling a continuum-level model (FEA) to a cellular-level model (ABM) has enabled this computational framework to capture the response of blood vessels to increased or decreased levels of growth factors, proteases and other signaling molecules (on the micro scale) as well as altered blood pressure...
August 19, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/28805306/bioprocess-scale-up-down-as-integrative-enabling-technology-from-fluid-mechanics-to-systems-biology-and-beyond
#12
Frank Delvigne, Ralf Takors, Rob Mudde, Walter van Gulik, Henk Noorman
Efficient optimization of microbial processes is a critical issue for achieving a number of sustainable development goals, considering the impact of microbial biotechnology in agrofood, environment, biopharmaceutical and chemical industries. Many of these applications require scale-up after proof of concept. However, the behaviour of microbial systems remains unpredictable (at least partially) when shifting from laboratory-scale to industrial conditions. The need for robust microbial systems is thus highly needed in this context, as well as a better understanding of the interactions between fluid mechanics and cell physiology...
August 14, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28794899/an-extended-model-for-culture-dependent-heterogenous-gene-expression-and-proliferation-dynamics-in-mouse-embryonic-stem-cells
#13
Simon Godwin, Daniel Ward, Elisa Pedone, Martin Homer, Alexander G Fletcher, Lucia Marucci
During development, pluripotency is a transient state describing a cell's ability to give rise to all three germ layers and germline. Recent studies have shown that, in vitro, pluripotency is highly dynamic: exogenous stimuli provided to cultures of mouse embryonic stem cells, isolated from pre-implantation blastocysts, significantly affect the spectrum of pluripotency. 2i/LIF, a recently defined serum-free medium, forces mouse embryonic stem cells into a ground-state of pluripotency, while serum/LIF cultures promote the co-existence of ground-like and primed-like mouse embryonic stem cell subpopulations...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28791758/agent-based-computational-model-of-retinal-angiogenesis-simulates-microvascular-network-morphology-as-a-function-of-pericyte-coverage
#14
Joseph Walpole, Feilim Mac Gabhann, Shayn M Peirce, John C Chappell
OBJECTIVE: Define a role for perivascular cells during developmental retinal angiogenesis in the context of endothelial cell Notch1-DLL4 signaling at the multicellular network level. METHODS: The retinal vasculature is highly sensitive to growth factor mediated intercellular signaling. Although endothelial cell signaling has been explored in detail, it remains unclear how pericytes function to modulate these signals that lead to a diverse set of vascular network patterns in health and disease...
August 8, 2017: Microcirculation: the Official Journal of the Microcirculatory Society, Inc
https://www.readbyqxmd.com/read/28774355/funding-quality-pre-kindergarten-slots-with-philadelphia-s-new-sugary-drink-tax-simulating-effects-of-using-an-excise-tax-to-address-a-social-determinant-of-health
#15
Brent A Langellier, Félice Lê-Scherban, Jonathan Purtle
OBJECTIVE: Philadelphia passed a 1·5-cent-per-ounce sweetened beverage tax (SBT). Revenue will fund 10 000 quality pre-kindergarten slots for poor children. It is imperative to understand how revenue from SBT can be used to fund programmes to address education and other social determinants of health. The objective of the present study was to simulate quality pre-kindergarten attendance, educational achievement and sugar-sweetened beverage (SSB) consumption among Philadelphia children and adolescents under six intervention scenarios: (i) no intervention; (ii) 10 000 additional quality pre-kindergarten slots; (iii) a 1·5-cent-per-ounce SBT; (iv) expanded pre-kindergarten and 1·5-cent-per-ounce SBT; (v) a 3-cent-per-ounce SBT; and (vi) expanded pre-kindergarten and 3-cent-per-ounce SBT...
September 2017: Public Health Nutrition
https://www.readbyqxmd.com/read/28756445/socialising-health-burden-through-different-network-topologies-a-simulation-study
#16
Adrian Peacock, Anthony Cheung, Peter Kim, Simon K Poon
An aging population and the expectation of premium quality health services combined with the increasing economic burden of the healthcare system requires a paradigm shift toward patient oriented healthcare. The guardian angel theory described by Szolovits [1] explores the notion of enlisting patients as primary providers of information and motivation to patients with similar clinical history through social connections. In this study, an agent based model was developed to simulate to explore how individuals are affected through their levels of intrinsic positivity...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28738861/the-risk-of-hiv-transmission-at-each-step-of-the-hiv-care-continuum-among-people-who-inject-drugs-a-modeling-study
#17
Daniel J Escudero, Mark N Lurie, Kenneth H Mayer, Maximilian King, Sandro Galea, Samuel R Friedman, Brandon D L Marshall
BACKGROUND: People who inject drugs (PWID) are at continued risk for HIV in the U.S., and experience disparities across the HIV care continuum compared to other high-risk groups. Estimates of the risk of HIV transmission at each stage of the care continuum may assist in identifying public health priorities for averting incident infections among PWID, in addition to transmissions to sexual partners of PWID. METHODS: We created an agent-based model simulating HIV transmission and the HIV care continuum for PWID in New York City (NYC) in 2012...
July 25, 2017: BMC Public Health
https://www.readbyqxmd.com/read/28737788/a-multiscale-agent-based-framework-integrated-with-a-constraint-based-metabolic-network-model-of-cancer-for-simulating-avascular-tumor-growth
#18
Mehrdad Ghadiri, Mahshid Heidari, Sayed-Amir Marashi, Seyed Hasan Mousavi
In recent years, many efforts have been made in the field of computational modeling of cancerous tumors, in order to obtain a better understanding and predictions of their growth patterns. Furthermore, constraint-based modeling of metabolic networks has become increasingly popular, which is appropriate for the systems-level reconstruction of cell physiology. The goal of the current study is to integrate a multiscale agent-based modeling framework with a constraint-based metabolic network model of cancer cells in order to simulate the three dimensional early growth of avascular tumors...
August 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28728997/sepsis-reconsidered-identifying-novel-metrics-for-behavioral-landscape-characterization-with-a-high-performance-computing-implementation-of-an-agent-based-model
#19
Chase Cockrell, Gary An
OBJECTIVES: Sepsis affects nearly 1 million people in the United States per year, has a mortality rate of 28-50% and requires more than $20 billion a year in hospital costs. Over a quarter century of research has not yielded a single reliable diagnostic test or a directed therapeutic agent for sepsis. Central to this insufficiency is the fact that sepsis remains a clinical/physiological diagnosis representing a multitude of molecularly heterogeneous pathological trajectories. Advances in computational capabilities offered by High Performance Computing (HPC) platforms call for an evolution in the investigation of sepsis to attempt to define the boundaries of traditional research (bench, clinical and computational) through the use of computational proxy models...
October 7, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28728002/development-of-an-integrated-generic-model-for-multi-scale-assessment-of-the-impacts-of-agro-ecosystems-on-major-ecosystem-services-in-west-africa
#20
Mahamadou Belem, Mehdi Saqalli
This paper presents an integrated model assessing the impacts of climate change, agro-ecosystem and demographic transition patterns on major ecosystem services in West-Africa along a partial overview of economic aspects (poverty reduction, food self-sufficiency and income generation). The model is based on an agent-based model associated with a soil model and multi-scale spatial model. The resulting Model for West-Africa Agro-Ecosystem Integrated Assessment (MOWASIA) is ecologically generic, meaning it is designed for all sudano-sahelian environments but may then be used as an experimentation facility for testing different scenarios combining ecological and socioeconomic dimensions...
July 17, 2017: Journal of Environmental Management
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