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"Agent-based modeling"

Matthieu Barbier, James R Watson
Predators of all kinds, be they lions hunting in the Serengeti or fishermen searching for their catch, display various collective strategies. A common strategy is to share information about the location of prey. However, depending on the spatial characteristics and mobility of predators and prey, information sharing can either improve or hinder individual success. Here, our goal is to investigate the interacting effects of space and information sharing on predation efficiency, represented by the expected rate at which prey are found and consumed...
October 2016: PLoS Computational Biology
Mark Pogson
Aggregation of many species of invertebrate is an example of a consensus decision, the success of which is central to survival. Personality is a stable form of behavioural diversity which has been observed in the aggregation process, but neither the reasons for its stability nor its effects on consensus decisions are well understood. By using an agent-based model of invertebrate aggregation, it is found that diverse personalities have only limited benefits to the experimental consensus decision-making process, but may have a more valuable role in natural settings...
2016: PloS One
Judith Pérez-Velázquez, Jana L Gevertz, Aleksandra Karolak, Katarzyna A Rejniak
A tumor vasculature that is functionally abnormal results in irregular gradients of metabolites and drugs within the tumor tissue. Recently, significant efforts have been committed to experimentally examine how cellular response to anti-cancer treatments varies based on the environment in which the cells are grown. In vitro studies point to specific conditions in which tumor cells can remain dormant and survive the treatment. In vivo results suggest that cells can escape the effects of drug therapy in tissue regions that are poorly penetrated by the drugs...
2016: Advances in Experimental Medicine and Biology
Kyle S Martin, Christopher D Kegelman, Kelley M Virgilio, Julianna A Passipieri, George J Christ, Silvia S Blemker, Shayn M Peirce
Numerous studies have pharmacologically modulated the muscle milieu in the hopes of promoting muscle regeneration; however, the timing and duration of these interventions are difficult to determine. This study utilized a combination of in silico and in vivo experiments to investigate how inflammation manipulation improves muscle recovery following injury. First, we measured macrophage populations following laceration injury in the rat tibialis anterior (TA). Then we calibrated an agent-based model (ABM) of muscle injury to mimic the observed inflammation profiles...
October 7, 2016: Annals of Biomedical Engineering
Mary E Northridge, Sara S Metcalf
BACKGROUND: Implementation science holds promise for better ensuring that research is translated into evidence-based policy and practice, but interventions often fail or even worsen the problems they are intended to solve due to a lack of understanding of real world structures and dynamic complexity. While systems science alone cannot possibly solve the major challenges in public health, systems-based approaches may contribute to changing the language and methods for conceptualising and acting within complex systems...
October 4, 2016: Health Research Policy and Systems
Erin Wild, Monica Gabriela Cojocaru
We investigate and generalize an existing model of competitive helping within a biological market, first introduced for a population of competing individuals in which one individual provides help to all others; the rest compete for the help available from this individual by providing help themselves. Our generalized model comprises two strategies in which each individual of a specific type provides the same amount of help as all other individuals of that type. Each individual's fitness function is dependent on this level of help, the cost of providing the help, and the fact that help is proportionally reciprocated by other individuals...
2016: PloS One
Negin Malekian, Jafar Habibi, Mohammad Hossein Zangooei, Hojjat Aghakhani
BACKGROUND AND OBJECTIVE: There are many cells with various phenotypic behaviors in cancer interacting with each other. For example, an apoptotic cell may induce apoptosis in adjacent cells. A living cell can also protect cells from undergoing apoptosis and necrosis. These survival and death signals are propagated through interaction pathways between adjacent cells called gap junctions. The function of these signals depends on the cellular context of the cell receiving them. For instance, a receiver cell experiencing a low level of oxygen may interpret a received survival signal as an apoptosis signal...
November 2016: Computer Methods and Programs in Biomedicine
François Vallée, Aurélien Luciani, Murray P Cox
Archeology, linguistics and increasingly genetics are clarifying how populations moved from mainland Asia, through Island Southeast Asia, and out into the Pacific during the farming revolution. Yet key features of this process remain poorly understood, particularly how social behaviors intersected with demographic drivers to create the patterns of genomic diversity observed across Island Southeast Asia today. Such questions are ripe for computer modeling. Here, we construct an agent-based model to simulate human mobility across Island Southeast Asia from the Neolithic period to the present, with a special focus on interactions between individuals with Asian, Papuan and mixed Asian-Papuan ancestry...
September 28, 2016: Genetics
Hua Wang, Mary E Northridge, Carol Kunzel, Qiuyi Zhang, Susan S Kum, Jessica L Gilbert, Zhu Jin, Sara S Metcalf
Social capital, as comprised of human connections in social networks and their associated benefits, is closely related to the health of individuals, communities, and societies at large. For disadvantaged population groups such as older adults and racial/ethnic minorities, social capital may play a particularly critical role in mitigating the negative effects and reinforcing the positive effects on health. In this project, we model social capital as both cause and effect by simulating dynamic networks. Informed in part by a community-based health promotion program, an agent-based model is contextualized in a GIS environment to explore the complexity of social disparities in oral and general health as experienced at the individual, interpersonal, and community scales...
June 2016: Soc Cult Behav Model (2016)
Wayne M Getz, Colin Carlson, Eric Dougherty, Travis C Porco Francis, Richard Salter
The winter 2014-15 measles outbreak in the US represents a significant crisis in the emergence of a functionally extirpated pathogen. Conclusively linking this outbreak to decreases in the measles/mumps/rubella (MMR) vaccination rate (driven by anti-vaccine sentiment) is critical to motivating MMR vaccination. We used the NOVA modeling platform to build a stochastic, spatially-structured, individual-based SEIR model of outbreaks, under the assumption that R 0 ≈ 7 for measles. We show this implies that herd immunity requires vaccination coverage of greater than approximately 85%...
April 2016: Agent Dir Simul Symp
J C L Alfonso, N S Schaadt, R Schönmeyer, N Brieu, G Forestier, C Wemmert, F Feuerhake, H Hatzikirou
Scattered inflammatory cells are commonly observed in mammary gland tissue, most likely in response to normal cell turnover by proliferation and apoptosis, or as part of immunosurveillance. In contrast, lymphocytic lobulitis (LLO) is a recurrent inflammation pattern, characterized by lymphoid cells infiltrating lobular structures, that has been associated with increased familial breast cancer risk and immune responses to clinically manifest cancer. The mechanisms and pathogenic implications related to the inflammatory microenvironment in breast tissue are still poorly understood...
2016: Scientific Reports
Chaitra Gopalappa, Paul G Farnham, Yao-Hsuan Chen, Stephanie L Sansom
BACKGROUND: HIV transmission is the result of complex dynamics in the risk behaviors, partnership choices, disease stage and position along the HIV care continuum-individual characteristics that themselves can change over time. Capturing these dynamics and simulating transmissions to understand the chief sources of transmission remain important for prevention. METHODS: The Progression and Transmission of HIV/AIDS (PATH 2.0) is an agent-based model of a sample of 10,000 people living with HIV (PLWH), who represent all men who have sex with men (MSM) and heterosexuals living with HIV in the U...
September 19, 2016: Medical Decision Making: An International Journal of the Society for Medical Decision Making
Megan Wong, Xiaoye Liang, Matt Smart, Le Tang, Richard Moore, Brian Ingalls, Tao G Dong
: In the host and natural environments, microbes often exist in complex multispecies communities. The molecular mechanisms through which such communities develop and persist - despite significant antagonistic interactions between species - are not well understood. The type VI secretion system (T6SS) is a lethal weapon commonly employed by Gram-negative bacteria to inhibit neighboring species through delivery of toxic effectors. It is well established that intra-species protection is conferred by immunity proteins that neutralize effector toxicities...
September 16, 2016: Applied and Environmental Microbiology
Hsing-Fu Huang, Hwong-Wen Ma
To determine the actual status of individuals in a system and the trading interaction between polluters, this study uses an agent-based model to set up a virtual world that represents the Kaohsiung and Pingtung regions in Taiwan, which are under the country's air emissions cap and trade program. The model can simulate each controlled industry's dynamic behavioral condition with the bottom-up method and can investigate the impact of the program and determine the industry's emissions reduction and trading condition...
December 1, 2016: Journal of Environmental Management
Cody J Dey, Evan Richardson, David McGeachy, Samuel A Iverson, H Grant Gilchrist, Christina Semeniuk
Climate change can influence interspecific interactions by differentially affecting species-specific phenology. In seasonal ice environments, there is evidence that polar bear predation of Arctic bird eggs is increasing because of earlier sea ice break-up, which forces polar bears into near-shore terrestrial environments where Arctic birds are nesting. Because polar bears can consume a large number of nests before becoming satiated, and because they can swim between island colonies, they could have dramatic influences on seabird and seaduck reproductive success...
September 10, 2016: Global Change Biology
Azadeh Ghanbari, Jaber Dehghany, Timo Schwebs, Mathias Müsken, Susanne Häussler, Michael Meyer-Hermann
Pseudomonas aeruginosa often colonises immunocompromised patients and the lungs of cystic fibrosis patients. It exhibits resistance to many antibiotics by forming biofilms, which makes it hard to eliminate. P. aeruginosa biofilms form mushroom-shaped structures under certain circumstances. Bacterial motility and the environment affect the eventual mushroom morphology. This study provides an agent-based model for the bacterial dynamics and interactions influencing bacterial biofilm shape. Cell motility in the model relies on recently published experimental data...
2016: Scientific Reports
Alexander Doroshenko, Weicheng Qian, Nathaniel D Osgood
BACKGROUND: Pertussis control remains a challenge due to recently observed effects of waning immunity to acellular vaccine and suboptimal vaccine coverage. Multiple outbreaks have been reported in different ages worldwide. For certain outbreaks, public health authorities can launch an outbreak response immunization (ORI) campaign to control pertussis spread. We investigated effects of an outbreak response immunization targeting young adolescents in averting pertussis cases. METHODS: We developed an agent-based model for pertussis transmission representing disease mechanism, waning immunity, vaccination schedule and pathogen transmission in a spatially-explicit 500,000-person contact network representing a typical Canadian Public Health district...
2016: PeerJ
Slawomir A Lux, Andrzej Wnuk, Heidrun Vogt, Tim Belien, Andreas Spornberger, Marcin Studnicki
The paper reports application of a Markov-like stochastic process agent-based model and a "virtual farm" concept for enhancement of site-specific Integrated Pest Management. Conceptually, the model represents a "bottom-up ethological" approach and emulates behavior of the "primary IPM actors"-large cohorts of individual insects-within seasonally changing mosaics of spatiotemporally complex faming landscape, under the challenge of the local IPM actions. Algorithms of the proprietary PESTonFARM model were adjusted to reflect behavior and ecology of R...
2016: Frontiers in Physiology
Marco Ajelli, Stefano Merler, Laura Fumanelli, Ana Pastore Y Piontti, Natalie E Dean, Ira M Longini, M Elizabeth Halloran, Alessandro Vespignani
BACKGROUND: Among the three countries most affected by the Ebola virus disease outbreak in 2014-2015, Guinea presents an unusual spatiotemporal epidemic pattern, with several waves and a long tail in the decay of the epidemic incidence. METHODS: Here, we develop a stochastic agent-based model at the level of a single household that integrates detailed data on Guinean demography, hospitals, Ebola treatment units, contact tracing, and safe burial interventions. The microsimulation-based model is used to assess the effect of each control strategy and the probability of elimination of the epidemic according to different intervention scenarios, including ring vaccination with the recombinant vesicular stomatitis virus-vectored vaccine...
2016: BMC Medicine
Barbara Entwisle, Nathalie E Williams, Ashton M Verdery, Ronald R Rindfuss, Stephen J Walsh, George P Malanson, Peter J Mucha, Brian G Frizzelle, Philip M McDaniel, Xiaozheng Yao, Benjamin W Heumann, Pramote Prasartkul, Yothin Sawangdee, Aree Jampaklay
This is a study of migration responses to climate shocks. We construct an agent-based model that incorporates dynamic linkages between demographic behaviors, such as migration, marriage, and births, and agriculture and land use, which depend on rainfall patterns. The rules and parameterization of our model are empirically derived from qualitative and quantitative analyses of a well-studied demographic field site, Nang Rong district, Northeast Thailand. With this model, we simulate patterns of migration under four weather regimes in a rice economy: 1) a reference, 'normal' scenario; 2) seven years of unusually wet weather; 3) seven years of unusually dry weather; and 4) seven years of extremely variable weather...
September 2016: Population and Environment
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