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"Agent-based modeling"

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https://www.readbyqxmd.com/read/28716770/data-preparation-for-west-nile-virus-agent-based-modelling-protocol-for-processing-bird-population-estimates-and-incorporating-arcmap-in-anylogic
#1
Hamid Reza Nasrinpour, Alexander A Reimer, Marcia R Friesen, Robert D McLeod
BACKGROUND: West Nile Virus (WNV) was first isolated in 1937. Since the 1950s, many outbreaks have occurred in various countries. The first appearance of infected birds in Manitoba, Canada was in 2002. OBJECTIVE: This paper describes the data preparation phase of setting up a geographic information system (GIS) simulation environment for WNV Agent-Based Modelling in Manitoba. METHODS: The main technology used in this protocol is based on AnyLogic and ArcGIS software...
July 17, 2017: JMIR Research Protocols
https://www.readbyqxmd.com/read/28716030/modeling-de-novo-granulation-of-anaerobic-sludge
#2
Anna Doloman, Honey Varghese, Charles D Miller, Nicholas S Flann
BACKGROUND: A unique combination of mechanical, physiochemical and biological forces influences granulation during processes of anaerobic digestion. Understanding this process requires a systems biology approach due to the need to consider not just single-cell metabolic processes, but also the multicellular organization and development of the granule. RESULTS: In this computational experiment, we address the role that physiochemical and biological processes play in granulation and provide a literature-validated working model of anaerobic granule de novo formation...
July 17, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28714879/the-influence-of-spatial-configuration-of-residential-area-and-vector-populations-on-dengue-incidence-patterns-in-an-individual-level-transmission-model
#3
Jeon-Young Kang, Jared Aldstadt
Dengue is a mosquito-borne infectious disease that is endemic in tropical and subtropical countries. Many individual-level simulation models have been developed to test hypotheses about dengue virus transmission. Often these efforts assume that human host and mosquito vector populations are randomly or uniformly distributed in the environment. Although, the movement of mosquitoes is affected by spatial configuration of buildings and mosquito populations are highly clustered in key buildings, little research has focused on the influence of the local built environment in dengue transmission models...
July 15, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28693495/an-agent-based-model-of-triple-negative-breast-cancer-the-interplay-between-chemokine-receptor-ccr5-expression-cancer-stem-cells-and-hypoxia
#4
Kerri-Ann Norton, Travis Wallace, Niranjan B Pandey, Aleksander S Popel
BACKGROUND: Triple-negative breast cancer lacks estrogen, progesterone, and HER2 receptors and is thus not possible to treat with targeted therapies for these receptors. Therefore, a greater understanding of triple-negative breast cancer is necessary for the treatment of this cancer type. In previous work from our laboratory, we found that chemokine ligand-receptor CCL5-CCR5 axis is important for the metastasis of human triple-negative breast cancer cell MDA-MB-231 to the lymph nodes and lungs, in a mouse xenograft model...
July 11, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28679174/invited-commentary-causal-inference-across-space-and-time-quixotic-quest-worthy-goal-or-both
#5
Jessie K Edwards, Catherine R Lesko, Alexander P Keil
The g-formula and agent-based models (ABMs) are 2 approaches used to estimate causal effects. In the current issue of the Journal, Murray et al. (Am J Epidemiol. 2017;000(0):000-000) compare the performance of the g-formula and ABMs to estimate causal effects in 3 target populations. In their thoughtful paper, the authors outline several reasons that a causal effect estimated using an ABM may be biased when parameterized from at least 1 source external to the target population. The authors have addressed an important issue in epidemiology: Often causal effect estimates are needed to inform public health decisions in settings without complete data...
June 30, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28673036/invited-commentary-agent-based-models-bias-in-the-face-of-discovery
#6
Katherine M Keyes, Melissa Tracy, Stephen J Mooney, Aaron Shev, Magdalena Cerdá
Agent-based models (ABMs) have grown in popularity in epidemiologic applications, but the assumptions necessary for valid inference have only partially been articulated. In this issue, Murray et al. (Am J Epidemiol. 2017;000(0):000-000) provided a much-needed analysis of the consequence of some of these assumptions, comparing analysis using an ABM to a similar analysis using the parametric g-formula. In particular, their work focused on the biases that can arise in ABMs that use parameters drawn from distinct populations whose causal structures and baseline outcome risks differ...
June 30, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28672001/host-seeking-efficiency-can-explain-population-dynamics-of-the-tsetse-fly-glossina-morsitans-morsitans-in-response-to-host-density-decline
#7
Jennifer S Lord, Zinhle Mthombothi, Vitalis K Lagat, Fatumah Atuhaire, John W Hargrove
Females of all blood-feeding arthropod vectors must find and feed on a host in order to produce offspring. For tsetse-vectors of the trypanosomes that cause human and animal African trypanosomiasis-the problem is more extreme, since both sexes feed solely on blood. Host location is thus essential both for survival and reproduction. Host population density should therefore be an important driver of population dynamics for haematophagous insects, and particularly for tsetse, but the role of host density is poorly understood...
July 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28667661/recovery-and-immune-priming-modulate-the-evolutionary-trajectory-of-infection-induced-reproductive-strategies
#8
Hoang Luu, Ann T Tate
In response to parasite exposure, organisms from a variety of taxa undergo a shift in reproductive investment that may trade off with other life history traits including survival and immunity. By suppressing reproduction in favor of somatic and immunological maintenance, hosts can enhance the probability of survival and recovery from infection. By plastically enhancing reproduction through terminal investment, on the other hand, hosts under the threat of disease-induced mortality could enhance their lifetime reproductive fitness through reproduction rather than survival...
July 1, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28665960/dynamics-of-organizational-culture-individual-beliefs-vs-social-conformity
#9
Christos Ellinas, Neil Allan, Anders Johansson
The complex nature of organizational culture challenges our ability to infer its underlying dynamics from observational studies. Recent computational studies have adopted a distinctly different view, where plausible mechanisms are proposed to describe a wide range of social phenomena, including the onset and evolution of organizational culture. In this spirit, this work introduces an empirically-grounded, agent-based model which relaxes a set of assumptions that describes past work-(a) omittance of an individual's strive for achieving cognitive coherence; (b) limited integration of important contextual factors-by utilizing networks of beliefs and incorporating social rank into the dynamics...
2017: PloS One
https://www.readbyqxmd.com/read/28658972/programming-microphysiological-systems-for-children-s-health-protection
#10
T B Knudsen, B Klieforth, W Slikker
Microphysiological systems (MPS) and computer simulation models that recapitulate the underlying biology and toxicology of critical developmental transitions are emerging tools for developmental effects assessment of drugs/chemicals. Opportunities and challenges exist for their application to alternative, more public health relevant and efficient chemical toxicity testing methods. This is especially pertinent to children's health research and the evaluation of complex embryological and reproductive impacts of drug/chemical exposure...
January 1, 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28649958/modeling-mechanical-interactions-in-growing-populations-of-rod-shaped-bacteria
#11
James Winkle, Oleg A Igoshin, Matthew Bennett, Kreso Josic, William Ott
Advances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand, as cellular growth and division as well as extra-cellular fluid flow lead to complex, changing arrangements of cells within the population. To rationally engineer and control the behavior of cell collectives we need theoretical and computational tools to understand their emergent spatiotemporal dynamics. Here, we present an agent-based model that allows growing cells to detect and respond to mechanical interactions...
June 26, 2017: Physical Biology
https://www.readbyqxmd.com/read/28645858/vascular-adaptation-pattern-formation-and-cross-validation-between-an-agent-based-model-and-a-dynamical-system
#12
Marc Garbey, Stefano Casarin, Scott A Berceli
Myocardial infarction is the global leading cause of mortality (Go et al., 2014). Coronary artery occlusion is its main etiology and it is commonly treated by Coronary Artery Bypass Graft (CABG) surgery (Wilson et al, 2007). The long-term outcome remains unsatisfactory (Benedetto, 2016) as the graft faces the phenomenon of restenosis during the post-surgery, which consists of re-occlusion of the lumen and usually requires secondary intervention even within one year after the initial surgery (Harskamp, 2013)...
June 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28622934/selection-to-outsmart-the-germs-the-evolution-of-disease-recognition-and-social-cognition
#13
Sharon E Kessler, Tyler R Bonnell, Richard W Byrne, Colin A Chapman
The emergence of providing care to diseased conspecifics must have been a turning point during the evolution of hominin sociality. On a population level, care may have minimized the costs of socially transmitted diseases at a time of increasing social complexity, although individual care-givers probably incurred increased transmission risks. We propose that care-giving likely originated within kin networks, where the costs may have been balanced by fitness increases obtained through caring for ill kin. We test a novel hypothesis of hominin cognitive evolution in which disease may have selected for the cognitive ability to recognize when a conspecific is infected...
July 2017: Journal of Human Evolution
https://www.readbyqxmd.com/read/28606814/does-cost-effectiveness-of-influenza-vaccine-choice-vary-across-the-u-s-an-agent-based-modeling-study
#14
Jay V DePasse, Mary Patricia Nowalk, Kenneth J Smith, Jonathan M Raviotta, Eunha Shim, Richard K Zimmerman, Shawn T Brown
BACKGROUND: In a prior agent-based modeling study, offering a choice of influenza vaccine type was shown to be cost-effective when the simulated population represented the large, Washington DC metropolitan area. This study calculated the public health impact and cost-effectiveness of the same four strategies: No Choice, Pediatric Choice, Adult Choice, or Choice for Both Age Groups in five United States (U.S.) counties selected to represent extremes in population age distribution. METHODS: The choice offered was either inactivated influenza vaccine delivered intramuscularly with a needle (IIV-IM) or an age-appropriate needle-sparing vaccine, specifically, the nasal spray (LAIV) or intradermal (IIV-ID) delivery system...
July 13, 2017: Vaccine
https://www.readbyqxmd.com/read/28606148/development-of-a-stochastic-agent-based-model-to-evaluate-surveillance-strategies-for-detection-of-emergent-porcine-reproductive-and-respiratory-syndrome-strains
#15
A G Arruda, Z Poljak, D Knowles, A McLean
BACKGROUND: The objective of the current study was to develop a stochastic agent-based model using empirical data from Ontario (Canada) swine sites in order to evaluate different surveillance strategies for detection of emerging porcine reproductive and respiratory syndrome virus (PRRSV) strains at the regional level. Four strategies were evaluated, including (i) random sampling of fixed numbers of swine sites monthly; (ii) risk-based sampling of fixed numbers, specifically of breeding sites (high-consequence sites); (iii) risk-based sampling of fixed numbers of low biosecurity sites (high-risk); and (iv) risk-based sampling of breeding sites that are characterized as low biosecurity sites (high-risk/high-consequence)...
June 12, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28601116/nonlinearities-in-behavioral-macroeconomics
#16
Orlando Gomes
This article undertakes a journey across the literature on behavioral macroeconomics, with attention concentrated on the nonlinearities that the behavioral approach typically suggests or implies. The emphasis is placed on thinking the macro economy as a living organism, composed of many interacting parts, each one having a will of its own, which is in sharp contrast with the mechanism of the orthodox view (well represented by the neoclassical or new Keynesian dynamic stochastic general equilibrium - DSGE - model)...
July 2017: Nonlinear Dynamics, Psychology, and Life Sciences
https://www.readbyqxmd.com/read/28593562/assessing-the-impacts-of-the-changes-in-farming-systems-on-food-security-and-environmental-sustainability-of-a-chinese-rural-region-under-different-policy-scenarios-an-agent-based-model
#17
Chengcheng Yuan, Liming Liu, Xiaoxing Qi, Yonghu Fu, Jinwei Ye
Since China has undergone a series of economic reforms and implemented opening up policies, its farming systems have significantly changed and have dramatically influenced the society, economy, and environment of China. To assess the comprehensive impacts of these changes on food security and environmental sustainability, and establish effective and environment-friendly subsidy policies, this research constructed an agent-based model (ABM). Daligang Town, which is located in the two-season rice region of Southern China, was selected as the case study site...
July 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/28589364/how-to-simulate-a-germinal-center
#18
Philippe A Robert, Ananya Rastogi, Sebastian C Binder, Michael Meyer-Hermann
Germinal centers host a mini-evolutionary environment where B cells can mutate their receptor and be selected depending on its affinity to target antigens in a process called affinity maturation. Starting from founder cells with a weak B cell receptor affinity, germinal centers release output cells as antibody-secreting cells or memory cells with a very high affinity, a property which is essential for pathogen clearance and immune memory. Therapeutic interventions on the germinal centers are tantalizing approaches to improve vaccines or to support rejection of chronic pathogens such as HIV...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28585809/bsim-2-0-an-advanced-agent-based-cell-simulator
#19
Antoni Matyjaszkiewicz, Gianfranco Fiore, Fabio Annunziata, Claire S Grierson, Nigel J Savery, Lucia Marucci, Mario di Bernardo
Agent-based models (ABMs) provide a number of advantages relative to traditional continuum modeling approaches, permitting incorporation of great detail and realism into simulations, allowing in silico tracking of single-cell behaviors and correlation of these with emergent effects at the macroscopic level. In this study we present BSim 2.0, a radically new version of BSim, a computational ABM framework for modeling dynamics of bacteria in typical experimental environments including microfluidic chemostats...
June 23, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28577533/an-agent-based-model-simulation-of-influenza-interactions-at-the-host-level-insight-into-the-influenza-related-burden-of-pneumococcal-infections
#20
Hélène Arduin, Matthieu Domenech de Cellès, Didier Guillemot, Laurence Watier, Lulla Opatowski
BACKGROUND: Host-level influenza virus-respiratory pathogen interactions are often reported. Although the exact biological mechanisms involved remain unelucidated, secondary bacterial infections are known to account for a large part of the influenza-associated burden, during seasonal and pandemic outbreaks. Those interactions probably impact the microorganisms' transmission dynamics and the influenza public health toll. Mathematical models have been widely used to examine influenza epidemics and the public health impact of control measures...
June 2, 2017: BMC Infectious Diseases
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