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"Agent-based modeling"

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https://www.readbyqxmd.com/read/28805306/bioprocess-scale-up-down-as-integrative-enabling-technology-from-fluid-mechanics-to-systems-biology-and-beyond
#1
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
#2
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
#3
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
#4
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...
August 4, 2017: Public Health Nutrition
https://www.readbyqxmd.com/read/28756445/socialising-health-burden-through-different-network-topologies-a-simulation-study
#5
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
#6
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
#7
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...
July 24, 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
#8
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...
July 18, 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
#9
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
https://www.readbyqxmd.com/read/28725407/the-contribution-of-marine-aggregate-associated-bacteria-to-the-accumulation-of-pathogenic-bacteria-in-oysters-an-agent-based-model
#10
Andrew M Kramer, J Evan Ward, Fred C Dobbs, Melissa L Pierce, John M Drake
Bivalves process large volumes of water, leading to their accumulation of bacteria, including potential human pathogens (e.g., vibrios). These bacteria are captured at low efficiencies when freely suspended in the water column, but they also attach to marine aggregates, which are captured with near 100% efficiency. For this reason, and because they are often enriched with heterotrophic bacteria, marine aggregates have been hypothesized to function as important transporters of bacteria into bivalves. The relative contribution of aggregates and unattached bacteria to the accumulation of these cells, however, is unknown...
October 2016: Ecology and Evolution
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
H Luu, A 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 favour 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
#19
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
#20
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
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