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Justin Caccavale, David Fiumara, Michael Stapf, Liedeke Sweitzer, Hannah J Anderson, Jonathan Gorky, Prasad Dhurjati, Deni S Galileo
BACKGROUND: Glioblastoma multiforme (GBM) is a devastating brain cancer for which there is no known cure. Its malignancy is due to rapid cell division along with high motility and invasiveness of cells into the brain tissue. Simple 2-dimensional laboratory assays (e.g., a scratch assay) commonly are used to measure the effects of various experimental perturbations, such as treatment with chemical inhibitors. Several mathematical models have been developed to aid the understanding of the motile behavior and proliferation of GBM cells...
December 11, 2017: BMC Systems Biology
Cristian Jimenez-Romero, Jeffrey Johnson
The scientific interest attracted by Spiking Neural Networks (SNN) has lead to the development of tools for the simulation and study of neuronal dynamics ranging from phenomenological models to the more sophisticated and biologically accurate Hodgkin-and-Huxley-based and multi-compartmental models. However, despite the multiple features offered by neural modelling tools, their integration with environments for the simulation of robots and agents can be challenging and time consuming. The implementation of artificial neural circuits to control robots generally involves the following tasks: (1) understanding the simulation tools, (2) creating the neural circuit in the neural simulator, (3) linking the simulated neural circuit with the environment of the agent and (4) programming the appropriate interface in the robot or agent to use the neural controller...
2017: Neural Computing & Applications
Alfredo Colosimo
This contribution reports on the simulation of some dynamical events observed in the collective behavior of different kinds of populations, ranging from shape-changing cells in a Petri dish to functionally correlated brain areas in vivo. The unifying methodological approach, based upon a Multi-Agent Simulation (MAS) paradigm as incorporated in the NetLogo™ interpreter, is a direct consequence of the cornerstone that simple, individual actions within a population of interacting agents often give rise to complex, collective behavior...
2018: Methods in Molecular Biology
Faisal Riaz, Muaz A Niazi
This paper presents the concept of a social autonomous agent to conceptualize such Autonomous Vehicles (AVs), which interacts with other AVs using social manners similar to human behavior. The presented AVs also have the capability of predicting intentions, i.e. mentalizing and copying the actions of each other, i.e. mirroring. Exploratory Agent Based Modeling (EABM) level of the Cognitive Agent Based Computing (CABC) framework has been utilized to design the proposed social agent. Furthermore, to emulate the functionality of mentalizing and mirroring modules of proposed social agent, a tailored mathematical model of the Richardson's arms race model has also been presented...
2017: PloS One
Pablo Granda Araujo, Anna Gras, Marta Ginovart
Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs) using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo...
2016: Computational and Structural Biotechnology Journal
Hugh Trenchard, Andrew Renfree, Derek M Peters
PURPOSE: Drafting in cycling influences collective behaviour of pelotons. Whilst evidence for collective behaviour in competitive running events exists, it is not clear if this results from energetic savings conferred by drafting. This study modelled the effects of drafting on behavior in elite 10,000 m runners. METHODS: Using performance data from a men's elite 10,000 m track running event, computer simulations were constructed using Netlogo 5.1 to test the effects of three different drafting quantities on collective behaviour: no drafting, drafting to 3m behind with up to ~8% energy savings (a realistic running draft); and drafting up to 3m behind with up to 38% energy savings (a realistic cycling draft)...
August 24, 2016: International Journal of Sports Physiology and Performance
Pablo Araujo Granda, Anna Gras, Marta Ginovart, Vincent Moulton
We have developed an individual-based model for denitrifying bacteria. The model, called INDISIM-Paracoccus, embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM, and is designed to simulate the bacterial cell population behavior and the product dynamics within the culture. The INDISIM-Paracoccus model assumes a culture medium containing succinate as a carbon source, ammonium as a nitrogen source and various electron acceptors such as oxygen, nitrate, nitrite, nitric oxide and nitrous oxide to simulate in continuous or batch culture the different nutrient-dependent cell growth kinetics of the bacterium Paracoccus denitrificans...
August 21, 2016: Journal of Theoretical Biology
Pere-Joan Cardona, Clara Prats
Infection with Mycobacterium tuberculosis (Mtb) can induce two kinds of lesions, namely proliferative and exudative. The former are based on the presence of macrophages with controlled induction of intragranulomatous necrosis, and are even able to stop its physical progression, thus avoiding the induction of active tuberculosis (TB). In contrast, the most significant characteristic of exudative lesions is their massive infiltration with polymorphonuclear neutrophils (PMNs), which favor enlargement of the lesions and extracellular growth of the bacilli...
2016: Frontiers in Microbiology
Susa H Stonedahl, Kevin R Roche, Forrest Stonedahl, Aaron I Packman
Advective exchange between the pore space of sediments and the overlying water column, called hyporheic exchange in fluvial environments, drives solute transport in rivers and many important biogeochemical processes. To improve understanding of these processes through visual demonstration, we created a hyporheic flow simulation in the multi-agent computer modeling platform NetLogo. The simulation shows virtual tracer flowing through a streambed covered with two-dimensional bedforms. Sediment, flow, and bedform characteristics are used as input variables for the model...
November 18, 2015: Journal of Visualized Experiments: JoVE
Mário Veloso
A multiplicity of natural history studies of multiple sclerosis provides valuable knowledge of the disease progression but individualized prognosis remains elusive. A few decision support tools that assist the clinician in such task have emerged but have not received proper attention from clinicians and patients. The objective of the current work is to implement a web-based tool, conveying decision relevant prognostic scientific evidence, which will help clinicians discuss prognosis with individual patients...
September 2014: Multiple Sclerosis and related Disorders
Jagpreet Chhatwal, Tianhua He
Agent-based modelling (ABM) is a relatively new technique, which overcomes some of the limitations of other methods commonly used for economic evaluations. These limitations include linearity, homogeneity and stationarity. Agents in ABMs are autonomous entities, who interact with each other and with the environment. ABMs provide an inductive or 'bottom-up' approach, i.e. individual-level behaviours define system-level components. ABMs have a unique property to capture emergence phenomena that otherwise cannot be predicted by the combination of individual-level interactions...
May 2015: PharmacoEconomics
Richard R Chapleau, Peter J Robinson, John J Schlager, Jeffery M Gearhart
BACKGROUND: One of the leading causes of death and illness within the agriculture industry is through unintentionally ingesting or inhaling organophosphate pesticides. OP intoxication directly inhibits acetylcholinesterase, resulting in an excitatory signaling cascade leading to fasciculation, loss of control of bodily fluids, and seizures. METHODS: Our model was developed using a discrete, rules-based modeling approach in NetLogo. This model includes acetylcholinesterase, the nicotinic acetylcholine receptor responsible for signal transduction, a single release of acetylcholine, organophosphate inhibitors, and a theoretical novel medical countermeasure...
2014: Theoretical Biology & Medical Modelling
Ferdinando Chiacchio, Marzio Pennisi, Giulia Russo, Santo Motta, Francesco Pappalardo
Several components that interact with each other to evolve a complex, and, in some cases, unexpected behavior, represents one of the main and fascinating features of the mammalian immune system. Agent-based modeling and cellular automata belong to a class of discrete mathematical approaches in which entities (agents) sense local information and undertake actions over time according to predefined rules. The strength of this approach is characterized by the appearance of a global behavior that emerges from interactions among agents...
2014: BioMed Research International
Luis F Schettino
Young students struggle with concepts that involve the parallel activity of large numbers of similar entities, precisely the kind of concepts that abound in neuroscience. While a direct experience to laboratory work cannot be replaced, such activities include a steep learning curve and may be impractical in certain course settings. This article describes a set of computer simulations of a number of neural processes using NetLogo (Wilensky, 1999), a software environment for the design and implementation of multi-agent simulations that has an intuitive graphical interface and minimal learning curve...
2014: Journal of Undergraduate Neuroscience Education: JUNE: a Publication of FUN, Faculty for Undergraduate Neuroscience
Haiyan Liu, Xia Chen, Bo Zhang
In the social sciences, computer-based modeling has become an increasingly important tool receiving widespread attention. However, the derivation of the quantitative relationships linking individual moral behavior and social morality levels, so as to provide a useful basis for social policy-making, remains a challenge in the scholarly literature today. A quantitative measurement of morality from the perspective of complexity science constitutes an innovative attempt. Based on the NetLogo platform, this article examines the effect of various factors on social morality levels, using agents modeling moral behavior, immoral behavior, and a range of environmental social resources...
2013: PloS One
Rafael Bravo, David E Axelrod
BACKGROUND: Normal colon crypts consist of stem cells, proliferating cells, and differentiated cells. Abnormal rates of proliferation and differentiation can initiate colon cancer. We have measured the variation in the number of each of these cell types in multiple crypts in normal human biopsy specimens. This has provided the opportunity to produce a calibrated computational model that simulates cell dynamics in normal human crypts, and by changing model parameter values, to simulate the initiation and treatment of colon cancer...
2013: Theoretical Biology & Medical Modelling
Alexey Solovyev, Maxim Mikheev, Leming Zhou, Joyeeta Dutta-Moscato, Cordelia Ziraldo, Gary An, Yoram Vodovotz, Qi Mi
Multi-scale modeling of complex biological systems remains a central challenge in the systems biology community. A method of dynamic knowledge representation known as agent-based modeling enables the study of higher level behavior emerging from discrete events performed by individual components. With the advancement of computer technology, agent-based modeling has emerged as an innovative technique to model the complexities of systems biology. In this work, the authors describe SPARK (Simple Platform for Agent-based Representation of Knowledge), a framework for agent-based modeling specifically designed for systems-level biomedical model development...
2010: International Journal of Agent Technologies and Systems
Matthew B Biggs, Jason A Papin
Multiscale modeling is used to represent biological systems with increasing frequency and success. Multiscale models are often hybrids of different modeling frameworks and programming languages. We present the MATLAB-NetLogo extension (MatNet) as a novel tool for multiscale modeling. We demonstrate the utility of the tool with a multiscale model of Pseudomonas aeruginosa biofilm formation that incorporates both an agent-based model (ABM) and constraint-based metabolic modeling. The hybrid model correctly recapitulates oxygen-limited biofilm metabolic activity and predicts increased growth rate via anaerobic respiration with the addition of nitrate to the growth media...
2013: PloS One
James W Reinhardt, Daniel A Krakauer, Keith J Gooch
Using a top-down approach, an agent-based model was developed within NetLogo where cells and extracellular matrix (ECM) fibers were composed of multiple agents to create deformable structures capable of exerting, reacting to, and transmitting mechanical force. At the beginning of the simulation, long fibers were randomly distributed and cross linked. Throughout the simulation, imposed rules allowed cells to exert traction forces by extending pseudopodia, binding to fibers and pulling them towards the cell. Simulated cells remodeled the fibrous matrix to change both the density and alignment of fibers and migrated within the matrix in ways that are consistent with previous experimental work...
July 1, 2013: Journal of Biomechanical Engineering
Kenneth H Schatten
This article focuses on mapping the Sun's large-scale magnetic fields. In particular, the model considers how photospheric fields evolve in time. Our solar field mapping method uses Netlogo's cellular automata software via algorithms to carry out the movement of magnetic field on the Sun via agents. This model's entities consist of two breeds: blue and red agents. The former carry a fixed amount of radially outward magnetic flux: 10(23) Mx, and the latter, the identical amount of inward directed flux. The individual agents are distinguished, for clarity, by various shades of blue and red arrows whose orientation indicates the direction the agents are moving, relative to the near-steady bulk fluid motions...
December 2013: SpringerPlus
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