This repository is an Example using GitHub Actions [egge] for the Advanced Programming with R class. The project consists of a quarto document updated once a week or whenever there’s a push or pull request. It performs a search on PubMed looking for the latest papers about Agent-Based Models. The last update was on 2024-10-27 00:51:31.
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AMBER: A Modular Model for Tumor Growth, Vasculature and Radiation Response.
Kunz LV, Bosque JJ, Nikmaneshi M, Chamseddine I, Munn LL, Schuemann J, Paganetti H, Bertolet A.
Bull Math Biol. 2024 Oct 26;86(12):139. doi: 10.1007/s11538-024-01371-4.
In particular, agent-based models (ABMs) tracking individual agents and their interactions are useful for their flexibility and ability to model complex behaviors. …Additionally, the integration into tumor ABMs of precise radiation dose calculations …
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Do COVID-19 Infectious Disease Models Incorporate the Social Determinants of Health? A Systematic Review.
John-Baptiste AA, Moulin M, Li Z, Hamilton D, Crichlow G, Klein DE, Alemu FW, Ghattas L, McDonald K, Asaria M, Sharpe C, Pandya E, Moqueet N, Champredon D, Moghadas SM, Cooper LA, Pinto A, Stranges S, Haworth-Brockman MJ, Galvani A, Ali S.
Public Health Rev. 2024 Oct 10;45:1607057. doi: 10.3389/phrs.2024.1607057. eCollection 2024.
Most pertained to multiple countries (n = 15), the United States (n = 12), or China (n = 7). Most models were compartmental (n = 45) and agent-based (n = 7). Age was the most incorporated SDH (n = 74), followed by gender (n = 15), race/ethnicity (n = 7) and r …
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PhysiMeSS - a new physiCell addon for extracellular matrix modelling.
Noël V, Ruscone M, Shuttleworth R, Macnamara CK.
GigaByte. 2024 Oct 16;2024:gigabyte136. doi: 10.46471/gigabyte.136. eCollection 2024.
The extracellular matrix, composed of macromolecules like collagen fibres, provides structural support to cells and acts as a barrier that metastatic cells degrade to spread beyond the primary tumour. While agent-based frameworks, such as PhysiCell, can simulate the …
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Neutrophils under the microscope: neutrophil dynamics in infection, inflammation, and cancer revealed using intravital imaging.
Yam AO, Jakovija A, Gatt C, Chtanova T.
Front Immunol. 2024 Oct 8;15:1458035. doi: 10.3389/fimmu.2024.1458035. eCollection 2024.
Finally, we highlight how computational modeling techniques, especially agent-based modeling, complement experimental data by elucidating neutrophil kinetics at the level of individual cells as well as their collective behavior. …
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Gardens reduce seasonal hunger gaps for farmland pollinators.
Timberlake TP, Tew NE, Memmott J.
Proc Biol Sci. 2024 Oct;291(2033):20241523. doi: 10.1098/rspb.2024.1523. Epub 2024 Oct 23.
Consistent with this pattern, bumblebee activity increased in gardens relative to farmland during early spring and late summer. An agent-based model reinforces this point, showing that timing, not quantity, of garden nectar supply enhances bumblebee colony gr …
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Tuning collective actuation of active solids by optimizing activity localization.
Lazzari D, Dauchot O, Brito C.
Soft Matter. 2024 Oct 21. doi: 10.1039/d4sm00868e. Online ahead of print.
Here, we investigate numerically how localizing activity to a fraction of modes enables the selection of non-trivial collective actuation. We perform numerical simulations of an agent-based model on triangular and disordered lattices and vary the concentratio …
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Enhancing Medical Training Through Learning From Mistakes by Interacting With an Ill-Trained Reinforcement Learning Agent.
Kakdas YC, Kockara S, Halic T, Demirel D.
IEEE Trans Learn Technol. 2024;17:1248-1260. doi: 10.1109/tlt.2024.3372508. Epub 2024 Mar 4.
This allows students to experience many outlier cases they might not encounter in an in-class educational model. In the assessment mode, an IRL-based method is used to evaluate how effective the participant is at correcting the mistakes performed by the RL agent. …
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OMIBONE: Omics-driven computer model of bone regeneration for personalized treatment.
Jaber M, Schmidt J, Kalkhof S, Gerstenfeld L, Duda GN, Checa S.
Bone. 2024 Oct 18;190:117288. doi: 10.1016/j.bone.2024.117288. Online ahead of print.
Here, we introduce a novel framework that allows to predict bone regeneration outcome using combined proteomic and mechanical analyses in a computer model. The framework uses Ingenuity Pathway Analysis (IPA) software to link protein changes to alterations in biological pro …
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Building multiscale models with PhysiBoSS, an agent-based modeling tool.
Ruscone M, Checcoli A, Heiland R, Barillot E, Macklin P, Calzone L, Noël V.
Brief Bioinform. 2024 Sep 23;25(6):bbae509. doi: 10.1093/bib/bbae509.
Multiscale models provide a unique tool for analyzing complex processes that study events occurring at different scales across space and time. …This article introduces three examples of multiscale models which rely on the framework PhysiBoSS, an add-on of PhysiCel …
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Application of H(2)N-Fe(3)O(4) Nanoparticles for Prostate Cancer Magnetic Resonance Imaging in an Animal Model.
Blasiak B, MacDonald D, Jasiński K, Cheng FY, Tomanek B.
Int J Mol Sci. 2024 Sep 26;25(19):10334. doi: 10.3390/ijms251910334.
This paper presents the efficacy of a contrast agent based on H(2)N-Fe(3)O(4) nanoparticles for the detection of prostate cancer in an animal model using a preclinical 9.4 T MRI system. …
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