From 0fc9ea66c942e9aa3dbe08c592fdc027d3158247 Mon Sep 17 00:00:00 2001 From: gvegayon Date: Sun, 14 Jul 2024 00:44:06 +0000 Subject: [PATCH] Commit from GitHub Actions (Build it) --- README.md | 194 +++++++++++++++++++++++++++--------------------------- 1 file changed, 97 insertions(+), 97 deletions(-) diff --git a/README.md b/README.md index 99730d6..09da3a9 100644 --- a/README.md +++ b/README.md @@ -9,147 +9,147 @@ 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 2024-07-07 00:43:19. +update was on 2024-07-14 00:44:04.
-1. **An agent-based model for cell microenvironment simulation using - FLAMEGPU2.** +1. **Dissecting the Spatially Restricted Effects of + Microenvironment-Mediated Resistance on Targeted Therapy + Responses.** - Borau C, Chisholm R, Richmond P, Walker D. + Miti T, Desai B, Miroshnychenko D, Basanta D, Marusyk A. - Comput Biol Med. 2024 Jul 5;179:108831. doi: - 10.1016/j.compbiomed.2024.108831. Online ahead of print. + Cancers (Basel). 2024 Jun 29;16(13):2405. doi: + 10.3390/cancers16132405. - > This work presents an advanced agent-based model developed within - > the FLAMEGPU2 framework, aimed at simulating the intricate - > dynamics of cell microenvironments. …Through four example - > applications, we demonstrate the model’s versatility in capt … + > To address this problem, we integrated spatial inferences of + > proliferation-death dynamics from an experimental animal model of + > targeted therapy responses with spatial mathematical modeling. … -2. **HPVsim: An agent-based model of HPV transmission and cervical - disease.** +2. **In Vivo PET Detection of Lung Micrometastasis in Mice by Targeting + Endothelial VCAM-1 Using a Dual-Contrast PET/MRI Probe.** - Stuart RM, Cohen JA, Kerr CC, Mathur P; National Disease Modelling - Consortium of India; Abeysuriya RG, Zimmermann M, Rao DW, Boudreau - MC, Lee S, Yang L, Klein DJ. + Melemenidis S, Knight JC, Kersemans V, Perez-Balderas F, Zarghami N, + Soto MS, Cornelissen B, Muschel RJ, Sibson NR. - PLoS Comput Biol. 2024 Jul 5;20(7):e1012181. doi: - 10.1371/journal.pcbi.1012181. Online ahead of print. + Int J Mol Sci. 2024 Jun 28;25(13):7160. doi: 10.3390/ijms25137160. - > Open-source modelling tools are needed to shift the capacity for - > such evaluations in-country. Here, we introduce the Human - > papillomavirus simulator (HPVsim), a new open-source software - > package for creating flexible agent-based models parameterised - > with … + > We have previously demonstrated that an antibody-targeted MRI + > contrast agent based on microparticles of iron oxide (MPIO; 1 mum + > diameter) enables the imaging of endothelial vascular cell + > adhesion molecule-1 (VCAM-1). Using a mouse model of lung + > metastasis, up … -3. **ENERGY Pro: Spatially explicit agent-based model on achieving - positive energy districts.** +3. **Agent-based model predicts that layered structure and 3D movement + work synergistically to reduce bacterial load in 3D in vitro models + of tuberculosis granuloma.** - Derkenbaeva E, Hofstede GJ, van Leeuwen E, Halleck Vega S, Wolfers - J. + Petrucciani A, Hoerter A, Kotze L, Du Plessis N, Pienaar E. - MethodsX. 2024 May 28;12:102779. doi: 10.1016/j.mex.2024.102779. - eCollection 2024 Jun. + PLoS Comput Biol. 2024 Jul 12;20(7):e1012266. doi: + 10.1371/journal.pcbi.1012266. Online ahead of print. - > This article describes the ENERGY Pro agent-based model using the - > Overview, Design Concept, and Details + Human Decision-making - > (ODD+D protocol). …The article also describes sensitivity - > analysis, validation results, and how to use and adapt the model … + > Previously we developed a biomimetic 3D spheroid granuloma model + > that controls bacteria better than a traditional monolayer culture + > counterpart. We used agent-based simulations to predict the + > mechanistic reason for this difference. … -4. **Influential individuals can promote prosocial practices in - heterogeneous societies: a mathematical and agent-based model.** +4. **Correction to “A seven-step guide to spatial, agent-based + modelling of tumour evolution”.** - Crabtree SA, Wren CD, Dixit A, Levin SA. + \[No authors listed\] - PNAS Nexus. 2024 Jul 2;3(7):pgae224. doi: 10.1093/pnasnexus/pgae224. + Evol Appl. 2024 Jul 9;17(7):e13756. doi: 10.1111/eva.13756. eCollection 2024 Jul. - > We construct a general theoretical framework to examine a - > game-theoretic model to assess the ease of achieving a cooperative - > outcome. We then build a dynamic agent-based model to examine - > three distinct governance types in a heterogenous population: mon - > … +5. **Deep learning-based dimensional emotion recognition for + conversational agent-based cognitive behavioral therapy.** -5. **Use of Individual-Based Mathematical Modelling to Understand More - About Antibiotic Resistance Within-Host.** + Striegl J, Richter JW, Grossmann L, Bråstad B, Gotthardt M, Rück C, + Wallert J, Loitsch C. - Saula AY, Rowlatt C, Bowness R. + PeerJ Comput Sci. 2024 Jun 24;10:e2104. doi: 10.7717/peerj-cs.2104. + eCollection 2024. - Methods Mol Biol. 2024;2833:93-108. doi: - 10.1007/978-1-0716-3981-8_10. + > This model significantly outperforms existing state-of-the-art + > models in detecting the dimensions of valence, arousal, and + > dominance, achieving a Pearson correlation coefficient of r = + > 0.90, r = 0.77, and r = 0.64, respectively. Furthermore, a + > feasibility study invo … - > To model complex systems, individual-based models (IBMs), - > sometimes called “agent-based models” (ABMs), describe a - > simplification of the system through an adequate representation of - > the elements. …Events that seldom occur such as the accumulat … +6. **Modeling the Impact of Proactive Community Case Management on + Reducing Confirmed Malaria Cases in Sub-Saharan African Countries.** -6. **Epidemic spreading on spatial higher-order network.** + Wang Y, Wang X, Gurbaxani B, Gutman JR, Keskinocak P, Smalley HK, + Thwing J. - Gu W, Qiu Y, Li W, Zhang Z, Liu X, Song Y, Wang W. + Am J Trop Med Hyg. 2024 Jul 9:tpmd230844. doi: + 10.4269/ajtmh.23-0844. Online ahead of print. - Chaos. 2024 Jul 1;34(7):073105. doi: 10.1063/5.0219759. + > Pilot experiments have shown the potential of ProCCM for + > controlling malaria transmission; identifying the best strategy + > for administering ProCCM in terms of interval timings and number + > of sweeps could lead to further reductions in malaria infections. + > We developed an agent … - > Therefore, this study attempts to model and simulate higher-order - > interactions among mobile populations and explore their impact on - > epidemic transmission. This study simulated the spread of the - > epidemic in a spatial high-order network based on agent-based … +7. **Building multiscale models with PhysiBoSS, an agent-based modeling + tool.** -7. **PhysiCell Studio: a graphical tool to make agent-based modeling - more accessible.** + Ruscone M, Checcoli A, Heiland R, Barillot E, Macklin P, Calzone L, + Noël V. - Heiland R, Bergman D, Lyons B, Waldow G, Cass J, Lima da Rocha H, - Ruscone M, Noël V, Macklin P. + ArXiv \[Preprint\]. 2024 Jun 26:arXiv:2406.18371v1. - GigaByte. 2024 Jun 19;2024:gigabyte128. doi: 10.46471/gigabyte.128. - eCollection 2024. + > Multiscale models provide a unique tool for studying 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 PhysiCell … - > In the best case, the model will be defined using some format - > specification - a markup language - that will provide easy model - > sharing (and a minimal step toward reproducibility). PhysiCell is - > an open-source, physics-based multicellular simulation framework - > with an … - -8. **Balancing long-term and short-term strategies in a sustainability - game.** +8. **An agent-based model for cell microenvironment simulation using + FLAMEGPU2.** - Bertolotti F, Roman S. + Borau C, Chisholm R, Richmond P, Walker D. - iScience. 2024 May 27;27(6):110020. doi: 10.1016/j.isci.2024.110020. - eCollection 2024 Jun 21. + Comput Biol Med. 2024 Jul 5;179:108831. doi: + 10.1016/j.compbiomed.2024.108831. Online ahead of print. - > This article aims to enhance the understanding of this issue by - > analyzing how sustainability concerns change over time by means of - > a game, and the effect of this variation on the final status of a - > system. Leveraging insights from the game, we implement an - > agent-based … + > This work presents an advanced agent-based model developed within + > the FLAMEGPU2 framework, aimed at simulating the intricate + > dynamics of cell microenvironments. …Through four example + > applications, we demonstrate the model’s versatility in capt … -9. **Minimal cellular automaton model with heterogeneous cell sizes - predicts epithelial colony growth.** +9. **HPVsim: An agent-based model of HPV transmission and cervical + disease.** - Lange S, Schmied J, Willam P, Voss-Böhme A. + Stuart RM, Cohen JA, Kerr CC, Mathur P; National Disease Modelling + Consortium of India; Abeysuriya RG, Zimmermann M, Rao DW, Boudreau + MC, Lee S, Yang L, Klein DJ. - J Theor Biol. 2024 Jun 27:111882. doi: 10.1016/j.jtbi.2024.111882. - Online ahead of print. + PLoS Comput Biol. 2024 Jul 5;20(7):e1012181. doi: + 10.1371/journal.pcbi.1012181. Online ahead of print. - > Cellular automata (CA) have been employed in the past as - > numerically efficient mathematical models to study the dynamics of - > cell ensembles, but they are not suitable to explore the origins - > of contact inhibition as such agent-based models assume fixed c … + > Open-source modelling tools are needed to shift the capacity for + > such evaluations in-country. Here, we introduce the Human + > papillomavirus simulator (HPVsim), a new open-source software + > package for creating flexible agent-based models parameterised + > with … -10. **Models of bee responses to land use and land cover changes in - agricultural landscapes - a review and research agenda.** +10. **ENERGY Pro: Spatially explicit agent-based model on achieving + positive energy districts.** - Rouabah A, Rabolin-Meinrad C, Gay C, Therond O. + Derkenbaeva E, Hofstede GJ, van Leeuwen E, Halleck Vega S, Wolfers + J. - Biol Rev Camb Philos Soc. 2024 Jun 28. doi: 10.1111/brv.13109. - Online ahead of print. + MethodsX. 2024 May 28;12:102779. doi: 10.1016/j.mex.2024.102779. + eCollection 2024 Jun. - > Here, we reviewed 42 studies that developed non-correlative models - > to explore the impact of land use and land cover changes on bee - > populations, and synthesised information about the modelled - > systems, modelling approaches, and key model characteristics … + > This article describes the ENERGY Pro agent-based model using the + > Overview, Design Concept, and Details + Human Decision-making + > (ODD+D protocol). …The article also describes sensitivity + > analysis, validation results, and how to use and adapt the model … ## Code of Conduct