From 81c309f96bd4d00240f0915457eb4f5bbd3930dc Mon Sep 17 00:00:00 2001 From: gvegayon Date: Sun, 21 Jul 2024 00:43:57 +0000 Subject: [PATCH] Commit from GitHub Actions (Build it) --- README.md | 195 +++++++++++++++++++++++++++--------------------------- 1 file changed, 98 insertions(+), 97 deletions(-) diff --git a/README.md b/README.md index 09da3a9..eb5ec00 100644 --- a/README.md +++ b/README.md @@ -9,147 +9,148 @@ 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 2024-07-14 00:44:04. +update was on 2024-07-21 00:43:54.
-1. **Dissecting the Spatially Restricted Effects of - Microenvironment-Mediated Resistance on Targeted Therapy - Responses.** +1. **Dual-modal imaging-guided agent based on NIR-II + aggregation-induced emission luminogens with balanced + phototheranostic performance.** - Miti T, Desai B, Miroshnychenko D, Basanta D, Marusyk A. + Dong C, Zhang Z, Wu H, Liang X, Pang S, Wu K, Sun J, Dong X, Sun L, + Gu X, Zhao C. - Cancers (Basel). 2024 Jun 29;16(13):2405. doi: - 10.3390/cancers16132405. + Chem Sci. 2024 Jun 7;15(28):10969-10979. doi: 10.1039/d4sc01916d. + eCollection 2024 Jul 17. - > 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. … + > These nanoparticles were applied to fluorescence-photothermal + > dual-mode imaging-guided photothermal ablation in a HeLa tumor + > xenograft mouse model, resulting in favorable photothermal + > clearance outcomes…. -2. **In Vivo PET Detection of Lung Micrometastasis in Mice by Targeting - Endothelial VCAM-1 Using a Dual-Contrast PET/MRI Probe.** +2. **Role of heterogeneity: National scale data-driven agent-based + modeling for the US COVID-19 Scenario Modeling Hub.** - Melemenidis S, Knight JC, Kersemans V, Perez-Balderas F, Zarghami N, - Soto MS, Cornelissen B, Muschel RJ, Sibson NR. + Chen J, Bhattacharya P, Hoops S, Machi D, Adiga A, Mortveit H, + Venkatramanan S, Lewis B, Marathe M. - Int J Mol Sci. 2024 Jun 28;25(13):7160. doi: 10.3390/ijms25137160. + Epidemics. 2024 Jun 27;48:100779. doi: 10.1016/j.epidem.2024.100779. + Online ahead of print. - > 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 … + > UVA-EpiHiper is a national scale agent-based model to support the + > US COVID-19 Scenario Modeling Hub (SMH). …We then discuss how the + > detailed output produced by UVA-EpiHiper can be analyzed to obtain + > interesting insights. We find that despite the comp … -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.** +3. **A three-dimensional lattice-free agent-based model of + intracellular ice formation and propagation and intercellular + mechanics in liver tissues.** - Petrucciani A, Hoerter A, Kotze L, Du Plessis N, Pienaar E. + Amiri F, Benson JD. - PLoS Comput Biol. 2024 Jul 12;20(7):e1012266. doi: - 10.1371/journal.pcbi.1012266. Online ahead of print. + R Soc Open Sci. 2024 Jul 17;11(7):231337. doi: 10.1098/rsos.231337. + eCollection 2024 Jul. - > 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. … + > Understanding how ice spreads can accelerate protocol development + > and enable model-based decision-making. Previous models of + > intracellular ice formation in individual cells have been extended + > to one-cell-wide arrays to establish the theory of intercellular + > ice propa … -4. **Correction to “A seven-step guide to spatial, agent-based - modelling of tumour evolution”.** +4. **Linking discrete and continuous models of cell birth and + migration.** - \[No authors listed\] + Martinson WD, Volkening A, Schmidtchen M, Venkataraman C, Carrillo + JA. - Evol Appl. 2024 Jul 9;17(7):e13756. doi: 10.1111/eva.13756. + R Soc Open Sci. 2024 Jul 17;11(7):232002. doi: 10.1098/rsos.232002. eCollection 2024 Jul. -5. **Deep learning-based dimensional emotion recognition for - conversational agent-based cognitive behavioral therapy.** + > Discrete models provide straightforward interpretations by + > tracking each individual yet can be computationally expensive. …We + > illustrate our approach on an example motivated by zebrafish-skin + > pattern formation, in which we create a continuous framework + > describing the mov … - Striegl J, Richter JW, Grossmann L, Bråstad B, Gotthardt M, Rück C, - Wallert J, Loitsch C. +5. **An agent-based modelling framework to study growth mechanisms in + EGFR-L858R mutant cell alveolar type II cells.** - PeerJ Comput Sci. 2024 Jun 24;10:e2104. doi: 10.7717/peerj-cs.2104. - eCollection 2024. + Coggan H, Weeden CE, Pearce P, Dalwadi MP, Magness A, Swanton C, + Page KM. - > 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 … + R Soc Open Sci. 2024 Jul 17;11(7):240413. doi: 10.1098/rsos.240413. + eCollection 2024 Jul. -6. **Modeling the Impact of Proactive Community Case Management on - Reducing Confirmed Malaria Cases in Sub-Saharan African Countries.** +6. **Modeling the dynamic impacts of maritime network blockage on + global supply chains.** - Wang Y, Wang X, Gurbaxani B, Gutman JR, Keskinocak P, Smalley HK, - Thwing J. + Qu S, She Y, Zhou Q, Verschuur J, Zhao LT, Liu H, Xu M, Wei YM. - Am J Trop Med Hyg. 2024 Jul 9:tpmd230844. doi: - 10.4269/ajtmh.23-0844. Online ahead of print. + Innovation (Camb). 2024 Jun 5;5(4):100653. doi: + 10.1016/j.xinn.2024.100653. eCollection 2024 Jul 1. - > 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 … + > A salient example is the March 2021 Suez Canal blockage, which + > delayed 432 vessels carrying cargo valued at $92.7 billion, + > triggering widespread supply chain disruptions. Our ability to + > model the spatiotemporal ramifications of such incidents remains + > limited. To fill this … -7. **Building multiscale models with PhysiBoSS, an agent-based modeling - tool.** +7. **Clonal dynamics of surface-driven growing tissues.** - Ruscone M, Checcoli A, Heiland R, Barillot E, Macklin P, Calzone L, - Noël V. + Mukhamadiarov RI, Ciarchi M, Olmeda F, Rulands S. - ArXiv \[Preprint\]. 2024 Jun 26:arXiv:2406.18371v1. + Phys Rev E. 2024 Jun;109(6-1):064407. doi: + 10.1103/PhysRevE.109.064407. - > 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 … + > To this end, we derive the clone size distributions using + > analytical calculations in the limit of negligible cell migration + > and cell death, and we test our predictions with an agent-based + > stochastic sampling technique. We show that for surface-driven + > growth the clon … -8. **An agent-based model for cell microenvironment simulation using - FLAMEGPU2.** +8. **Noisy kinetic-exchange opinion model with aging.** - Borau C, Chisholm R, Richmond P, Walker D. + Vieira AR, Llabrés J, Toral R, Anteneodo C. - Comput Biol Med. 2024 Jul 5;179:108831. doi: - 10.1016/j.compbiomed.2024.108831. Online ahead of print. + Phys Rev E. 2024 Jun;109(6-1):064119. doi: + 10.1103/PhysRevE.109.064119. - > 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 … + > We study the critical behavior of a noisy kinetic opinion model + > subject to resilience to change depending on aging, defined as the + > number of interactions before a change of opinion state. …For the + > opinion dynamics in a complete graph, we obtain analytical + > predictions for … -9. **HPVsim: An agent-based model of HPV transmission and cervical - disease.** +9. **Admission screening testing of patients and staff N95 masks are + cost-effective in reducing COVID-19 hospital acquired infections.** - 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. + McAndrew F, Abeysuriya RG, Sacks-Davis R, Sammann M, Lister DM, West + D, Majumdar S, Scott N. - PLoS Comput Biol. 2024 Jul 5;20(7):e1012181. doi: - 10.1371/journal.pcbi.1012181. Online ahead of print. + J Hosp Infect. 2024 Jul 15:S0195-6701(24)00236-6. doi: + 10.1016/j.jhin.2024.06.015. Online ahead of print. - > 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 … + > This study assessed the cost-effectiveness of clinical staff N95 + > masks and admission screening testing of patients to reduce + > COVID-19 hospital-acquired infections. METHODS: An agent-based + > model was calibrated to data on 178 outbreaks in acute care + > settings in … -10. **ENERGY Pro: Spatially explicit agent-based model on achieving - positive energy districts.** +10. **Stress sharing as cognitive glue for collective intelligences: A + computational model of stress as a coordinator for morphogenesis.** - Derkenbaeva E, Hofstede GJ, van Leeuwen E, Halleck Vega S, Wolfers - J. + Shreesha L, Levin M. - MethodsX. 2024 May 28;12:102779. doi: 10.1016/j.mex.2024.102779. - eCollection 2024 Jun. + Biochem Biophys Res Commun. 2024 Jul 14;731:150396. doi: + 10.1016/j.bbrc.2024.150396. 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 … + > One mechanism that has been proposed for enabling individual cells + > to coordinate toward specific morphological outcomes is the + > sharing of stress (where stress is a physiological parameter that + > reflects the current amount of error in the context of a + > homeostatic loop). Here, we co … ## Code of Conduct