Commit from GitHub Actions (Build it)

README.md

@@ -9,150 +9,152 @@ document updated once a week or whenever there’s a push or pull request.
 It performs a search on PubMed looking for the <a
 href="https://pubmed.ncbi.nlm.nih.gov/?term=agent-based+model&amp;sort=date"
 target="_blank">latest papers about Agent-Based Models</a>. The last
-update was on 2024-04-21 00:38:47.
+update was on 2024-04-28 00:39:18.
 
 <div class="cell">
 
 </div>
 
-1.  **Integrating multiplexed imaging and multiscale modeling identifies
-    tumor phenotype conversion as a critical component of therapeutic T
-    cell efficacy.**
+1.  **Spatial transcriptome-guided multi-scale framework connects P.
+    aeruginosa metabolic states to oxidative stress biofilm
+    microenvironment.**
 
-    Hickey JW, Agmon E, Horowitz N, Tan TK, Lamore M, Sunwoo JB, Covert
-    MW, Nolan GP.
+    Kuper TJ, Islam MM, Peirce-Cottler SM, Papin JA, Ford RM.
 
-    Cell Syst. 2024 Apr 17;15(4):322-338.e5. doi:
-    10.1016/j.cels.2024.03.004.
+    PLoS Comput Biol. 2024 Apr 26;20(4):e1012031. doi:
+    10.1371/journal.pcbi.1012031. eCollection 2024 Apr.
 
-    > Here, we integrated CODEX multiplexed tissue imaging with
-    > multiscale modeling software to model key action points that
-    > influence the outcome of T cell therapies with cancer. …The
-    > results suggest new design criteria and patient selection metrics
-    > for T cell therapie …
+    > With the generation of spatially resolved transcriptomics of
+    > microbial biofilms, computational tools can be used to integrate
+    > this data to elucidate the multi-scale mechanisms controlling
+    > heterogeneous biofilm metabolism. This work presents a Multi-scale
+    > model of Metabolis …
 
-2.  **Empirical and simulated investigation of the solid waste reverse
-    supply chain: A complex adaptive system perspective.**
+2.  **Screening Strategies to Reduce COVID-19 Mortality in Nursing
+    Homes.**
 
-    Ma G, Pan X, Zhang Y, Liu T, Wang D.
+    Dong S, Jutkowitz E, Giardina J, Bilinski A.
 
-    J Environ Manage. 2024 Apr 17;358:120924. doi:
-    10.1016/j.jenvman.2024.120924. Online ahead of print.
+    JAMA Health Forum. 2024 Apr 5;5(4):e240688. doi:
+    10.1001/jamahealthforum.2024.0688.
 
-    > In the multi-layer system, different layers communicate with each
-    > other through the material and financial flows and have
-    > cross-layer impacts. An agent-based model is developed to
-    > investigate the multi-layer feedforward influence mechanism of
-    > changes in key l …
+    > OBJECTIVE: To evaluate the cost-effectiveness of screening
+    > strategies in reducing COVID-19 mortality in nursing homes. DESIGN
+    > AND SETTING: An agent-based model was developed to simulate
+    > SARS-CoV-2 transmission in the nursing home setting. …The
+    > population us …
 
-3.  **Methods for health workforce projection model: systematic review
-    and recommended good practice reporting guideline.**
+3.  **Conformity and Mass Media Influence in the Sznajd Model on Regular
+    Lattices.**
 
-    Lee JT, Crettenden I, Tran M, Miller D, Cormack M, Cahill M, Li J,
-    Sugiura T, Xiang F.
+    Wołoszyn M.
 
-    Hum Resour Health. 2024 Apr 17;22(1):25. doi:
-    10.1186/s12960-024-00895-z.
+    Entropy (Basel). 2024 Mar 30;26(4):307. doi: 10.3390/e26040307.
 
-    > The review identified at least eight distinct types of health
-    > workforce projection models commonly used in recent literature:
-    > population-to-provider ratio models (n = 7), utilization models (n
-    > = 10), needs-based models (n = 25), skill-mixed models …
+    > Understanding the dynamics governing those processes is,
+    > therefore, one of the main aims of sociophysics. In this work, the
+    > Sznajd model of opinion dynamics is investigated with Monte Carlo
+    > simulations performed on four different regular lattices:
+    > triangular, honeycomb, an …
 
-4.  **T-cell commitment inheritance-an agent-based multi-scale model.**
+4.  **Protective effects of antibiotic resistant bacteria on
+    susceptibles in biofilm: Influential factors, mechanism, and
+    modeling.**
 
-    Andersson E, Rothenberg EV, Peterson C, Olariu V.
+    Xu F, Jiang M, Li D, Yu P, Ma H, Lu H.
 
-    NPJ Syst Biol Appl. 2024 Apr 17;10(1):40. doi:
-    10.1038/s41540-024-00368-y.
+    Sci Total Environ. 2024 Apr 23:172668. doi:
+    10.1016/j.scitotenv.2024.172668. Online ahead of print.
 
-    > T-cell development provides an excellent model system for studying
-    > lineage commitment from a multipotent progenitor. …However, the
-    > exact timing between decision-making and commitment stage remains
-    > unexplored. To this end, we implemented an agent-based multi …
+    > Compared to AmpS, AmpR displayed superiority in adhesion,
+    > antibiotic degradation, motility, and quorum sensing, allowing
+    > them to preferentially colonize biofilm edge and areas with higher
+    > ampicillin. An agent-based model incorporating protective effects
+    > succe …
 
-5.  **Collective behavior from surprise minimization.**
+5.  **Selective social interactions and speed-induced leadership in
+    schooling fish.**
 
-    Heins C, Millidge B, Da Costa L, Mann RP, Friston KJ, Couzin ID.
+    Puy A, Gimeno E, Torrents J, Bartashevich P, Miguel MC,
+    Pastor-Satorras R, Romanczuk P.
 
-    Proc Natl Acad Sci U S A. 2024 Apr 23;121(17):e2320239121. doi:
-    10.1073/pnas.2320239121. Epub 2024 Apr 17.
+    Proc Natl Acad Sci U S A. 2024 Apr 30;121(18):e2309733121. doi:
+    10.1073/pnas.2309733121. Epub 2024 Apr 25.
 
-    > However, organisms are not particles; they are probabilistic
-    > decision-makers. Here, we introduce an approach to modeling
-    > collective behavior based on active inference. This cognitive
-    > framework casts behavior as the consequence of a single
-    > imperative: to minimize surprise. …
+    > Here, we introduce a force map technique suitable for the analysis
+    > of the alignment forces experienced by individuals. After
+    > validating it using an agent-based model, we apply the force map
+    > to experimental data of schooling fish. …This mechanism implies
+    > the …
 
-6.  **It’s about time: Feeding competition costs of sociality are
-    affected more by temporal characteristics than spatial
-    distribution.**
+6.  **Noise and opinion dynamics: how ambiguity promotes pro-majority
+    consensus in the presence of confirmation bias.**
 
-    Ekanayake-Weber M, Mathew N, Cunha D, Payen N, Grimm V, Koenig A.
+    Steiglechner P, Keijzer MA, E Smaldino P, Moser D, Merico A.
 
-    Ecol Evol. 2024 Apr 16;14(4):e11209. doi: 10.1002/ece3.11209.
+    R Soc Open Sci. 2024 Apr 24;11(4):231071. doi: 10.1098/rsos.231071.
     eCollection 2024 Apr.
 
-    > However, these models did not fully account for the fact that
-    > gregariousness has multiple experiences and can vary in relation
-    > to ecological variables and foraging competition. Here, we present
-    > an agent-based model for testing how ecological variables …
+    > Opinion dynamics are affected by cognitive biases and noise. While
+    > mathematical models have focused extensively on biases, we still
+    > know surprisingly little about how noise shapes opinion patterns.
+    > Here, we use an agent-based opinion dynamics model to …
 
-7.  **Modelling the impact of hybrid immunity on future COVID-19
-    epidemic waves.**
+7.  **A Role for Cross-linking Proteins in Actin Filament Network
+    Organization and Force Generation.**
 
-    Le TP, Abell I, Conway E, Campbell PT, Hogan AB, Lydeamore MJ,
-    McVernon J, Mueller I, Walker CR, Baker CM.
+    Hill JM, Cai S, Carver MD, Drubin DG.
 
-    BMC Infect Dis. 2024 Apr 16;24(1):407. doi:
-    10.1186/s12879-024-09282-4.
+    bioRxiv \[Preprint\]. 2024 Apr 20:2024.04.19.590161. doi:
+    10.1101/2024.04.19.590161.
 
-    > METHODS: To investigate the role of hybrid immunity, we use an
-    > agent-based model of COVID-19 transmission with waning immunity to
-    > simulate outbreaks in populations with varied past attack rates
-    > and past vaccine coverages, basing the demographics and past hist
-    > …
+    > Endocytic internalization is severely impeded in the absence of
+    > fimbrin, an actin filament crosslinking protein called Sac6 in
+    > budding yeast. Here, we combine live-cell imaging and mathematical
+    > modeling to gain new insights into the role of actin filament
+    > crosslinking prot …
 
-8.  **An agent-based model on antimicrobial de-escalation in intensive
-    care units: Implications on clinical trial design.**
+8.  **Controlling inter-particle distances in crowds of motile,
+    cognitive, active particles.**
 
-    Huo X, Liu P.
+    Negi RS, Iyer P, Gompper G.
 
-    PLoS One. 2024 Apr 16;19(4):e0301944. doi:
-    10.1371/journal.pone.0301944. eCollection 2024.
+    Sci Rep. 2024 Apr 24;14(1):9443. doi: 10.1038/s41598-024-59022-6.
 
-    > This paper conducts computer simulations to assess the ecological
-    > effects of de-escalation on the resistance prevalence of
-    > Pseudomonas aeruginosa-a frequent pathogen causing nosocomial
-    > infections. Synthetic data produced by the models are then used to
-    > estimate the sample s …
+    > This becomes particularly relevant in systems of active agents,
+    > which can sense their environment and react by adjusting their
+    > direction of motion. We employ agent-based simulations to
+    > investigate the complex interplay between agent activity,
+    > characterized by Peclet …
 
-9.  **Coupling an agent-based model and an ensemble Kalman filter for
-    real-time crowd modelling.**
+9.  **Hierarchically embedded scales of movement shape the social
+    networks of vampire bats.**
 
-    Suchak K, Kieu M, Oswald Y, Ward JA, Malleson N.
+    Hartman CRA, Wilkinson GS, Razik I, Hamilton IM, Hobson EA, Carter
+    GG.
 
-    R Soc Open Sci. 2024 Apr 10;11(4):231553. doi: 10.1098/rsos.231553.
-    eCollection 2024 Apr.
+    Proc Biol Sci. 2024 Apr 30;291(2021):20232880. doi:
+    10.1098/rspb.2023.2880. Epub 2024 Apr 24.
 
-    > Agent-based modelling has emerged as a powerful tool for modelling
-    > systems that are driven by discrete, heterogeneous individuals and
-    > has proven particularly popular in the realm of pedestrian
-    > simulation. …This paper addresses this challenge by integ …
+    > Using existing data from common vampire bats (Desmodus rotundus),
+    > we created an agent-based model of how three nested scales of
+    > movement-among roosts, clusters and grooming partners-each
+    > influence a bat’s grooming network centrality. …Simulations
+    > revealed h …
 
-10. **Modeling the implications of policy reforms on pesticide risk for
-    Switzerland.**
+10. **Is chromium(III) pharmacologically relevant? An update focused on
+    studies with diabetic rodent models.**
 
-    Dueri S, Mack G.
+    Vincent JB.
 
-    Sci Total Environ. 2024 Apr 15;928:172436. doi:
-    10.1016/j.scitotenv.2024.172436. Online ahead of print.
+    J Trace Elem Med Biol. 2024 Apr 20;84:127453. doi:
+    10.1016/j.jtemb.2024.127453. Online ahead of print.
 
-    > Therefore, we introduced crop-specific pesticide quantities and
-    > pesticide risk scores into a sample of 1907 bio-economic farm
-    > optimization models. The models were used to predict farmers’
-    > adoption decisions regarding voluntary direct payment programs
-    > from 2019 to 20 …
+    > A decade ago, the author assessed the status of chromium as the
+    > trivalent ion as an essential element and as a therapeutic agent
+    > based on rodent studies for this journal. The current review was
+    > undertaken to update considerations regarding the status of
+    > chromium, fo …
 
 ## Code of Conduct