Merge branch 'master' of github.com:UofUEpiBio/PHS-7045-egga

README.md

@@ -9,13 +9,69 @@ 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 2025-01-05 00:52:11.
+update was on 2025-01-06 04:53:48.
 
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 </div>
 
-1.  **Long-range organization of intestinal 2D-crypts using exogenous
+1.  **The SARS-CoV-2 test scale-up in the USA: an analysis of the number
+    of tests produced and used over time and their modelled impact on
+    the COVID-19 pandemic.**
+
+    Santos S, Humbard M, Lambrou AS, Lin G, Padilla Y, Chaitram J,
+    Natrajan MS, Kirking HL, Courtney S, Del Guercio K, Roberts S,
+    Gaspar F, Iademarco MF, Hamel J, Salerno RM.
+
+    Lancet Public Health. 2025 Jan;10(1):e47-e57. doi:
+    10.1016/S2468-2667(24)00279-2.
+
+    > Tests produced (TDWG), reported test positivity (US Centers for
+    > Disease Control and Prevention \[CDC\]’s COVID-19 Electronic
+    > Laboratory Reporting system and the Federal Direct Report testing
+    > data), reported COVID-19 case counts (CDC), hospitalisations
+    > (Department of Health and Huma …
+
+2.  **Analysis of inoculation strategies during COVID-19 pandemic with
+    an agent-based simulation approach.**
+
+    Kulaç O, Toy AÖ, Kabak KE.
+
+    Comput Biol Med. 2025 Jan 3;186:109564. doi:
+    10.1016/j.compbiomed.2024.109564. Online ahead of print.
+
+    > METHOD: In this study we have implemented a highly detailed
+    > Agent-Based Simulation (ABS) model that extends classical SEIR
+    > Model by including five more additional states: Asymptomatic (A),
+    > Quarantine (Q), Hospitalized (H), Dead (D) and Immune (M) which …
+
+3.  **Complexity Control in Artificial Self-Organizing Systems: The Case
+    of Bottom-Up versus Top-Down Intervention When Managing Pandemic
+    Contagion.**
+
+    Mahmoodi K, Hazy JK.
+
+    Nonlinear Dynamics Psychol Life Sci. 2025 Jan;29(1):135-164.
+
+    > We model an adaptive agent-based environment using selfish
+    > algorithm agents (SA-agents) that make decisions along three
+    > choice dimensions as they play the multi-round prisoner’s dilemma
+    > game. The dynamics that emerge from mutual interactions among the
+    > SA-agen …
+
+4.  **Introduction to Emergence in Social Systems.**
+
+    Hazy JK, Lichtenstein B, Guastello SJ.
+
+    Nonlinear Dynamics Psychol Life Sci. 2025 Jan;29(1):1-4.
+
+    > Applications include work teams, organizations, ecologies of
+    > organizations, and societies. Prominent methodologies include
+    > agent-based modeling, qualitative analysis of publicly available
+    > business and governmental reports, structured analyses of team
+    > discussi …
+
+5.  **Long-range organization of intestinal 2D-crypts using exogenous
     Wnt3a micropatterning.**
 
     Larrañaga E, Marin-Riera M, Abad-Lázaro A, Bartolomé-Català D, Otero
@@ -30,7 +86,7 @@ update was on 2025-01-05 00:52:11.
     > crypt-like regions in primary epithelial monolayers. Additionally,
     > an agent-based …
 
-2.  **Mathematical modeling of impacts of patient differences on
+6.  **Mathematical modeling of impacts of patient differences on
     renin-angiotensin system and applications to COVID-19 lung fibrosis
     outcomes.**
 
@@ -44,7 +100,7 @@ update was on 2025-01-05 00:52:11.
     > fibrosis dynamics model to investigate the effects of
     > patient-group-specific factors in the systemic alteration of …
 
-3.  **Modelling the Impact of HIF on Metabolism and the Extracellular
+7.  **Modelling the Impact of HIF on Metabolism and the Extracellular
     Matrix: Consequences for Tumour Growth and Invasion.**
 
     Spinicci K, Powathil G, Stéphanou A.
@@ -57,7 +113,7 @@ update was on 2025-01-05 00:52:11.
     > focus on the Warburg effect and collagen remodelling processes.
     > Therefore, we present an agent-based model (ABM) of tumour gr …
 
-4.  **Lifetime Disability-adjusted Life Year assessment of indolent
+8.  **Lifetime Disability-adjusted Life Year assessment of indolent
     systemic mastocytosis.**
 
     Mounié M, Derumeaux Burel H, Molinier L, Costa N, Bulai Livideanu C.
@@ -71,7 +127,7 @@ update was on 2025-01-05 00:52:11.
     > DALY calculation. An agent-based model was developed to more accu
     > …
 
-5.  **Epidemiological models to estimate the burden of snakebite
+9.  **Epidemiological models to estimate the burden of snakebite
     envenoming: A systematic review.**
 
     Gololo AA, Veettil SK, Anantachoti P, Taychakhoonavudh S, Patikorn
@@ -85,7 +141,7 @@ update was on 2025-01-05 00:52:11.
     > factors. RESULTS: Thirty-nine modelling studies were included from
     > 2426 retrieved articles, comprising statistical models …
 
-6.  **Matrix-producing cells’ orientation order facilitates Bacillus
+10. **Matrix-producing cells’ orientation order facilitates Bacillus
     subtilis biofilm self-healing.**
 
     Li J, Wang J, Wu J, Wang X.
@@ -97,67 +153,6 @@ update was on 2025-01-05 00:52:11.
     > employed to simulate the self-healing processes of biofilms at two
     > ages. …
 
-7.  **Theoretical modeling of hepatitis C acute infection in
-    liver-humanized mice support pre-clinical assessment of candidate
-    viruses for controlled-human-infection studies.**
-
-    Shi Z, Mhlanga A, Ishida Y, Josephson A, Collier NT, Abe-Chayama H,
-    Tateno-Mukaidani C, Cotler SJ, Ozik J, Major M, Feld JJ, Chayama K,
-    Dahari H.
-
-    Sci Rep. 2024 Dec 30;14(1):31826. doi: 10.1038/s41598-024-83104-0.
-
-    > Designing and carrying out a controlled human infection (CHI)
-    > model for hepatitis C virus (HCV) is critical for vaccine
-    > development. However, key considerations for a CHI model protocol
-    > include understanding of the earliest viral-host kinetic events
-    > during the acute …
-
-8.  **An agent based simulation of COVID-19 history in Catalonia using
-    extensive real datasets.**
-
-    Bosman M, Cordon Y, Duran-Sala M, Gabbanelli L, García-Pérez C,
-    Jordan X, Manera M, Masjuan P, Medina A, Mir LM, Oròs A, Vitagliano
-    V.
-
-    Sci Rep. 2024 Dec 30;14(1):31858. doi: 10.1038/s41598-024-83238-1.
-
-    > During the COVID-19 pandemic, effective public policy
-    > interventions have been crucial in combating virus transmission,
-    > sparking extensive debate on crisis management strategies and
-    > emphasizing the necessity for reliable models to inform
-    > governmental decisions, particularly …
-
-9.  **Plaque heterogeneity influences in-stent restenosis following
-    drug-eluting stent implantation: Insights from patient-specific
-    multiscale modelling.**
-
-    Corti A, Dal Ferro L, Akyildiz AC, Migliavacca F, McGinty S,
-    Chiastra C.
-
-    J Biomech. 2024 Dec 16;179:112485. doi:
-    10.1016/j.jbiomech.2024.112485. Online ahead of print.
-
-    > Here, an original patient-specific multiscale agent-based
-    > modelling framework was developed to investigate the interplay
-    > between drug release, plaque composition and intervention-induced
-    > inflammation on in-stent restenosis following drug-eluting stent
-    > implant …
-
-10. **Cost-Effectiveness Analysis of Vaccination Compliance Strategies
-    Using a Novel Hybrid Model for Influenza Vaccination.**
-
-    You D, Zhou Y, Yan Y, Chen F, Lu M, Shao F.
-
-    China CDC Wkly. 2024 Dec 13;6(50):1337-1342. doi:
-    10.46234/ccdcw2024.265.
-
-    > This study evaluated the cost-effectiveness of vaccination
-    > compliance strategies by comparing an “adherence” strategy, which
-    > promoted continuous vaccination uptake, with a “volunteer”
-    > strategy through model-based simulations. METHODS: We developed a
-    > novel hybrid model …
-
 ## Code of Conduct
 
 Please note that the PHS-7045-egga project is released with a