With advances in computing, agent-based models (ABMs) have become a feasible and appealing tool to study biological systems. ABMs are seeing increased incorporation into both the biology and mathematics classrooms as powerful modeling tools to study processes involving substantial amounts of stochasticity, nonlinear interactions, and/or heterogeneous spatial structures. Here we present a brief synopsis of the agent-based modeling approach with an emphasis on its use to simulate biological systems, and provide a discussion of its role and limitations in both the biology and mathematics classrooms.
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http://dx.doi.org/10.1007/s11538-020-00778-z | DOI Listing |
Front Biosci (Schol Ed)
December 2024
Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
Background: Alternative cleavage and polyadenylation (APA) is a crucial post-transcriptional gene regulation mechanism that regulates gene expression in eukaryotes by increasing the diversity and complexity of both the transcriptome and proteome. Despite the development of more than a dozen experimental methods over the last decade to identify and quantify APA events, widespread adoption of these methods has been limited by technical, financial, and time constraints. Consequently, APA remains poorly understood in most eukaryotes.
View Article and Find Full Text PDFFront Biosci (Elite Ed)
December 2024
Polytechnic School, University of Vale do Itajaí (Univali), Itajaí, SC 88302-202, Brazil.
Background: Enhanced biological phosphorus removal (EBPR) systems utilize phosphorus-accumulating organisms (PAOs) to remove phosphorus from wastewater since excessive phosphorus in water bodies can lead to eutrophication. This study aimed to characterize a newly isolated PAO strain for its potential application in EBPR systems and to screen for additional biotechnological potential. Here, sequencing allowed for genomic analysis, identifying the genes and molecules involved, and exploring other potentials.
View Article and Find Full Text PDFFront Biosci (Elite Ed)
October 2024
Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, 1983969411 Tehran, Iran.
Background: Regenerative endodontics requires an innovative delivery system to release antibiotics/growth factors in a sequential trend. This study focuses on developing/characterizing a thermoresponsive core-shell hydrogel designed for targeted drug delivery in endodontics.
Methods: The core-shell chitosan-alginate microparticles were prepared by electrospraying to deliver bone morphogenic protein-2 for 14 days and transforming growth factor-beta 1 (TGF-β1) for 7-14 days.
CJC Open
December 2024
University Health Network, Toronto, Ontario, Canada.
Background: Patients with heart failure (HF) can experience a poor quality-of-life (QOL), recurring hospitalizations, and progressive disease symptoms. Patient-reported outcome measures (PROMs) integrate patients' voices into clinical care, by assessing patient symptoms, function, and QOL. In 2022, PROMs were incorporated into the electronic health record system (Epic) at a large academic hospital in Toronto, Ontario, Canada.
View Article and Find Full Text PDFJACS Au
December 2024
Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States.
Understanding the origin and effect of the confinement of molecules and transition states within the micropores of a zeolite can enable targeted design of such materials for catalysis, gas storage, and membrane-based separations. Linear correlations of the thermodynamic parameters of molecular adsorption in zeolites have been proposed; however, their generalizability across diverse molecular classes and zeolite structures has not been established. Here, using molecular simulations of >3500 combinations of adsorbates and zeolites, we show that linear trends hold in many cases; however, they collapse for highly confined systems.
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