scholarly journals Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks

2015 ◽  
Vol 7 (9) ◽  
pp. 987-997 ◽  
Author(s):  
J. Walpole ◽  
J. C. Chappell ◽  
J. G. Cluceru ◽  
F. Mac Gabhann ◽  
V. L. Bautch ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Time Lapse ◽  
Confocal Imaging ◽  
Agent Based Model ◽  
Agent Based

We developed an agent-based model of endothelial sprout initiations based on time-lapse confocal imaging in vitro that outperforms Monte Carlo simulations, suggesting that sprout location and frequency are not purely stochastic behaviors.

scholarly journals Isolation, Characterization, and Agent-Based Modeling of Mesenchymal Stem Cells in a Bio-construct for Myocardial Regeneration Scaffold Design

Data ◽  
2019 ◽  
Vol 4 (2) ◽  
pp. 71 ◽  
Author(s):  
Diana Victoria Ramírez López ◽  
María Isabel Melo Escobar ◽  
Carlos A. Peña-Reyes ◽  
Álvaro J. Rojas Arciniegas ◽  
Paola Andrea Neuta Arciniegas
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
In Silico ◽  
Cardiac Tissue ◽  
Cellular Level ◽  
Cell Behavior ◽  
Agent Based Model ◽  
Agent Based ◽  
And Migration

Regenerative medicine involves methods to control and modify normal tissue repair processes. Polymer and cell constructs are under research to create tissue that replaces the affected area in cardiac tissue after myocardial infarction (MI). The aim of the present study is to evaluate the behavior of differentiated and undifferentiated mesenchymal stem cells (MSCs) in vitro and in silico and to compare the results that both offer when it comes to the design process of biodevices for the treatment of infarcted myocardium in biomodels. To assess in vitro behavior, MSCs are isolated from rat bone marrow and seeded undifferentiated and differentiated in multiple scaffolds of a gelled biomaterial. Subsequently, cell behavior is evaluated by trypan blue and fluorescence microscopy, which showed that the cells presented high viability and low cell migration in the biomaterial. An agent-based model intended to reproduce as closely as possible the behavior of individual MSCs by simulating cellular-level processes was developed, where the in vitro results are used to identify parameters in the agent-based model that is developed, and which simulates cellular-level processes: Apoptosis, differentiation, proliferation, and migration. Thanks to the results obtained, suggestions for good results in the design and fabrication of the proposed scaffolds and how an agent-based model can be helpful for testing hypothesis are presented in the discussion. It is concluded that assessment of cell behavior through the observation of viability, proliferation, migration, inflammation reduction, and spatial composition in vitro and in silico, represents an appropriate strategy for scaffold engineering.

6 ANEUPLOIDY TOLERANCE IN RHESUS MACAQUE PRE-IMPLANTATION EMBRYOS VIA MICRONUCLEI FORMATION, CELLULAR FRAGMENTATION, AND BLASTOMERE EXCLUSION

2017 ◽  
Vol 29 (1) ◽  
pp. 110 ◽  
Author(s):  
B. L. Daughtry ◽  
J. L. Rosenkrantz ◽  
N. Lazar ◽  
N. Redmayne ◽  
K. A. Nevonen ◽  
...  
Keyword(s):  
Rhesus Macaque ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Time Lapse ◽  
Confocal Imaging ◽  
Chromosomal Mosaicism ◽  
Human Embryos ◽  
Cleavage Stage ◽  
Chromosomal Breakage

A primary contributor to in vitro fertilization (IVF) failure is the presence of unbalanced chromosomes in pre-implantation embryos. Previous array-based and next-generation sequencing (NGS) studies determined that ~50 to 80% of human embryos are aneuploid at the cleavage stage. During early mitotic divisions, many human embryos also sequester mis-segregated chromosomes into micronuclei and concurrently undergo cellular fragmentation. We hypothesised that cellular fragmentation represents a response to mis-segregated chromosomes that are encapsulated into micronuclei. Here, we utilised the rhesus macaque pre-implantation embryo as a model to study human embryonic aneuploidy using a combination of EevaTM time-lapse imaging for evaluating cell divisions, single-cell/-fragment DNA-Sequencing (DNA-Seq), and confocal microscopy of nuclear structures. Results from our time-lapse image analysis demonstrated that there are considerable differences in the timing of the first and third mitotic divisions between rhesus blastocysts and those that arrested before this stage in development (P < 0.01; ANOVA). By examining the chromosome content of each blastomere from cleavage stage embryos via DNA-Seq, we determined that rhesus embryos have an aneuploidy frequency up to ~62% (N = 26) with several embryos exhibiting chromosomal mosaicism between blastomeres (N = 6). Certain blastomeres also exhibited reciprocal whole chromosomal gains or losses, indicating that these embryos had undergone mitotic non-disjunction early in development. In addition, findings of reciprocal sub-chromosomal deletions/duplications among blastomeres suggest that chromosomal breakage had occurred in some embryos as well. Embryo immunostaining for the nuclear envelope protein, LAMIN-B1, demonstrated that fragmented cleavage-stage rhesus embryos often contain micronuclei and that cellular fragments can enclose DNA. Our DNA-Seq analysis confirmed that cellular fragments might encapsulate whole and/or partial chromosomes lost from blastomeres. When embryos were immunostained with gamma-H2AX, a marker of chromatin fragility, we observed distinct foci solely in micronuclei and DNA-containing cellular fragments. This suggests that micronuclei may be ejected from blastomeres through the process of cellular fragmentation and, once sequestered, these mis-segregated chromosomes become highly unstable and undergo DNA degradation. Finally, we also observed that ~10% of embryos prevented cellular fragments or large blastomeres from incorporating into the inner cell mass or trophectoderm at the blastocyst stage (n = 5). Upon confocal imaging, multiple nuclei and intense gamma-H2AX foci were found in a large unincorporated blastomere in one of the blastocysts. Altogether, our findings demonstrate that the rhesus embryo responds to segregation errors by eliminating chromosome-containing micronuclei via cellular fragmentation and/or selecting against aneuploid blastomeres that fail to divide during pre-implantation development with significant implications for human IVF.

Monte Carlo Physarum Machine: An Agent-based Model for Reconstructing Complex 3D Transport Networks

2020 ◽  
Author(s):  
Oskar Elek ◽  
Joseph N. Burchett ◽  
J. Xavier Prochaska ◽  
Angus G. Forbes
Keyword(s):  
Monte Carlo ◽  
Agent Based Model ◽  
Transport Networks ◽  
Agent Based

Evolution of tag-based cooperation on Erdős–Rényi random graphs

2014 ◽  
Vol 25 (06) ◽  
pp. 1450006 ◽  
Author(s):  
F. W. S. Lima ◽  
Tarik Hadzibeganovic ◽  
Dietrich Stauffer
Keyword(s):  
Monte Carlo ◽  
Random Graph ◽  
Random Graphs ◽  
Phenotypic Traits ◽  
Artificial Agents ◽  
Agent Based Model ◽  
Agent Based ◽  
Mode Of Reproduction ◽  
Interacting Agents ◽  
Short Period

Here, we study an agent-based model of the evolution of tag-mediated cooperation on Erdős–Rényi random graphs. In our model, agents with heritable phenotypic traits play pairwise Prisoner's Dilemma-like games and follow one of the four possible strategies: Ethnocentric, altruistic, egoistic and cosmopolitan. Ethnocentric and cosmopolitan strategies are conditional, i.e. their selection depends upon the shared phenotypic similarity among interacting agents. The remaining two strategies are always unconditional, meaning that egoists always defect while altruists always cooperate. Our simulations revealed that ethnocentrism can win in both early and later evolutionary stages on directed random graphs when reproduction of artificial agents was asexual; however, under the sexual mode of reproduction on a directed random graph, we found that altruists dominate initially for a rather short period of time, whereas ethnocentrics and egoists suppress other strategists and compete for dominance in the intermediate and later evolutionary stages. Among our results, we also find surprisingly regular oscillations which are not damped in the course of time even after half a million Monte Carlo steps. Unlike most previous studies, our findings highlight conditions under which ethnocentrism is less stable or suppressed by other competing strategies.

scholarly journals Monte Carlo simulations guided by imaging to predict the in vitro ranking of radiosensitizing nanoparticles

2016 ◽  
Vol Volume 11 ◽  
pp. 6169-6179 ◽  
Author(s):  
Paul Retif ◽  
Aurélie Reinhard ◽  
Héna Paquot ◽  
Valérie Jouan-Hureaux ◽  
Alicia Chateau ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations
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