This is the repository to create the graphics used in the slides for my seminar talk. The code to create the graphics is either included here or in the noted repository below; if it is adapted from a paper, then the link to the appropriate citation is provided.
Chesebro, AG, Mujica-Parodi, LR, Weistuch, C. Ion gradient-driven bifurcations of a multi-scale neuronal model. Chaos, Solitons, and Fractals. (2023); 167:113120. https://content.api.getguru.com/files/view/42352b6f-8bec-4eb6-b0f7-d043bfa90d6a.
Code to generate Figures 2-5 for this paper can be found at: https://github.com/lcneuro/larter-breakspear-bifurcation.
- Slide 3: Dukart et al. PLOS Comp. Bio. (2013). https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002987
- Slide 4: Baeza-Lehnert et al., Cell Metabolism. (2019). https://www.cell.com/cell-metabolism/fulltext/S1550-4131(18)30682-X?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS155041311830682X%3Fshowall%3Dtrue
- Slides 6-7: Taken from Chesebro et al. Images created in BioRender.
- Slides 9-10: Taken from my talk at the Gordon Research Seminar on Stochastic Physics in Biology. Repository to generate these images here: https://github.com/agchesebro/stochastic-physics-biology-2023. Note the Neimark-Sacker bifurcations require the repository from Chesebro et al. to work.
- Slides 11-14: Taken from Chesebro et al. Repository linked above.
- Slide 17: Antal et al. (2023). arXiv preprint: https://arxiv.org/abs/2303.13746
- Slide 18:
- Ma et al. J. Neurosci. (2007). https://www.jneurosci.org/content/27/14/3618
- Mujica-Parodi et al. PNAS (2020). https://www.pnas.org/doi/10.1073/pnas.1913042117.
- van Nieuwenhuizen et al. (2023). https://www.biorxiv.org/content/10.1101/2023.05.10.540257v1.
- Slides 19-20, 22: Transcriptomic maps derived using the tool from Gryglewski et al. NeuroImage. (2018). https://www.sciencedirect.com/science/article/abs/pii/S1053811918303884?via%3Dihub
- Slide 20: Additional graphics from the Allen Human Brain Atlas: https://human.brain-map.org
- Slide 21: Image adapted from Adapted from Hansen et al. Nat. Neurosci. (2022). https://www.nature.com/articles/s41593-022-01186-3
- Slide 22: Tau PET maps derived using data from the ADNI cohort: https://adni.loni.usc.edu. Graphics of evolution on the brain surface over time can be generated using this repository, along with the BrainSurfaceAnimation toolbox developed by J.O. Stuart: https://github.com/StuartJO/BrainSurfaceAnimation. Simply copy the code and data here into the main repository from that link and it should run! The output will be the same as voila.gif (used in the slide).