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Anna Kishida Thomas

Publications and source records attributed to Anna Kishida Thomas.

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Multiple timescale dynamics of conductance-based models of brainstem locomotor neurons

The pedunculopontine nucleus (PPN) is a heterogeneous brainstem locomotor hub implicated in Parkinson's disease and potentially relevant for its treatment. We propose single-compartment, conductance-based models for three classes of PPN neurons, such that each model reproduces relevant experimentally observed stimulus-dependent responses, including post-inhibitory rebound dynamics, transient low-threshold activity, and gamma band oscillations. To understand the mechanisms underlying these transient responses to current stimulation, we leverage the models' intrinsic multi-timescale structure and apply dynamical system methods designed for multiple timescale systems. By separating fast membrane and channel-gating dynamics from slower gating and calcium processes, we identify specific ionic mechanisms underlying hallmark dynamics across cell types. We also generate new predictions about PPN behavior under a post-inhibitory facilitation protocol.

math.DS

XPPLORE: Import, visualize, and analyze XPPAUT data in MATLAB

The analysis of ordinary differential equation (ODE) dynamical systems, particularly in applied disciplines such as mathematical biology and neuroscience, often requires flexible computational workflows tailored to model-specific questions. XPPAUT is a widely used tool combining numerical integration and continuation methods. Various XPPAUT toolboxes have emerged to customize analyses, however, they typically rely on summary '.dat' files and cannot parse the more informative '.auto' files, which contain detailed continuation data, e.g. periodic orbits and boundary value problem solutions. We present XPPLORE, a user-friendly and structured MATLAB toolbox overcoming this limitation through the handling of '.auto' files. This free software enables post-processing of continuation results, facilitates analyses such as manifold reconstruction and averaging, and it supports the creation of high-quality visualizations suitable for scientific publications. This paper introduces the core data structures of XPPLORE and demonstrates the software's exploration capabilities, highlighting its value as a customizable and accessible extension for researchers working with ODE-based dynamical systems.

math.DS