Work Description

Title: Epileptogenesis modulates spontaneous and responsive brain state dynamics - Code & Data Open Access Deposited

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Methodology
  • This study employs the intrahippocampal tetanus toxin rat model. Six rats were injected with a single dose of tetanus toxin and monitored using epidural electrodes for 6-8 weeks. During this time, periodic electrical stimulation was preformed to evoked response from the brain. This way, we were able to study spontaneous (seizures) and responsive (evoked responses) brain activity throughout the course of epileptogenesis. Seizure onset features inspired by invariant brain state dynamics (Jirsa et al. 2014) were computed from the seizure onset waveform. Power spectral density estimates were computed as features for the evoked responses. To show that both features sets changes over the course of epileptogenesis, data was segmented into Pre-seizure emergence, Rising-seizure phases, and Falling-seizure phase, which all describe the three characteristics stages of the tetanus toxin model (latency, disease progression, remission). A divergence measure was computed between each of the three phases for the evoked responses, and between the final two phases for the seizure onsets. Our divergence measurement was the Henze-Penrose Statistic. For each computed statistic, a divergence measure was also computed for each of 10,000 random label permutation to provide a baseline measurement of intrinsic data separability.
Description
  • The data and the scripts are to show that seizure onset dynamics and evoked responses change over the progression of epileptogenesis defined in this intrahippocampal tetanus toxin rat model. All tests explored in this study can be repeated with the data and scripts included in this repository.

  • Dataset citation: Crisp, D.N., Cheung, W., Gliske, S.V., Lai, A., Freestone, D.R., Grayden, D.B., Cook, MJ., Stacey, W.C. (2019). Epileptogenesis modulates spontaneous and responsive brain state dynamics [Data set]. University of Michigan Deep Blue Data Repository.  https://doi.org/10.7302/r6vg-9658
Creator
Depositor
  • woodbr@umich.edu
Contact information
Discipline
Funding agency
  • Other Funding Agency
  • National Institutes of Health (NIH)
Other Funding agency
  • University of Melbourne

  • University of Michigan

  • NHMRC Project Grant (1065638)
Keyword
Citations to related material
  • Crisp, D. N., Cheung, W., Gliske, S. V., Lai, A., Freestone, D. R., Grayden, D. B., Cook, M. J., & Stacey, W. C. (2020). Quantifying epileptogenesis in rats with spontaneous and responsive brain state dynamics. Brain Communications, 2(1). https://doi.org/10.1093/braincomms/fcaa048
Resource type
Curation notes
  • On Mar. 5, 2020, A further revised version of data (REVISED_V2) was added after review and feedback by journal. Changes include a few new analyses, and minor alterations to 2 previous scripts. See 'Changelog for REVISED_V2_Epileptogenesis_Code_Repository.docx ' for details.

  • On July 25, 2019, revised code and documentation were added to record, including enhanced context, minor corrections, and organization. See file "Crisp_Epileptogenesis_ChangeLog_20190718.txt" for details.
Last modified
  • 08/28/2021
Published
  • 05/21/2019
Language
DOI
  • https://doi.org/10.7302/r6vg-9658
License
To Cite this Work:
Crisp, D. N., Cheung, W., Gliske, S. V., Lai, A., Freestone, D. R., Grayden, D. B., Cook, M. J., Stacey, W. C. (2019). Epileptogenesis modulates spontaneous and responsive brain state dynamics - Code & Data [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/r6vg-9658

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Files (Count: 5; Size: 4.42 GB)

Thumbnailthumbnail-column Title Original Upload Last Modified File Size Access Actions
EChangelog for REVISED_V2_Epilep....docx 2020-03-05 2020-03-05 15 KB Open Access
REVISED_V2_Epileptogenesis Code ...y.zip 2020-03-05 2020-03-05 2.59 GB Open Access
Crisp_Epileptogenesis_ChangeLog_...8.txt 2019-07-25 2019-07-25 1.4 KB Open Access
REVISED_Epileptogenesis_Code_Rep...y.zip 2019-07-25 2019-07-25 1.11 GB Open Access
Epileptogenesis_Code_Repository.zip 2019-05-14 2019-05-21 736 MB Open Access

Changes – 7/18/2019

Data Analysis > Evoked Response
1. Added 3 more data folders (‘Control 1’, ‘Control 2’, and ‘Control 3’)
2. This data is identical in structure and meaning to the rest of the data in this folder, with the exception that it is derived from sham control animals.
3. The README file in this folder was modified to reflect these additions.

Data Analysis > Code
1. Added “dataAnalysisDriver_EvokedResponse_Control.m”
a. Same as “dataAnalysisDriver_EvokedResponse.”, but with the following changes:
i. Specifically formatted for control data
ii. Only computes the features and plots it over time. This file does not contain statistical comparisons between seizure epochs, because the control data does not include seizures.
2. Added “EvokedResponses_TimeCorrelation_Con_VS_Exp.m”
a. This code is used to determine the differences in time dependency between experimental and control evoked response features.
3. Added “ResponseAnalyzer.m”
a. Illustrates two important concepts: (1) the data analysis process for evoked response features and (2) the progression of raw data to features over the course of the experiment in one animal.
4. Overhauled the README file to explain these added scripts as well as help users better orient themselves to the content of this folder.

Data Analysis
1. Updated the initial README to reflect the additions.

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