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A Markovian Entropy Measure for the Analysis of Calcium Activity Time Series

Marken, John P. and Halleran, Andrew D. and Rahman, Atiqur and Odorizzi, Laura and LeFew, Michael C. and Golino, Caroline A. and Kemper, Peter and Saha, Margaret S. (2016) A Markovian Entropy Measure for the Analysis of Calcium Activity Time Series. PLOS ONE, 11 (12). Art. No. e0168342. ISSN 1932-6203. PMCID PMC5158058. https://resolver.caltech.edu/CaltechAUTHORS:20170126-160544721

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[img] Image (TIFF) (S1 Fig. Distributions of Markovian Entropy and other analysis measures of calcium activity from raw, non-detrended time series from Xenopus laevis neural progenitors) - Supplemental Material
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[img] Image (TIFF) (S2 Fig. Parameter choices do not qualitatively change the biological interpretation of our markovian entropy measure) - Supplemental Material
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[img] Image (TIFF) (S3 Fig. Separation between calcium activity distributions from two biologically distinct populations as a function of sample size) - Supplemental Material
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[img] Image (TIFF) (S4 Fig. The relationship between spike counts and Markovian Entropy in cells in the pH 7.2 condition of the synaptic neuron dataset) - Supplemental Material
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[img] Image (TIFF) (S5 Fig. The choice of amplitude threshold for spike counting algorithms can influence the qualitative interpretation of the analysis results) - Supplemental Material
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[img] MS Excel (S1 Table. Separation of Biologically Distinct Populations by Markovian Information Entropy, Average Power, and Hurst Exponent for raw, non-detrended Xenopus laevis time series) - Supplemental Material
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[img] MS Excel (S2 Table. Parameter choices do not qualitatively change the biological interpretation of our markovian entropy measure) - Supplemental Material
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[img] PDF (S1 File. Traces of every time series from Xenopus stage 14 dataset, baseline corrected) - Supplemental Material
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[img] PDF (S2 File. Traces of every time series from Xenopus stage 18 dataset, baseline corrected) - Supplemental Material
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[img] PDF (S3 File. Traces of every time series from Xenopus stage 22 dataset, baseline corrected) - Supplemental Material
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[img] PDF (S4 File. Traces of every time series from Xenopus stage 14 dataset) - Supplemental Material
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[img] PDF (S5 File. Traces of every time series from Xenopus stage 18 dataset) - Supplemental Material
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[img] PDF (S6 File. Traces of every time series from Xenopus stage 22 dataset) - Supplemental Material
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[img] PDF (S7 File. Traces of every time series from the Ruffault et al. dataset in the pH 7.2 condition) - Supplemental Material
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[img] PDF (S8 File. Traces of every time series from the Ruffault et al. dataset in the pH 7.4 condition) - Supplemental Material
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Abstract

Methods to analyze the dynamics of calcium activity often rely on visually distinguishable features in time series data such as spikes, waves, or oscillations. However, systems such as the developing nervous system display a complex, irregular type of calcium activity which makes the use of such methods less appropriate. Instead, for such systems there exists a class of methods (including information theoretic, power spectral, and fractal analysis approaches) which use more fundamental properties of the time series to analyze the observed calcium dynamics. We present a new analysis method in this class, the Markovian Entropy measure, which is an easily implementable calcium time series analysis method which represents the observed calcium activity as a realization of a Markov Process and describes its dynamics in terms of the level of predictability underlying the transitions between the states of the process. We applied our and other commonly used calcium analysis methods on a dataset from Xenopus laevis neural progenitors which displays irregular calcium activity and a dataset from murine synaptic neurons which displays activity time series that are well-described by visually-distinguishable features. We find that the Markovian Entropy measure is able to distinguish between biologically distinct populations in both datasets, and that it can separate biologically distinct populations to a greater extent than other methods in the dataset exhibiting irregular calcium activity. These results support the benefit of using the Markovian Entropy measure to analyze calcium dynamics, particularly for studies using time series data which do not exhibit easily distinguishable features.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://dx.doi.org/10.1371/journal.pone.0168342DOIArticle
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168342PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5158058/PubMed CentralArticle
Additional Information:© 2016 Marken et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: July 19, 2016; Accepted: November 29, 2016; Published: December 15, 2016. Data Availability: All relevant data are within the paper and its Supporting Information files or deposited at https://github.com/jpmarken/markovian-entropy-calcium. This study was supported by National Institutes of Health grants R15NS067566 and 1R15HD077624-01 to MS, National Science Foundation grant 1257895 to MS, Howard Hughes Medical Institute grant 52006919 to the College of William and Mary, Arnold and Mabel Beckman Foundation Beckman Scholar Award to AH. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Author Contributions: Conceptualization: MSS JPM ADH PK. Data curation: JPM ADH MCL CAG. Formal analysis: JPM ADH AR PK MCL CAG. Funding acquisition: MSS. Investigation: LO. Methodology: MSS PK JPM ADH AR. Project administration: MSS PK. Resources: MSS. Software: JPM ADH AR PK. Supervision: MSS PK. Validation: MSS JPM ADH. Visualization: CAG. Writing – original draft: JPM ADH. Writing – review & editing: JPM ADH PK MSS. The authors have declared that no competing interests exist.
Funders:
Funding AgencyGrant Number
NIHR15NS067566
NIH1R15HD077624-01
NSFIOS-1257895
Howard Hughes Medical Institute (HHMI)52006919
Arnold and Mabel Beckman FoundationUNSPECIFIED
Issue or Number:12
PubMed Central ID:PMC5158058
Record Number:CaltechAUTHORS:20170126-160544721
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170126-160544721
Official Citation:Marken JP, Halleran AD, Rahman A, Odorizzi L, LeFew MC, Golino CA, et al. (2016) A Markovian Entropy Measure for the Analysis of Calcium Activity Time Series. PLoS ONE 11(12): e0168342. doi:10.1371/journal.pone.0168342
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:73764
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:27 Jan 2017 15:45
Last Modified:03 Oct 2019 16:31

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