Abstract
Hidden Markov models have been used to restore recorded signals of single ion channels buried in background noise. Parameter estimation and signal restoration are usually carried out through likelihood maximization by using variants of the Baum-Welch forward-backward procedures. This paper presents an alternative approach for dealing with this inferential task. The inferences are made by using a combination of the framework provided by Bayesian statistics and numerical methods based on Markov chain Monte Carlo stochastic simulation. The reliability of this approach is tested by using synthetic signals of known characteristics. The expectations of the model parameters estimated here are close to those calculated using the Baum-Welch algorithm, but the present methods also yield estimates of their errors. Comparisons of the results of the Bayesian Markov Chain Monte Carlo approach with those obtained by filtering and thresholding demonstrate clearly the superiority of the new methods.
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Selected References
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- Ball F. G., Rice J. A. Stochastic models for ion channels: introduction and bibliography. Math Biosci. 1992 Dec;112(2):189–206. doi: 10.1016/0025-5564(92)90023-p. [DOI] [PubMed] [Google Scholar]
- Ball F. G., Sansom M. S. Ion-channel gating mechanisms: model identification and parameter estimation from single channel recordings. Proc R Soc Lond B Biol Sci. 1989 May 22;236(1285):385–416. doi: 10.1098/rspb.1989.0029. [DOI] [PubMed] [Google Scholar]
- Chung S. H., Moore J. B., Xia L. G., Premkumar L. S., Gage P. W. Characterization of single channel currents using digital signal processing techniques based on Hidden Markov Models. Philos Trans R Soc Lond B Biol Sci. 1990 Sep 29;329(1254):265–285. doi: 10.1098/rstb.1990.0170. [DOI] [PubMed] [Google Scholar]
- Colquhoun D., Hawkes A. G. On the stochastic properties of bursts of single ion channel openings and of clusters of bursts. Philos Trans R Soc Lond B Biol Sci. 1982 Dec 24;300(1098):1–59. doi: 10.1098/rstb.1982.0156. [DOI] [PubMed] [Google Scholar]
- Fredkin D. R., Rice J. A. Bayesian restoration of single-channel patch clamp recordings. Biometrics. 1992 Jun;48(2):427–448. [PubMed] [Google Scholar]
- Fredkin D. R., Rice J. A. Maximum likelihood estimation and identification directly from single-channel recordings. Proc Biol Sci. 1992 Aug 22;249(1325):125–132. doi: 10.1098/rspb.1992.0094. [DOI] [PubMed] [Google Scholar]
- Kienker P. Equivalence of aggregated Markov models of ion-channel gating. Proc R Soc Lond B Biol Sci. 1989 Apr 22;236(1284):269–309. doi: 10.1098/rspb.1989.0024. [DOI] [PubMed] [Google Scholar]
- Magleby K. L., Song L. Dependency plots suggest the kinetic structure of ion channels. Proc Biol Sci. 1992 Aug 22;249(1325):133–142. doi: 10.1098/rspb.1992.0095. [DOI] [PubMed] [Google Scholar]
- doi: 10.1098/rspb.1999.0867. [DOI] [PMC free article] [Google Scholar]
- Stark J. A., Hladky S. B. Adjustments for the display of quantized ion channel dwell times in histograms with logarithmic bins. Biophys J. 2000 Feb;78(2):662–667. doi: 10.1016/S0006-3495(00)76624-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zimmer B. D., Bickel P., Dittrich A. Changes of simple somatic parameters by delta-9-trans-tetrahydrocannabinol (delta-9-THC) in a double-blind-study. Short communication. Arzneimittelforschung. 1976;26(8):1614–1616. [PubMed] [Google Scholar]