Level detection in ion channel records via idealization by statistical filtering and likelihood optimization

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 352, Issue 1349, 1997, Pages 39-51

  Pastushenko, Vassili Ph ^a   Sghindler, Hansgeorg ^a  

^a JOHANNES KEPLER UNIVERSITY LINZ   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0031589852     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.1997.0004     Document Type: Article

References (45)

1. Abramowitz, M. & Stegun, I. A. 1965 Handbook of mathematical functions with formulas, graphs and mathematical tables. New York: Dover.
2. Becker, J. D., Honerkamp, J., Hirsch, J., Fröbe, U., Schlatter, E. & Greger, R. 1994 Analysing ion channels with hidden Markov models. Pflügers Arch. GES. Physiol. 426, 328-332.
3. Box, G. E. P., Jenkins, G. M. & Reinsel, G. C. 1994 Time series analysis. Forecasting and control. Englewood Cliffs, New Jersey: Prentice-Hall.
4. Chung, S. H. & Kennedy, R. A. 1991 Forward-backward non-linear filtering technique for extracting small biological signals from noise. J. neurosci. Methods 40, 71-86.
5. Chung, S. H. Moore J. B, Xia, L., Premkumar, L. S., & Gage, P. W. 1990 Characterization of single channel currents using digital processing techniques based on hidden Markov Models. Phil. Trans. R. Soc. Lond. B. 329, 265-285.
6. Colquhoun, D. 1987 Practical analysis of single channel records. In Microelectrode Techniques. The Plymouth Workshop Handbook (ed. N. B. Standen, P. T. Gra & M. J. Whitaker), pp. 83-104. Cambridge.
7. Colquhoun, D. & Hawkes, A. G. 1983 The principles of the stochastic interpretation of ion channel mechanism. In Single channel recording (ed. B. Sakmann & E. Neher), pp. 135-175. New York: Plenum Press.
8. Colquhoun, D. & Sigworth, F. J. 1983 Fitting and statistical analysis of single channel records. In Single channel recording (ed. B. Sakmann & E. Neher), pp. 191-263. New York: Plenum Press.
9. Dempster, A. P., Laird, N. M. & Rubin, D. B. 1977 Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. B. 39, 1-38.
10. Fox, J. A. 1987 Ion channel subconductancc states. J. Membrane Biol. 97, 1-8.
11. Fredkin, D. R. & Rice, J. A. 1992a Maximum likelihood estimation and identification directly from single-channel recordings. Proc. R. Soc. Lond. B. 249, 125-132.
12. Fredkin, D. R. & Rice, J. A. 1992b Bayesian restoration of single-channel patch clamp recordings. Biometrics 48, 427-448.
13. French, R. J. & Wonderlin, W. F. 1992 Software for acquisition and analysis of ion channel data: choices, tasks, and strategies. In Methods in enzymology. Ion channels vol. 207 (ed. B. Rudy & L. E. Iverson), pp. 711-728. Academic Press, Inc.
14. Hafner, R. 1989 Wahrscheinlichkeitsrechnung und Statistik, Wien. New York: Springer-Verlag.
15. Heinemann, S. H. 1995 Guide to data acquisition and analysis. In Single channel recording, 2nd edn (eds. B. Sakmann & E. Neher), pp. 53-91. New York, London: Plenum Press.
16. Heinemann, S. H. & Sigworth, F. J. 1991 Open channel noise. Analysis of amplitude histograms to determine rapid kinetic parameters. Biophys. J. 60, 577-587.
17. Heinhold, J. & Gaede, H. 1968 Ingeneur-statistik. München, Wien: R. Oldenbourg.
18. Horn, R. 1987 Statistical methods for model discrimination: application to gating kinetics and permeation of acetyl-choline receptor channel. Biophys. J. 51, 255-263.
19. Horn R. & Lange, K. 1983 Estimating kinetic constants from single channel data. Biophys. J. 43, 207-223.
20. Jackson, M. B. 1992 Stationary single-channel analysis. In Methods in enzymology. Ion channels vol. 207 (ed. B. Rudy & L. E. Iverson), pp. 729-746. Academic Press.
21. Kirlin, R. L. & Moghaddamjoo, A. 1986 A robust-window detector and estimator for step-signals in contaminated gaussian noise. IEEE Trans. Acoustic, Speech, Signal Processing. 34, 816-823.
22. Korn, S. J. & Horn, R. 1988 Statistical discrimination of fractal and markov models of single-channel gating. Biophys. J. 54, 871-877.
23. Magleby, K. L. 1992 Preventing artifacts and reducing errors in single-channel analysis. In Methods in Enzymology. Ion channels, vol. 207 (ed. B. Rudy & L. E. Iverson), pp. 763-791. Academic Press
24. Magleby, K. L. & Weiss, D. S. 1990a Estimating kinetic parameters for single channels with simulation. Biophys. J. 58, 1411-1426.
25. Magleby, K. L. & Weiss, D. S. 1990b Identifying kinetic gating mechanisms by using two-dimensional distributions of simulated dwell times. Proc. R. Soc. Lond. B. 241, 220-228.
26. Moghaddamjoo, A. 1988 Step-like signal processing with distinct finite number of levels. IEEE Trans. Indust. Electron. 35, 489-493.
27. Moghaddamjoo, A. 1989 Constraint optimum well-log signal segmentation. IEEE Trans. Geosci. Remote Sensing 27, 633-641.
28. Moghaddamjoo, A. 1991 Automatic segmentation and classification of ionic-channel signals. IEEE Trans. Biomed. Eng. 38, 149-155.
29. Oppenheim, A. V. & Schaefer, R. W. 1975 Digital signal processing. Englewood Cliffs, New Jersey: Prentice Hall.
30. Pastushenko, V. Ph. & Schindler, H. 1993 Statistical filtering of the single ion channel records. Acta Pharm. 43, 7-13.
31. Pastushenko, V. Ph. & Schindler, H. 1994 Idealization of ion channel records by Student's t-test filtering with subsequent optimization of level distribution likelihood. Biophys. J. 66, A440.
32. Pastushenko, V. Ph. & Schindler, H. 1995 Epoch oriented likelihood maximization of an idealized ion channel record. Biophys. J. 68, A148.
33. Pastushenko, V. Ph., Schindler, H. & Reza, A. M. 1997 Predictive optimality criterion for idealization of ion channel data and exact akaike's criterion. Eur. Biophys. J. (Submitted.)
34. Pastushenko, V. Ph., Schindler, H., Waldl, H. & Hafner, R. 1996 A new statistical test for analysis of patch-clamp data. Biophys. J. 70, A200.
35. Patlak, J. B. 1988 Sodium channel subconductance events measured with a new Variance-Mean Analysis. Biophys. J. 54, 413-430.
36. Petracchi, D., Barbi, M., Pellegrini, M., Pellegrino, M. & Simoni, A. 1991 Use of conditional distributions in the analysis of ion channel recordings. Eur. Biophys. J. 20, 31-39.
37. Qin, F., Auerbach, A. & Sachs, F. 1996 Estimating single-channel kinetic parameters from idealized patch-clamp data containing missed events. Biophys. J. 70, 264-280.
38. Rabiner, L. R. 1989 A tutorial on hidden markov models and selected applications in speech recognition. Proc. IEEE. 77, 257-285.
39. Sachs, F. 1983 Automated analysis of single-channel records. In Single channel recording (ed. B. Sakmann & E. Neher), pp. 265-285. New York: Plenum Press.
40. Schindler, H. & Pastushenko V. Ph. 1992 Statistical filtering of ion channel data. Biophys J. 61, 1-248
41. Schultze, R. & Draber, S. 1993 A nonlinear filter algorithm for the detection of jumps in patch-clamp data. J. Membrane Biol. 132, 41-52.
42. Sigworth, F. J. 1983 An example of analysis. In Single channel recording (ed. B. Sakmann & E. Neher), pp. 301-321. New York: Plenum Press.
43. Terrien, C. W. 1992 Discrete random signals and statistical signal processing. Englewood Cliffs: Prentice Hall.
44. Tyerman, S. D., Terry, B. R. & Findlay, G. P. 1992 Multiple conductances in the large K channel from Chara corallina shown by a transient analysis method. Biophys. J. 61, 736-749.
45. VanDongen, A. M. J. 1996 A new algorithm for idealizing single ion channel data containing multiple unknown conductance levels. Biophys. J. 70, 1303-1315.