Texture analysis of poly-adenylated mRNA staining following global brain ischemia and reperfusion

Computer Methods and Programs in Biomedicine

Volumn 105, Issue 1, 2012, Pages 81-94

  Szymanski, Jeffrey J ^a   Jamison, Jill T ^a   DeGracia, Donald J ^a  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Brain ischemia and reperfusion; Cycloheximide; Fractal dimension; MRNA granules; Texture analysis

Indexed keywords

BRAIN ISCHEMIA; CEREBRAL ISCHEMIA; CYCLOHEXIMIDE; CYCLOHEXIMIDES; GRANULE FORMATIONS; MICROSCOPE IMAGES; MORPHOLOGICAL CHANGES; MRNA GRANULES; PROTEIN SYNTHESIS; PYRAMIDAL CELL; REGION CA3; REPERFUSION; TEXTURE ANALYSIS;

ANIMALS; BIOSYNTHESIS; CELL DEATH; FRACTAL DIMENSION; TEXTURES;

GRANULATION;

CYCLOHEXIMIDE; MESSENGER RNA; POLYADENYLATED RNA;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BRAIN ISCHEMIA; COMPUTER PROGRAM; CONTROLLED STUDY; CYTOPLASM; GRANULATION TISSUE; HIPPOCAMPUS; IMAGE ANALYSIS; MALE; MICROPHOTOGRAPHY; NONHUMAN; POLYADENYLATION; POLYSOME; PYRAMIDAL NERVE CELL; RAT; REPERFUSION INJURY; STAINING; TEXTURE ANALYSIS;

ANIMALS; BRAIN ISCHEMIA; CELL DEATH; MALE; POLY A; RATS; RATS, LONG-EVANS; REPERFUSION; RNA, MESSENGER; SOFTWARE; STAINING AND LABELING;

EID: 84855202774     PISSN: 01692607     EISSN: 18727565     Source Type: Journal    
DOI: 10.1016/j.cmpb.2011.03.005     Document Type: Article

References (43)

1. Abramoff M.D., Magelhaes P.J., Ram S.J. Image processing with ImageJ. Biophoton. Int. 2004, 11:36-42.
2. Chen W.S., Yuan S.Y., Hsieh C.H. Two algorithms to estimate fractal dimension of gray level images. Opt. Eng. 2003, 42:2452-2464.
3. Collewet G., Strzelecki M., Mariette F. Influence of MRI acquisition protocols and image intensity normalization methods on texture classification. J. Magn. Reson. Imaging 2004, 22:81-91.
4. Comanicu D., Meer P. Mean shift: a robust approach toward feature space analysis. IEEE Trans. Pattern Anal. Mach. Intell. 2002, 24:603-619.
5. De Vico G., Peretti V., Losa G.A. Fractal organization of feline oocyte cytoplasm. Eur. J. Histochem. 2005, 49:151-156.
6. DeGracia D.J., Hu B.R. Irreversible translation arrest in the reperfused brain. J. Cereb. Blood Flow Metab. 2007, 27:875-893.
7. DeGracia D.J., Jamison J.T., Szymanski J.R., Marshall M.K. Translation arrest and ribonomics in post-ischemic brain: layers and layers of players. J. Neurochem. 2008, 106:2288-2301.
8. Deshpande J., Bergstedt K., Lindén T., Kalimo H., Wieloch T. Ultrastructural changes in the hippocampal CA1 region following cerebral ischemia: evidence against programmed cell death. Exp. Brain Res. 1992, 88:91-105.
9. Dirnagl U., Macleod M.R. Stroke research at a road block: the streets from adversity should be paved with meta-analysis and good laboratory practice. Br. J. Pharmacol. 2009, 157(7):1154-1156.
10. Haralick R., Shanmugam K., Dinstein I. Textural features for image classification. IEEE Trans. Syst. Man Cybern. 1973, 3:610-621.
11. Haralick R. Statistical and structural approaches to texture. Proc. IEEE 1979, 67:786-804.
12. Harrison L.C., Luukkaala T., Pertovaara H., et al. Non-Hodgkin lymphoma response evaluation with MRI texture classification. J. Exp. Clin. Cancer Res. 2009, 28:87.
13. Hossmann K.A. Disturbances of cerebral protein synthesis and ischemic cell death. Prog. Brain Res. 1993, 96:167-177.
14. Hu B.R., Janelidze S., Ginsberg M.D., Busto R., et al. Protein aggregation after focal brain ischemia and reperfusion. J. Cereb. Blood Flow Metab. 2001, 21:865-875.
15. Hu B.R., Martone M.E., Jones Y.Z., Liu C.L. Protein aggregation after transient cerebral ischemia. J. Neurosci. 2000, 20:3191-3199.
16. Iftekharuddin K., Jia W., Marsh R. Fractal analysis of tumor in brain MR images. Mach. Vis. Appl. 2003, 13:352-362.
17. Jain A. Fundamentals of Digital Image Processing 1989, Prentice-Hall International, Englewood Cliffs.
18. Jamison J.T., Kayali F., Rudolph J., Marshall M.K., Kimball S.R., DeGracia D.J. Persistent redistribution of poly-adenylated mRNAs correlates with translation arrest and cell death following global brain ischemia and reperfusion. Neuroscience 2008, 154:504-520.
19. Kassner A., Thornhill R.E. Texture analysis: a review of neurologic MR imaging applications. Am. J. Neuroradiol. 2010, 31:809-816.
20. Kayali F., Montie H.L., Rafols J.A., DeGracia D.J. Prolonged translation arrest in reperfused hippocampal cornu Ammonis 1 is mediated by stress granules. Neuroscience 2005, 134:1223-1245.
21. Kedersha N., Anderson P. Mammalian stress granules and processing bodies. Methods Enzymol. 2007, 431:61-81.
22. Kedersha N., Cho M.R., Li W., et al. Dynamic shuttling of TIA-1 accompanies the recruitment of mRNA to mammalian stress granules. J. Cell Biol. 2000, 11151:1257-1268.
23. Kleihues P., Hossmann K. Protein synthesis in the cat brain after prolonged cerebral ischemia. Brain Res. 1971, 35:409-418.
24. Krzanowski W. Principles of Multivariable Data Analysis 1988, Oxford University Press.
25. Lerski R., Straughan K., Shad L., Boyce D., Bluml S., Zuna I. MR image texture analysis an approach to tissue characterization. Magn. Reson. Imaging 1993, 11:873-887.
26. Lipton P. Ischemic cell death in brain neurons. Physiol. Rev. 1999, 79:1431-1568.
27. Lopes R., Steinling M., Szurhaj W., Maouche S., Dubois P., Betrouni N. Fractal features for localization of temporal lobe epileptic foci using SPECT imaging. Comput. Biol. Med. 2010, 40:469-477.
28. Losa G.A., Castelli C. Nuclear patterns of human breast cancer cells during apoptosis: characterisation by fractal dimension and co-occurrence matrix statistics. Cell Tissue Res. 2005, 322:257-267.
29. Mallat S.G. Multifrequency channel decompositions of images and wavelet models. IEEE Trans. Acoust. Speech Signal Process. 1989, 37:2091-2110.
30. Mattson M.P., Furukawa K. Anti-apoptotic actions of cycloheximide: blockade of programmed cell death or induction of programmed cell life?. Apoptosis 1997, 2:257-264.
31. Mili S., Steitz J.A. Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. RNA 2004, 10:1692-1694.
32. Meer P., Stewart C.V., Tyler D.E. Robust computer vision: an interdisciplinary challenge. Comput. Vis. Image Underst. 2000, 78:1-7.
33. Papas S., Crépel V., Hasboun D., Jorquera I., Chinestra P., Ben-Ari Y. Cycloheximide reduces the effects of anoxic insult in vivo and in vitro. Eur. J. Neurosci. 1992, 4:758-765.
34. Pestka S. Inhibitors of ribosome functions. Annu. Rev. Microbiol. 1971, 25:487-562.
35. Press W., Teukolsky S., Vetterling W., Flannery B. Numerical Recipes in C 1996, Cambridge University Press.
36. Roberts G.G., Di Loreto M.J., Marshall M., Wang J., DeGracia D.J. Hippocampal cellular stress responses after global brain ischemia and reperfusion. Antioxid. Redox Signal. 2007, 9:2265-2275.
37. Schürman J. Pattern Classification 1996, John Wiley & Sons.
38. Smith M.L., Bendek G., Dahlgren N., Rosen I., Wieloch T., Siesjo B.K. Models for studying long-term recovery following forebrain ischemia in the rat 2. A 2-vessel occlusion model. Acta Neurol. Scand. 1984, 69:385-401.
39. Souquere S., Mollet S., Kress M., Dautry F., Pierron G., Weil D. Unraveling the ultrastructure of stress granules and associated P-bodies in human cells. J. Cell Sci. 2009, 122:3619-3626.
40. Swets D., Weng J. Using discriminant eigenfeatures for image retrieval. IEEE Trans. Pattern Anal. Mach. Intell. 1996, 18:831-836.
41. Szczypiński P.M., Strzelecki M., Materka A., Klepaczko A. MaZda - a software package for image texture analysis. Comput. Methods Programs Biomed. 2009, 94:66-76.
42. Tuceryan M., Jain A. Texture analysis. Handbook of Pattern Recognition and Computer Vision 1993, 235-276. World Scientific Press. C.H. Chen, L.F. Pau, P.S.P. Wang (Eds.).
43. Uppal S.O., Voronine D.V., Wendt E., Heckman C.A. Morphological fractal analysis of shape in cancer cells treated with combinations of microtubule-polymerizing and -depolymerizing agents. Microsc. Microanal. 2010, 16:472-477.