I have table of abbreviations at the end of the introduction section. Should explain an abbrevation if it was explained in that table, at other sections of the paper.
I answered a very similar question here, so I shan't repeat all of it. Briefly, however, I think that it worthwhile to repeat the meaning of abbreviations at the point of their first occurrence in each new chapter ... unless you are certain that the reader could not possibly misunderstand or have forgotten your intended meaning.
Theses are different from journal articles, and the approach to abbreviations should be adapted accordingly.