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While Calibre is great at converting different text ebooks, it has some problems with equations in my experience. Source format seems to work best with academical texts as far as I can tell, which inevitibly almost always boils down to PDF. A reader with PDF support is thus adviceable, and with reflow issues that generally also means getting a larger reader than 6" - I sometimes read journal articles on my 6" Sony Touch and aside from the few text-based articles this is no great joy with images and graphs appearing on different pages and equations appearing distorted or simply not parsed at all.
Using the original PDF's these issues mostly go away, only to make place for the new issue that to read a two-column PDF I am constantly zooming in and panning.
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