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There was a relevant question asked on Slashdot today - someone asked for an e-ink-reader for academic papers. The OP is asking specifically about PDF's on a Kindle, but in the comments of the Slashdot discussion I found someone who posted about a utility they wrote that could help in this situation.

I wrote a small script that takes research papers and splits them up if they have two columns. It tries to figure out when you have figures, and to strip away the header/footer etc. It produces epubs (which you can convert with Calibre)
github.com/JohannesBuchner/research2epub
The pages are first converted to images, the white spaces figured out, and the page sliced and diced. The linearized content is a sequence of page number, and rectangle definitions. You could make those into a pdf again, but I just stick to images and html (epub).

DISCLAIMER: Although I plan to use it myself, I haven't yet.


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