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none of the android pdf readers can compare to the sony stock. you will have a lot of frustration trying to use anything else. the best feature of the stock sony reader in my opinion is the ability to highlight a word or sentence and have a little pad pop wherein draw/diagram/write your notes, as they'll be linked thru the software but not, for example, adobe acrobat or other desktop pdf readers.
if your scientific pdfs are not journal articles, but like huge textbooks style, as most of mine are. the sony reader's TOC is quite robust and functional.
think about getting an entourage edge, which is a hybrid tablet/reader, so you can use ezpdf and other android apps that embed annotations and notes in a more compatible form. if your lucky you can get it for around $70 on ebay.
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