PDFTOHTML is a very good Opensource tool for converting PDF files to HTML so it can then be parsed with other tools. It can be found here: http://pdftohtml.sourceforge.net/
A problem that you will find is processing some if not all double column articles. The specific problem that I am solving is automatically converting the PDF to a text file and I need to have access to the code to connect it to the rest of the application. I am currently programming my own since I gave up on alternatives. PDF TOTEXT will solve all other single column documents.
If you have specific portion of text to extract you can try to use pdftableconverter.com or its downloadable version online.
If you are looking for a PDF parser you may want to take a look at the datalogics libraries
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