Thanks for your comment.

The PDF format will ignore some structures of paper and `draw` contents on a fixed-layout flat document. For a char, e-readers cannot know it belongs a paragraph, a figure caption or a formula. Plus, publishers render original paper with the specific style. It is a problem. Some research concentrate to improve PDF format, extract infos for scholarly papers, like articles on DocEng - a compute science conference: http://dl.acm.org/event.cfm?id=RE135. Then I read the spec of PDF format...

Anyway, that's hurt.