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That may not be a good example, since when you try to copy
text from that PDF, within Acrobat, the text gets selected
across columns.

However I found another PDF file
(www.louisville.edu/speed/bioengineering/
ieee-embs-mmb/Smpl_Mnuscrpt_EMBS.pdf) where, when you copy
the text in Acrobat, it is possible to select a single
column, but when I use pdftohtml, the lines from the two
columns are intermixed.

I am not sure how the two files differ internally, but if
you could fix this it would be a great help. Thanks for the
good work.