I tested whether a different encoding would fix it in version 0.16.7-3. Done did.
Here's how I tested all the available encodings:
$ for encoding in $(pdftotext -listenc | sed 1d) ; do pdftotext -enc
$encoding -layout -nopgbrk /tmp/pone.0009339.pdf - ; done | egrep
"Atractylodes japonica" | less
Thanks,
Kingsley
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