That patent was filed in the US on 2004-10-21.
IANAL, but to me, that’s a point against that patent in the USA.
So if the paper was indeed published in Oct 2003 then all is well.
https://www.science.org/content/article/patent-first-publish...: “According to U.S. law, a patent cannot be obtained if an invention was previously known or used by other people in the U.S., or was already patented or published anywhere in the world. Furthermore, publicly using or selling an invention more than 1 year prior to filing a patent application completely bars you from ever winning a patent on that invention.
[…]
In Europe, for instance, there is no 1-year grace period--the chances of winning patent protection is lost the instant an invention becomes public”
Only if the paper was released between 2003-10-22 and 2003-12-31 would it meet the one year grace period requirement.
Looks like it’s not relevant in this case since they got a provisional patent in 2002, but that’s likely what the above was referring to as “a point against that patent”.
... in return for disclosing said innovation for use by others (in the patent) instead of keeping it secret. If the disclosure has already happened without the prospect of royalties (such as in a journal article), then the deal is off. But indeed various places have grace periods for that.