[bdowling]

First of all, a patent is presumed valid unless proven otherwise. (35 U.S.C. §282). However, this is challengable. In litigation, the patentee would argue that the invention at issue is a process and that, in the language of your citation, is one to "transform a particular article into a different state." Here the "article" in question is a "subject exhibiting symptoms..." who is transformed into the state of being a subject who has been treated.

The scope of the invention is stated by the claims, not what is disclosed in the specification. So, as you wrote, the "diet protocol" does have to be followed exactly, and all other other elements of the claim need to be present in order for there to be literal infringement of that claim.