Shifty was faced with his worst nightmare; he was back in the hands of scientists. He turned into his mind for solace; remembering a past that had changed his life for the better.
Because we know in the comics she's in and out of stasis for near 21 years only being let out for assignments/assassinations and experimental procedures. I am convinced they are talking about project: changeling
When melina talks about a project in conjuction with the winter soldier project and she mentions about a brain being dissected and reconstructed and I can't help but imagine how that was Yelizaveta