Thesis includes three chapters that are amended versions of published manuscripts. The appendix includes the three published manuscripts. All are permitted as the publisher is Elsevier. Elsevier has a policy of allowing published articles to remain in theses.  https://www.elsevier.com/about/policies/copyright/permissions (click on Can I include/use my article in my thesis/dissertation)
All the chapters are amended versions this thesis has not been treated as a thesis by publication.
LM 05/02/20