This invention provides systems, methods and compositions for the prevention of diseases caused by amyloid based deposits of proteins. This invention teaches procedures and therapeutic models for controlling amyloids and related plaque deposits as applicable to common diseases including, but not limited to: Alzheimer's, cardiovascular, stroke, arterial sclerosis, etc. By addressing plaque development at its earliest stage involving protein-protein interaction, ongoing plaque growth is arrested or substantially decreased while the balance of plaque deposition/management for expulsion of existing plaques is switched to favor the body's natural aberrant protein removal mechanisms. The preferred embodiment implements a dual approach for: a) attacking protein dimerization and oligomerization that serves as the cornerstone of the disease, and b) rebalancing the body's natural processes to enhance removal of existing plaques through inflammation management in concert with cessation of ongoing plaque formation. In normal disease progression, the body's adaptive mechanisms amplify inflammation that interferes with plaque expulsion and exacerbates the problem through reactive oxygen and pro-inflammatory chemokine release. This imbalance increases severity as the plaques continue to grow and proliferate. However, stopping new plaque deposits while concurrently supporting the natural destruction of existing plaques reverses the disease processes and immediately improves patient's conditions. The invention also provides procedures and/or kits for effective analysis to achieve earliest detection for maximum effect.