Let's say aloud you could control medical research funds... please read on?
Answers: I wouldn't target any one disease. Diseases aren't the central problem. There are countless possible microbes which can impose disease, and it doesn't make sense to develop vaccines and cures for respectively one.
Instead, I'd put all of the funds into researching a channel to greatly strengthen the human immune system. This might involve stem cell research, pharmaceuticals, or nanotechnology.
If i could only choose one disease to cure and not spread the research funding over several diseases, consequently i would definitely settle next to one. i'd pick cancer.
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