Advice for Funded Research Fellowship

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That's a great opportunity! Especially if you are interested in academics. Do you have a home ENT dept? I would definitely start there as they most certainly can provide advice and direction, if not help you set something up that piggybacks off someone's current research.
 
This is really a question for the faculty member you're working with. Coming up with an innovative research question to pursue as an MS3 is not going to happen without a good mentor. I would email some faculty members with labs or significant clinical research projects -- most would love to have a funded student working with them for the year.