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With depression, the "why" is never easy to suss out, even when something is stated, is that really the reason?

Academia can be very toxic and PhD students are the most vulnerable as their Prof holds all the cards. This needs real checks and balances.

Getting a paper into nature and being a top-ranked school almost certainly says it was a high-pressure environment.

But there is certainly a process for handling advisor-advisee issues at a big school like Stanford:

I have a feeling that depression relies on many pillars of your mind breaking.