What is the process for sending updates to programs, i.e. manuscripts etc. Do you email PDs or PCs directly, or ask your med school admin to email them?
Also, is this a good idea?
No. In most cases it would not make a difference.
Not the op, but what if a paper was accepted at a high impact journal? Is that worth telling programs?
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As someone who reads these and interviews applicants:
I think that acceptances to higher impact journals (think multispecialty like Stroke, the JAMA imprints, PNAS, etc.) are worth letting programs know about. At our shop, after your portfolio is created, no one really looks at it until 10 minutes before you meet them for interviews, and I personally do gloss through the sea of Cureus and Surgical Neurology International case reports to try and find the higher quality papers. At the very least a good paper may spur a conversation that doesn't center around "why are you going into neurosurgery!?"
I personally would have the program coordinator be your go to person for all communications except in very specific circumstances. The PD is usually inundated with emails and sending him an update will result in the update never making into your file at best or be seen as an obnoxious cold-call at worst. A short, polite message along the lines of "here is a paper accepted for publication that I was hoping to get into my file" with the formatted reference will suffice.