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Does any one have advice for crafting this update?
Include the pertinents (citation, PMID, or acceptance email), and keep it short and sweet. As a general rule of thumb, write what you would want to read if you were busy and needed to go through a trove of these letters
 
So I attach the acceptance letter to the email? Or put it below my text if I’m uploading a letter to the portal? What should I title the document: accepted publication to journal or should I refer to it as a manuscript?
Sounds like you're overthinking it. Just title your document however you need to, write a short and sweet update letter saying "I'd like to update my application with an acceptance of my manuscript to journal XYZ", a one liner about your interest in the school, a thank you, and bam you're done. Or better yet, just wait until the paper is done being edited by the editors then send the update letter when you have a citation. Acceptance to publication doesn't take that long.
 
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