I am sending in an article to a ScholarOne journal: should I mark my prefix Dr. or Mr./Ms. if I have an M.D. but not a Ph.D.?
First, note that the title that you give to a ScholarOne manuscript handling system probably doesn't matter at all --- more than anything else, that is in there to avoid offending you if you are particular about being given your title. The actual publication of the paper will typically omit titles, so putting in the title just regulates what the system will call you in email.
That said, Dr. is a correct title to use as an M.D. In fact, many people will argue that opposite, that it is Ph.D.-holders whose use of the title is dubious!
I don't always use the prefix, as it has no relevance when I'm, for example, out drinking with friends. But I do sometimes use Dr. with my name, for several reasons. Sometimes it is just fun. Women actually like to call me Dr. Hurst (I could never get a single one to call me Master after I got my MPA). It is just a sign of respect. But sometimes if I am discussing an issue dealing with economics, my Ph.D. field, I will add Dr. to ward off trolls who think they know all about economics and want to educate me about how I'm wrong.
It also made a difference in my work. On one job, my company bought out a competitor and absorbed some of their workers. One supervisor in the modeling department where I worked used to insist that his methodologies were superior to others we were using, which was not true. In order to push his models, he always had to point out that the top modeler on his team had a Ph.D. I kept my mouth shut for a while, until one day in a meeting he made a big issue of it, and my boss said "Well, I have a Ph.D. on my team also, Dr. Hurst." That guy was really embarrassed and shut up and never brought it up again.