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How do you request explanation if are not sure what the speaker means by one specific word? I have noticed people barely say "What do you mean by ..." I assume it is not the appropriate way of asking the meaning of something. Is my assumption correct? If yes, what are the potential substitutions to it? Is "what are you referring to by ..." a good choice?

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Instead of asking

What do you mean by something?

similar to asking questions here on ELL, it might be better to ask

By something do you mean?
Does something mean your understanding? (which you tried to figure out from context)

the speaker will then have some frame of reference of your understanding in order to help you

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Using

What do you mean by ...

or

What are you referring to ...

are valid phrases, but they might be interpreted as negative or argumentative.

If the only problem is that you do not understand some word or phrase, my first choice would be to ask a friend or co-worker.

But if you need to ask directly, I would use a polite form:

I'm sorry, but I do not understand the word/phrase xxx. Would you please rephrase it for me?

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    Quite right. Whether this expression is perceived as the start of an argument or a simply inquiry depends much on the tone of the speaker's voice. – J.R. Feb 18 '16 at 10:20

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