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My question involves the usage of "that is." I would like to use this construction in such a way that it will provide further qualification to the previous passage or sentence.

An example might be something like this:

"However, it is far less clear whether the fluent processing of a word will have the opposite effect, that is, will the reaction time to a given stimulus show a decreased latency."

What would be correct usage of punctuation, semi-colon, questions marks etc...? Or perhaps does this type of construction not even make much sense?

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Welcome to ELU. I think you've got a typo -- shouldn't that be something like "it is far less likely that"? – StoneyB Jun 13 '13 at 11:25
Your first paragraph is correct regarding one usage of that is, but I don't understand what you example is trying to say. 1) I assume that that should be than that? 2) what do you mean by the fluent processing of a word? 3) opposite effect from what? 4) I don't understand the relationship between reaction time to a given stimulus show[ing] a decreased latency and fluent processing of a word, especially as the former is phrased as a question and the latter as a statement. Please clarify. – TrevorD Jun 13 '13 at 11:28
Thanks for the notes, 1) I've clarified the sentence, I hope. 2) This would be clear from the preceding passage, but in summary it means that the word is processed (ie. understood) quickly. 3) Again, this would be clear from the previous sentence which demonstrates that disfluent processing shows increased latencies. I probably should a simpler sentence for this example. – skleene Jun 13 '13 at 11:48

It is acceptable to employ a comma before that is; but I would prefer a stronger disjunction, either a colon or a dash, simply to make the structure of this long sentence clearer. A comma after that is is conventional.

You do need to restructure the clause following that is as an indicative rather than an interrogative: that is, as "the reaction time to a given stimulus will show a decreased latency."

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Another +1. (I'm just going through some of the questions in the 'Unanswered' list, which I gather actually means "No answers with a positive vote"!) – TrevorD Jul 10 '13 at 13:35

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