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Normally, commas are used to mark an appositive NP as supplementary, thus non-restrictive, and since John can only have one youngest brother of course, it's reasonable to treat "Jim" is a supplementary appositive. By contrast, integrated appositives are normally semantically restrictive. But they don't have to be. Your example could be written as “John's youngest brother Jim arrived at noon”. There's no implication that John has more than one youngest brother: the integrated construction simply provides a succinct way of saying that the person concerned arrived at noon and his name was Jim.