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Suppose one files a provisional that describes methods A and B, then publishes a paper describing methods A and B, then files a non-provisional that claims the benefit of the provisional and describes method A only, then more than a year after publishing the paper files a continuation of the non-provisional that describes method B and makes a claim related to method B. Does the paper count as prior art against the continuation?

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You can chain back through the first non-povisional to get benefit of the provisional. But you do need to specify the chain of applications in the new application. The USPTO has a summary of the rules for this here.

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