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In 2151, Dr. Phlox failed to run a submolecular scan on Ethan Novakovich and thus did not detect the stray neutron present in tropolisine atoms which released an undetectable toxin into Novakovich’s bloodstream. (ENT: "Strange New World")
Submolecular scans were also a finishing step in the refinement of kemocite. While performing such a scan, Gralik Durr was challenged by other Xindi about the need for what he was doing. He claimed that he did not allow kemocite to leave his facility unless it was "perfectly calibrated", suggesting that the scan, at least as used in his field, was a quality control check. (ENT: "The Shipment")