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Starfleet R & D was a special branch present within Starfleet. Commander Elizabeth Shelby was part of the initiative working to develop new anti-Borg technology, which included special interfaces that could link with the Borg Collective. Defiant class vessels were one of the developments of the R & D's initiative.
After the publication of The Genesis Report in 2286, recommendations were made for further secret research to be conducted by Starfleet's Research and Development division. (TNG novel: The Genesis Wave, Book One)
In 2369, a team from Starfleet Research and Development joined similar teams from Starfleet Intelligence and the Starfleet Corps of Engineers in boarding Deep Space 9 after the Cardassians had left the space station. (DS9 reference: Star Trek: Deep Space Nine Technical Manual)
Later in 2382 on Stardate 60334.46, Admiral Owen Paris of Starfleet Research and Development gave orders for the Mobile emitter to be confiscated and taken to the Starfleet facility on Galor IV for study. (ST website: The Path to 2409)