Strained relations between Eli Lilly and its research partners caused the drug maker some setbacks this week.In one case, a federal jury found Lilly must pay at least $65 million in damages to Ariad Pharmaceuticals and several academic institutions over a patent dispute.The Boston jury said Lilly’s osteoporosis drug Evista and septic-shock drug Xigris infringe on technology controlled by Ariad, which exclusively licensed the technology from Massachusetts Institute of Technology, the Whitehead Institute for Biomedical Research and the president and fellows of Harvard College. Ariad and the institutions sued Lilly for patent infringement in 2002.Maintaining it discovered the drugs years before the plaintiffs made their discovery, Lilly said it will appeal.In addition to back royalties, the jury also awarded a 2.3% royalty on future US sales of Evista and Xigris until the patents expire in 2019.Evista had worldwide sales of $1.04 billion in 2005, while Xigris had sales of $214.6 million, Lilly said.In a case involving another Lilly osteoporosis drug, a federal judge in Indianapolis ordered the transfer of the international patent on a pill form of Forteo to Emisphere Technologies, Lilly’s erstwhile research partner.Lilly had applied for the patent in 2002, the same year an injectable form of Forteo came on the market.The drug maker plans to appeal the order, which could delay any transfer.