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SAN FRANCISCO _ When voters overwhelmingly approved California's novel $3-billion stem cell initiative, they counted on a promise spelled out on the ballot: The state would earn back as much as $1.1 billion in royalties from scientific discoveries.

But those hypothetical profits are now looking increasingly dubious.

The California Institute for Regenerative Medicine last month proudly rolled out a groundbreaking plan to require universities and nonprofit research institutes that receive public grants to channel a 25% return back to the state on discoveries yielding more than $500,000 in revenues.

But in recent weeks, the University of Wisconsin foundation that claims broad patent rights to all embryonic stem cell lines in the U.S. has vowed to demand payments from California. That could spur a bitter court fight, even as pending litigation has so far kept the state from issuing the voter-approved bonds.

"Theoretically, could they close down research activity in California? Yes," said Ed Penhoet, vice chairman of the institute's oversight committee.

A spokesman for the Wisconsin Alumni Research Foundation said talks with the institute are continuing. "We feel there should...