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The longest-ever federal shutdown may be over, putting a stop to financial bleeding for many research universities covering the costs of ongoing research, but colleges across the country aren't declaring victory.

The deal reached between congressional Democrats and the White House last week means at least a three-week reprieve from the shutdown. But it's not yet clear whether lawmakers will reach a new spending deal for agencies like the National Science Foundation or the National Aeronautics and Space Administration, or pass another continuing resolution.

And the impact of the standoff will likely linger for institutions that rely on federal support for their research enterprises.

"We're going to feel the effects of this shutdown for many months," said David Conover, vice president for research and innovation at the University of Oregon, at a meeting Monday of research vice presidents at the Association of Public and Land-grant Universities. “I worry mostly about our youngest faculty who are on the tenure track and their career depends in part on their ability to attract federal funding. When there's such a huge delay that is really going to last for months in terms of impact, it's really hard to put it into numbers.”

Officials from more than a dozen institutions visited Capitol Hill for meetings with lawmakers and their staffs. And the uncertainty over federal funding promised to be a top issue in those discussions.

The shutdown means reviews of new grant proposals at federal agencies are delayed for at least a month, and likely more. And it resulted in delayed selection for graduate research fellowships at NSF. That means careers of younger scientists are negatively affected, along with progress on potential research advances.

Sandra Brown, vice chancellor for research at University of California, San Diego, said the shutdown has taken a toll on the morale of graduate students and postdocs.

“This is part of the long-term impact for the U.S.,” said Brown, who chairs the APLU’s Council of Research.

For institutions themselves, the open-ended shutdown posed questions about how long they could fund research on their own. Universities typically put up their own money to pay for investigations and then invoice federal agencies. While the shutdown was ongoing, they burned through millions of their own funds to keep labs open.

The University of Virginia spent about $2.6 million over the past month to back research supported by NSF. The University of Maryland Baltimore County spent about $3 million.

The federal government should reimburse those funds now. But there would have been "truly great consequences" on those institutions' finances if the shutdown lasted another week, said Cynthia Sagers, vice president of research at Arizona State University, as the capacity of colleges to shoulder the cost of research enterprises without affecting other operations would be pushed to the limit.

And the uncertainty over funding has hampered long-term planning for scientific projects, top officials said. During the shutdown, resources that would have been used to recruit new graduate students were directed to those already pursuing work on campus, said Melur Ramasubramanian, vice president for research at the University of Virginia.

"Priorities have shifted to a short-term, immediate focus," he said.

Congressional lawmakers passed and sent to the president's desk spending bills for most federal agencies last year. But they didn't pass legislation to fund a quarter of agencies, including NSF, NASA and the U.S. Department of Agriculture before a December deadline -- largely because of a standoff over money for a border wall. Numbers negotiated at the end of last year would boost NSF spending by nearly 4 percent, to $8.075 billion. That's less than what APLU had recommended to Congress but much more than the $7.47 billion requested by the White House. Even if a deal is reached soon to resolve the border security fight, however, the stalemate will have long-term effects.

With the shutdown over, those top research leaders are counseling patience with academics on campus hoping to make contact with officials at agencies that back their work.

"Imagine how many people want to talk to each program officer," said Conover.

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