At least twice, the affidavit said, witnesses interviewed for the investigation warned both McAteer and the school that they were breaking the law. A consulting firm hired in 2008 also made similar warnings, the document said.
"We will slowly work on making this right, but we can't afford to do it at this time," McAteer is said to have told top university officials in response to the consulting firm's conclusion, according to the affidavit.
Documents the agent obtained indicate the school's board of directors deliberately circumvented federal spending rules "for the purpose of sustaining ... its general, non-federal program educational areas."
McAteer also is director of its National Technology Transfer Center and its Erma Ora Byrd Center for Education Technologies, which is named for the wife of the late longtime U.S. Sen. Robert C. Byrd.
The technology transfer center does work on mine safety and health, missile defense, health technology and small business partnerships. The Center for Educational Technologies has housed the NASA-sponsored "Classroom of the Future" program since 1990. The space agency began construction of the center in 1993 and later helped build the educational technologies center.
Between fiscal years 2000 and 2009, NASA gave Wheeling Jesuit more than $116 million, more than $65 million of that after McAteer took over the school's Sponsored Programs Office in 2005.
A finance manager in that office told the investigator that McAteer created the Combined Cost Management Service Center when he took over. Merging the billing of the two centers allowed him "to control and consolidate all the expenses, regardless of whether such expenses were related to the federal awards."
The affidavit calls the handling of federal dollars at Wheeling Jesuit "arbitrary and fraudulent," and cites a 2007 incident in which the Missile Defense Agency "expressed outrage" that McAteer and others weren't working on the agency's program but were still billing 6 percent of the center's expenses to the grant.
In 2008, an unidentified witness sent then-university president Julio Giulietti a letter outlining his concerns that McAteer wanted to charge 75 percent of his salary to the Sponsored Programs Office and 25 percent to the school.
"I cannot legally do this," the employee wrote in a letter marked personal and confidential that was included in the affidavit. "...These matters concern me professionally, ethically and legally."
In correspondence, McAteer denied doing anything wrong and called the employee's charges "absolutely false."
When Giulietti was fired in August 2009, McAteer replaced him as interim president and served until January 2011, when Richard Allen Beyer began work. The school's board never publicly said why Giulietti was let go.
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