Now, the Lis are booted from Emory, their laboratory shuttered, their tale an example of the rising scrutiny of ethnic Chinese scientists that has rattled campuses from coast to coast.

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The university fired them abruptly in May — 23 years after they arrived at the prestigious Emory School of Medicine in Atlanta. It charged that the professors failed to fully disclose foreign sources of research funding and the extent of their work for institutions and universities in China. Both scientists are naturalized U.S. citizens.

Xiao-Jiang Li, who held tenure at Emory as a distinguished professor of human genetics, disputes the university’s account. “I routinely disclosed my Chinese affiliations and Chinese funding in my publications,” he said recently in an email from China.

The couple’s departure underscores the roiling debate over how to preserve the culture of free academic exchange and international cooperation that is a hallmark of American universities, while preventing China and other nations from abusing that trust.

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In the research arena, federal officials in recent years have sounded alarms about violations of funding disclosure rules, breaches of confidential grant proposals and even outright espionage orchestrated by the Chinese government. NIH has sent letters about potential violations to more than 60 research institutions within the past year, according to Michael S. Lauer, NIH deputy director for extramural research, questioning the conduct of “well over 100” scientists.

The FBI and other federal agencies are working with universities to tighten enforcement of rules and laws.

Critics denounce the crackdown as ethnic profiling that will weaken science and stigmatize innocent researchers. Advocates call it a prudent response to an emerging threat.

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In April, FBI Director Christopher A. Wray said China is taking “a societal approach to stealing innovation in any way it can” from universities and other sources. “I do think that the academic sector needs to be much more sophisticated and thoughtful about how others may exploit the very open, collaborative research environment that we have in this country,” Wray told the Council on Foreign Relations in Washington.

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Warnings about malign foreign influence on college campuses come as President Trump has sparred with China over tariffs and trade and his administration has moved to limit visas for Chinese graduate students in certain research fields. Lawmakers on Capitol Hill have proposed bills to prevent academic espionage.

It is hard to overstate the importance of China for U.S. colleges and universities. China is by far the leading supplier of international students to the United States, with more than 130,000 graduate students and 148,000 undergraduates enrolled in 2017-2018. Those students bring vital tuition dollars into the U.S. system. China’s own universities are also rapidly developing research capacity that the United States cannot ignore. New York and Duke universities have opened outposts in China.

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Now, some academics in the United States worry about a repeat of the “Red Scare” over communist infiltration that Sen. Joseph R. McCarthy (R-Wis.) fomented in the 1950s.

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Yiguang Ju, a professor of mechanical and aerospace engineering at Princeton University, said he senses “increasing fear of a new McCarthyism” if conflicts with China intensify. Ju, 55, earned a bachelor’s degree in his native China and a doctorate in Japan before moving to the United States in 2001 and eventually becoming a naturalized U.S. citizen.

He spoke in late June at the China Institute, a cultural and educational organization in New York. The event was called “The New Normal: The perils of being a Chinese scientist in the U.S.”

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Ju said faculty have long abided by rules protecting intellectual property and controlling the export of sensitive technology. Now, many are frustrated, he said, at questions about foreign influence in academia. They want clear guidance. “This is the tough part: Where do you draw the line between foreign influence and academic exchange?” he asked.

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Ju, who receives federal funding for his research on combustion, energy and propulsion, said in a telephone interview that he routinely collaborates with peers from Germany, France, Ireland, Britain and elsewhere. Sometimes, Chinese scholars visit his lab. “People look at things from different angles,” he said. “It helps you think outside the box.”

NIH officials say the rules they are enforcing have long been clear: Scientists who seek federal funding must disclose professional affiliations and sources of financial support, and they must protect the confidentiality of grant proposals submitted for peer review. Those proposals provide a precious window into cutting-edge science.

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“To have faith in the system, the system has to run according to agreed-upon rules and norms of behavior,” said Lauer, who oversees more than $25 billion a year in NIH grants. “This is not new.”

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The rules are meant to uphold transparency, prevent the loss of intellectual property and ensure conflicts of interest do not taint research findings.

The FBI alerted NIH to potential rule violations in 2016, Lauer said. Many cases arose through information from the FBI or internal NIH reviews, he said, and others are based on tips from whistleblowers. Universities have also notified NIH of problems they have discovered on their own.

Not all of those identified as potential rule-breakers were of Chinese descent, Lauer said, but the majority were. “It’s not based on ethnicity,” he said. “It’s based on specific behavior.”

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The investigations have led to the ouster of the Lis and three scientists of Asian descent from the University of Texas MD Anderson Cancer Center, according to news reports. Lauer confirmed a June 26 report from the journal Science that universities have quietly fired others and refunded the government hundreds of thousands of dollars in grants. He declined to elaborate.

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The Lis, who declined to provide their ages, have been in the United States for decades and were part of a wave of Chinese immigrants who joined American faculties in the past 30 years. Xiao-Jiang Li and Shihua Li both earned medical degrees from Jiangxi Medical College in China in 1982, according to their résumés. Xiao-Jiang Li earned a doctorate in pharmacology in 1991 from a school then named Oregon Health Sciences University. He was on the faculty of Johns Hopkins University before joining Emory as an assistant professor in 1996. Shihua Li started at Emory that year as a senior research associate.

After settling in Georgia, the couple maintained ties to China. Xiao-Jiang Li notes on a résumé prepared for NIH that he was honored in 2010 as a professor in the “Thousand Talents” program, an initiative to attract top scientists to work in China. He also kept professional ties to Chinese institutions, including a recent appointment at Jinan University in Guangzhou.

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Thousand Talents has drawn fire in recent years. Critics call the program a ploy to help China achieve technological and scientific supremacy. NIH said the program is a “known prominent player.”

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Emory declined to make officials available to discuss why the Lis were terminated. Shihua Li declined to comment. Her husband said in an email that he has disclosed to Emory his time and the nature of his work in China every year since 2012. He said the couple’s NIH-funded projects had no overlap with his research in China.

“We were not charged with any crimes or accused of stealing technology, and were not contacted by FBI either,” Xiao-Jiang Li said.

An attorney for Xiao-Jiang Li, Peter R. Zeidenberg, said Li was fired before being given a chance to respond to evidence against him. “He was a tenured professor,” Zeidenberg said. “No due process.”

Emory replied in an email: “Dr. Li was provided an opportunity to respond. Under Emory policies, he has the opportunity to appeal the decision and he has done so.”

For Emory and other universities, the stakes in these investigations are high. They seek to ensure they will not lose access to government funding, but they do not want to alienate campus communities that value what foreigners and immigrants contribute.

“It is important to note that Emory remains committed to the free exchange of ideas and research and to our vital collaborations with researchers from around the world,” Emory said.

Denis Wirtz, vice provost for research at Johns Hopkins, lamented what he called a “palpable” level of anxiety among foreign-born scholars. Wirtz — himself a Belgian immigrant — said universities must reassure them that they are welcome, or else they will leave. “These people have options,” he said. Pushing them out would be “really shooting ourselves in the foot.”

The president of the Massachusetts Institute of Technology, L. Rafael Reif, said universities “must take great care not to create a toxic atmosphere of unfounded suspicion and fear.”

“Looking at cases across the nation, small numbers of researchers of Chinese background may indeed have acted in bad faith, but they are the exception and very far from the rule,” Reif said in a June 25 email to the university. “Yet faculty members, post-docs, research staff and students tell me that, in their dealings with government agencies, they now feel unfairly scrutinized, stigmatized and on edge — because of their Chinese ethnicity alone.”

Xiaoxing Xi, 61, a Temple University physicist who is Chinese American, says he knows well what it is like to be stigmatized. In 2015, FBI agents stormed his house and arrested him in front of his wife and daughters on an accusation that he had illicitly shared information about a superconductor device with colleagues in China. The government, which obtained evidence through intercepted emails, dropped the charges after Xi showed that what he had shared was public knowledge.

Xi is suing the government for damages for what he says was a violation of his constitutional rights that harmed his career. He is also speaking out about the dangers of a security crackdown.