Years of investigations and a lengthy trial failed to win any convictions against Sami Al-Arian, the professor who was fired by the University of South Florida in 2003 after he was indicted on charges of helping terrorist groups. Last month, a federal jury in Florida cleared him of some charges and deadlocked on others.

While the evidence in the trial failed to convince jurors of Al-Arian's guilt, it is now being used by a pro-Israel group in a campaign against Brandeis University for hiring a Palestinian scholar who was a participant in phone calls that were taped as part of the investigation into Al-Arian and his associates. The campaign against a university founded by Jewish leaders is the latest sign of how contentious it can be these days to work in Middle Eastern studies.

Khalil Shikaki, the scholar who is being accused by critics of links to terrorist groups, has never been charged with anything and is known as a moderate. He did not return messages Thursday, but Brandeis officials and others say that there is no credible evidence linking him to terrorism and that he is a respected scholar being unfairly tarnished.

Shikaki is director of the Palestinian Center for Policy and Survey Research and much of his research is based on his polling of Palestinians. Unlike some Palestinian scholars, Shikaki has ties to Israeli institutions as well, and Brandeis officials noted that he recently helped a fund raising effort for Hebrew University in Jerusalem.

The article in The New York Sun that publicized Shikaki's bit part in the Al-Arian trial noted that he was heard in a wiretapped conversation with Sameeh Hammoudeh, an associate of Al-Arian's who was on trial with him and who was acquitted on all counts. In the conversation, Hammoudeh tells Shikaki: "If you please, do us a favor. There is an amount of money for orphans in Nablus." The U.S. government argued that "orphans" was code for the Palestinian Islamic Jihad.

Linda Moreno, one of Al-Arian's lawyers, called the government theory "nonsense," and she noted that the jury acquitted Hammoudeh on all charges -- and might not have done so had its members believed that "orphans" referred to terrorists. Al-Arian and his co-defendants argued that they were being tried for making statements that criticized the U.S. and Israeli governments or for providing funds to legitimate nonprofit groups.

"The money went to charity. Period. The money didn't go to terrorism or terrorists," Moreno said.

She called the attempts to like Shikaki to terrorism "rather desperate." Moreno said that the phone call transcript was never used to charge Shikaki with any crime, and that the person it was used against was vindicated in court.

The Zionist Organization of America, however, based on The New York Sun article, is calling for Brandeis to "act" against Shikaki or face a boycott.

"We urge Jewish donors and indeed all supporters of Brandeis to make their deep concern and shock at these revelations linking a Brandeis faculty member with foreign terrorists known to the University authorities and we also urge them to rethink their support for Brandeis if the University fails to address their concerns in a timely and appropriate manner, said Morton A. Klein, in a statement released by the association. "We particularly urge parents who are considering appropriate colleges for their children's studies to also consider directing them elsewhere if Brandeis does not address this serious issue."

Both the Sun article and the Zionist association statement noted that a Brandeis student was killed in Israel in 1995 by terrorists affiliated with Palestinian Islamic Jihad. But supporters of Shikaki said that is irrelevant since he never helped that group.

Jehuda Reinharz, president of Brandeis, said through a spokesman that there was no reason for him to take any action against Shikaki. "We live in a country where people are presumed innocent until proven guilty," he said. "If someone has real evidence, let them bring it forward. The university has full faith in law enforcement in America. In the future, if something arises we will act accordingly, but at this moment there is absolutely no evidence of any offenses."

Shikaki has been a popular teacher at Brandeis. An article in The Justice, the student newspaper there, noted that he taught a class last semester together with scholars from Israel and Egypt and quoted one student as calling the course "fantastic."

Zachary Lockman, who teaches modern Middle Eastern history at New York University, said he does not know Shikaki, but that the campaign against Brandeis is part of something larger.

"I think there is definitely an assault under way against scholars of the Middle East and of Islam. it is organized in the sense that there are a number of groups and Web sites that have targeted various individuals and have sought to pressure the institutions where they work to silence them," Lockman said.

Lockman said that NYU's administration has supported the academic freedom of scholars of the Middle East. But Lockman, who is Jewish, said that the campaigns against scholars who, like he does, sometimes criticize U.S. and Israeli policies, seem particularly strong at institutions with large Jewish donor bases. (Brandeis is nonsectarian, but was founded by Jewish leaders and has always relied on Jewish philanthropists for support.)

These critical groups, Lockman said, make false accusations. He said that he was once accused of supporting a boycott of Israeli colleges -- something he said he would never do. "People will find ammunition if they want to," he said.

Universities need to respond forcefully when these events take place, he said. "Scholars and academic leaders need to make it clear that they will defend the principle of academic freedom," he said. "Universities are one of the few places where you can have a full and open discussion of these issues. If we allow these kinds of attacks to close down that space for free discussion, we'll be in worse shape."