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NEW YORK – A reputed al-Qaida operative who was recently captured in Libya made his first public appearance Tuesday in a packed courtroom in Manhattan, seeming far more dour and haggard than defiant.

The suspect, Nazih Abdul-Hamed al-Ruqai, wearing sweat pants and a dark shirt, was advised of his rights by U.S. District Court Judge Lewis A. Kaplan.

David E. Patton, a federal public defender, entered a not-guilty plea on his behalf.

Al-Ruqai, speaking through an Arabic interpreter, responded briefly to the judge’s questions, indicating that he understood his rights. A Quran belonging to al-Ruqai was on the table in front of him.

A federal prosecutor, Nicholas J. Lewin, told the judge that al-Ruqai “presents a clear danger to the community” and is a flight risk. The judge ordered al-Ruqai detained pending trial.

Al-Ruqai was indicted here in 2000 on conspiracy charges stemming from al-Qaida’s 1998 bombings of two U.S. Embassies in East Africa, which killed 224 people. He had been a fugitive for years, and was seen as potentially possessing a wealth of intelligence information about al-Qaida, from its earliest days to the present.

Al-Ruqai, who is known as Abu Anas al-Libi, was captured by U.S. commandos in Tripoli, Libya, on Oct. 5. He spent a week in military custody aboard a Navy ship in the Mediterranean, where he was interrogated without a lawyer. Saturday, al-Ruqai was transferred abruptly into the criminal-justice system after his chronic health problems worsened aboard the ship, where he had stopped eating and drinking, officials have said.

While Patton represented al-Ruqai at the proceeding in Manhattan, a new lawyer is expected to be appointed because the Public Defender’s Office had represented another defendant in the same indictment years ago. Last week, Patton asked the judge to appoint counsel for al-Ruqai while he was in military detention, but the request was denied.

“We are pleased that the government has now brought him into federal court and appointed him an attorney,” Patton said after the proceeding. “We continue to believe that the government should have done so earlier in accordance with federal law.”

“The presumption of innocence is not a small technicality here,” he added.

Patton said al-Ruqai was mentioned only briefly in a 150-page indictment, relating to conduct in 1993 and 1994. He also said that there were no allegations in the charges “that he had any connection to al-Qaida after 1994, and he is eager to move forward with the legal process in this case.”

Preet Bharara, the U.S. attorney in Manhattan, watched the proceeding with other senior prosecutors; his office declined to comment.