WASHINGTON, Aug 3: Five years after her mysterious disappearance in Karachi, the FBI has finally conceded that an MIT-trained Pakistani neuroscientist is alive and is in US custody in Afghanistan.

Aafia Siddiqui, 36, disappeared with her three children while visiting her parents’ home in Karachi in March 2003, around the same time the FBI announced that it wanted to question her over her alleged links to Al Qaeda.

Her family’s lawyer Elaine Whitfield Sharp said she believed recent media reports about Mrs Siddiqui’s incarceration increased pressure on the US and Pakistani authorities to divulge more information.

“I don’t believe that they just found Aafia,” she said. “I believe that she was there all along.”

The fate of her three young, American-born children is still unknown.

Before her disappearance, Mrs Siddiqui lived in a Boston suburb of Roxbury and studied at Brandeis University as well as the Massachusetts Institute of Technology.

In a 2006 report, Amnesty International listed Mrs Siddiqui as among a number of “disappeared” suspects in the war on terrorism. On July 6, 2007, AI listed Mrs Siddiqui as a possible CIA “secret detainee”, although she was still on the FBI’s Seeking Information - Terrorism list. Late last week, Mrs Siddiqui’s photo still appeared on the FBI’s list of people wanted for questioning.

Since no charges were ever filed against her, human rights groups treated her case as that of “extrajudicial detention”, although no government ever claimed detaining her.

Even the FBI does not mention any charges in the notice seeking information about her. “Although the FBI has no information indicating this individual is connected to specific terrorist activities, the FBI would like to locate and question this individual,” says the notice.

The “gray lady of Bagram”: On July 7, a British journalist Yvonne Ridley told a news conference in Islamabad that a Pakistani woman had been held in solitary confinement for years at the Bagram US base near Kabul. The identity of this prisoner remains unconfirmed. She has been nicknamed the “gray lady of Bagram”. Ms Ridley, however, speculated that she was Aafia Siddiqui.

Moazzam Begg and several other former captives also have reported that a female prisoner, prisoner 650, was held in Bagram. The former captives claim that she has lost her sanity and cries all the time.

Although it is still not clear if the “gray lady of Bagram” is Aafia Siddiqui, her family’s attorney told reporters on Friday that the FBI had finally conceded that Mrs Siddiqui is in US custody.

“It has been confirmed by the FBI that Aafia Siddiqui is alive,” said Ms Sharp, who said she spoke to an FBI official on Thursday.

“She is injured but alive, and she is in Afghanistan.”

For five years, US and Pakistani authorities denied knowing her whereabouts. But human rights groups and Mrs Siddiqui’s relatives had long suspected that she had been captured in Karachi and secretly taken into custody.

On Thursday, an FBI official visited Mrs Siddiqui’s brother in Houston to deliver the news that she was alive and in custody, Ms Sharp said.

FBI officials, however, would not say who was holding her or reveal the fate of her children.

“If she’s in US custody, they want to know where she is,” Ms Sharp said. “Who has got her? And does she need medical care?”

The FBI and the Justice Department declined to comment.

US military documents declassified in recent years suggest that Mrs Siddiqui is suspected of having ties to several key terrorism suspects being held at the Guantanamo Bay detention centre.

She is believed to have links to Khalid Sheikh Mohammed, alleged mastermind of the Sept. 11, 2001, terrorist attacks, and allegedly arranged travel documents for another suspected terrorist.

Papers in Guantanamo Bay also indicate that she married Ali Abd Al Aziz Ali, an alleged Al Qaeda facilitator who intended to blow up petrol stations or poison water reservoirs in the United States.

The three men were among 14 high-value suspects brought to Guantanamo Bay in 2006 after years of secret detention in CIA prisons in Eastern Europe.