Aafia Siddiqui, a Pakistani national and MIT graduate wanted for questioning by the FBI in relation to terrorism cases, appeared in a New York court on Tuesday after being charged with attempting to kill US soldiers. Before being taken into custody in Afghanistan last month, Ms. Siddiqui was last seen in Karachi, Pakistan, in 2003. Her reappearance raises questions about the Pakistan government's practice of illegally detaining terror suspects in secret security centers.

Although Siddiqui was accused of having links to the Al Qaeda leadership and has been wanted for questioning by the FBI since 2003, she appeared in court on charges of attempted killing, reports the Times Online.

The US Government alleges that Aafia Siddiqui, a Pakistani mother of three with a biology degree from Massachusetts Institute of Technology and a doctorate in behavioural neuroscience from Brandeis University, near Boston, is married to the nephew of Khalid Sheikh Mohammed, the man who claims to have organised the September 11 terror attacks in 2001.

She is charged with attempted murder and assault for allegedly trying to kill an American interrogator in a gun battle after she was arrested outside an Afghan government compound with a handbag full of chemicals and information on chemical, biological and radiological weapons, as well as descriptions of "various landmarks" in the United States.

Siddiqui was arrested in the Ghazni Province of Afghanistan, outside the governor's compound there, by the Afghanistan National Police. The next day, Siddiqui attacked US soldiers and FBI agents preparing to question her, reports ABC News.

The day after her arrest by Afghani authorities on July 17th, Siddiqui was shot twice in the torso, US officials said, when she grabbed a US soldier's M-4 carbine and attempted to shoot another officer as a team of US soldiers and FBI agents prepared to question her. A US interpreter threw off her aim when he pushed the gun. She then was shot twice with a .9 millimeter handgun, authorities said. According to the US Government, despite her wounds, she shouted that she "wanted to kill Americans," and struggled with her captors before they subdued her.

Siddiqui's family maintains that she has been illegally detained by Pakistani security agencies for the past five years, reports the BBC.

Rights groups say she has spent the last five years in secret US jails....

According to her family, Ms Siddiqui has not been seen since returning to Pakistan on a visit from the US in 2003....

At a news conference on Tuesday in the Pakistani port city of Karachi, Ms Siddiqui's sister said: "Aafia was tortured for five years until one day US authorities announce that they have found her in Afghanistan."

Fauzia Siddiqui said her sister had spent "five years in detention" despite being "innocent of any crime".

Ms Siddiqui's family deny she has connections to al-Qaeda.

The BBC reports that the FBI and Pakistan government in 2003 denied having anything to do with Siddiqui's disappearance. She was never officially listed as wanted by any American or Pakistani agency. Even after her reappearance in Afghanistan, the US government maintains that her whereabouts have remained unknown.

Human rights groups say that Siddiqui is only one of hundreds, possibly thousands, of Pakistanis who have been illegally detained in secret security centers where they are tortured and forced to confess to terrorism. In June, the Asian Human Rights Commission reported that 52 illegal detention centers maintained by various security agencies had been identified across Pakistan.

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