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For Samira Ibrahim, and many other Egyptians, the struggle to remake their country didn't end with the ouster last year of Hosni Mubarak.

Ibrahim, a 25-year-old from southern Egypt, was arrested by the military during a protest in Cairo's Tahrir Square in March of last year, a month after Mubarak was overthrown.

While in custody, Ibrahim said, she and six other young women were subjected to a so-called "virginity check" — a forced penetration to check for hymen blood. Amnesty International has called the procedure a form of torture.

After her release, Ibrahim filed suit against the military in a closely watched case as the country's military rulers have come under increasing scrutiny.

Earlier this month, a military tribunal ruled against Ibrahim, who stepped out of the courtroom sobbing. But the verdict only seemed to strengthen the resolve of Egyptian activists who want to put an end to military trials of civilians.

Caught In The Military's Crackdown

The episode involving Ibrahim took place just a month after the military took over from Mubarak. Dozens were arrested when the military forcibly broke up a protest in Tahrir Square, and Ibrahim was among a group of seven women singled out by the military.

"First they made us take off our clothes to search us," Ibrahim says, describing what happened after her arrest. "There were soldiers and military officers standing and watching while we were being searched, naked. And also when we were subjected to the virginity testing, they were watching, they were making fun, they were humiliating us."

Reem Saad, the head of the Middle East Studies Center at the American University in Cairo, was among Ibrahim's supporters outside the military court during a recent hearing.

"It is unprecedented that just a young woman from Upper Egypt comes out and challenges the military and the patriarchal order in a way that is very difficult for someone in her position," Saad says.

In December, Ibrahim won a legal victory in a separate civil court case to make virginity checks illegal.

But the military court found the doctor accused of carrying out the check not guilty. The ruling was in effect a denial that the incident happened at all.

"We know that this happened," says Heba Morayef, the Egypt researcher for Human Rights Watch, and a witness in the case. "We know that this happened to seven women, on March 10th, and it was a long struggle to even get this case referred to court."

A Broader Campaign Against Military Rule

Mohamed Kadry Said, a retired major general in the army who is now a senior analyst at the Ahram Center for Political and Strategic Studies, says the virgin testing procedure took place regularly and called it a "very bad process."

He described it as a remnant of the past, adding that it will take time for such abusive practices to be fully eliminated.

Despite the verdict against Ibrahim, activists are optimistic about their campaign against the military justice and detention system.

The controversial system of military courts has been criticized for its hasty trials, harsh sentences and lack of legal protections.

According to human rights groups, more than 12,000 civilians have gone through the process since Egypt's revolution in February of last year. But the number of civilians being referred to military trials has dropped significantly in recent months.

Military trials have become the focus of popular anger and debate in the media. Mona Seif, the coordinator for the campaign, says increasing public pressure has been a major factor in changing the way the ruling generals speak about military trials.

"We have managed to make the Supreme Council of the Armed Forces ashamed of using military trials," Seif says.

Kadry Said, the retired general, says that initially, the Supreme Council of the Armed Forces, or SCAF, was simply following the letter of military law. But public criticism has made it roll back the number of cases that are tried in a military court.

"They want, by any means, to satisfy the public, even by not applying the law as it is written," Seif says.

Civilians Being Released

He points out that the army has freed a large number of civilians convicted in military courts.

The ruling generals have issued statements saying they have halted the use of military trials, with the exception of cases covered under the code of military justice.

But Morayef of Human Rights Watch says the types of charges covered in this code are numerous and flexible.

"The military, over the last month, has made a number of very misleading statements indicating — implying — that they have limited the use of military tribunals," Morayef says. "But when you look at the actual text, the actual words of their statements, what is clear is that on the contrary, they are keen on maintaining the discretion to use military tribunals to try civilians when they wish to."

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