Islamists are among several groups campaigning against Mubarak
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At least 400 Muslim Brotherhood members have been detained after nationwide anti-government protests.
The outlawed group is campaigning for political reform and an end to Hosni Mubarak's 24-year career as president.
Wednesday's protests ended in clashes in several towns and police fired tear gas to disperse crowds, activists said.
One report citing judicial sources said the number of detainees reached 1,000. They were held for demonstrating without proper authorisation.
"The detained people insisted on gathering and demonstrating without authorisation, thus threatening public order," a police official was quoted as saying.