Pope Benedict has apologized for comments that have fueled rage in the Muslim world, but protests continue.

In Indian-controlled Kashmir, shops, businesses and schools shut down in response to a strike call by the head of a hard-line Muslim separatist leader to denounce Benedict. For the third day running, people burned tires and shouted “Down with the pope.”

Protests also broke out in Iraq, where angry demonstrators burned an effigy of the pope in Basra, and in Indonesia, where more than 100 people rallied in front of the heavily guarded Vatican Embassy in Jakarta, waving banners that said the “Pope is building religion on hatred.”

The pope on Sunday said he was “deeply sorry” about the angry reaction to his speech last week in which he cited the words of a Byzantine emperor who characterized some of the teachings of Islam’s Prophet Muhammad as “evil and inhuman” and referred to spreading Islam “by the sword.”

Benedict said the remarks came from a text that didn’t reflect his own opinion.

“I hope that this serves to appease hearts and to clarify the true meaning of my address, which in its totality was and is an invitation to frank and sincere dialogue, with great mutual respect,” he said during his weekly appearance before pilgrims in Italy.

The statement of regret — the pope’s second in two days — helped ease some tensions.

In Turkey, where outrage against Benedict’s remarks had been swift, Catholic bishops decided Monday that no changes were necessary in his upcoming visit in November — his first to a Muslim country, Vatican spokesman George Marovic said.

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