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But the Pope's supporters will be hoping that by visiting Muslim holy sites - he was the first pontiff to go to the great compound of al-Aqsa mosque in Jerusalem - he will have improved the overall tone of relations between the Catholic Church and some at least of Islam's believers.
BBC: Reflections on Pope's Holy Land tour
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The BBC's Middle East correspondent, Paul Wood, says the call by some Palestinian officials for people to defend the Haram al-Sharif or Temple Mount, site of the al-Aqsa mosque, comes amid rumours of plans by Jewish extremists to take control of the area.
BBC: US envoy George Mitchell postpones Israel visit
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In Jerusalem, triumphant Muslims built the Al-Aqsa mosque on top of the Jews' revered Temple Mount.
CENTERFORSECURITYPOLICY: A shrine to Shariah?