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Looks like the New York Times was wrong again. After first insinuating that only civilians were killed with this photo, and down right saying it in the accompanying article here, ABC News now reports that 3 major al-Qaeda members were killed in the attacks. They were:

1) Abu Khabab al-Masri - Al-Qaeda lead bomb maker. Had $5 million reward for his capture. "His explosives training manual is still regarded as the bible for al Qaeda terrorists around the world." - ABC Report
2) Khalid Habib, the al Qaeda operations chief for Pakistan and Afghanistan
3) Abdul Rehman al Magrabi, a senior operations commander for al Qaeda

And although they said that it was highly unlikely that Ayman al-Zawahiri was dead, this quote sums it up very well.

"Zawahiri, if he slept three hours on a normal night, he's sleeping an hour and a half right now with his eyes wide open," [former FBI Agent Jack] Cloonan said. "He's looking around right now and wondering who handed him up. Not a nice feeling."