Sorry to hear that guy_tensed...In my opinion, reapply again and get supporting letters from ur department and write a personal letter/statement saying that you will come back to nepal after u complete ur phd...By looking at your situation, you should be renewed Visa. The US embassy is giving Visas to people who don't really qualify but if you're already working towards ur PHD and half done, i dont' understand why they would stop you !

And Bidroh, You don't need to have Valid Visa in United States to be in Status. Expiring F1 visa doesn't mean you're out of status. If you're not sure about anything, you shouldn't reply to the sincere threads..and the SAJHA has the same intetion. If you're not sure about the Answer do not reply.