updated sampleQuery.nt and inputTriples.nt to remove BOM characters (per http://isites.harvard.edu/icb/icb.do?keyword=k97402&panel=icb.pagecontent1356729%3Arforum%3Fforum_id%3D139234&pageid=icb.page626866&pageContentId=icb.pagecontent1356729&view=message&viewParam_message_id=902464#a_icb_pagecontent1356729), and fixed bugs in QueryEngine and KnowledgeGraph that were causing problems with the queries