Income Taxes	6 Months Ended
Mar. 31, 2013
Income Taxes	12. Income Taxes The Company recorded income tax provisions associated with income from continuing operations of $0.9 million and $1.2 million for the three months ended March 31, 2013 and 2012, respectively, representing effective tax rates of 21.2% and 39.0%, respectively. The Company recorded income tax provisions associated with income from continuing operations of $2.8 million and $2.5 million for the six months ended March 31, 2013 and 2012, respectively, representing effective tax rates of 26.7% and 37.5%, respectively. The difference between the U.S. federal statutory tax rate of 35.0% and the Company’s effective tax rate for the three and six months ended March 31, 2013 and 2012 reflects the impact of state income taxes, permanent tax items and discrete tax benefits of $0.4 million and $0.6 million for the three and six months ended March 31, 2013, respectively. Discrete tax items primarily relate to capital loss carrybacks and the January 2013 signing of the American Taxpayer Relief Act of 2012 which retroactively reinstated the U.S. R&D tax credit to the beginning of calendar 2012. The six months ended March 31, 2013 also reflects the impact of gains on the sale of Vessix, OctoPlus and certain debt securities in our available-for-sale investment portfolio for which there is tax expense recognized which has been offset by the reversal of valuation allowances. The Company recorded an income tax expense from discontinued operations of $0.3 million for the three and six months ended March 31, 2013. The Company recorded an income tax expense from discontinued operations of $0.1 million and $1.0 million for the three and six months ended March 31, 2012, respectively. The Company recorded an income tax benefit of $0.1 million and $0.7 million from the sale of discontinued operations for the three and six months ended March 31, 2012, respectively. The effective tax rate applied to discontinued operations was 32.8% for the three and six months ended March 31, 2013. The effective tax rate applied to discontinued operations was 14.4% and 51.4% for the three and six months ended March 31, 2012, respectively. The total amount of unrecognized tax benefits including interest and penalties that, if recognized, would affect the effective tax rate as of March 31, 2013 and September 30, 2012, respectively, are $1.4 million for each period. Currently, the Company does not expect the liability for unrecognized tax benefits to change significantly in the next 12 months with the above balances classified on the condensed consolidated balance sheets in other long-term liabilities. Interest and penalties related to unrecognized tax benefits are recorded in income tax expense. The Company files income tax returns, including returns for its subsidiaries, in the U.S. federal jurisdiction and in various state jurisdictions. Uncertain tax positions are related to tax years that remain subject to examination. The Internal Revenue Service (“IRS”) commenced an examination of the Company’s U.S. income tax return for fiscal 2010 in the first quarter of fiscal 2012. The IRS completed its examination in the third quarter of fiscal 2012 and a payment was made in the fourth quarter of fiscal 2012 associated with a timing adjustment. U.S. income tax returns for years prior to fiscal 2009 are no longer subject to examination by federal tax authorities. Tax returns for state and local jurisdictions for fiscal years 2004 through 2011 remain subject to examination by state and local tax authorities.

12. Income Taxes

The Company recorded income tax provisions associated with income from continuing operations of $0.9 million and $1.2 million for the three months ended March 31, 2013 and 2012, respectively, representing effective tax rates of 21.2% and 39.0%, respectively. The Company recorded income tax provisions associated with income from continuing operations of $2.8 million and $2.5 million for the six months ended March 31, 2013 and 2012, respectively, representing effective tax rates of 26.7% and 37.5%, respectively. The difference between the U.S. federal statutory tax rate of 35.0% and the Company’s effective tax rate for the three and six months ended March 31, 2013 and 2012 reflects the impact of state income taxes, permanent tax items and discrete tax benefits of $0.4 million and $0.6 million for the three and six months ended March 31, 2013, respectively. Discrete tax items primarily relate to capital loss carrybacks and the January 2013 signing of the American Taxpayer Relief Act of 2012 which retroactively reinstated the U.S. R&D tax credit to the beginning of calendar 2012. The six months ended March 31, 2013 also reflects the impact of gains on the sale of Vessix, OctoPlus and certain debt securities in our available-for-sale investment portfolio for which there is tax expense recognized which has been offset by the reversal of valuation allowances.

The Company recorded an income tax expense from discontinued operations of $0.3 million for the three and six months ended March 31, 2013. The Company recorded an income tax expense from discontinued operations of $0.1 million and $1.0 million for the three and six months ended March 31, 2012, respectively. The Company recorded an income tax benefit of $0.1 million and $0.7 million from the sale of discontinued operations for the three and six months ended March 31, 2012, respectively. The effective tax rate applied to discontinued operations was 32.8% for the three and six months ended March 31, 2013. The effective tax rate applied to discontinued operations was 14.4% and 51.4% for the three and six months ended March 31, 2012, respectively.

The total amount of unrecognized tax benefits including interest and penalties that, if recognized, would affect the effective tax rate as of March 31, 2013 and September 30, 2012, respectively, are $1.4 million for each period. Currently, the Company does not expect the liability for unrecognized tax benefits to change significantly in the next 12 months with the above balances classified on the condensed consolidated balance sheets in other long-term liabilities. Interest and penalties related to unrecognized tax benefits are recorded in income tax expense.

The Company files income tax returns, including returns for its subsidiaries, in the U.S. federal jurisdiction and in various state jurisdictions. Uncertain tax positions are related to tax years that remain subject to examination. The Internal Revenue Service (“IRS”) commenced an examination of the Company’s U.S. income tax return for fiscal 2010 in the first quarter of fiscal 2012. The IRS completed its examination in the third quarter of fiscal 2012 and a payment was made in the fourth quarter of fiscal 2012 associated with a timing adjustment. U.S. income tax returns for years prior to fiscal 2009 are no longer subject to examination by federal tax authorities. Tax returns for state and local jurisdictions for fiscal years 2004 through 2011 remain subject to examination by state and local tax authorities.