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Income Taxes (Tables) | 12 Months Ended
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Dec. 31, 2013
Income Tax Disclosure [Abstract] |
Schedule of the components of income tax benefit | The components of the income tax benefit for continuing operations are as follows (in thousands):
| Year Ended December 31,
| 2013 |  | 2012 |  | 2011
Current expense (benefit): |  |  |  |  |
Federal | $ | — |  |  | $ | 3 |  |  | $ | 520 |
State | 33 |  |  | 16 |  |  | 139 |
| 33 |  |  | 19 |  |  | 659 |
Deferred expense (benefit): |  |  |  |  |
Federal | 404 |  |  | (913 | ) |  | (10,803 | )
State | (63 | ) |  | (297 | ) |  | (3,126 | )
| $ | 374 |  |  | $ | (1,191 | ) |  | $ | (13,270 | )
Schedule of deferred tax assets and liabilities |
| December 31,
| 2013 |  | 2012
| (in thousands)
Deferred assets: |  |  |
Net operating loss carryforwards | $ | 196,421 |  |  | $ | 198,445 |
Research and AMT credit carryforwards | 30,092 |  |  | 27,169 |
Fixed assets and intangibles | 17,293 |  |  | 23,763 |
Accrued expenses | 1,474 |  |  | 1,366 |
Contingent liabilities | 582 |  |  | 1,779 |
Deferred revenue | 760 |  |  | 1,013 |
Present value of royalties | 12,175 |  |  | 10,836 |
Organon termination asset | (4,073 | ) |  | (4,503 | )
Organon termination liability | 4,073 |  |  | 4,503 |
Royalty obligation | — |  |  | 861 |
Deferred rent | 1,634 |  |  | 2,635 |
Lease termination costs | — |  |  | — |
Capital loss carryforwards | 148 |  |  | 298 |
Other | 3,701 |  |  | 1,844 |
| 264,280 |  |  | 270,009 |
Valuation allowance for deferred tax assets | (249,470 | ) |  | (254,870 | )
Net deferred tax assets | $ | 14,810 |  |  | $ | 15,139 |
Deferred tax liabilities: |  |  |
Retrophin fair value adjustment | $ | (859 | ) |  | $ | — |
Identified intangibles | (13,984 | ) |  | (15,139 | )
Identified indefinite lived intangibles | (2,639 | ) |  | (2,298 | )
Total | $ | (2,672 | ) |  | $ | (2,298 | )
Schedule of effective income tax rate reconciliation | A reconciliation of income taxes from continuing operations to the amount computed by applying the statutory federal income tax rate to the net loss from continuing operations is summarized as follows:
| Years Ended December 31,
| 2013 |  | 2012 |  | 2011
Amounts computed at statutory federal rate | $ | (3,131 | ) |  | $ | 1,317 |  |  | $ | 1,204 |
State taxes net of federal benefit | (293 | ) |  | 196 |  |  | (2 | )
Meals & entertainment | (10 | ) |  | (8 | ) |  | (9 | )
Acquisition related transaction costs | — |  |  | — |  |  | (37 | )
Imputed interest | (285 | ) |  | (259 | ) |  | (255 | )
CVRs | (2,027 | ) |  | 695 |  |  | (601 | )
Stock-based compensation | 556 |  |  | 581 |  |  | (597 | )
Expired NOLs | — |  |  | (6,847 | ) |  | (678 | )
Expired research and development credits | 641 |  |  | (1,984 | ) |  | (1,200 | )
R&D credit study | 3,940 |  |  | — |  |  | — |
Change in uncertain tax positions | (364 | ) |  | 830 |  |  | — |
Rate change for changes in state law | (901 | ) |  | (3,388 | ) |  | — |
Increase in deferred tax assets from completion of 382 analysis | (786 | ) |  | 53,257 |  |  | — |
Change in valuation allowance | 3,509 |  |  | (41,768 | ) |  | 15,486 |
Other | (1,223 | ) |  | (1,431 | ) |  | (41 | )
| $ | (374 | ) |  | $ | 1,191 |  |  | $ | 13,270 |
Schedule of unrecognized tax benefits | A reconciliation of the amount of unrecognized tax benefits at December 31, 2013 and 2012 is as follows (in thousands):
Balance at December 31, 2011 | $ | 8,906 |
Additions based on tax positions related to the current year | 38 |
Reductions for tax positions of prior years | (877 | )
Balance at December 31, 2012 | 8,067 |
Additions based on tax positions related to the current year | 417 |
Additions for tax positions of prior years | 20 |
Balance at December 31, 2013 | $ | 8,504 |

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- Definition Tabular disclosure of the components of income tax expense attributable to continuing operations for each year presented including, but not limited to: current tax expense (benefit), deferred tax expense (benefit), investment tax credits, government grants, the benefits of operating loss carryforwards, tax expense that results from allocating certain tax benefits either directly to contributed capital or to reduce goodwill or other noncurrent intangible assets of an acquired entity, adjustments of a deferred tax liability or asset for enacted changes in tax laws or rates or a change in the tax status of the entity, and adjustments of the beginning-of-the-year balances of a valuation allowance because of a change in circumstances that causes a change in judgment about the realizability of the related deferred tax asset in future years. + References Reference 1: http://www.xbrl.org/2003/role/presentationRef -Publisher FASB -Name Accounting Standards Codification -Topic 740 -SubTopic 10 -Section 50 -Paragraph 9 -URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32639-109319 + Details
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- Definition Tabular disclosure of the components of net deferred tax asset or liability recognized in an entity's statement of financial position, including the following: the total of all deferred tax liabilities, the total of all deferred tax assets, the total valuation allowance recognized for deferred tax assets. + References Reference 1: http://www.xbrl.org/2003/role/presentationRef -Publisher FASB -Name Accounting Standards Codification -Topic 740 -SubTopic 10 -Section 50 -Paragraph 2 -URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32537-109319 + Details
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- Definition Tabular disclosure of the reconciliation using percentage or dollar amounts of the reported amount of income tax expense attributable to continuing operations for the year to the amount of income tax expense that would result from applying domestic federal statutory tax rates to pretax income from continuing operations. + References Reference 1: http://www.xbrl.org/2003/role/presentationRef -Publisher FASB -Name Accounting Standards Codification -Topic 740 -SubTopic 10 -Section 50 -Paragraph 12 -URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32687-109319 + Details
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- Definition Tabular disclosure of the change in unrecognized tax benefits, excluding amounts pertaining to examined tax returns. + References Reference 1: http://www.xbrl.org/2003/role/presentationRef -Publisher FASB -Name Accounting Standards Codification -Topic 740 -SubTopic 10 -Section 50 -Paragraph 15A -URI http://asc.fasb.org/extlink&oid=6907707&loc=SL6600010-109319 + Details
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