Acorda Therapeutics (ACORQ) 10-Q 7 Nov 16 2016 Q3 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	9 Months Ended
	Sep. 30, 2016	Oct. 31, 2016
Document and Entity Information
Entity Registrant Name	ACORDA THERAPEUTICS INC
Entity Central Index Key	1,008,848
Document Type	10-Q
Document Period End Date	Sep. 30, 2016
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		46,114,306
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	Q3

Consolidated Balance Sheets

Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 127,940	$ 153,204
Restricted cash		6,032
Short-term investments		200,101
Trade accounts receivable, net of allowances of $957 and $884, as of September 30, 2016 and December 31, 2015, respectively	48,575	31,466
Prepaid expenses	15,639	16,079
Finished goods inventory	40,935	36,476
Other current assets	4,863	7,959
Total current assets	237,952	451,317
Property and equipment, net of accumulated depreciation	35,777	40,204
Goodwill	284,029	183,636
Deferred tax asset	2,951	2,128
Intangible assets, net of accumulated amortization	749,415	430,856
Non-current portion of deferred cost of license revenue	2,430	2,906
Other assets	5,814	247
Total assets	1,318,368	1,111,294
Current liabilities:
Accounts payable	18,557	14,233
Accrued expenses and other current liabilities	89,374	66,158
Current portion of deferred license revenue	9,057	9,057
Current portion of convertible notes payable	1,134	1,144
Total current liabilities	118,122	90,592
Convertible senior notes (due 2021)	297,111	290,420
Acquired contingent consideration	75,400	63,500
Non-current portion of deferred license revenue	34,720	41,513
Non-current portion of convertible notes payable		1,107
Deferred tax liability	91,429	12,146
Other non-current liabilities	34,820	8,991
Commitments and contingencies
Stockholders' equity:
Common stock, $0.001 par value. Authorized 80,000,000 shares at September 30, 2016 and December 31, 2015; issued 46,144,900 and 43,440,324 shares, including those held in treasury, as of September 30, 2016 and December 31, 2015, respectively	46	43
Treasury stock at cost (12,420 shares at September 30, 2016 and December 31, 2015)	(329)	(329)
Additional paid-in capital	911,540	812,782
Accumulated deficit	(240,876)	(209,352)
Accumulated other comprehensive loss	(3,615)	(119)
Total stockholders' equity	666,766	603,025
Total liabilities and stockholders' equity	$ 1,318,368	$ 1,111,294

Consolidated Balance Sheets (Pa

Consolidated Balance Sheets (Parenthetical) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Consolidated Balance Sheets
Trade accounts receivable, allowances (in dollars)	$ 957	$ 884
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, Authorized shares	80,000,000	80,000,000
Common stock, issued shares	46,144,900	43,440,324
Treasury stock, shares	12,420	12,420

Consolidated Statements of Oper

Consolidated Statements of Operations - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Revenues:
Net product revenues	$ 128,508	$ 141,330	$ 359,350	$ 342,394
Royalty revenues	4,841	4,605	12,831	12,571
License revenue	2,264	2,264	6,793	6,793
Total net revenues	135,613	148,199	378,974	361,758
Costs and expenses:
Cost of sales	27,644	24,741	77,265	65,896
Cost of license revenue	159	159	476	476
Research and development	54,777	43,356	149,640	105,221
Selling, general and administrative	54,805	51,056	176,388	152,645
Changes in fair value of acquired contingent consideration	3,700	3,200	11,900	7,400
Total operating expenses	141,085	122,512	415,669	331,638
Operating (loss) income	(5,472)	25,687	(36,695)	30,120
Other (expense) income (net):
Interest and amortization of debt discount expense	(4,404)	(4,037)	(12,161)	(12,098)
Interest income	46	120	309	281
Realized loss on foreign currency transactions	(179)		(1,674)
Other (expense) income		(59)	10,026	411
Total other (expense), (net)	(4,537)	(3,976)	(3,500)	(11,406)
(Loss) income before taxes	(10,009)	21,711	(40,195)	18,714
(Provision for) benefit from income taxes	(3,023)	(17,770)	7,686	(16,861)
Net (loss) income	(13,032)	3,941	(32,509)	1,853
Net loss attributable to non-controlling interest	307		985
Net (loss) income attributable to Acorda Therapeutics, Inc.	$ (12,725)	$ 3,941	$ (31,524)	$ 1,853
Net (loss) income per share attributable to Acorda Therapeutics, Inc.-basic	$ (0.28)	$ 0.09	$ (0.70)	$ 0.04
Net (loss) income per share attributable to Acorda Therapeutics, Inc.-diluted	$ (0.28)	$ 0.09	$ (0.70)	$ 0.04
Weighted average common shares outstanding used in computing net (loss) income per share attributable to Acorda Therapeutics, Inc.-basic	45,378	42,174	45,178	42,097
Weighted average common shares outstanding used in computing net (loss) income per share attributable to Acorda Therapeutics, Inc.-diluted	45,378	43,432	45,178	43,434

Consolidated Statements of Comp

Consolidated Statements of Comprehensive (Loss) Income - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Consolidated Statements of Comprehensive (Loss) Income
Net (loss) income	$ (13,032)	$ 3,941	$ (32,509)	$ 1,853
Other comprehensive (loss) income, net of tax:
Foreign currency translation adjustment	1,097		(3,615)
Unrealized gains on available for sale securities		17		31
Reclassification of net losses to net income			119
Other comprehensive income (loss), net of tax	1,097	17	(3,496)	31
Comprehensive (loss) income	(11,935)	$ 3,958	(36,005)	$ 1,884
Other comprehensive income (loss) attributable to noncontrolling interest	$ 17		$ (110)

Consolidated Statements of Cash

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Cash flows from operating activities:
Net (loss) income	$ (32,509)	$ 1,853
Adjustments to reconcile net (loss) income to net cash provided by operating activities:
Recognition of deferred product revenue- Zanaflex		(22,186)
Share-based compensation expense	27,392	24,748
Amortization of net premiums and discounts on investments	467	2,372
Amortization of debt discount and debt issuance costs	7,158	6,383
Amortization of revenue interest issuance cost		15
Depreciation and amortization expense	15,775	11,153
Change in acquired contingent consideration obligation	11,900	7,400
Realized gain on foreign currency transaction	(10,484)
Deferred tax (benefit) provision	(10,522)	16,861
Changes in assets and liabilities:
(Increase) decrease in accounts receivable	(17,018)	455
Decrease in prepaid expenses and other current assets	5,820	1,408
Increase in inventory	(4,459)	(20,001)
Decrease in non-current portion of deferred cost of license revenue	476	476
Decrease in other assets	25	25
Increase (decrease) in accounts payable, accrued expenses, other current liabilities	9,612	(2,158)
Decrease in revenue interest liability interest payable		(124)
Decrease in non-current portion of deferred license revenue	(6,793)	(6,793)
Decrease in deferred product revenue-Zanaflex		(988)
Decrease (increase) in restricted cash	6,032	(4,743)
Net cash provided by operating activities	2,872	16,156
Cash flows from investing activities:
Purchases of property and equipment	(4,633)	(5,025)
Purchases of intangible assets	(482)	(781)
Acquisitions, net of cash received	(268,107)
Purchases of investments	(40,214)	(359,968)
Proceeds from maturities of investments	239,966	249,500
Net cash used in investing activities	(73,470)	(116,274)
Cash flows from financing activities:
Proceeds from issuance of common stock and option exercises	74,673	8,000
Purchase of noncontrolling interest	(27,946)
Debt issuance costs	(1,559)
Repayments of revenue interest liability	(41)	(215)
Net cash provided by financing activities	45,127	7,785
Effect of exchange rate changes on cash and cash equivalents	207
Net decrease in cash and cash equivalents	(25,264)	(92,333)
Cash and cash equivalents at beginning of period	153,204	182,170
Cash and cash equivalents at end of period	127,940	89,837
Supplemental disclosure:
Cash paid for interest	3,040	4,279
Cash paid for taxes	$ 3,564	$ 2,152

Organization and Business Activ

Organization and Business Activities	9 Months Ended
	Sep. 30, 2016
Organization and Business Activities
Organization and Business Activities	(1) Organization and Business Activities Acorda Therapeutics, Inc. (“Acorda” or the “Company”) is a biotechnology company focused on developing therapies that restore function and improve the lives of people with neurological disorders. The accompanying unaudited consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States (GAAP) for interim financial information, Accounting Standards Codification (ASC) Topic 270-10 and with the instructions to Form 10-Q. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. In management’s opinion, all adjustments considered necessary for a fair presentation have been included in the interim periods presented and all adjustments are of a normal recurring nature. The Company has evaluated subsequent events through the date of this filing. Operating results for the three and nine-month periods ended September 30, 2016 are not necessarily indicative of the results that may be expected for the year ending December 31, 2016. When used in these notes, the terms “Acorda” or “the Company” mean Acorda Therapeutics, Inc. The December 31, 2015 consolidated balance sheet data was derived from audited financial statements, but does not include all disclosures required by GAAP. You should read these unaudited interim condensed consolidated financial statements in conjunction with the consolidated financial statements and footnotes included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2015. Certain reclassifications were made to prior period amounts in the interim consolidated financial statements and accompanying notes to conform with the current presentation.

Summary of Significant Accounti

Summary of Significant Accounting Policies	9 Months Ended
	Sep. 30, 2016
Summary of Significant Accounting Policies
Summary of Significant Accounting Policies	(2) Summary of Significant Accounting Policies Our critical accounting policies are detailed in our Annual Report on Form 10-K for the year ended December 31, 2015. As of September 30, 2016, with the exception of the addition of our policy on translation of foreign currency, the modification of our policy on segment and geographic information to reflect sales of Selincro and the adoption of ASU 2015-03, “Interest — Imputation of Interest” (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs (ASU 2015-03), our critical accounting policies have not changed materially from December 31, 2015. Foreign Currency Translation — The functional currency of operations outside the United States of America is deemed to be the currency of the local country, unless otherwise determined that the United States dollar would serve as a more appropriate functional currency given the economic operations of the entity. Accordingly, the assets and liabilities of the Company’s foreign subsidiary, Biotie, are translated into United States dollars using the period-end exchange rate; and income and expense items are translated using the average exchange rate during the period; and equity transactions are translated at historical rates. Cumulative translation adjustments are reflected as a separate component of equity. Foreign currency transaction gains and losses are charged to operations. Segment and Geographic Information The Company is managed and operated as one business which is focused on the identification, development and commercialization of novel therapies to improve the lives of people with neurological disorders. The entire business is managed by a single management team that reports to the Chief Executive Officer. The Company does not operate separate lines of business with respect to any of its products or product candidates and the Company does not prepare discrete financial information with respect to separate products or product candidates or by location. Accordingly, the Company views its business as one reportable operating segment. Net product revenues reported to date are derived from the sales of Ampyra, Zanaflex and Qutenza in the U.S. Subsequent Events Subsequent events are defined as those events or transactions that occur after the balance sheet date, but before the financial statements are filed with the Securities and Exchange Commission. The Company completed an evaluation of the impact of any subsequent events through the date these financial statements were issued, and determined the following subsequent events required disclosure in these financial statements. In October 2016, the Company entered into a 10 year lease agreement for approximately 26,000 square feet of lab/office space in Waltham, MA. The lease provides for monthly rental payments over the lease term. The Company expects to take occupancy of the space in January 2017. Recently Issued / Adopted Accounting Pronouncements In April 2015, the FASB issued Accounting Standards Update 2015-03, “Interest — Imputation of Interest” (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs (ASU 2015-03), which requires that debt issuance costs related to a recognized debt liability be presented in the balance sheet as a direct deduction from the debt liability rather than as an asset. ASU-2015-03 is effective for fiscal years and interim periods therein beginning after December 15, 2015, with early adoption permitted. The Company adopted this guidance retrospectively effective in the three-month period ended March 31, 2016. The impact of the adoption of this guidance on the Company’s consolidated balance sheet as of December 31, 2015 was a reclassification of approximately $5.0 million representing the unamortized balance of debt issuance costs as of December 31, 2015 from Other Assets to the Convertible Senior Notes liability. (In thousands) Balance at December 31, 2015 Revised As Previously Other assets $ $ Convertible notes payable — due 2021 $ ) $ ) In March 2016, the FASB issued Accounting Standards Update 2016-09, “Compensation — Stock Compensation” (Topic 718). The main objective of this update is to simplify the accounting, and reporting classifications for certain aspects of share-based payment transactions. This ASU is effective for fiscal years beginning after December 15, 2016, including interim periods within those fiscal years. The Company is currently evaluating the new guidance to determine the impact it may have on its financial statements. In August 2016, the FASB issued Accounting Standards update 2016-15, “Statement of Cash Flows” (Topic 230). The main objective of this update is to reduce diversity in how certain cash receipts and cash payments are presented and classified in the statement of cash flows. This ASU is effective for fiscal years beginning after December 15, 2017, including interim periods within those fiscal years, with early adoption permitted. The Company is currently evaluating the new guidance to determine the impact it may have on its financial statements.

Acquisitions

Acquisitions	9 Months Ended
	Sep. 30, 2016
Acquisitions
Acquisitions	(3) Acquisitions Biotie Therapies Corp. On April 18, 2016, the Company acquired a controlling interest in Biotie Therapies Corp. (“Biotie”) pursuant to a combination agreement entered into in January 2016. The acquisition of Biotie positions the Company as a leader in Parkinson’s disease therapeutic development, with three clinical-stage compounds that have the potential to improve the lives of people with Parkinson’s disease. In accordance with the combination agreement, the Company closed a public tender offer for all of Biotie’s capital stock, pursuant to which the Company acquired approximately 93% of the fully diluted capital stock of Biotie for a cash purchase price of approximately $350 million. On May 4, 2016, the Company acquired an additional approximately 4% of Biotie’s fully diluted capital stock pursuant to a subsequent public offer to Biotie stockholders that did not tender their shares in the initial tender offer. The purchase consideration for the subsequent tender offer was approximately $14.5 million. The acquisition of the additional 4% of Biotie’s fully diluted capital stock resulted in the Company owning approximately 97% of the fully diluted capital stock of Biotie (the “Acquisition”) as of June 30, 2016. On September 30, 2016, the Company acquired the remaining approximately 3% of Biotie’s fully diluted capital stock in exchange for the payment of a cash security deposit of approximately $13.5 million, as determined by the arbitral tribunal administering the redemption proceedings. Accordingly, the Company owned 100% of the fully diluted capital stock of Biotie as of September 30, 2016. The Company estimated the preliminary fair value of the assets acquired and liabilities assumed as of the date of acquisition based on the information available at that time. During the three-month period ended September 30, 2016, the Company recorded a measurement-period adjustment to its preliminary purchase price allocation of $1.2 million, which reduced other long-term liabilities with a corresponding decrease to goodwill. The valuation of the assets and liabilities is subject to further analysis. As the Company finalizes the fair values of the assets acquired and liabilities assumed, additional purchase price adjustments may be recorded during the measurement period and such adjustments could be material. The Company will reflect measurement period adjustments, if any, in the period in which the adjustments are recognized. The following table presents the preliminary allocation of the purchase price to the estimated fair values of the assets acquired and liabilities assumed as of the acquisition date of April 18, 2016, as adjusted through the period ended September 30, 2016: (In thousands) Preliminary Measurement Preliminary Cash and cash equivalents $ $ — $ Other current assets — Other long-term assets — Intangible assets (indefinite-lived) — Intangible assets (definite-lived) — Current liabilities ) — ) Deferred taxes ) — ) Other long-term liabilities ) ) Fair value of assets and liabilities acquired Goodwill ) Total purchase price — Less: Noncontrolling interests ) — ) Purchase consideration on date of acquisition $ $ — $ The Company accounted for the Acquisition as a business combination using the acquisition method of accounting. Under the acquisition method of accounting, the total purchase price of the acquisition is allocated to the net tangible and identifiable intangible assets acquired and liabilities assumed based on their fair values as of the date of acquisition. The Company incurred approximately $17.7 million in acquisition related expenses to date. For the three and nine-month periods ended September 30, 2016, the Company incurred approximately $0.4 million and $17.1 million, respectively, in acquisition related expenses, all of which were expensed and included in selling, general and administrative expenses in the consolidated statements of operations. The results of Biotie’s operations have been included in the consolidated statements of operations from the acquisition date of April 18, 2016. The definite-lived intangible asset will be amortized on a straight line basis over the period in which the Company expects to receive economic benefit and will be reviewed for impairment when facts and circumstances indicate that the carrying value of the asset may not be recoverable. The fair value of the IPR&D will be capitalized as of the acquisition date and subsequently accounted for as indefinite-lived intangible assets until disposition of the assets or completion or abandonment of the associated research and development efforts. Accordingly, during the development period after the completion of the acquisition, these assets will not be amortized into earnings; rather, these assets will be subject to periodic impairment testing. Upon successful completion of the development efforts, the useful lives of the IPR&D assets will be determined and the assets will be considered definite-lived intangible assets and amortized over their expected useful lives. Goodwill is calculated as the excess of the purchase price and the noncontrolling interest over the estimated fair value of the assets acquired and liabilities assumed. The goodwill recorded is primarily related to establishing a deferred tax liability for the IPR&D intangible assets which have no tax basis and, therefore, will not result in a future tax deduction. None of the goodwill is deductible for tax purposes. The revenue of Biotie included in the consolidated statements of operations for the three-month period ended September 30, 2016 and the year to date period April 18, 2016 through September 30, 2016 was $1.1 million and $1.9 million, respectively. The net loss of Biotie included in the consolidated statement of operations for the three-month period ended September 30, 2016 and the year to date period April 18, 2016 through September 30, 2016 was $11.7 million and $26.5 million, respectively. Noncontrolling Interests The fair value of the noncontrolling interest was comprised of the fair value of Biotie’s equity interests not acquired by the Company. The fair value of the noncontrolling interest was determined by quoted market price, which is considered to be a Level 1 input under the fair value measurements and disclosure guidance. The noncontrolling interest in Biotie was presented as permanent equity in the Company’s consolidated balance sheet. Noncontrolling interests are generally adjusted for the net income or loss and other comprehensive income or loss attributable to the noncontrolling shareholders and any additional acquisition of noncontrolling interests. On September 30, 2016, the Company acquired shares representing the remaining approximately 3% of Biotie’s fully diluted capital stock, which eliminated the noncontrolling interest as of September 30, 2016. Activity attributable to stockholders’ equity - Acorda and noncontrolling interests for the nine-month period ended September 30, 2016 is as follows: (In thousands) Stockholders’ Non- Total Balance at December 31, 2015 $ $ — $ Net loss ) ) ) Other comprehensive loss ) ) ) Noncontrolling interest at date of acquisition — Purchase of noncontrolling interest ) ) ) Private Placement, net of issuance costs — Stock compensation expense and option exercises — Balance at September 30, 2016 $ $ — $ Financial Instruments The Company does not enter into hedging transactions in the normal course of business. However, as a result of the Biotie acquisition which was completed in Euros, the Company was exposed to fluctuations in exchange rates between the U.S. dollar and the Euro until the completion of the transaction. To mitigate this risk, the Company entered into foreign currency options to limit its exposure to fluctuations in exchange rates between the U.S. dollar and the Euro until the transaction was completed. As of May 2, 2016, there were no foreign currency options outstanding. The Company had a realized gain on the foreign currency options of approximately $9.9 million, which is included in other income in the consolidated statements of operations for the nine month period ended September 30, 2016. Pro-Forma Financial Information Associated with the Biotie Acquisition (Unaudited) The following table summarizes certain supplemental pro forma financial information for the three and nine-month periods ended September 30, 2016 and 2015 as if the Acquisition had occurred as of January 1, 2015. The unaudited pro forma financial information for the three and nine months ended September 30, 2016 reflects ( i) the net impact to amortization expense based on the fair value adjustments to the intangibles assets; (ii) the impact to operations resulting from the reversal of transaction costs related to the Acquisition; (iii) the impact to operations resulting from the reversal of the unrealized and realized gains on the foreign currency option; (iv) the impact to interest expense based on the fair value adjustments to the debt acquired from Biotie; (v) the tax effects of those adjustments; and (vi) the net loss attributable to the noncontrolling interests resulting from the Acquisition. The unaudited pro forma financial information for the three and nine-month periods ended September 30, 2015 reflects (i) the net impact to amortization expense based on the fair value adjustments to the intangible assets acquired from Biotie; (ii) the impact to interest expense based on the fair value adjustments to the debt acquired from Biotie; and (iii) the net loss attributable to the noncontrolling interests resulting from the Acquisition, and the related tax effects of those adjustments. Three-month Nine-month (In thousands) 2016 2015 2016 2015 Revenues $ $ $ $ Loss from continuing operations attributable to Acorda $ ) $ ) $ ) $ )

Intangible Assets and Goodwill

Intangible Assets and Goodwill	9 Months Ended
	Sep. 30, 2016
Intangible Assets and Goodwill
Intangible Assets and Goodwill	(4) Intangible Assets and Goodwill Intangible Assets In connection with the acquisition of Biotie (Note 3), the Company acquired global rights to tozadenant, SYN-120, and BTT-1023. Tozadenant is an oral adenosine A2a receptor antagonist currently in Phase 3 development as an adjunctive treatment to levodopa in Parkinson’s disease patients to reduce OFF periods. SYN-120 is an oral, dual antagonist with the potential to facilitate pro-cognitive and antipsychotic activities for patients with neurodegenerative diseases, such as Parkinson’s and Alzheimer’s. BTT-1023 is a fully human monoclonal antibody which targets vascular adhesion for the potential treatment of inflammatory/fibrotic disease, such as rheumatoid arthritis and psoriasis. The Company also acquired rights to Selincro, an orally administered drug used for the treatment of alcohol dependence. Selincro received European Medicines Agency approval in 2013 and is currently marketed across Europe by Biotie’s partner H. Lundbeck A/S, a Danish pharmaceutical company. In accordance with the acquisition method of accounting, the Company allocated the acquisition cost for the transaction to the underlying assets acquired and liabilities assumed, based upon the estimated fair values of those assets and liabilities at the date of acquisition. The Company classified the fair value of the acquired IPR&D as indefinite lived intangible assets until the successful completion or abandonment of the associated research and development efforts. The Company classified the fair value of Selincro as a definite lived intangible asset. The fair value assigned to Selincro will be amortized over the estimated remaining useful life of 7 years. The value allocated to the indefinite lived intangible assets was $260.5 million. The value allocated to Selincro was $65 million. Information regarding intangible assets is as follows: September 30, 2016 December 31, 2015 (Dollars In thousands) Estimated Cost Accumulated Foreign Net Cost Accumulated Net In-process research & development (1) Indefinite-lived $ $ — $ ) $ $ $ — $ Selincro ) ) — — — Ampyra milestones ) — ) Ampyra CSRO royalty buyout ) — ) Website development costs ) — ) Website development costs — in process n/a — — — $ $ ) $ ) $ $ $ ) $ (1) Includes the fair values of: CVT-301: $423.0 million; tozadenant: $232.0 million; SYN-120: $24.2 million and BTT-1023: $4.3 million The Company recorded $2.8 million and $6.2 million in amortization expense related to these intangibles assets during the three and nine-month periods ended September 30, 2016, respectively. The Company recorded $0.7 million and $2.3 million in amortization expense related to these intangibles assets during the three and nine month periods ended September 30, 2015. Estimated future amortization expense for intangible assets subsequent to September 30, 2016 is as follows: (In thousands) 2016 $ 2017 2018 2019 2020 Thereafter $ Goodwill Changes in the carrying amount of goodwill were as follows: In thousands Balance at December 31, 2015 $ Goodwill associated with the acquisition of Biotie Therapies Decrease to goodwill for measurement period adjustment ) Foreign currency translation adjustment ) Balance at September 30, 2016 $

Share-based Compensation

Share-based Compensation	9 Months Ended
	Sep. 30, 2016
Share-based Compensation
Share-based Compensation	(5) Share-based Compensation During the three-month periods ended September 30, 2016 and 2015, the Company recognized share-based compensation expense of $10.0 million and $8.9 million, respectively. During the nine-month periods ended September 30, 2016 and 2015, the Company recognized share-based compensation expense of $27.4 million and $24.7 million. Activity in options and restricted stock during the nine-month period ended September 30, 2016 and related balances outstanding as of that date are reflected below. The weighted average fair value per share of options granted to employees for the three-month periods ended September 30, 2016 and 2015 were approximately $11.21 and $14.74, respectively. The weighted average fair value per share of options granted to employees for the nine-month periods ended September 30, 2016 and 2015 were approximately $13.65 and $15.89, respectively. The following table summarizes share-based compensation expense included within the consolidated statements of operations: For the three-month For the nine-month period ended September 30, period ended September 30, (In millions) 2016 2015 2016 2015 Research and development $ $ $ $ Selling, general and administrative Total $ $ $ $ A summary of share-based compensation activity for the nine-month period ended September 30, 2016 is presented below: Stock Option Activity Number of Weighted Weighted Intrinsic Balance at January 1, 2016 $ Granted Cancelled ) Exercised ) Balance at September 30, 2016 $ $ Vested and expected to vest at September 30, 2016 $ $ Vested and exercisable at September 30, 2016 $ $ Restricted Stock Activity (In thousands) Restricted Stock Number of Nonvested at January 1, 2016 Granted Vested ) Forfeited ) Nonvested at September 30, 2016 Unrecognized compensation cost for unvested stock options, restricted stock awards and performance stock units as of September 30, 2016 totaled $63.7 million and is expected to be recognized over a weighted average period of approximately 2.4 years.

Earnings Per Share

Earnings Per Share	9 Months Ended
	Sep. 30, 2016
Earnings Per Share
Earnings Per Share	(6) Earnings Per Share The following table sets forth the computation of basic and diluted earnings per share for the three and nine-month periods ended September 30, 2016 and 2015: (In thousands, except per share data) Three- Three- Nine-month Nine-month Basic and diluted Net (loss) income $ ) $ $ ) $ Weighted average common shares outstanding used in computing net (loss) income per share—basic Plus: net effect of dilutive stock options and restricted common shares — — Weighted average common shares outstanding used in computing net (loss) income per share—diluted Net (loss) income per share—basic $ ) $ $ ) $ Net (loss) income per share—diluted $ ) $ $ ) $ The difference between basic and diluted shares is that diluted shares include the dilutive effect of the assumed exercise of outstanding securities. The Company’s stock options and unvested shares of restricted common stock could have the most significant impact on diluted shares. Securities that could potentially be dilutive are excluded from the computation of diluted earnings per share when a loss from continuing operations exists or when the exercise price exceeds the average closing price of the Company’s common stock during the period, because their inclusion would result in an anti-dilutive effect on per share amounts. The following amounts were not included in the calculation of net income per diluted share because their effects were anti-dilutive: (In thousands) Three- Three- Nine-month Nine-month Denominator Stock options and restricted common shares Convertible note — Saints Capital Additionally, the impact of the convertible debt and the impact of the convertible capital loan assumed from Biotie were determined to be anti-dilutive and excluded from the calculation of net loss per diluted share for the three and nine-month periods ended September 30, 2016.

Income Taxes

Income Taxes	9 Months Ended
	Sep. 30, 2016
Income Taxes
Income Taxes	(7) Income Taxes The Company’s effective income tax rate differs from the U.S. statutory rate principally due to state taxes, foreign taxes related to the Company’s Puerto Rico operations, Federal research and development tax credits, jurisdictions with pretax losses from the acquisition of Biotie for which no tax benefit can be recognized and certain other permanent tax items. The annual rate depends on a number of factors, including the jurisdiction in which operating profit is earned and the timing and nature of discrete items. For the three-month periods ended September 30, 2016 and 2015, the Company recorded a $3.0 million and $17.8 million provision for income taxes, respectively. The effective income tax rates for the Company for the three-month periods ended September 30, 2016 and 2015 were 30% and 82%, respectively. The variance in the effective tax rates for the three-month period ended September 30, 2016 as compared to the three-month period ended September 30, 2015 was due primarily to the valuation allowance recorded on jurisdictions with pretax losses from the acquisition of Biotie during three-month period ended June 30, 2016 for which no tax benefit can be recognized, partially offset by a non-deductible $8.8 million payment in July 2015 to the former equity holders of Neuronex and the Company being able to receive a benefit in 2016 for the Federal research and development tax credits as a result of passed legislation making the tax credit permanent. The Company was not able to benefit from the Federal research and development tax credits for the three-month period ended September 30, 2015, however, the Company was able to receive the benefit for this tax credit in the effective tax rate at December 31, 2015. For the nine-month periods ended September 30, 2016 and 2015, the Company recorded a $7.7 million benefit and $16.9 million provision for income taxes, respectively. The effective income tax rates for the Company for the nine-month periods ended September 30, 2016 and 2015 were 19% and 90%, respectively. The variance in the effective tax rates for the nine-month period ended September 30, 2016 as compared to the nine-month period ended September 30, 2015 was due primarily to the valuation allowance recorded on jurisdictions with pretax losses from the acquisition of Biotie during the six-month period ended June 30, 2016 for which no tax benefit can be recognized, partially offset by a non-deductible $8.8 million payment in July 2015 to the former equity holders of Neuronex and the Company being able to receive a benefit in 2016 for the Federal research and development tax credits as a result of passed legislation making the tax credit permanent. The Company was not able to benefit from the Federal research and development tax credits for the nine-month period ended September 30, 2015, however, the Company was able to receive the benefit for this tax credit in the effective tax rate at December 31, 2015. The Company continues to evaluate the realizability of its deferred tax assets on a quarterly basis and will adjust such amounts in light of changing facts and circumstances including, but not limited to, future projections of taxable income, tax legislation, rulings by relevant tax authorities, the progress of ongoing tax audits and the regulatory approval of products currently under development. Any changes to the valuation allowance or deferred tax assets and liabilities in the future would impact the Company’s income taxes.

Fair Value Measurements

Fair Value Measurements	9 Months Ended
	Sep. 30, 2016
Fair Value Measurements
Fair Value Measurements	(8) Fair Value Measurements The following table presents information about the Company’s assets and liabilities measured at fair value on a recurring basis as of September 30, 2016 and December 31, 2015 and indicates the fair value hierarchy of the valuation techniques utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize quoted prices (unadjusted) in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize data points that are observable, such as quoted prices, interest rates, exchange rates and yield curves. Fair values determined by Level 3 inputs utilize unobservable data points for the asset or liability. The Company’s Level 1 assets consist of time deposits, money market funds and investments in a Treasury money market fund and the Company’s Level 2 assets consist of high-quality government bonds that are valued using observable market prices. The Company’s Level 3 liabilities represent acquired contingent consideration related to the acquisition of Civitas and are valued using a probability weighted discounted cash flow valuation approach. No changes in valuation techniques occurred during the three or nine-month periods ended September 30, 2016. The estimated fair values of all of our financial instruments approximate their carrying values at September 30, 2016, except for the fair value of the Company’s convertible senior notes, which was approximately $276 million as of September 30, 2016. The Company estimates the fair value of its notes utilizing market quotations for the debt (Level 2). (In thousands) Level 1 Level 2 Level 3 September 30, 2016 Assets Carried at Fair Value: Cash equivalents $ $ — $ — Liabilities Carried at Fair Value: Acquired contingent consideration — — December 31, 2015 Assets Carried at Fair Value: Cash equivalents $ $ $ — Short-term investments — — Liabilities Carried at Fair Value: Acquired contingent consideration — — The following table presents additional information about liabilities measured at fair value on a recurring basis and for which the Company utilizes Level 3 inputs to determine fair value. Acquired contingent consideration (In thousands) Three- Three- Nine-month Nine-month Acquired contingent consideration: Balance, beginning of period $ $ $ $ Fair value change to contingent consideration (unrealized) included in the statement of operations Balance, end of period $ $ $ $ The Company estimates the fair value of its acquired contingent consideration using a probability weighted discounted cash flow valuation approach based on estimated future sales expected from CVT-301, a phase 3 candidate for the treatment of OFF periods of Parkinson’s disease and CVT-427, a Phase I candidate. CVT-427 is an inhaled triptan intended for acute treatment of migraine using the ARCUS delivery system. Using this approach, expected future cash flows are calculated over the expected life of the agreement, are discounted, and then exercise scenario probabilities are applied. Some of the more significant assumptions made in the valuation include (i) the estimated CVT-301 and CVT 427 revenue forecasts, (ii) probabilities of success, and (iii) discount periods and rate. The probability of achievement of revenue milestones ranged from 43.9% to 70% with milestone payment outcomes ranging from $0 to $54 million in the aggregate for CVT-301 and CVT-427. The valuation is performed quarterly. Gains and losses are included in the statement of operations. For the three and nine-month periods ended September 30, 2016, changes in the fair value of the acquired contingent consideration were due to the re-calculation of cash flows for the passage of time and updates to certain other estimated assumptions. The acquired contingent consideration is classified as a Level 3 liability as its valuation requires substantial judgment and estimation of factors that are not currently observable in the market. If different assumptions were used for the various inputs to the valuation approach, including but not limited to, assumptions involving probability adjusted sales estimates for CVT-301 and CVT-427 and estimated discount rates, the estimated fair value could be significantly higher or lower than the fair value determined.

Investments

Investments	9 Months Ended
	Sep. 30, 2016
Investments
Investments	(9) Investments The Company held no short-term available-for-sale debt securities at September 30, 2016 as compared to $200.1 million at December 31, 2015 as these investments were either sold or matured during the three-month period ended March 31, 2016 to facilitate the Biotie acquisition. The contractual maturities of available-for-sale debt securities held at December 31, 2015 were greater than 3 months but less than 1 year. (In thousands) Amortized Gross Gross Estimated September 30, 2016 U.S. Treasury bonds $ — $ — $ (— ) $ — December 31, 2015 U.S. Treasury bonds — ) Short-term investments with maturities of three months or less from date of purchase have been classified as cash equivalents, and amounted to $25.5 million and $83.5 million as of September 30, 2016 and December 31, 2015, respectively. Unrealized holding gains and losses are reported within accumulated other comprehensive (loss) (AOCI) in the statements of comprehensive income. The changes in AOCI associated with the unrealized holding (losses) on available-for-sale investments during the nine-month period ended September 30, 2016, were as follows (in thousands): (In thousands) Net Balance at December 31, 2015 $ ) Other comprehensive loss before reclassifications: — Amounts reclassified from accumulated other comprehensive loss Net current period other comprehensive income Balance at September 30, 2016 $ —

Debt Obligations

Debt Obligations	9 Months Ended
	Sep. 30, 2016
Debt Obligations
Debt Obligations	(10) Debt Obligations Asset Based Loan On June 1, 2016, the Company and certain of its subsidiaries entered into a Credit Agreement (the “Credit Agreement”) with JPMorgan Chase Bank, N.A., as the sole initial lender and the administrative agent for the lenders (the “Administrative Agent”). The Credit Agreement provides the Company with a three-year senior secured revolving credit facility in the maximum amount of $60 million. Availability under the facility is subject to a borrowing base, which is based on eligible accounts receivable, inventory and equipment of the Company and certain of its U.S. subsidiaries, after adjusting for customary factors that are subject to modification from time to time by the Administrative Agent at its discretion (not to be exercised unreasonably). Based on the Company’s eligible accounts receivable and inventory and other components of the borrowing base, the availability under the facility was approximately $60 million as of September 30, 2016. Amounts drawn under the facility will bear interest, at the Company’s option, at (i) an alternate base rate (the highest of (a) the prime rate, (b) the federal funds effective rate or the overnight bank funding rate plus 0.5%, and (c) the LIBOR rate (adjusted for statutory reserve requirements for eurocurrency liabilities) plus 1%) plus 1.5%, or (ii) the LIBOR rate (adjusted for statutory reserve requirements for eurocurrency liabilities) plus 2.5%. The facility is subject to an annual commitment fee of either 0.375% or 0.50%, depending on the amounts already drawn under the facility. As of September 30, 2016, there were no amounts drawn under the facility. The Company’s obligations under the facility are guaranteed by its U.S. subsidiaries (other than its U.S. subsidiary of Biotie Therapies Oyj). The Company’s obligations under the facility and its subsidiaries’ obligations under the related guarantees are secured by first priority security interests in collateral that includes, subject to certain exceptions: · U.S. accounts receivable, inventory and manufacturing equipment; · Equity interests in the Company’s U.S. subsidiaries (other than its U.S. subsidiary of Biotie Therapies Oyj) and up to 65% of the voting equity interests of its directly owned foreign subsidiaries; and · Substantially all other tangible and intangible assets, including equipment, contract rights and intellectual property (other than intellectual property related to Ampyra). The facility contains certain covenants that, among other things, limit the Company’s ability and the ability of certain of its subsidiaries to (i) incur additional debt or issue redeemable preferred stock, (ii) pay dividends, repurchase shares or make certain other restricted payments or investments, (iii) incur liens, (iv) sell assets, (v) incur restrictions on future liens and incur restrictions on the ability of our subsidiaries to pay dividends or to make other payments to us, (vi) enter into affiliate transactions, (vii) engage in sale and leaseback transactions, and (viii) consolidate or merge. These covenants are subject to significant exceptions and qualifications. In addition, the Company will not be permitted to allow its ratio of (a) EBITDA minus Unfinanced Capital Expenditures to (b) Fixed Charges to be less than 1.10 to 1.00 on a trailing four quarter basis as of the end of any fiscal quarter during any period. The facility has customary representations and warranties including, as a condition to borrowing, that all such representations and warranties are true and correct, in all material respects, on the date of the borrowing, including representations as to no material adverse effect on the Company’s business or financial condition since December 31, 2015. The facility also has customary defaults, including a cross-default to material indebtedness of the Company and its subsidiaries. The Administrative Agent may declare any outstanding obligations under the facility immediately due and payable upon the occurrence, and during the continuance, of an event of default. In addition, any outstanding obligations under the facility will be immediately due and payable in the event that the Company or certain of its subsidiaries become the subject of voluntary or involuntary proceedings under any bankruptcy, insolvency or similar law. Non-convertible Capital Loans Non-convertible capital loans (“Tekes Loans”) granted by Tekes, a Finnish Funding Agency for Technology and Innovation, with an adjusted acquisition-date fair value of $23.3 million (€20.6 million) and a carrying value of $23.2 million as of September 30, 2016. The Tekes Loans are comprised of fourteen non-convertible loans granted by Tekes. The maturity dates for the Tekes Loans range from eight to ten years. These loans bear interest based on the greater of 3% or the base rate set by Finland’s Ministry of Finance minus one (1) percentage point. According to certain terms and conditions of the Tekes Loans, Biotie may repay the principal amounts of these loans and the accrued and unpaid interest only if the restricted equity of Biotie, including its consolidated subsidiaries, is positive (fully covered). Convertible Capital Loan Convertible capital loan issued to certain shareholders and venture capital organizations with an acquisition-date fair value of $6.0 million (€5.3 million) and a carrying value of $6.0 million as of September 30, 2016. The loan bears cash interest at a rate of 10% per annum, payable annually each year. The convertible capital loan is subject to certain terms and restrictive conditions as it relates to interest payments and repayment of the loan. The loan will yield interest from the fiscal years in which the financial statements do not present sufficient funds available for profit distribution; however, interest on the loan may be paid if Biotie, including its subsidiaries, has sufficient funds for profit distribution as of the most recently ended fiscal year. The loan may be repaid only if the restricted equity of Biotie, including its consolidated subsidiaries, for the last financial period is sufficient to repay the loan. Pursuant to the terms of the loan agreement, the loan is convertible at any time at the option of the holders into 828,000 common shares of Biotie. The conversion rates for the loan are €1.8688 per share for 540,000 of the shares and €2.3359 for the remaining 288,000 of the shares. Research and Development Loans Research and Development Loans (“R&D Loans”) granted by Tekes with an acquisition-date fair value of $2.9 million (€2.6 million) and a carrying value of $3.0 million as of September 30, 2016. The R&D Loans bear interest based on the greater of 1% or the base rate set by Finland’s Ministry of Finance minus three (3) percentage points. The repayment of these loans shall be initiated after five years, thereafter the loan principal shall be paid in equal installments over a 5 year period.

Commitments and Contingencies

Commitments and Contingencies	9 Months Ended
	Sep. 30, 2016
Commitments and Contingencies
Commitments and Contingencies	(11) Commitments and Contingencies The Company’s long-term contractual obligations include commitments and estimated purchase obligations entered into in the normal course of business. Under certain supply agreements and other agreements with manufacturers and suppliers, the Company is required to make payments for the manufacture and supply of its clinical and approved products. The Company’s major outstanding contractual obligations are for payments related to its convertible notes, capital loans, operating leases and commitments to purchase inventory. The following table summarizes the contractual obligations at September 30, 2016 and the effect such obligations are expected to have on the Company’s liquidity and cash flow in future periods: Payments due by period (1)(9) (In thousands) Total Less than 1-3 years 4-5 years Convertible Senior Notes (2) $ $ $ $ Convertible note payable (3) — — Capital loans (4) (6) — — — Research and development loans (5) (6) Operating leases (7) Inventory purchase commitments (8) — — Total $ $ $ $ (1) Excludes a liability for uncertain tax positions totaling $6.3 million. This liability has been excluded because the Company cannot currently make a reliable estimate of the period in which the liability will be payable, if ever. (2) Represents the future payments of principal and interest to be made on the Convertible Senior Notes issued in June 2014 and due in 2021. (3) Represents the remaining annual payment of principal and interest to be made on the convertible note payable to Saints Capital. (4) Represents payments for the convertible and non-convertible capital loans. The convertible capital loan and the non-convertible capital loans have a stated maturity of less than one year. However, the repayment of these loans and payment of accrued interest thereon are governed by a restrictive condition, according to which the loan principal must only be repaid if Biotie’s consolidated restricted equity is fully covered. Accrued interest must only be paid if Biotie, including its subsidiaries, has sufficient funds for profit distribution as of the most recently ended fiscal year. Interest accrues in the interim. (5) Represents the future principal payments on the R&D loans acquired from Biotie. (6) The amounts do not include interest costs at the loans’ applicable interest rates. (7) Represents payments for the operating leases of the Company’s Ardsley, NY headquarters, the Company’s manufacturing facility in Chelsea, MA, Biotie’s headquarters at Turku, Finland, and Biotie’s clinical operations in South San Francisco, CA. (8) Represents Ampyra, Zanaflex, and Qutenza inventory commitments. The Ampyra inventory commitment is an estimate as the price paid for Ampyra inventory is based on a percentage of the net product sales during the quarter Alkermes ships inventory to us. Under our supply agreement with Alkermes, we provide Alkermes with monthly written 18-month forecasts, and with annual written five-year forecasts for our supply requirements of Ampyra and two-year forecasts for our supply requirements of Zanaflex Capsules. In each of the five months for Zanaflex and three months for Ampyra following the submission of our written 18-month forecast we are obligated to purchase the quantity specified in the forecast, even if our actual requirements are greater or less. We have agreed to purchase at least 75% of our annual requirements of Ampyra from Alkermes, unless Alkermes is unable or unwilling to meet its requirements, for a percentage of net product sales and the quantity of product shipped by Alkermes to us. (9) Pursuant to the UCB Termination and Transition Agreement, Biotie is required to pay up to $4.3 million (€ 3.9 million) to UCB. The amount that will be paid will be determined based on a percentage of future consideration Biotie will receive from tozadenant. The liability is excluded as the Company cannot currently estimate the period in which the liability will be payable, if ever. The Company is currently party to various legal proceedings which are principally patent litigation matters. The Company has assessed such legal proceedings and does not believe that it is probable that a liability has been incurred or that the amount of any potential liability or range of losses can be reasonably estimated. As a result, the Company did not record any loss contingencies for any of these matters. While it is not possible to determine the outcome of these matters the Company believes that the resolution of all such matters will not have a material adverse effect on its consolidated financial position or liquidity, but could possibly be material to the Company’s consolidated results of operations in any one accounting period. Litigation expenses are expensed as incurred. Operating Leases Biotie Leases In connection with the acquisition of Biotie, the Company assumed two existing leases in Turku, Finland and South San Francisco, California. The lease for Biotie’s headquarters in Turku, Finland, was entered into on June 27, 2013. This lease will expire in November 2016, after which Biotie may extend the lease for an additional six months. The lease provides for monthly rent payments during the lease term. On August 20, 2013, Biotie entered into a 60-month lease for its clinical space located in South San Francisco, California. This lease provides for monthly rent payments during the lease term. This lease will expire in December 2018. Future minimum commitments under all of the Company’s non-cancelable operating leases subsequent to September 30, 2016 are as follows: (In thousands) 2016 $ 2017 2018 2019 2020 Later years $ Rent expense under the Company’s operating leases during the three and nine-month periods ended September 30, 2016, was approximately $1.6 million, and $4.3 million, respectively.

Summary of Significant Accoun18

Summary of Significant Accounting Policies (Policies)	9 Months Ended
	Sep. 30, 2016
Summary of Significant Accounting Policies
Foreign Currency Translation	Foreign Currency Translation — The functional currency of operations outside the United States of America is deemed to be the currency of the local country, unless otherwise determined that the United States dollar would serve as a more appropriate functional currency given the economic operations of the entity. Accordingly, the assets and liabilities of the Company’s foreign subsidiary, Biotie, are translated into United States dollars using the period-end exchange rate; and income and expense items are translated using the average exchange rate during the period; and equity transactions are translated at historical rates. Cumulative translation adjustments are reflected as a separate component of equity. Foreign currency transaction gains and losses are charged to operations.
Segment and Geographic Information	Segment and Geographic Information The Company is managed and operated as one business which is focused on the identification, development and commercialization of novel therapies to improve the lives of people with neurological disorders. The entire business is managed by a single management team that reports to the Chief Executive Officer. The Company does not operate separate lines of business with respect to any of its products or product candidates and the Company does not prepare discrete financial information with respect to separate products or product candidates or by location. Accordingly, the Company views its business as one reportable operating segment. Net product revenues reported to date are derived from the sales of Ampyra, Zanaflex and Qutenza in the U.S.
Subsequent Events	Subsequent Events Subsequent events are defined as those events or transactions that occur after the balance sheet date, but before the financial statements are filed with the Securities and Exchange Commission. The Company completed an evaluation of the impact of any subsequent events through the date these financial statements were issued, and determined the following subsequent events required disclosure in these financial statements. In October 2016, the Company entered into a 10 year lease agreement for approximately 26,000 square feet of lab/office space in Waltham, MA. The lease provides for monthly rental payments over the lease term. The Company expects to take occupancy of the space in January 2017.
Recently Issued / Adopted Accounting Pronouncements	Recently Issued / Adopted Accounting Pronouncements In April 2015, the FASB issued Accounting Standards Update 2015-03, “Interest — Imputation of Interest” (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs (ASU 2015-03), which requires that debt issuance costs related to a recognized debt liability be presented in the balance sheet as a direct deduction from the debt liability rather than as an asset. ASU-2015-03 is effective for fiscal years and interim periods therein beginning after December 15, 2015, with early adoption permitted. The Company adopted this guidance retrospectively effective in the three-month period ended March 31, 2016. The impact of the adoption of this guidance on the Company’s consolidated balance sheet as of December 31, 2015 was a reclassification of approximately $5.0 million representing the unamortized balance of debt issuance costs as of December 31, 2015 from Other Assets to the Convertible Senior Notes liability. (In thousands) Balance at December 31, 2015 Revised As Previously Other assets $ $ Convertible notes payable — due 2021 $ ) $ ) In March 2016, the FASB issued Accounting Standards Update 2016-09, “Compensation — Stock Compensation” (Topic 718). The main objective of this update is to simplify the accounting, and reporting classifications for certain aspects of share-based payment transactions. This ASU is effective for fiscal years beginning after December 15, 2016, including interim periods within those fiscal years. The Company is currently evaluating the new guidance to determine the impact it may have on its financial statements. In August 2016, the FASB issued Accounting Standards update 2016-15, “Statement of Cash Flows” (Topic 230). The main objective of this update is to reduce diversity in how certain cash receipts and cash payments are presented and classified in the statement of cash flows. This ASU is effective for fiscal years beginning after December 15, 2017, including interim periods within those fiscal years, with early adoption permitted. The Company is currently evaluating the new guidance to determine the impact it may have on its financial statements.

Summary of Significant Accoun19

Summary of Significant Accounting Policies (Tables)	9 Months Ended
	Sep. 30, 2016
Summary of Significant Accounting Policies
Schedule of new accounting pronouncement	(In thousands) Balance at December 31, 2015 Revised As Previously Other assets $ $ Convertible notes payable — due 2021 $ ) $ )

Acquisitions (Tables)

Acquisitions (Tables)	9 Months Ended
	Sep. 30, 2016
Acquisitions
Schedule of preliminary allocation of purchase price to estimated fair values of assets acquired and liabilities assumed	(In thousands) Preliminary Measurement Preliminary Cash and cash equivalents $ $ — $ Other current assets — Other long-term assets — Intangible assets (indefinite-lived) — Intangible assets (definite-lived) — Current liabilities ) — ) Deferred taxes ) — ) Other long-term liabilities ) ) Fair value of assets and liabilities acquired Goodwill ) Total purchase price — Less: Noncontrolling interests ) — ) Purchase consideration on date of acquisition $ $ — $
Schedule of activity attributable to stockholders' equity - Acorda and noncontrolling interests	(In thousands) Stockholders’ Non- Total Balance at December 31, 2015 $ $ — $ Net loss ) ) ) Other comprehensive loss ) ) ) Noncontrolling interest at date of acquisition — Purchase of noncontrolling interest ) ) ) Private Placement, net of issuance costs — Stock compensation expense and option exercises — Balance at September 30, 2016 $ $ — $
Summary of supplemental pro forma financial information	Three-month Nine-month (In thousands) 2016 2015 2016 2015 Revenues $ $ $ $ Loss from continuing operations attributable to Acorda $ ) $ ) $ ) $ )

Intangible Assets and Goodwill

Intangible Assets and Goodwill (Tables)	9 Months Ended
	Sep. 30, 2016
Intangible Assets and Goodwill
Schedule of intangible assets	September 30, 2016 December 31, 2015 (Dollars In thousands) Estimated Cost Accumulated Foreign Net Cost Accumulated Net In-process research & development (1) Indefinite-lived $ $ — $ ) $ $ $ — $ Selincro ) ) — — — Ampyra milestones ) — ) Ampyra CSRO royalty buyout ) — ) Website development costs ) — ) Website development costs — in process n/a — — — $ $ ) $ ) $ $ $ ) $ (1) Includes the fair values of: CVT-301: $423.0 million; tozadenant: $232.0 million; SYN-120: $24.2 million and BTT-1023: $4.3 million
Schedule of estimated future amortization expense for intangible assets	(In thousands) 2016 $ 2017 2018 2019 2020 Thereafter $
Schedule of changes in carrying amount of goodwill	In thousands Balance at December 31, 2015 $ Goodwill associated with the acquisition of Biotie Therapies Decrease to goodwill for measurement period adjustment ) Foreign currency translation adjustment ) Balance at September 30, 2016 $

Share-based Compensation (Table

Share-based Compensation (Tables)	9 Months Ended
	Sep. 30, 2016
Share-based Compensation
Schedule of share-based compensation expense	For the three-month For the nine-month period ended September 30, period ended September 30, (In millions) 2016 2015 2016 2015 Research and development $ $ $ $ Selling, general and administrative Total $ $ $ $
Schedule of stock option activity	Number of Weighted Weighted Intrinsic Balance at January 1, 2016 $ Granted Cancelled ) Exercised ) Balance at September 30, 2016 $ $ Vested and expected to vest at September 30, 2016 $ $ Vested and exercisable at September 30, 2016 $ $
Schedule of restricted stock activity	(In thousands) Restricted Stock Number of Nonvested at January 1, 2016 Granted Vested ) Forfeited ) Nonvested at September 30, 2016

Earnings Per Share (Tables)

Earnings Per Share (Tables)	9 Months Ended
	Sep. 30, 2016
Earnings Per Share
Schedule of computation of basic and diluted earnings per share	(In thousands, except per share data) Three- Three- Nine-month Nine-month Basic and diluted Net (loss) income $ ) $ $ ) $ Weighted average common shares outstanding used in computing net (loss) income per share—basic Plus: net effect of dilutive stock options and restricted common shares — — Weighted average common shares outstanding used in computing net (loss) income per share—diluted Net (loss) income per share—basic $ ) $ $ ) $ Net (loss) income per share—diluted $ ) $ $ ) $
Schedule of antidilutive securities excluded from calculation of net income per diluted share	(In thousands) Three- Three- Nine-month Nine-month Denominator Stock options and restricted common shares Convertible note — Saints Capital

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	9 Months Ended
	Sep. 30, 2016
Schedule of assets and liabilities measured at fair value on a recurring basis	(In thousands) Level 1 Level 2 Level 3 September 30, 2016 Assets Carried at Fair Value: Cash equivalents $ $ — $ — Liabilities Carried at Fair Value: Acquired contingent consideration — — December 31, 2015 Assets Carried at Fair Value: Cash equivalents $ $ $ — Short-term investments — — Liabilities Carried at Fair Value: Acquired contingent consideration — —
Contingent liability
Schedule of contingent liabilities	(In thousands) Three- Three- Nine-month Nine-month Acquired contingent consideration: Balance, beginning of period $ $ $ $ Fair value change to contingent consideration (unrealized) included in the statement of operations Balance, end of period $ $ $ $

Investments (Tables)

Investments (Tables)	9 Months Ended
	Sep. 30, 2016
Investments
Schedule of available-for-sale securities	(In thousands) Amortized Gross Gross Estimated September 30, 2016 U.S. Treasury bonds $ — $ — $ (— ) $ — December 31, 2015 U.S. Treasury bonds — )
Schedule of changes in accumulated other comprehensive (loss) income	The changes in AOCI associated with the unrealized holding (losses) on available-for-sale investments during the nine-month period ended September 30, 2016, were as follows (in thousands): (In thousands) Net Balance at December 31, 2015 $ ) Other comprehensive loss before reclassifications: — Amounts reclassified from accumulated other comprehensive loss Net current period other comprehensive income Balance at September 30, 2016 $ —

Commitments and Contingencies (

Commitments and Contingencies (Tables)	9 Months Ended
	Sep. 30, 2016
Commitments and Contingencies
Summary of minimum significant contractual obligations	Payments due by period (1)(9) (In thousands) Total Less than 1-3 years 4-5 years Convertible Senior Notes (2) $ $ $ $ Convertible note payable (3) — — Capital loans (4) (6) — — — Research and development loans (5) (6) Operating leases (7) Inventory purchase commitments (8) — — Total $ $ $ $ (1) Excludes a liability for uncertain tax positions totaling $6.3 million. This liability has been excluded because the Company cannot currently make a reliable estimate of the period in which the liability will be payable, if ever. (2) Represents the future payments of principal and interest to be made on the Convertible Senior Notes issued in June 2014 and due in 2021. (3) Represents the remaining annual payment of principal and interest to be made on the convertible note payable to Saints Capital. (4) Represents payments for the convertible and non-convertible capital loans. The convertible capital loan and the non-convertible capital loans have a stated maturity of less than one year. However, the repayment of these loans and payment of accrued interest thereon are governed by a restrictive condition, according to which the loan principal must only be repaid if Biotie’s consolidated restricted equity is fully covered. Accrued interest must only be paid if Biotie, including its subsidiaries, has sufficient funds for profit distribution as of the most recently ended fiscal year. Interest accrues in the interim. (5) Represents the future principal payments on the R&D loans acquired from Biotie. (6) The amounts do not include interest costs at the loans’ applicable interest rates. (7) Represents payments for the operating leases of the Company’s Ardsley, NY headquarters, the Company’s manufacturing facility in Chelsea, MA, Biotie’s headquarters at Turku, Finland, and Biotie’s clinical operations in South San Francisco, CA. (8) Represents Ampyra, Zanaflex, and Qutenza inventory commitments. The Ampyra inventory commitment is an estimate as the price paid for Ampyra inventory is based on a percentage of the net product sales during the quarter Alkermes ships inventory to us. Under our supply agreement with Alkermes, we provide Alkermes with monthly written 18-month forecasts, and with annual written five-year forecasts for our supply requirements of Ampyra and two-year forecasts for our supply requirements of Zanaflex Capsules. In each of the five months for Zanaflex and three months for Ampyra following the submission of our written 18-month forecast we are obligated to purchase the quantity specified in the forecast, even if our actual requirements are greater or less. We have agreed to purchase at least 75% of our annual requirements of Ampyra from Alkermes, unless Alkermes is unable or unwilling to meet its requirements, for a percentage of net product sales and the quantity of product shipped by Alkermes to us. (9) Pursuant to the UCB Termination and Transition Agreement, Biotie is required to pay up to $4.3 million (€ 3.9 million) to UCB. The amount that will be paid will be determined based on a percentage of future consideration Biotie will receive from tozadenant. The liability is excluded as the Company cannot currently estimate the period in which the liability will be payable, if ever.
Schedule of future minimum commitments under all of the Company's non-cancelable operating leases	(In thousands) 2016 $ 2017 2018 2019 2020 Later years $

Summary of Significant Accoun27

Summary of Significant Accounting Policies (Details) $ in Thousands	1 Months Ended	9 Months Ended
	Oct. 31, 2016ft²	Sep. 30, 2016USD ($)segment	Dec. 31, 2015USD ($)
Recently Issued / Adopted Accounting Pronouncements
Other assets		$ 5,814	$ 247
Convertible notes payable - due 2021		$ (297,111)	(290,420)
Segment and Geographic Information
Number of operating segments | segment		1
Number of reportable operating segments | segment		1
Subsequent Events | Lease for office space in Waltham, MA
Subsequent Event
Lease term	10 years
Area of lab/office | ft²	26,000
Accounting Standards Update 2015-03 | Other Noncurrent Assets
Recently Issued / Adopted Accounting Pronouncements
Unamortized debt issuance cost			(5,000)
Accounting Standards Update 2015-03 | Convertible notes payable - due 2021
Recently Issued / Adopted Accounting Pronouncements
Unamortized debt issuance cost			5,000
As Previously Reported
Recently Issued / Adopted Accounting Pronouncements
Other assets			5,296
Convertible notes payable - due 2021			$ (295,469)

Acquisitions - Biotie Therapies

Acquisitions - Biotie Therapies Corp (Details) - USD ($) $ in Thousands	Sep. 30, 2016	May 04, 2016	Apr. 18, 2016	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2016	Sep. 30, 2015	Jun. 30, 2016	Dec. 31, 2015
Preliminary allocation of purchase price to estimated fair values of assets acquired and liabilities assumed
Goodwill	$ 284,029			$ 284,029		$ 284,029	$ 284,029			$ 183,636
Net revenues				135,613	$ 148,199		378,974	$ 361,758
Net (loss) income				$ (13,032)	$ 3,941		$ (32,509)	$ 1,853
Biotie Therapies Corp.
Acquisitions
Voting interest acquired (as a percent)			93.00%
Aggregate equity purchase price			$ 350,000
Additional voting interest acquired (as a percent)	3.00%	4.00%		3.00%		3.00%	3.00%
Voting interest acquired including subsequent acquisition (as a percent)	100.00%			100.00%		100.00%	100.00%		97.00%
Purchase consideration for subsequent acquisition		$ 14,500
Payment of cash security deposit	$ 13,500
Preliminary allocation of purchase price to estimated fair values of assets acquired and liabilities assumed
Cash and cash equivalents	73,854		73,854	$ 73,854		$ 73,854	$ 73,854
Other current assets	2,208		2,208	2,208		2,208	2,208
Other long-term assets	4,962		4,962	4,962		4,962	4,962
Intangible assets (indefinite-lived)	260,500		260,500	260,500		260,500	260,500
Intangible assets (definite-lived)	65,000		65,000	65,000		65,000	65,000
Current liabilities	(17,547)		(17,547)	(17,547)		(17,547)	(17,547)
Deferred taxes	(89,038)		(89,038)	(89,038)		(89,038)	(89,038)
Other long-term liabilities	(25,556)		(26,715)	(25,556)		(25,556)	(25,556)
Fair value of assets and liabilities acquired	274,383		273,224	274,383		274,383	274,383
Goodwill	101,517		102,676	101,517		101,517	101,517
Total purchase price	375,900		375,900	375,900		375,900	375,900
Less: Noncontrolling interests	(25,736)		(25,736)	(25,736)		(25,736)	(25,736)
Purchase consideration on date of acquisition	350,164		350,164	350,164		350,164	350,164
Acquisition-related expenses						17,700
Goodwill deductible for tax purposes			0
Net revenues				1,100		1,900
Net (loss) income				(11,700)		(26,500)	(32,509)
Biotie Therapies Corp. | IPR&D
Preliminary allocation of purchase price to estimated fair values of assets acquired and liabilities assumed
Intangible assets (indefinite-lived)			$ 260,500
Biotie Therapies Corp. | Selling, general, and administrative
Preliminary allocation of purchase price to estimated fair values of assets acquired and liabilities assumed
Acquisition-related expenses				400			17,100
Biotie Therapies Corp. | Measurement Period Adjustments
Preliminary allocation of purchase price to estimated fair values of assets acquired and liabilities assumed
Other long-term liabilities	1,159			1,159		1,159	1,159
Fair value of assets and liabilities acquired	1,159			1,159		1,159	1,159
Goodwill	$ (1,159)			$ (1,159)		$ (1,159)	$ (1,159)

Acquisitions - Noncontrolling I

Acquisitions - Noncontrolling Interests (Details) - USD ($) $ in Thousands	3 Months Ended		5 Months Ended	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2016	Sep. 30, 2015	May 04, 2016
Activity attributable to common stockholders' equity and noncontrolling interests
Net loss	$ (13,032)	$ 3,941		$ (32,509)	$ 1,853
Other comprehensive loss	1,097	$ 17		(3,496)	$ 31
Stockholders' Equity Acorda
Activity attributable to common stockholders' equity and noncontrolling interests
Beginning balance				603,025
Net loss				(31,524)
Other comprehensive loss				(3,496)
Purchase of noncontrolling interest				(3,305)
Stock compensation expense and option exercises				29,972
Ending balance	$ 666,766		$ 666,766	666,766
Stockholders' Equity Acorda | Private Placement
Activity attributable to common stockholders' equity and noncontrolling interests
Private Placement, net of issuance costs				$ 72,094
Biotie Therapies Corp.
Noncontrolling Interests
Additional voting interest acquired (as a percent)	3.00%		3.00%	3.00%		4.00%
Activity attributable to common stockholders' equity and noncontrolling interests
Beginning balance				$ 603,025
Net loss	$ (11,700)		$ (26,500)	(32,509)
Other comprehensive loss				(3,606)
Noncontrolling interest at date of acquisition				25,736
Purchase of noncontrolling interest				(27,946)
Stock compensation expense and option exercises				29,972
Ending balance	$ 666,766		$ 666,766	666,766
Biotie Therapies Corp. | Private Placement
Activity attributable to common stockholders' equity and noncontrolling interests
Private Placement, net of issuance costs				72,094
Biotie Therapies Corp. | Non-Controlling Interest
Activity attributable to common stockholders' equity and noncontrolling interests
Net loss				(985)
Other comprehensive loss				(110)
Noncontrolling interest at date of acquisition				25,736
Purchase of noncontrolling interest				$ (24,641)

Acquisitions - Financing Instru

Acquisitions - Financing Instruments (Details) - Biotie Therapies Corp. - Foreign currency option - USD ($) $ in Millions	9 Months Ended
	Sep. 30, 2016	May 02, 2016
Acquisitions
Notional value of foreign currency option		$ 0
Other income
Acquisitions
Realized gain on foreign currency options	$ 9.9

Acquisitions - Pro-Forma Financ

Acquisitions - Pro-Forma Financial Information (Details) - Biotie Therapies Corp. - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Pro-Forma Financial Information
Revenues	$ 135,613	$ 149,076	$ 380,032	$ 365,092
Loss from continuing operations attributable to Acorda	$ (12,168)	$ (7,255)	$ (55,376)	$ (30,362)

Intangible Assets and Goodwil32

Intangible Assets and Goodwill - Intangible Assets (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Apr. 18, 2016	Dec. 31, 2015
Intangible Assets
Finite-lived intangible asset, Accumulated Amortization	$ (19,899)		$ (19,899)			$ (13,664)
Finite-lived intangible asset, Net Carrying Amount	66,934		66,934
Intangible asset, Cost	770,401		770,401			444,520
Intangible asset, Foreign Currency Translation Adjustments	(1,087)		(1,087)
Intangible asset, Net Carrying Amount	749,415		749,415			430,856
Amortization expense	2,800	$ 700	6,200	$ 2,300
Biotie Therapies Corp.
Intangible Assets
Value allocated to indefinite-lived intangible asset	260,500		260,500		$ 260,500
IPR&D
Intangible Assets
Indefinite-lived intangible asset, Cost	683,500		683,500			423,000
Indefinite-lived intangible assets, Foreign Currency Translation	(307)		(307)
Indefinite-lived intangible assets, Net Carrying Amount	683,193		683,193			423,000
IPR&D | Biotie Therapies Corp.
Intangible Assets
Value allocated to indefinite-lived intangible asset					$ 260,500
IPR&D | CVT-301
Intangible Assets
Indefinite-lived intangible asset, Cost	423,000		423,000
IPR&D | Tozadenant
Intangible Assets
Indefinite-lived intangible asset, Cost	232,000		232,000
IPR&D | SYN-120
Intangible Assets
Indefinite-lived intangible asset, Cost	24,200		24,200
IPR&D | BTT-1023
Intangible Assets
Indefinite-lived intangible asset, Cost	4,300		$ 4,300
Selincro
Intangible Assets
Estimated Remaining Useful Lives (Years)			7 years
Finite-lived intangible asset, Cost	65,000		$ 65,000
Finite-lived intangible asset, Accumulated Amortization	(4,229)		(4,229)
Finite-lived intangible assets, Foreign Currency Translation	(780)		(780)
Finite-lived intangible asset, Net Carrying Amount	59,991		$ 59,991
Ampyra milestones
Intangible Assets
Estimated Remaining Useful Lives (Years)			11 years
Finite-lived intangible asset, Cost	5,750		$ 5,750			5,750
Finite-lived intangible asset, Accumulated Amortization	(2,603)		(2,603)			(2,380)
Finite-lived intangible asset, Net Carrying Amount	3,147		$ 3,147			3,370
Ampyra CSRO royalty buyout
Intangible Assets
Estimated Remaining Useful Lives (Years)			4 years
Finite-lived intangible asset, Cost	3,000		$ 3,000			3,000
Finite-lived intangible asset, Accumulated Amortization	(2,035)		(2,035)			(1,817)
Finite-lived intangible asset, Net Carrying Amount	965		$ 965			1,183
Website development costs
Intangible Assets
Estimated Remaining Useful Lives (Years)			3 years
Finite-lived intangible asset, Cost	13,083		$ 13,083			12,504
Finite-lived intangible asset, Accumulated Amortization	(11,032)		(11,032)			(9,467)
Finite-lived intangible asset, Net Carrying Amount	2,051		2,051			3,037
Website development costs - in process
Intangible Assets
Finite-lived intangible asset, Cost	68		68			266
Finite-lived intangible asset, Net Carrying Amount	$ 68		$ 68			$ 266

Intangible Assets and Goodwil33

Intangible Assets and Goodwill - Future Amortization Expense (Details) $ in Thousands	Sep. 30, 2016USD ($)
Estimated future amortization expense
2,016	$ 2,857
2,017	10,994
2,018	10,298
2,019	9,987
2,020	9,602
Thereafter	23,196
Finite-lived intangible asset, Net Carrying Amount	$ 66,934

Intangible Assets and Goodwil34

Intangible Assets and Goodwill - Goodwill (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2016USD ($)
Changes in carrying amount of goodwill
Beginning balance	$ 183,636
Goodwill associated with the acquisition of Biotie Therapies	102,676
Decrease to goodwill for measurement period adjustment	(1,159)
Foreign currency translation adjustment	(1,124)
Ending balance	$ 284,029

Share-based Compensation - Expe

Share-based Compensation - Expense (Details) - USD ($) $ / shares in Units, $ in Millions	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Share based compensation disclosure
Share-based compensation expense recognized	$ 10	$ 8.9	$ 27.4	$ 24.7
Stock Options and Restricted Stock Awards
Share based compensation disclosure
Weighted average fair value of options granted (in dollars per share)	$ 11.21	$ 14.74	$ 13.65	$ 15.89
Research and development
Share based compensation disclosure
Share-based compensation expense recognized	$ 2.9	$ 2.2	$ 7.7	$ 6.2
Selling, general, and administrative
Share based compensation disclosure
Share-based compensation expense recognized	$ 7.1	$ 6.7	$ 19.7	$ 18.5

Share-based Compensation - Stoc

Share-based Compensation - Stock Options and Restricted Stock (Details) $ / shares in Units, shares in Thousands, $ in Thousands	9 Months Ended
	Sep. 30, 2016USD ($)$ / sharesshares
Share based compensation, other disclosures
Total unrecognized compensation costs related to unvested stock options and restricted stock awards that the company expects to recognize | $	$ 63,700
Weighted average period	2 years 4 months 24 days
Stock Options
Stock Option Activity
Beginning balance (in shares)	8,223
Granted (in shares)	1,717
Cancelled (in shares)	(526)
Exercised (in shares)	(141)
Ending balance (in shares)	9,273
Vested and expected to vest at end of period (in shares)	9,175
Vested and exercisable at end of period (in shares)	5,877
Weighted Average Exercise Price
Balance at the beginning of the period (in dollars per share) | $ / shares	$ 30.97
Granted (in dollars per share) | $ / shares	31.91
Cancelled (in dollars per share) | $ / shares	34.22
Exercised (in dollars per share) | $ / shares	18.33
Balance at the end of the period (in dollars per share) | $ / shares	31.15
Vested and expected to vest at the end of the period (in dollars per share) | $ / shares	31.13
Vested and exercisable at the end of the period (in dollars per share) | $ / shares	$ 29.60
Weighted Average Remaining Contractual Term
Balance at the end of the period	6 years 4 months 24 days
Vested and expected to vest at the end of the period	6 years 4 months 24 days
Vested and exercisable at the end of the period	5 years 3 months 18 days
Intrinsic Value
Balance at the end of the period | $	$ 816
Vested and expected to vest at the end of the period | $	816
Vested and exercisable at the end of the period | $	$ 816
Restricted Stock
Restricted Stock Activity
Nonvested at the beginning of the period (in shares)	441
Granted (in shares)	659
Vested (in shares)	(19)
Forfeited (in shares)	(219)
Nonvested at the end of the period (in shares)	862

Earnings Per Share - EPS (Detai

Earnings Per Share - EPS (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Basic and diluted
Net (loss) income	$ (12,725)	$ 3,941	$ (31,524)	$ 1,853
Weighted average common shares outstanding used in computing net (loss) income per share-basic	45,378	42,174	45,178	42,097
Plus: net effect of dilutive stock options and restricted common shares		1,258		1,337
Weighted average common shares outstanding used in computing net (loss) income per share-diluted	45,378	43,432	45,178	43,434
Net (loss) income per share-basic	$ (0.28)	$ 0.09	$ (0.70)	$ 0.04
Net (loss) income per share-diluted	$ (0.28)	$ 0.09	$ (0.70)	$ 0.04

Earnings Per Share - Amounts no

Earnings Per Share - Amounts not included (Details) - shares shares in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Stock options and restricted common shares
Antidilutive Securities
Anti-dilutive securities excluded from computation of earnings per share (in shares)	8,278	4,630	7,821	4,517
Convertible note - Saints Capital
Antidilutive Securities
Anti-dilutive securities excluded from computation of earnings per share (in shares)	10	19	10	19

Income Taxes (Details)

Income Taxes (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Jul. 31, 2015	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Reconciliation of statutory federal income tax rate to effective income tax rate
Income tax (provision) benefit		$ (3,023)	$ (17,770)	$ 7,686	$ (16,861)
Effective income tax rate (as a percent)		30.00%	82.00%	19.00%	90.00%
Payment to the former equity holders	$ 8,800

Fair Value Measurements - Recur

Fair Value Measurements - Recurring (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Assets Carried at Fair Value:
Short-term investments		$ 200,101
Level 2
Liabilities Carried at Fair Value:
Convertible senior notes	$ 276,000
Recurring basis | Level 1
Assets Carried at Fair Value:
Cash equivalents	25,519	70,504
Recurring basis | Level 2
Assets Carried at Fair Value:
Cash equivalents		13,009
Short-term investments		200,101
Recurring basis | Level 3 | Contingent liability
Liabilities Carried at Fair Value:
Acquired contingent consideration	$ 75,400	$ 63,500

Fair Value Measurements - Level

Fair Value Measurements - Level 3 (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Assets and liabilities measured at fair value on a recurring basis utilizing Level 3 inputs
Balance, beginning of period	$ 71,700	$ 56,800	$ 63,500	$ 52,600
Fair value change to contingent consideration (unrealized) included in the statement of operations	3,700	3,200	11,900	7,400
Balance, end of period	$ 75,400	$ 60,000	$ 75,400	$ 60,000
Contingent liability
Assets and liabilities measured at fair value on a recurring basis utilizing Level 3 inputs
Milestone payment, minimum (as a percent)	43.90%		43.90%
Milestone payment, maximum (as a percent)	70.00%		70.00%
Milestone payment, minimum	$ 0		$ 0
Milestone payment, maximum	$ 54,000		$ 54,000

Investments - Available-for-sal

Investments - Available-for-sale (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Sep. 30, 2016
Investments
Short-term available-for-sale debt securities	$ 200,100	$ 0
Short-term investments classified as cash and cash equivalents	$ 83,500	$ 25,500
Minimum
Investments
Short-term investments maturity term	3 months
Maximum
Investments
Short-term investments maturity term	1 year
U.S. Treasury bonds
Investments
Amortized Cost	$ 200,244
Gross unrealized losses	(143)
Estimated fair value	$ 200,101

Investments - AOCI (Details)

Investments - AOCI (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Changes in accumulated other comprehensive (loss) income
Balance at the beginning of the period			$ (119)
Amounts reclassified from accumulated other comprehensive loss			119
Net current period other comprehensive income	$ 1,097	$ 17	(3,496)	$ 31
Balance at the end of the period	$ (3,615)		(3,615)
Net Unrealized Gains (Losses) on Marketable Securities
Changes in accumulated other comprehensive (loss) income
Balance at the beginning of the period			(119)
Amounts reclassified from accumulated other comprehensive loss			119
Net current period other comprehensive income			$ 119

Debt Obligations - Asset Based

Debt Obligations - Asset Based Loan (Details) - JPMorgan Chase Bank, N.A. - Senior secured revolving credit facility - USD ($) $ in Millions	Jun. 01, 2016	Sep. 30, 2016
Line of Credit Facility Line Items
Term of credit facility	3 years
Maximum borrowing capacity	$ 60
Initial availability under the facility		$ 60
Amounts drawn under the facility		$ 0
Voting equity interests	65.00%
Minimum
Line of Credit Facility Line Items
Commitment fee percentage	0.375%
EBITDA minus Unfinanced Capital Expenditures to Fixed Charges	1.10
Maximum
Line of Credit Facility Line Items
Commitment fee percentage	0.50%
Federal funds effective rate
Line of Credit Facility Line Items
Basis Spread (as a percent)	0.50%
LIBOR
Line of Credit Facility Line Items
Basis Spread (as a percent)	1.50%
Floor rate	1.00%
LIBOR 1
Line of Credit Facility Line Items
Basis Spread (as a percent)	2.50%

Debt Obligations - Non-converti

Debt Obligations - Non-convertible Capital Loans, Convertible Capital Loan, Research and Development Loans (Details) € / shares in Units, € in Millions, $ in Millions	9 Months Ended
	Sep. 30, 2016EUR (€)item€ / sharesshares	Sep. 30, 2016USD ($)
Non-convertible Capital Loans
Debt Instrument [Line Items]
Fair value of debt	€ 20.6	$ 23.3
Carrying value of debt		$ 23.2
Number of loans | item	14
Non-convertible Capital Loans | Finland's Ministry of Finance
Debt Instrument [Line Items]
Basis Spread to be reduced (as a percent)	1.00%
Non-convertible Capital Loans | Minimum
Debt Instrument [Line Items]
Maturity date	8 years
Non-convertible Capital Loans | Minimum | Finland's Ministry of Finance
Debt Instrument [Line Items]
Interest rate	3.00%	3.00%
Non-convertible Capital Loans | Maximum
Debt Instrument [Line Items]
Maturity date	10 years
Convertible Senior Notes
Debt Instrument [Line Items]
Fair value of debt	€ 5.3	$ 6
Carrying value of debt		$ 6
Interest rate	10.00%	10.00%
Common shares issued by conversion of loan | item	828,000
Conversion rate for 540,000 shares | € / shares	€ 1.8688
Number of shares with conversion rate of 1.8688 | shares	540,000
Conversion rate for 288,000 shares | € / shares	€ 2.3359
Number of shares with conversion rate of 2.3359 | shares	288,000
Research and development loans
Debt Instrument [Line Items]
Fair value of debt	€ 2.6	$ 2.9
Carrying value of debt		$ 3
Research and development loans | Finland's Ministry of Finance
Debt Instrument [Line Items]
Basis Spread to be reduced (as a percent)	3.00%
Loan repayment initiation (in period)	5 years
Period in which equal installments to be paid	5 years
Research and development loans | Minimum | Finland's Ministry of Finance
Debt Instrument [Line Items]
Interest rate	1.00%	1.00%

Commitments and Contingencies -

Commitments and Contingencies - Minimum Significant Contractual Obligations (Details) - 9 months ended Sep. 30, 2016 $ in Thousands, € in Millions	EUR (€)	USD ($)
Operating leases
Total		$ 31,659
Less than 1 year		6,255
1-3 years		12,258
4-5 years		13,146
Inventory purchase commitments
Total		34,980
Less than 1 year		34,980
Total
Total		465,449
Less than 1 year		49,017
1-3 years		25,534
4-5 years		370,809
Liability for uncertain tax position		6,300
Biotie Therapies Corp.
Operating leases
Total		44,142
Less than 1 year		1,564
Biotie Therapies Corp. | Maximum
Total
Required amount to be paid to UCB for Termination and Transition Agreement	€ 3.9	$ 4,300
Alkermes | Ampyra
Total
Monthly written forecasts (in months)	18 months	18 months
Annual written forecasts (in years)	5 years	5 years
Period for obligation to purchase quantity specified in forecasts (in months)	3 months	3 months
Minimum agreed percentage of annual requirements for purchase	75.00%	75.00%
Alkermes | Zanaflex
Total
Annual written forecasts (in years)	2 years	2 years
Period for obligation to purchase quantity specified in forecasts (in months)	5 months	5 months
Convertible Senior Notes
Long term debt
Total		$ 374,575
Less than 1 year		6,038
1-3 years		12,075
4-5 years		356,462
Convertible note payable
Long term debt
Total		1,144
Less than 1 year		1,144
Capital loans
Long term debt
Total		20,089
Research and development loans
Long term debt
Total		3,002
Less than 1 year		600
1-3 years		1,201
4-5 years		$ 1,201

Commitments and Contingencies47

Commitments and Contingencies - Operating Leases (Details) $ in Thousands	Aug. 20, 2013	Sep. 30, 2016USD ($)	Sep. 30, 2016USD ($)lease
Future minimum commitments under all non-cancelable operating leases
2,016		$ 6,255	$ 6,255
Total		31,659	$ 31,659
Biotie Therapies Corp.
Operating Leases
Number of assumed existing leases | lease			2
Future minimum commitments under all non-cancelable operating leases
2,016		1,564	$ 1,564
2,017		6,252	6,252
2,018		6,347	6,347
2,019		5,821	5,821
2,020		5,966	5,966
Later years		18,192	18,192
Total		44,142	44,142
Rent expense under operating leases		$ 1,600	$ 4,300
Lease for headquarters in Turku, Finland | Biotie Therapies Corp.
Operating Leases
Additional lease term (in months)			6 months
Lease for clinical space located in South San Francisco | Biotie Therapies Corp.
Operating Leases
Lease term (in months)	60 months