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CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($)
$ in Thousands
9 Months Ended 12 Months Ended
Dec. 31, 2013
Dec. 31, 2015
Dec. 31, 2014
CASH FLOWS FROM OPERATING ACTIVITIES:      
Net (loss) income $ 17,649 $ (227,163) $ (30,061)
Adjustments to reconcile net loss to cash flows from operating activities:      
Depreciation and amortization 70,765 85,596 98,087
Share-based compensation expense 33,409 97,341 59,579
Deferred income taxes (15,393) (37,580) (19,192)
Excess tax benefit from share-based compensation (11,394) (28,576) (32,367)
Gain on sale of investment in Civitas Therapeutics, Inc.     (29,564)
Gain on the Gainesville Transaction   (9,636)  
Decrease in the fair value of contingent consideration   2,300  
(Gain) loss on sale of property, plant and equipment 129 (3,272) (40,099)
Gain on sale of investment of Acceleron Pharma Inc.     (15,296)
Other non-cash charges (5,860) (1,351) 9,192
Changes in assets and liabilities, net of divestiture:      
Receivables (9,534) (16,455) (17,397)
Inventory, prepaid expenses and other assets (6,345) 19,618 (31,237)
Accounts payable and accrued expenses 16,126 76,155 56,896
Deferred revenue 4,051 (629) (996)
Other long-term liabilities (1,382) 3,292 3,594
Cash flows (used in) provided by operating activities 92,221 (40,360) 11,139
CASH FLOWS FROM INVESTING ACTIVITIES:      
Additions of property, plant and equipment (19,054) (52,877) (33,651)
Proceeds from the sale of equipment 52 535 44,365
Net proceeds from the Gainesville Transaction   49,966  
Investment in Civitas Therapeutics, Inc. (1,191)   27,190
Purchases of investments (135,643) (508,683) (642,455)
Sales and maturities of investments 90,470 467,573 341,154
Cash flows used in investing activities (65,366) (43,486) (263,397)
CASH FLOWS FROM FINANCING ACTIVITIES:      
Proceeds from the issuance of ordinary shares, net     248,406
Proceeds from the issuance of ordinary shares under share-based compensation arrangements 49,077 44,969 47,577
Excess tax benefit from share-based compensation 11,394 28,576 32,367
Employee taxes paid related to net share settlement of equity awards (11,665) (25,904) (12,840)
Principal payments of long-term debt (5,060) (6,750) (6,750)
Cash flows provided by financing activities 43,746 40,891 308,760
NET (DECREASE) INCREASE IN CASH AND CASH EQUIVALENTS 70,601 (42,955) 56,502
CASH AND CASH EQUIVALENTS - Beginning of period 96,961 224,064 167,562
CASH AND CASH EQUIVALENTS - End of period 167,562 181,109 224,064
SUPPLEMENTAL CASH FLOW DISCLOSURE:      
Cash paid for interest 9,596 12,323 12,489
Cash paid for taxes 704 705 2,799
Non-cash investing and financing activities:      
Purchased capital expenditures included in accounts payable and accrued expenses $ 1,969 6,054 $ 3,483
Fair value of warrants received as part of the Gainesville Transaction   2,123  
Fair value of contingent consideration received as part of the Gainesville Transaction   $ 57,600