7. Stockholders’ Equity

Option activity under our stock-based compensation plans during the six months ended June 30, 2014 was as follows (in thousands except per share amounts):

	Shares Underlying Outstanding Options (in thousands)			Weighted-Average Exercise Price Per Share		Weighted-Average Remaining Contractual Term (years)		Aggregate Intrinsic Value (in thousands)
Balance at December 31, 2013		15,765		$	3.17
Options granted		5,455			1.69
Options exercised		(25	)		0.54
Options cancelled:
Options forfeited (unvested)		(454	)		2.70
Options cancelled (vested)		(587	)		3.64
Balance at June 30, 2014		20,154			2.77		6.14	$	647
Vested and expected to vest at June 30, 2014		20,154			2.77		6.14	$	647
Exercisable at June 30, 2014		11,588			3.27		3.88	$	548

Restricted stock unit activity under our stock-based compensation plans during the six months ended June 30, 2014 was as follows (in thousands except per share amounts):

	Number of Shares (In thousands)			Weighted-Average Grant-Date Fair Value
Non-vested as of December 31, 2013		1,275		$	3.93
Granted		1,555		$	1.79
Vested		-		$	-
Forfeited or expired		(1,025	)	$	4.24
Non-vested as of June 30, 2014		1,805		$	1.71

The aggregate intrinsic value of the restricted stock units outstanding as of June 30, 2014, based on our stock price on that date, was $2.9 million.

As of June 30, 2014, approximately 1,100,000 shares underlying stock options and restricted stock units awards with performance-based vesting criteria were outstanding.

Under our stock-based compensation plans, option awards generally vest over a four-year period contingent upon continuous service and expire ten years from the date of grant (or earlier upon termination of continuous service). The fair value-based measurement of each option is estimated on the date of grant using the Black-Scholes option valuation model.

The fair value-based measurements and weighted-average assumptions used in the calculations of these measurements are as follows:

	Stock Options						Stock Options						Employee Stock Purchase Plan
	Three Months Ended						Six Months Ended						Six Months Ended
	June 30,						June 30,						June 30,
	2014			2013			2014			2013			2014			2013
Weighted-average fair value	$	1.36		$	2.05		$	1.55		$	2.46		$	0.92		$	1.46
Risk-free interest rate		1.9	%		0.9	%		1.8	%		1.0	%		0.2	%		0.2	%
Expected life (in years)		5.8			6.0			5.9			5.9			1.1			1.3
Volatility		1.3			1.4			1.4			1.4			0.9			0.7

We recognized stock-based compensation expense of $1.7 million and $3.7 million for the three months ended June 30, 2014 and 2013, respectively. Stock-based compensation during the three months ended June 30, 2013 included $1.9 million of expense for accelerated vesting of stock options related to management continuity and severance arrangements. We recognized stock-based compensation expense of $2.9 million and $8.0 million for the six months ended June 30, 2014 and 2013, respectively. Stock-based compensation during the six months ended June 30, 2013 included $3.9 million related to severance arrangements.

The components of stock-based compensation expense were (in thousands):

	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2014		2013		2014		2013
Research and development	$	738	$	1,027	$	1,430	$	2,350
General and administrative		938		2,709		1,516		5,652
Total	$	1,676	$	3,736	$	2,946	$	8,002

As of June 30, 2014, the total unrecognized compensation cost related to non-vested equity awards including all awards with time-based vesting amounted to $16.6 million, which is expected to be recognized over the remaining weighted-average vesting period of 3.03 years. Additionally, as of June 30, 2014, the total unrecognized compensation cost related to equity awards with performance-based vesting criteria not deemed probable of vesting amounted to $0.4 million.

Employee Stock Purchase Plan

As of June 30, 2014, 996,000 shares have been reserved and approved for issuance under the 2004 Employee Stock Purchase Plan, subject to adjustment for a stock split, any future stock dividend or other similar change in our common stock or capital structure. To date, employees have acquired 887,987 shares of our common stock under the 2004 Employee Stock Purchase Plan including 59,573 shares during the six months ended June 30, 2014. As of June 30, 2014, 108,013 shares of our common stock remained available for future purchases. In May 2014, stockholders of the Company approved the 2014 Employee Stock Purchase Plan, pursuant to which the Company may issue up to 500,000 shares of its common stock to its employees.

Warrants

As of June 30, 2014, warrants to purchase an aggregate of approximately 10,900,000 shares of our common stock were outstanding. The warrants are exercisable at a weighted average price of $1.50 per share and expire in the second quarter of 2015. During the six months ended June 30, 2014 and 2013 warrants were exercised to purchase an aggregate of approximately 100 and 84,000 shares of our common stock, respectively.

Preferred Stock Outstanding

As of June 30, 2014, there were 5,000,000 shares of preferred stock authorized and 43,430 shares of $0.001 par value Series B Convertible Preferred Stock outstanding. Each share of Series B Convertible Preferred Stock is convertible into 1,000 shares of common stock at any time at the holder’s option. However, the holder is prohibited from converting the Series B Convertible Preferred Stock into shares of common stock if, as a result of such conversion, the holder and its affiliates would own more than 9.98% of the total number of shares of common stock then issued and outstanding. In the event of the Company’s liquidation, dissolution, or winding up, holders of Series B Convertible Preferred Stock will receive a payment equal to $0.001 per share before any proceeds are distributed to the common stockholders. Shares of Series B Convertible Preferred Stock generally have no voting rights, except as required by law and except that the consent of holders of a majority of the outstanding Series B Convertible Preferred Stock is required to amend the terms of the Series B Convertible Preferred Stock. Holders of Series B Convertible Preferred Stock are not entitled to receive any dividends, unless and until specifically declared by the Company’s board of directors. The Series B Convertible Preferred Stock ranks senior to the Company’s common stock as to distributions of assets upon the Company’s liquidation, dissolution or winding up, whether voluntarily or involuntarily. The Series B Convertible Preferred Stock may rank senior to, on parity with or junior to any class or series of the Company’s capital stock created in the future depending upon the specific terms of such future stock issuance.