Health stocks were mixed in the middle of what's been -- and will likely continue to be -- a volatile week.

The Nasdaq and Amex biotech indices lagged by 0.8% and 1.2%, respectively. But big pharma did slightly better; the Amex pharmaceutical index edged up 0.6%.

A slew of big pharmas, including AstraZeneca ( AZN), King ( KG), Pfizer ( PFE), Sanofi Aventis ( SNY) and Wyeth ( WYE), registered more than 2% gains for the day.

Device maker Boston Scientific ( BSX) said Wednesday that a Delaware court ruled in favor of Johnson & Johnson ( JNJ) in a patent dispute regarding a J&J patent and Boston Scientifics NIR stent product, which hasn't been sold since 2004. The result, Boston Scientific will have to pay roughly $702 million in prejudgment interest and damages.

Boston Scientific shares fell $1.02, or 8.3%, to $11.25, while J&J's shares were off by $1.41, or 2.1%, at $67.87.

Advanced Life Sciences ( ADLS) said Wednesday that it submitted a new drug application in the U.S. for cethromycin, an antibiotic for respiratory tract infections. Separately, it said it signed a deal with Wyeth ( WYE) for development and commercialization of the drug in the Asia pacific region, excluding Japan.

In exchange for Asian rights to cethromycin, Wyeth agreed to purchase a 4.9% stake in Advanced Life Sciences and will pay milestones and sales royalties on the future development and sales of the antibiotic.

Advanced Life Sciences shares were off by 14 cents, or 17%, at 67 cents, while Wyeth shares were up $1.19 cents, or 3.2%, at $38.15.

Emergent Biosystems ( EBS) signed a new fixed-price contract through 2011 to with the U.S. Department of Health and Human Services (HHS) to supply an additional 14.5 million doses of BioThrax anthrax vaccine to be included in the national stockpile. The government will pay Emergent between $364 million and $404 million for the follow-on contract.

Emergent's shares were up 91 cents, or 6.9%, at $14.00.

Losing ground Wednesday, Cyberonics ( CYBX) said that its process to find a partner for VNS Therapy for depression hasn't produced a sufficient offer. The company, which is evaluating its alternatives, reaffirmed that it won't undertake a new trial without a partner.

Two post-marketing studies mandated by the FDA to maintain approval of the VNS Therapy for depression are expected to cost between $3.5 million and $4.0 million in the second half of 2009, less than $4 million in 2010 and less than $2 million in 2011. The company is generating $3 million a year in revenue from the depression indication. Shares were down $1.39, or 8.2%, at $15.61.

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