Out of the chute this morning, the S&P/Case-Shiller index rose 1.2% in July and gave the market a nice uptick for a while. Then came the report from the Conference Board that its consumer confidence index for September fell to 53.1 from 54.5 in August. What was worse is that economists had estimated a rise to 57 for the month. The soft confidence number is almost certainly due to people worried about losing their jobs. Right now, it could be that traders are waiting for Friday's unemployment report before jumping one way or the other. The negative news won out and the indexes traded down most of the day.

The numbers:

Dow

S&P 500

Nasdaq

Today was an unusually active day for extremely volume increases in several stocks which traded on news and rumors.

Shares in Sequenom (NASDAQ: SQNM) jumped over 10% on takevover rumors.

Rite Aide (NYSE: RAD) moved higher by 5% on larger than normal volume as it beat earnings estimates and Monsanto (NYSE: MON) traded up on strong numbers and took a number of agriculture stocks with it. Oracle (NASDAQ: ORCL) also benefited from earnings above Wall Street forecasts.

Palm (NASDAQ: PALM) traded higher as RBC upped its price target to $18 from $14, and MEMC (NYSE: WFR) fell on a downgrade from JPMorgan.

Douglas A. McIntyre is an editor at VSInvestor.com.

The Federal Reserve's cautious Beige Book may have been a small catalyst to keep a lid on the market, but the real weakness was after the 10-Year Treasury auction came in very weak and 10-year Treasury rates flirted with 4%. Higher draw-downs in oil inventories also kept energy prices higher. Here were today's unofficial closing bell levels:

Dow 8,739.02 -24.04 (-0.27%)
S&P 500 939.15 -3.28 (-0.35%)
Nasdaq 1,853.08 -7.05 (-0.38%)

Top Analyst Upgrades
Top Analyst Downgrades

Today was one of those days where the overall market direction never felt entrenched nor felt certain. The news of ten banks getting to pay back TARP funds created mixed reactions, as the news was expected. Positive guidance from a chip leader may have kept the wheels on the cart for technology stocks. Oil also spent much of the day flirting with the $70 per barrel mark.

With the swings we are seeing from positive to negative, it is just further evidence that there is a battleground between bulls and bears forming. So far the bulls are managing to keep the high ground. Here are today's unofficial closing bell levels:

DJIA
S&P500
NASDAQ

Top Analyst Upgrades
Top Analyst Downgrades

Here are some highlights from this past week's earnings coverage from BloggingStocks:

• Bristol-Myers Squibb Co. (NYSE: BMY) Q1 profit fell despite strong sales of Plavix and Abilify.
• Check Point Software Technologies Inc. (NASDAQ: CHKP) was downgraded based on its guidance.
• Domino's Pizza Inc. (NYSE: DPZ) strong Q1 results were boosted by early debt retirement.
• DreamWorks Animation SKG Inc. (NYSE: DWA) strong Q1 results were driven by Madagascar 2.
• Endo Pharmaceuticals Holdings Inc. (NASDAQ: ENDP) Q1 results led to an analyst's downgrade.
• E*Trade Financial Corp. (NASDAQ: ETFC) widened its Q1 loss, sending shares sharply lower.

Analyst upgrades:

• Stephens upgraded Arris (NASDAQ: ARRS) to Overweight from Equal Weight following the company's Q1 results and raised its target on shares to $15 from $8.
  
• Goldman upgraded Goodyear Tire (NYSE: GT) to Neutral from Sell and raised their target to $11 from $7 citing better earnings prospects and stabilizing volumes.
  
• KeyBanc upgraded Parkway Properties (NYSE: PKY) to Hold from Underweight citing the company's improved balance sheet and valuation.
• Digital River (NASDAQ: DRIV) was raised to Perform from Underperform at Oppenheimer.
  
• Barclays (NYSE: BCS) was raised to Buy from Sell at Royal Bank of Scotland.
  
• First Potomac (NYSE: FPO) was upgraded at RBC Capital to Sector Perform from Underperform.

Look for Sequenom, Inc. (NASDAQ: SQNM) to be smacked hard by selling pressure today. Late Wednesday, the company reported that improper handling of research and development test data and results by its employees has delayed the launch of its Down's Syndrome test. Sequenom said it's forming a special committee to investigate employee activity related to the tainted test data.

The company's SEQureDx tests the DNA of a fetus, via the mother's blood, in order to determine whether their blood groups are compatible. Although Sequenom can no longer rely on previously announced test data and results, Chief Executive Harry Stylli asserted, "We are not back at square one" on a conference call.

Analyst upgrades:

• Goldman upgraded Gerdau AmeriSteel (NYSE: GNA) to Buy from Neutral and has a $5.50 target on shares. Shares were upgraded due to the potential impact from infrastructure spending. Note that Goldman downgraded Steel Dynamics (NYSE: STLD) and Olympic Steel (NYSE: ZEUS) to Neutral from Buy.
  
• Banc of America/Merrill upgraded Coca-Cola Enterprises (NYSE: CCE) to Buy from Neutral and raised the price target to $18 from $15. The firm the strong Q1 report gives them greater confidence in shares.
  
• Roth Capital upgraded Halozyme (NASDAQ: HALO) to Buy from Hold due to increased clarity into Roche programs, the discontinuation of the chemophase program, and progress on insulin delivery.
• American Movil (NYSE: AMX) was raised to Overweight from Neutral at JP Morgan and to Hold from Sell at Citigroup.
  
• Barclays (NYSE: BCS) and Lloyds TSB Group (NYSE: LYG) were upgraded at HSBC to Overweight from Neutral.

Analyst upgrades:

• Jefferies upgraded Abiomed (NASDAQ: ABMD) to Hold from Underperform on valuation as it believes concerns over the company's Impella heart pump are priced in at current levels. The firm lowered its target price to $7 from $8.
  
• Suntrust upgraded Somanetics (NASDAQ: SMTS) to Neutral from Reduce. The firm believes most of the risk is out of Somanetics shares and that the Q1 report could be a positive catalyst.
  
• Banc of America/Merrill upgraded shares of Telecom Italia (NYSE: TI) to Buy from Neutral on valuation and believes the company's revenue trends are improving.
• China Petroleum & Chemical (NYSE: SNP) was raised to Buy from Neutral at UBS.
• Hexcel (NYSE: HXL) and Johnson Controls (NYSE: JCI) were upgraded to Buy from Neutral at Goldman.

Intermune (NASDAQ: ITMN) closed at $11.72. ITMN's Pirfenidone Capacity data is expected soon. ITMN February 12.5 straddle is priced at $7.40, April 12.5 straddle is at $9.80 and July 12.5 straddle is priced at $14.10 according to Track Data, suggesting large price movement.

Sequenom (NASDAQ: SQNM) closed at $23.09. SQNM will present Down's syndrome data after the market close today. SQNM February option implied volatility is at140; March is at 120; above its 26-week average of 103, according to Track Data, suggesting larger price movement.

Today would have likely felt like Day 3 of the market siege, but thankfully the master of the universe came to a key firm's rescue. The bad news is that the stock markets were mixed all day and the key index levels didn't gain at the end of the day. The good news is that there was no systematic free fall. Bernanke changed his tone marginally to convey a better bailout message, and Paulson was more on target today in conveying the need and lack of outright costs to the system. Things are so bad that the Presidential campaigns are being put on hold temporarily.

Here are today's unofficial closing bell levels:
DJIA 10,825.17 -29 -0.275%
NASDAQ 2,155.68 +2.35 +0.11%
S&P500 1,185.89 -2.23 -0.19%
10YR T-Note 3.771% (-0.07%)
Top Analyst Upgrades
Top Analyst Downgrades
52-Week Low Club

Goldman Sachs Group Inc. (NYSE: GS) was the real stabilizer today despite what the overall index levels closed at. It raised $5 billion in a stock sale and received a $5 billion investment from Warren Buffett. Shares were up almost 6% at $132.20 right before the close.

Sequenom (NASDAQ: SQNM) makes the MassARRAY system, a nucleic acid analysis platform that identifies and quantifies genetic target materials. The system is composed of electronic analysis equipment, related software and various consumables. It is used in biomedical research, livestock testing, oncology diagnoses, molecular medicine, noninvasive prenatal testing, and infectious disease identification. Customers include clinical research laboratories, biotechnology concerns, and universities.

The company surprised the Street last week, when it announced a successful trial of its prenatal test used to detect Down-syndrome in a mother's blood. In blinded studies involving 200 clinical samples, Sequenom's proprietary test identified all Down-syndrome samples with no false positives. The company pointed out that current testing options have a detection rate of 70-90%, with false-positive rates as high as 5%. Management said it will start a study of several thousand samples in the fourth quarter, in preparation for a U.S. launch of the test in the first half of 2009.

This was quite a week in biotechnology. You had a major premium buyout and had much data come out from the American Society of Clinical Oncology (ASCO) and others. This is far from all of the movers, but it is a brief summary of the major gainers from BioHealthInvestor.com showing how large some moves were in biotechnology this week.

Acorda Therapeutics Inc. (NASDAQ: ACOR) had a great week after it announced positive data from a second Phase III study of its Fampridine-SR for patients' walking abilities who suffer from multiple sclerosis (MS). FULL DETAILS

Auxilium Pharmaceuticals Inc. (NASDAQ: AUXL) was a strange stock this week. The company reported great news but shares slid before the market figured out it had misinterpreted news in the company. INITIAL DETAILS

Inspire Pharmaceuticals Inc. (NASDAQ: ISPH) saw a surge after it reached its primary endpoint in Phase III trial of Denufosol for Cystic Fibrosis. FULL DETAILS

MOST NOTEWORTHY: AU Optronics, General Steel and Sequenom were today's noteworthy initiations:

• Jefferies initiated AU Optronics (NYSE: AUO) with a Buy rating and $25 target and believes LCD trends will be healthy in 2008 despite a soft economy.
  
• General Steel (NYSE: GSI) shares were started at Merriman with a Buy rating, as the firm believes strong demand for steel in China should last for years and finds the valuation attractive at current levels.
  
• Cantor believes Sequenom (NASDAQ: SQNM) is positioned to establish sustainable market leadership as a provider of genome analytical products and molecular diagnostics. Shares were assumed with a Buy rating and $12 target.

OTHER INITIATIONS:

• UBS initiated Altria Group (NYSE: MO) with a Buy rating and $30 target.
  
• Canaccord Adams assumed Drugstore.com (NASDAQ: DSCM) with a Buy rating and $3.50 target.
  
• Goldman Sachs initiated DirecTV (NASDAQ: DTV) with a Buy rating and $30 target.

MOST NOTEWORTHY: Big 5 Sporting Goods (BGFV), Nutrition 21 (NXXI), Sonic Solutions (SNIC), AeroGrow (AERO) and Sequenom (SQNM) were today's noteworthy initiations:

• Nollenberger believes Big 5 Sporting Goods' (NASDAQ: BGFV) shares are fairly valued and would likely get more constructive near the $20 level and initiated shares with a Neutral rating.

• ThinkEquity said Nutrition 21 (NASDAQ: NXXI) has a number of clinically proven nutritional supplements that target the rapidly growing obesity and diabetes markets, and initiated shares with a Buy rating.

• SMH Capital initiated shares of Sonic Solutions (NASDQ: SNIC) with a Buy rating, on the belief that shares have been oversold.

• ThinkEquity is positive on AeroGrow's (NASDAQ: AERO) proprietary aeroponic technology and recurring revenue model and initiated shares with a Buy rating.

• Leerink Swann started shares of Sequenom (NASDAQ: SQNM) with an Outperform rating as MEDACorp researchers are positive regarding the company's MassARRAY system for genetic analysis, which is well-positioned for growth in follow-on SNP fine-mapping studies; Leerink anticipates in 2008, the company will launch iPLEX 3, which is currently in development, and reduce the cost of acquiring fine-mapping SNP data...

OTHER INITIATIONS:

• Dover (NYSE: DOV) was initiated at Morgan Stanley with an Overweight rating.

• Merrill started Akamai (NASDAQ: AKAM) with a Neutral rating.

• Pacific Crest started Wipro Ltd (NYSE: WIT) with a Sector perform.

• Susquehanna initiated Herman Miller (NASDAQ: MLHR) with a Positive rating.

• RBC Capital initiated Warren Resources (NASDAQ: WRES) with an Outperform rating.

Analyst summaries provided by TheFlyOnTheWall.com (subscription required).