**UNITEDSTATES**

**SECURITIESAND EXCHANGE COMMISSION**

**WASHINGTON, DC 20549**

 

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**Form 10-K/A**

 

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**Amendment No. 1**

 

**(Mark One)**
| **x**                                                | ** ** | **ANNUAL REPORT PURSUANT TO  SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934**                                                                                                                                                                                                                                                               |
|------------------------------------------------------|------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|                                                 |       |                                                                                                                                                                                                                                                                                                                                                              |
| **For the fiscal year ended December 31, 2008** |
|                                                 |
| **or**                                               |
|                                                 |       |                                                                                                                                                                                                                                                                                                                                                              |
| **o**                                                | ** ** | **TRANSITION REPORT PURSUANT TO  SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934**                                                                                                                                                                                                                                                           |
|                                                 |       |                                                                                                                                                                                                                                                                                                                                                              |
| ** **                                           | ** ** | **For the  transition period from                                to                        ** |

 

**Commission file number: 001-33291**

 

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**OptimerPharmaceuticals, Inc.**

(Exact Name of Registrant as Specified in its Charter)

 

| **Delaware**                                                                | **33-0830300**      |
|-----------------------------------------------------------------------------|---------------------|
| (State or Other Jurisdiction of                                             | (I.R.S. Employer    |
| Incorporation or Organization)                                              | Identification No.) |
|                                                                        | ** **          |
| **10110 Sorrento Valley Road, Suite C, San Diego,  California, 92121** |
| (Address of principal executive offices and zip code)                       |
|                                                                        |                |
| Registrant’s telephone number, including area code: **(858) 909-0736** |

 

Securities registered pursuant to Section 12(b) ofthe Act:

 
| **Title of  Each Class**                     | ** ** | **Name of  Each Exchange on Which Registered** |
|----------------------------------------------|------------|------------------------------------------------|
| **Common Stock, par value $0.001 per share** | ** ** | **Nasdaq Global Market**                       |

 

Securities registered pursuant to Section 12(g) ofthe Act:

**None**

 

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Indicateby check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405of the Securities Act. Yes o    No  x.

 

Indicateby check mark if the registrant is not required to file reports pursuant to Section 13or Section 15(d) of the Act. Yes o    No  x.

 

Indicateby check mark whether the registrant: (1) has filed all reports requiredto be filed by Section 13 or 15(d) of the Securities Exchange Act of1934 during the preceding 12 months (or for such shorter period that theregistrant was required to file such reports), and (2) has been subject tosuch filing requirements for the past 90 days.    Yes  x    No  o

 

Indicateby check mark if disclosure of delinquent filers pursuant to Item 405 ofRegulation S-K is not contained herein, and will not be contained, to the bestof the registrant’s knowledge, in definitive proxy or information statementsincorporated by reference in Part III of this Form 10-K or anyamendment to this Form 10-K.  x

 

Indicate by check mark whether the registrant is alarge accelerated filer, an accelerated filer, a non-accelerated filer, or asmaller reporting company. See the definitions of “large accelerated filer,” “acceleratedfiler,” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.(Check one):

 
| Large  accelerated filer  o | Accelerated filer  x | Non-accelerated filer  o | Smaller reporting company  o |
|---------------------------------------|--------------------------------|------------------------------------|----------------------------------------|

 

Indicateby check mark whether the registrant is a shell company (as defined in Rule 12b-2of the Exchange Act). Yes  o  No  x.

 

The aggregate market value of the registrant’s common stock held bynon-affiliates as of June 30, 2008 (without admitting that any personwhose shares are not included in such calculation is an affiliate), computed byreference to the price at which the common stock was last sold as of such dateon the Nasdaq Global Market, was $226,483,907.

 

Thenumber of outstanding shares of the registrant’s common stock, par value $0.001per share, as of March 11, 2009 was 33,037,661.

 

 

 

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**Explanatory Note**

 

OptimerPharmaceuticals, Inc. (the “Company”) is filing this Amendment No. 1to its Annual Report on Form 10-K for the year ended December 31,2008, as filed with the Securities and Exchange Commission on March 12,2009 (the “Original Filing”), to amend the certifications of the Company’sChief Executive Officer and Chief Financial Officer pursuant to Rule 13a-14of the Securities Exchange Act of 1934, as amended (the “Certifications”), tocorrect an inadvertent omission of a portion of paragraph 4 of theCertifications. The Certifications are included herewith as Exhibits 31.1 and31.2.  Item 15 and the Exhibit Indexof the Original Filing are being amended to reflect the filing of the amendedCertifications.

 

Exceptfor the filing of the amended Certifications and the amendments to Item 15 andthe Exhibit Index as described above, this Form 10-K/A does notmodify or update any previously reported financial statements or otherdisclosures in, or exhibits to, the Original Filing.

 

**Item 15.Exhibits and Financial Statement Schedules**

 

1. *Financial Statements*

 

See Index to Consolidated Financial Statements inItem 8 of the Company’s Annual Report on Form 10-K for the year endedDecember 31, 2008.

 

2. *FinancialStatement Schedules*

 

None

 

3. *Exhibits*

 
| **Exhibit No.** | ** ** | ** ** | **Description of Document**                                                                                                                                                                                                                                                    |
|----------------------|------------|------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 3.1                  | (3)        |       | Certificate of  Incorporation of Optimer Pharmaceuticals, Inc., as amended and restated.                                                                                                                                                                                            |
| 3.2                  | (7)        |       | Bylaws of Optimer  Pharmaceuticals, Inc., as amended.                                                                                                                                                                                                                               |
| 4.1                  | (4)        |       | Common Stock  Certificate of Optimer Pharmaceuticals, Inc.                                                                                                                                                                                                                          |
| 4.2                  | (1)        |       | Investors’ Rights  Agreement by and among Optimer Pharmaceuticals, Inc. and certain  stockholders of the registrant dated November 30, 2005, as amended and  restated.                                                                                                    |
| 4.3                  | (6)        |       | Registration Rights  Agreement, dated October 23, 2007, by and between Optimer  Pharmaceuticals, Inc. and the purchasers listed on the signature  pages thereto.                                                                                                          |
| 4.4                  | (11)       |       | Form of Warrant.                                                                                                                                                                                                                                                                    |
| 10.1                 | (1)*       |       | Master Service Agreement  between Optimer Pharmaceuticals, Inc. and Advanced Biologics, LLC  (subsequently INC Research, Inc.), dated November 16, 2005, as  amended.                                                                                                     |
| 10.2                 | (12)*      |       | Collaboration Research  and Development and License Agreement between Optimer  Pharmaceuticals, Inc. and Cempra Pharmaceuticals, Inc., dated  March 31, 2006, as amended.                                                                                                 |
| 10.3                 | (4)*       |       | Agreement between  Optimer Pharmaceuticals, Inc. and Sloan-Kettering Institute for Cancer  Research dated July 31, 2002, as amended.                                                                                                                                           |
| 10.4                 | (3)*       |       | License Agreement  between Optimer Pharmaceuticals, Inc. and Nippon Shinyaku Co., Ltd.,  dated June 10, 2004.                                                                                                                                                                  |
| 10.5                 | (1)*       |       | License Agreement  between Optimer Pharmaceuticals, Inc. and The Scripps Research Institute  dated July 23, 1999.                                                                                                                                                              |
| 10.6                 | (1)*       |       | License Agreement  between Optimer Pharmaceuticals, Inc. and The Scripps Research Institute  dated May 30, 2001.                                                                                                                                                               |
| 10.7                 | (1)*       |       | License Agreement  between Optimer Pharmaceuticals, Inc. and The Scripps Research Institute  dated May 30, 2001.                                                                                                                                                               |
| 10.8                 | (1)*       |       | License Agreement  between Optimer Pharmaceuticals, Inc. and The Scripps Research Institute  dated June 1, 2004.                                                                                                                                                               |
| 10.9                 | (3)        |       | Building Lease between  Optimer Pharmaceuticals, Inc. and Pacific Sorrento Technology Park dated  May 1, 2001, as amended by the First Amendment to Building Lease between  Optimer Pharmaceuticals, Inc. and Pacific Sorrento Technology Park dated  July 12, 2001. |
| 10.10                | (1)+       |       | Form of Employee  Proprietary Information Agreement of Optimer Pharmaceuticals, Inc.                                                                                                                                                                                           |
| 10.11                | (12)+      |       | Employment Agreement  between Optimer Pharmaceuticals, Inc. and Michael N. Chang dated  June 17, 2005, as amended on October 2, 2008.                                                                                                                                     |
| 10.12                | (1)+       |       | Offer letter between  Optimer Pharmaceuticals, Inc. and Sherwood L. Gorbach dated  October 6, 2005.                                                                                                                                                                            |

 

2

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| 10.13 | (12)+  |   | Offer letter between  Optimer Pharmaceuticals, Inc. and Kevin P. Poulos dated June 15,  2006, as amended on October 2, 2008.                                                                                                                                                  |
|-------|--------|--------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 10.14 | (12)+  |   | Offer letter between  Optimer Pharmaceuticals, Inc. and John D. Prunty dated May 10,  2006, as amended on October 2, 2008.                                                                                                                                                    |
| 10.15 | (1)+   |   | Offer letter between  Optimer Pharmaceuticals, Inc. and Tessie M. Che dated August 30,  2001.                                                                                                                                                                                      |
| 10.16 | (1)+   |   | Offer letter between  Optimer Pharmaceuticals, Inc. and Youe-Kong Shue dated February 18,  2000.                                                                                                                                                                                   |
| 10.17 | (1)+   |   | Form of  Indemnification Agreement between Optimer Pharmaceuticals, Inc. and its  directors and officers.                                                                                                                                                                          |
| 10.18 | (1)+   |   | 1998 Stock Plan of  Optimer Pharmaceuticals, Inc.                                                                                                                                                                                                                                       |
| 10.19 | (1)+   |   | Stock Plan Stock Option  Agreement of Optimer Pharmaceuticals, Inc.                                                                                                                                                                                                                     |
| 10.20 | (3)+   |   | 2006 Equity Incentive  Plan of Optimer Pharmaceuticals, Inc.                                                                                                                                                                                                                            |
| 10.21 | (7)+   |   | Employee Stock Purchase  Plan of Optimer Pharmaceuticals, Inc., as amended.                                                                                                                                                                                                             |
| 10.22 | (3)    |   | Prospective Buy-Back  Agreement between Optimer Pharmaceuticals, Inc. and Par  Pharmaceutical, Inc. dated January 19, 2007.                                                                                                                                                   |
| 10.23 | (5)*   |   | Supply Agreement with  Biocon Limited dated August 29, 2005, as amended.                                                                                                                                                                                                                |
| 10.24 | (5)*   |   | Assignment letter  between Par Pharmaceutical, Inc. and Biocon Limited dated  January 16, 2007.                                                                                                                                                                                    |
| 10.25 | (8)+   |   | Summary of Optimer  Pharmaceuticals, Inc. 2009 Incentive Compensation Plan.                                                                                                                                                                                                             |
| 10.26 | (9)    |   | Office Lease, dated  August 18, 2008, by and between Optimer Pharmaceuticals, Inc. and  Trizec Sorrento Towers, LLC.                                                                                                                                                               |
| 10.27 | (10)+  |   | Optimer  Pharmaceuticals, Inc. Severance Benefit Plan                                                                                                                                                                                                                                   |
| 23.1  | (12)   |   | Consent of Independent  Registered Public Accounting Firm.                                                                                                                                                                                                                                   |
| 31.1  |   |   | Certification of  principal executive officer required by Rule 13a-14(a) or  Rule 15d-14(a).                                                                                                                                                                                  |
| 31.2  |   |   | Certification of  principal financial officer required by Rule 13a-14(a) or  Rule 15d-14(a).                                                                                                                                                                                  |
| 32    | (12)   |   | Certification by the  Chief Executive Officer and the Chief Financial Officer of Optimer  Pharmaceuticals, Inc., as required by Rule 13a-14(b) or  15d-14(b) and Section 1350 of Chapter 63 of Title 18 of  the United States Code (18 U.S.C. 1350). |

 

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| +    |   | Indicates management  contract or compensatory plan.                                                                                                                                  |
|------|--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| *    |   | Confidential treatment  has been granted with respect to certain portions of this exhibit. Omitted  portions have been filed separately with the Securities and Exchange  Commission. |
| (1)  |   | Filed with Registrant’s  Registration Statement on Form S-1 on November 9, 2006.                                                                                       |
| (2)  |   | Filed with Registrant’s  Amendment No. 2 to Registration Statement on Form S-1 on  January 5, 2007.                                                               |
| (3)  |   | Filed with Registrant’s  Amendment No. 3 to Registration Statement on Form S-1 on  January 22, 2007.                                                              |
| (4)  |   | Filed with Registrant’s  Amendment No. 4 to Registration Statement on Form S-1 on  February 5, 2007.                                                              |
| (5)  |   | Filed with the  Registrant’s Current Report on Form 8-K on February 26, 2007.                                                                                          |
| (6)  |   | Filed with the  Registrant’s Current Report on Form 8-K on October 29, 2007.                                                                                           |
| (7)  |   | Filed with the  Registrant’s Current Report on Form 8-K on September 18, 2007.                                                                                         |
| (8)  |   | Filed with the  Registrant’s Current Report on Form 8-K on January 13, 2009.                                                                                           |
| (9)  |   | Filed with the  Registrant’s Current Report on Form 8-K on August 21, 2008.                                                                                            |
| (10) |   | Filed with the Registrant’s  Current Report on Form 8-K on October 8, 2008.                                                                                            |
| (11) |   | Filed with the  Registrant’s Current Report on Form 8-K on March 5, 2009.                                                                                              |
| (12) |   | Filed with the  Company’s Annual Report on Form 10-K for the year ended  December 31, 2008.                                                                            |

 

3

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**SIGNATURES**

 

     Pursuantto the requirements of Section 13 or 15(d) of the Securities ExchangeAct of 1934, as amended, the registrant has duly caused this Annual Report on Form 10-K/Ato be signed on its behalf by the undersigned, thereunto duly authorized.

 
|   | OPTIMER  PHARMACEUTICALS, INC. |
|--------|--------------------------------|
|   |                           |
|   | By:                            | /s/ MICHAEL N. CHANG |
|   |                           | Michael N. Chang |
|   |                           | *President and Chief Executive Officer* |
|   |                           | *(Principal Executive Officer)* |

 

Dated:April 1, 2009

 

4

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**EXHIBIT INDEX**

 
| **Exhibit No.** | ** ** | ** ** | **Description of Document**                                                                                                                                                                                                                                                    |
|----------------------|------------|------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 3.1                  | (3)        |       | Certificate of  Incorporation of Optimer Pharmaceuticals, Inc., as amended and restated.                                                                                                                                                                                            |
| 3.2                  | (7)        |       | Bylaws of Optimer  Pharmaceuticals, Inc., as amended.                                                                                                                                                                                                                               |
| 4.1                  | (4)        |       | Common Stock Certificate  of Optimer Pharmaceuticals, Inc.                                                                                                                                                                                                                          |
| 4.2                  | (1)        |       | Investors’ Rights  Agreement by and among Optimer Pharmaceuticals, Inc. and certain  stockholders of the registrant dated November 30, 2005, as amended and  restated.                                                                                                    |
| 4.3                  | (6)        |       | Registration Rights  Agreement, dated October 23, 2007, by and between Optimer  Pharmaceuticals, Inc. and the purchasers listed on the signature  pages thereto.                                                                                                          |
| 4.4                  | (11)       |       | Form of Warrant.                                                                                                                                                                                                                                                                    |
| 10.1                 | (1)*       |       | Master Service  Agreement between Optimer Pharmaceuticals, Inc. and Advanced Biologics,  LLC (subsequently INC Research, Inc.), dated November 16, 2005, as  amended.                                                                                                     |
| 10.2                 | (12)*      |       | Collaboration Research  and Development and License Agreement between Optimer  Pharmaceuticals, Inc. and Cempra Pharmaceuticals, Inc., dated  March 31, 2006, as amended.                                                                                                 |
| 10.3                 | (4)*       |       | Agreement between  Optimer Pharmaceuticals, Inc. and Sloan-Kettering Institute for Cancer  Research dated July 31, 2002, as amended.                                                                                                                                           |
| 10.4                 | (3)*       |       | License Agreement  between Optimer Pharmaceuticals, Inc. and Nippon Shinyaku Co., Ltd.,  dated June 10, 2004.                                                                                                                                                                  |
| 10.5                 | (1)*       |       | License Agreement  between Optimer Pharmaceuticals, Inc. and The Scripps Research Institute  dated July 23, 1999.                                                                                                                                                              |
| 10.6                 | (1)*       |       | License Agreement  between Optimer Pharmaceuticals, Inc. and The Scripps Research Institute  dated May 30, 2001.                                                                                                                                                               |
| 10.7                 | (1)*       |       | License Agreement  between Optimer Pharmaceuticals, Inc. and The Scripps Research Institute  dated May 30, 2001.                                                                                                                                                               |
| 10.8                 | (1)*       |       | License Agreement  between Optimer Pharmaceuticals, Inc. and The Scripps Research Institute  dated June 1, 2004.                                                                                                                                                               |
| 10.9                 | (3)        |       | Building Lease between  Optimer Pharmaceuticals, Inc. and Pacific Sorrento Technology Park dated  May 1, 2001, as amended by the First Amendment to Building Lease between  Optimer Pharmaceuticals, Inc. and Pacific Sorrento Technology Park dated  July 12, 2001. |
| 10.10                | (1)+       |       | Form of Employee  Proprietary Information Agreement of Optimer Pharmaceuticals, Inc.                                                                                                                                                                                           |
| 10.11                | (12)+      |       | Employment Agreement  between Optimer Pharmaceuticals, Inc. and Michael N. Chang dated  June 17, 2005, as amended on October 2, 2008.                                                                                                                                     |
| 10.12                | (1)+       |       | Offer letter between  Optimer Pharmaceuticals, Inc. and Sherwood L. Gorbach dated  October 6, 2005.                                                                                                                                                                            |
| 10.13                | (12)+      |       | Offer letter between  Optimer Pharmaceuticals, Inc. and Kevin P. Poulos dated June 15,  2006, as amended on October 2, 2008.                                                                                                                                              |
| 10.14                | (12)+      |       | Offer letter between  Optimer Pharmaceuticals, Inc. and John D. Prunty dated May 10,  2006, as amended on October 2, 2008.                                                                                                                                                |
| 10.15                | (1)+       |       | Offer letter between  Optimer Pharmaceuticals, Inc. and Tessie M. Che dated August 30,  2001.                                                                                                                                                                                  |
| 10.16                | (1)+       |       | Offer letter between  Optimer Pharmaceuticals, Inc. and Youe-Kong Shue dated February 18,  2000.                                                                                                                                                                               |
| 10.17                | (1)+       |       | Form of  Indemnification Agreement between Optimer Pharmaceuticals, Inc. and its  directors and officers.                                                                                                                                                                      |
| 10.18                | (1)+       |       | 1998 Stock Plan of  Optimer Pharmaceuticals, Inc.                                                                                                                                                                                                                                   |
| 10.19                | (1)+       |       | Stock Plan Stock Option  Agreement of Optimer Pharmaceuticals, Inc.                                                                                                                                                                                                                 |
| 10.20                | (3)+       |       | 2006 Equity Incentive  Plan of Optimer Pharmaceuticals, Inc.                                                                                                                                                                                                                        |
| 10.21                | (7)+       |       | Employee Stock Purchase  Plan of Optimer Pharmaceuticals, Inc., as amended.                                                                                                                                                                                                         |
| 10.22                | (3)        |       | Prospective Buy-Back  Agreement between Optimer Pharmaceuticals, Inc. and Par  Pharmaceutical, Inc. dated January 19, 2007.                                                                                                                                               |
| 10.23                | (5)*       |       | Supply Agreement with  Biocon Limited dated August 29, 2005, as amended.                                                                                                                                                                                                            |
| 10.24                | (5)*       |       | Assignment letter  between Par Pharmaceutical, Inc. and Biocon Limited dated  January 16, 2007.                                                                                                                                                                                |
| 10.25                | (8)+       |       | Summary of Optimer  Pharmaceuticals, Inc. 2009 Incentive Compensation Plan.                                                                                                                                                                                                         |
| 10.26                | (9)        |       | Office Lease, dated  August 18, 2008, by and between Optimer Pharmaceuticals, Inc. and  Trizec Sorrento Towers, LLC.                                                                                                                                                           |
| 10.27                | (10)+      |       | Optimer  Pharmaceuticals, Inc. Severance Benefit Plan                                                                                                                                                                                                                               |
| 23.1                 | (12)       |       | Consent of Independent  Registered Public Accounting Firm.                                                                                                                                                                                                                               |
| 31.1                 |       |       | Certification of  principal executive officer required by Rule 13a-14(a) or  Rule 15d-14(a).                                                                                                                                                                              |

 

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| 31.2 |   |   | Certification of  principal financial officer required by Rule 13a-14(a) or  Rule 15d-14(a).                                                                                                                                                                                  |
|------|--------|--------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 32   | (12)   |   | Certification by the  Chief Executive Officer and the Chief Financial Officer of Optimer  Pharmaceuticals, Inc., as required by Rule 13a-14(b) or  15d-14(b) and Section 1350 of Chapter 63 of Title 18 of  the United States Code (18 U.S.C. 1350). |

 

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| +    |   | Indicates management  contract or compensatory plan.                                                                                                                                  |
|------|--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| *    |   | Confidential treatment  has been granted with respect to certain portions of this exhibit. Omitted  portions have been filed separately with the Securities and Exchange  Commission. |
| (1)  |   | Filed with Registrant’s  Registration Statement on Form S-1 on November 9, 2006.                                                                                       |
| (2)  |   | Filed with Registrant’s  Amendment No. 2 to Registration Statement on Form S-1 on  January 5, 2007.                                                               |
| (3)  |   | Filed with Registrant’s  Amendment No. 3 to Registration Statement on Form S-1 on  January 22, 2007.                                                              |
| (4)  |   | Filed with Registrant’s  Amendment No. 4 to Registration Statement on Form S-1 on  February 5, 2007.                                                              |
| (5)  |   | Filed with the  Registrant’s Current Report on Form 8-K on February 26, 2007.                                                                                          |
| (6)  |   | Filed with the  Registrant’s Current Report on Form 8-K on October 29, 2007.                                                                                           |
| (7)  |   | Filed with the  Registrant’s Current Report on Form 8-K on September 18, 2007.                                                                                         |
| (8)  |   | Filed with the  Registrant’s Current Report on Form 8-K on January 13, 2009.                                                                                           |
| (9)  |   | Filed with the  Registrant’s Current Report on Form 8-K on August 21, 2008.                                                                                            |
| (10) |   | Filed with the  Registrant’s Current Report on Form 8-K on October 8, 2008.                                                                                            |
| (11) |   | Filed with the  Registrant’s Current Report on Form 8-K on March 5, 2009.                                                                                              |
| (12) |   | Filed with the  Company’s Annual Report on Form 10-K for the year ended  December 31, 2008.                                                                            |

 

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