Document:

Second Amendment to Credit Agreement

 EXHIBIT 10.13 
 SECOND AMENDMENT TO CREDIT AGREEMENT  
 This SECOND
AMENDMENT TO CREDIT AGREEMENT (this “Amendment”), dated as of December 27, 2012, is entered into by and among the undersigned with respect to that certain Credit Agreement, dated as of November 16, 2011, (the
“Credit Agreement”) by and among Great Lakes Aviation, Ltd., an Iowa corporation (“Great Lakes”), the financial institutions and other entities that are parties thereto as Lenders, Crystal Financial LLC (in its
individual capacity, “Crystal” or “Administrative Agent”) and GB Merchant Partners, LLC (in its individual capacity “GB Merchant” or “Collateral Agent”, and together with the
Administrative Agent, the “Agents” and each individually an “Agent”). 
 W I T N E S S E
T H: 
 WHEREAS, the Lenders have extended credit to Great Lakes, pursuant to the terms and subject to the conditions of the
Credit Agreement; 
 WHEREAS, Great Lakes has requested that Agents and the Lenders agree to amend the Credit Agreement upon the
terms and subject to the conditions set forth herein; and 
 WHEREAS, as an accommodation to Great Lakes, the Agents and the
undersigned Lenders (constituting Requisite Lenders) have agreed to amend the Credit Agreement, subject in all respects, however, to the terms and the conditions set forth herein. 

NOW, THEREFORE, in consideration of the foregoing and for other good and valid consideration, the receipt and sufficiency of which are
hereby acknowledged, the parties hereto, intending to be legally bound, hereby agree as follows: 
 1. Defined Terms.
Capitalized terms used but not defined herein shall have the respective meanings ascribed to such terms in the Credit Agreement. In addition, as used herein, the following terms shall have the following meanings: 

“Second Amendment Effective Date” means the date on which all of the conditions set forth in
Section 4 of this Amendment have been satisfied (or waived by the Requisite Lenders). 
 2. Amendment to Credit
Agreement. Effective upon the Second Amendment Effective Date, Annex A to the Credit Agreement is hereby amended by amending and restating the definition of Capital Expenditures in its entirety to read as follows: 

““Capital Expenditures” means, with respect to any Person for any period, the aggregate of all
expenditures by such Person and its Subsidiaries during such period that are capital expenditures as determined in accordance with GAAP, whether such expenditures are paid in cash or financed, provided, however it is understood and agreed

 
that Capital Expenditures do not include (i) any item customarily charged directly to expense or depreciated over a useful life of twelve (12) months or less in accordance with GAAP,
(ii) any capitalizable spares, rotables, aircraft parts, upgrades (software or hardware) or other flight equipment related to any Aircraft, (iii) an amount not to exceed $250,000 with respect to the Raddix reservation system license
upgrade, (iv) any capital expenditures attributable to the purchase of up to three (3) Aircraft, so long as such Aircraft are purchased after the Closing Date but on or prior to January 31, 2012, and (v) any capital expenditures
associated with the purchase of an additional (2) Aircraft, so long as such Aircraft are purchased after January 31, 2012 but on or prior to December 31, 2012 and the aggregate cash consideration paid for such Aircraft does not exceed
$1,800,000. For avoidance of doubt the capital expenditures attributable to the purchase of any Aircraft, other than the Aircraft that are explicitly excluded in the foregoing clauses (ii), (iv) and (v), shall be included in the calculation of
Capital Expenditures.” 
 3. Supplement to Aircraft Security Agreement. Within thirty (30) days of the date of
this Amendment, Great Lakes shall execute a Mortgage Supplement (as defined in the Aircraft Security Agreement) with respect to the Aircraft excluded from the definition of Capital Expenditures (after giving effect to this Amendment) pursuant to
clause (v) of the definition thereof. 
 4. Conditions to Effectiveness of Amendment. The effectiveness of this
Amendment is subject to the fulfillment, in a manner satisfactory to the Agents and the Requisite Lenders, of the following conditions precedent: 
 (a) the execution and delivery of this Amendment by Great Lakes, the Agents, and the Requisite Lenders; 
 (b) the representations and warranties set forth in Section 5 hereof shall be true and correct (and Great Lakes hereby certifies, by its signatures below that each of the following are true
and correct) as of the date hereof and as of the Second Amendment Effective Date; and 
 (c) no Default or Event
of Default shall exist after giving effect to this Amendment. 
 5. Representations and Warranties. Great Lakes hereby
represents and warrants to the Agents and each Lender as follows: 
 (a) Great Lakes is a corporation, duly
organized, validly existing and in good standing under the laws of the jurisdiction of its incorporation; 
 (b)
Great Lakes has the power and authority to execute, deliver and perform its obligations under this Amendment; 

(c) the execution, delivery and performance by Great Lakes of this Amendment has been duly authorized by all necessary
corporate action and does not and will not require any registration with, consent or approval of, notice to or action by, any Person; 

  
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 (d) this Amendment constitutes the legal, valid and binding obligation of
Great Lakes, enforceable against it in accordance with its terms; 
 (e) no Default or Event of Default shall
exist after giving effect to this Amendment; 
 (f) all representations and warranties contained in the Credit
Agreement and the Loan Documents are true and correct as of the date hereof, except to the extent made as of a specific date, in which case each such representation and warranty shall be true and correct as of such date; and 

(g) by its signature below, Great Lakes agrees that it shall constitute an Event of Default if any representation or warranty made herein
is untrue or incorrect in any material respect as of the date when made or deemed made. 
 6. Reaffirmation. Great Lakes
as debtor, grantor, pledgor, guarantor, assignor, or in any other similar capacity in which the grants liens or security interests in its property, hereby (i) ratifies and reaffirms all of its payment and performance obligations, contingent or
otherwise, under each of the Loan Documents and (ii) ratifies and reaffirms any liens on or security interests in any of its property pursuant to any Loan Document and confirms and agrees that such security interests and liens hereafter secure
all of the Obligations as amended hereby. Great Lakes hereby consents to this Amendment and acknowledges that each of the Loan Documents remains in full force and effect and is hereby ratified and reaffirmed. The execution of this Amendment shall
not operate as a waiver of any right, power or remedy of Agents or Lenders, or, except as expressly set forth herein, constitute a waiver of any provision of any of the Loan Documents, or serve to affect a novation of the Obligations. 

7. Miscellaneous. 
 (a) Reference to and Effect on the Loan Documents. Except for the amendments and modifications expressly set forth above, the execution, delivery and effectiveness of this Amendment shall not
operate as a waiver of any right, power or remedy of any Lender under any of the Loan Documents, nor constitute a waiver of, or a consent in connection with, any other provision of the Loan Documents. Any and all notices, requests, certificates and
other instruments executed and delivered after the execution and delivery of this Amendment may refer to the Credit Agreement without making specific reference to this Amendment but nevertheless all such references shall include this Amendment
unless the context otherwise requires. Great Lakes agrees that, except as expressly modified hereby, the Credit Agreement and other Loan Documents remain in full force and effect in accordance with their terms and are hereby ratified and reaffirmed.

 (b) Costs, Expenses and Taxes. Great Lakes agrees to reimburse the Lenders and each Agent on demand for all
out-of-pocket costs, expenses and charges incurred by them in connection with the preparation, reproduction, execution and delivery of this Amendment (including, without limitation, the fees and expenses of Proskauer Rose LLP) and any other
instruments and documents to be delivered hereunder. 

  
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 (c) Governing Law. This Amendment shall be construed and enforced in accordance with,
and the rights of the parties shall be governed by, the law of the State of New York, excluding choice-of-law principles of the law of such state that would require the application of the laws of a jurisdiction other than such state. 

(d) Headings. Section headings in this Amendment are included herein for convenience of reference only and shall not constitute a
part of this Amendment for any other purpose. 
 (e) Successors and Assigns. This Amendment shall be binding upon and
inure to the benefit of Great Lakes and its successors and assigns and each Agent and Lenders and their successors and assigns. 

(f) Counterparts. This Amendment may be executed in any number of counterparts, all of which taken together shall constitute one
and the same instrument, and any party hereto may execute this Amendment by signing any such counterpart. 
 [Remainder of Page
Intentionally Left Blank; Signature Pages Follow] 

  
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 IN WITNESS WHEREOF, this Second Amendment to Credit Agreement has been duly executed as of
the date first written above. 
  

			
	GREAT LAKES:
	
	GREAT LAKES AVIATION, LTD.
		
	By:	 	 /s/ Michael Matthews

	Name:	 	Michael Matthews
	Title:	 	Chief financial Officer

  

SECOND AMENDMENT TO CREDIT AGREEMENT 

 
			
	ADMINISTRATIVE AGENT:
	
	CRYSTAL FINANCIAL LLC
		
	By:	 	 /s/ Christopher A. Arnold

	Name:	 	Christopher A. Arnold
	Title:	 	Managing Director

  

SECOND AMENDMENT TO CREDIT AGREEMENT 

 
			
	COLLATERAL AGENT:
	
	GB MERCHANT PARTNERS, LLC
		
	By:	 	 /s/ Lawrence Klaff

	Name:	 	Lawrence Klaff
	Title:	 	Managing Director

  

SECOND AMENDMENT TO CREDIT AGREEMENT 

 
			
	LENDERS:
	
	CRYSTAL FINANCIAL SPV LLC
		
	By:	 	 /s/ Christopher A. Arnold

	Name:	 	Christopher A. Arnold
	Title:	 	Managing Director
	
	CRYSTAL FINANCIAL LLC
		
	By:	 	 /s/ Christopher A. Arnold

	Name:	 	Christopher A. Arnold
	Title:	 	Managing Director

  

SECOND AMENDMENT TO CREDIT AGREEMENT 

 
			
	1903 ONSHORE FUNDING, LLC
		
	By:	 	 /s/ Lawrence Klaff

	Name:	 	Lawrence Klaff
	Title:	 	Managing Director

  

SECOND AMENDMENT TO CREDIT AGREEMENTEX-10.40

 Exhibit 10.40 
 EXECUTION COPY 
 CONFIDENTIAL 

AMENDMENT TO 
 LICENSE & DEVELOPMENT AGREEMENT 
 This
AMENDMENT TO LICENSE & DEVELOPMENT AGREEMENT (this “Amendment”) is entered into as of January 4, 2013 (the
“Amendment Effective Date”), by and between ALEXZA PHARMACEUTICALS, INC., a Delaware corporation with a principal place of business at 2091 Stierlin Court, Mountain
View, CA 94043 (“Alexza”), and ROYALTY PHARMA a Delaware statutory trust with a principal place of business at 110 East 59th Street, 33rd Floor, New York, NY 10022 (acquiror of CYPRESS BIOSCIENCE, INC., a
Delaware corporation with a principal place of business at 4350 Executive Drive, Suite 325, San Diego, CA 92121 (“Cypress”)) (“Royalty Pharma”). Alexza and Royalty Pharma are sometimes
referred to herein individually as a “Party” and collectively as the “Parties”. 

RECITALS 

WHEREAS, Alexza and Cypress are parties to that certain License & Development Agreement, dated
August 25, 2010 (the “Agreement”); 
 WHEREAS, Cypress was acquired by
Royalty Pharma on January 5, 2011 and Royalty Pharma is Cypress’s successor in interest to the Agreement; 

WHEREAS, Alexza has completed activities contemplated by the Agreement as of the Amendment Effective Date, and
Royalty Pharma has fully paid Alexza for the work completed as of the Amendment Effective Date; and 

WHEREAS, Alexza and Royalty Pharma now desire to amend the terms and conditions of the Agreement, as outlined
below. 
 Now, THEREFORE, in consideration of the premises, and the mutual covenants contained herein, and
for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the Parties agree as follows: 
 1. STACCATO® NICOTINE PROJECT EQUIPMENT DISPOSITION. The
following new Section 3.6 is hereby added after Section 3.5 of the Agreement: 
 3.6 Purchased Equipment. During
the term of the Agreement, as of the Amendment Effective Date, various pieces of equipment were purchased by Royalty Pharma in support of the Alexza Development Plan and are still on-site at Alexza’s location at the address above (the
“Purchased Equipment”). Alexza and Royalty Pharma agree that the Purchased Equipment shall be owned by Alexza. Each Party agrees to take all further acts reasonably required to evidence such ownership and transfer.

  
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 EXECUTION COPY 

CONFIDENTIAL 
  

 2. PATENT PROSECUTION AND MAINTENANCE. Section 7.2 of the Agreement is
hereby deleted and replaced in its entirety with the following: 
 7.2 Patent Prosecution and Maintenance. As of the
Amendment Effective Date, Alexza shall have the right and authority to prepare, file, prosecute (including any interferences, reissue proceedings and reexaminations) and maintain the Alexza Patents, Cypress Patents and Joint Patents in any
jurisdiction in the world and all costs and expenses incurred by Alexza in connection with the preparation, prosecution, and maintenance of the Alexza Background Patents and Alexza Product Patents (other than the Alexza Nicotine Product Patents)
shall be borne by Alexza. For clarity, all costs and expenses incurred by Royalty Pharma in connection with the preparation, prosecution, and maintenance of the Alexza Nicotine Product Patents and the Cypress Patents prior to the Amendment Effective
Date shall be borne by Royalty Pharma. All reasonable, out-of-pocket documented costs and expenses incurred by Alexza accrued from and after October 1, 2012 in connection with the preparation, prosecution, and maintenance of the Alexza Nicotine
Product Patents and the Cypress Patents shall be reimbursed by Royalty Pharma, with such reimbursement payable by Royalty Pharma to Alexza within thirty (30) days of receipt of monthly invoices from Alexza. Each Party represents and warrants to
the other Party that, as of the Amendment Effective Date, it has fully disclosed to the other Party all Inventions. Subject to the foregoing representation and warranty, the Parties acknowledge and agree that, as of the Amendment Effective Date,
there are no Joint Patents or Joint Inventions the Parties desire to patent and the Parties do not anticipate filing any Joint Patents during the Term. Alexza shall keep Royalty Pharma reasonably informed of its prosecution activities with respect
to the Alexza Background Patents, Alexza Product Patents and Cypress Patents. If, in accordance with Section 7.8, the Parties agree that a particular Alexza Background Patent will be listed or would reasonably be expected to be listed in the Orange
Book, then such patent will hereinafter be called an “Orange Book Alexza Background Patent.” Alexza shall provide Royalty Pharma with a copy of material communications from any patent authority regarding any Orange Book
Alexza Background Patent, any Alexza Product Patent or any Cypress Patent and shall provide drafts of any material filings or responses to be made to such patent authorities regarding such Orange Book Alexza Background Patent, Alexza Product Patent
or Cypress Patent a reasonable amount of time in advance of submitting such filings or responses and Royalty Pharma shall have an opportunity to review and comment thereon within ten (10) business days of receipt thereof. Alexza shall discuss and
reasonably consider any comments received from Royalty Pharma. Alexza shall use commercially reasonable efforts to separate any Alexza Patent claims directed primarily toward a Product into distinct divisional (or equivalent) patent applications, to
the extent feasible and permitted under Applicable Laws, and to the extent Alexza does not reasonably believe that such separation would materially adversely affect the claim scope or likelihood or timing of patent issuance of any Alexza Patent, and
such 

  
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 EXECUTION COPY 

CONFIDENTIAL 
  

 
distinct divisional (or equivalent) patent applications shall be Alexza Nicotine Product Patents. Alexza shall have the right, in its sole discretion, to abandon, cease prosecution of or not
maintain any Alexza Patent or Cypress Patent anywhere in the world. Should Alexza determine to abandon prosecution of, or cease to maintain, any Alexza Product Patents or Cypress Patent in any jurisdiction, Alexza shall promptly so notify Royalty
Pharma and provided that Alexza has no reasonable objection shall permit Royalty Pharma, should Royalty Pharma choose to do so, at Royalty Pharma’s expense, to continue to prosecute or maintain such patent in such jurisdiction, and Alexza
shall, at the expense of Royalty Pharma, cooperate with Royalty Pharma in regard thereto. The Parties acknowledge and agree that it shall be unreasonable for Alexza to object pursuant to the preceding sentence if such Alexza Patent or Cypress Patent
proposed for abandonment is required to protect, or to extend the time of patent protection for, the Product in the jurisdiction where abandonment is proposed. Alexza and Royalty Pharma agree that the patent application entitled “NICOTINE
TRIFUMARATE” (U.S. Patent Application No. 61/512,763), filed July 28, 2011 will be abandoned. Alexza and Royalty Pharma agree that Alexza will file a patent application for the “nicotine salt formed with 3-hydroxybenzoic
acid” and such Alexza Nicotine Product Patent will be pursued by Alexza pursuant to the terms of this Section 7.2. 

3. TERMINATION. 
 (a) The following new Section 11.2(c) is hereby added after Section 11.2(b) of the Agreement: 
 (c) Royalty Pharma shall use commercially reasonable efforts to complete an Asset Sale or Asset License by September 30, 2013. Alexza shall have no additional development obligations or commitments
as a result of the foregoing. Alexza shall use commercially reasonable efforts, at Royalty Pharma’s expense, to support Royalty Pharma’s reasonable requests in connection with its Asset Sale or Asset License solely with respect to
necessary due diligence activities with any potential partner or licensee. Notwithstanding anything to the contrary in this Agreement, this Agreement shall terminate automatically if Royalty Pharma does not complete an Asset Sale or Asset License by
December 31, 2013. If Royalty Pharma completes an Asset Sale or Asset License by December 31, 2013, this Agreement shall not automatically terminate under this Section 11.2(c). 

(b) The first sentence of Section 11.3(a) of the Agreement is hereby amended as follows: 

“Section 11.2(a) or 11.2(b)” is hereby replaced with “Section 11.2(a), 11.2(b) or 11.2(c)” 

  
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 EXECUTION COPY 

CONFIDENTIAL 
  

 4. TERMINATION OF THE SUBLET AND ADMINISTRATIVE SERVICES AGREEMENT. The Parties
acknowledge and agree that the Sublet and Administrative Services Agreement between Alexza and Cypress, dated August 25, 2010 (the “Sublease”) is fully paid and shall be terminated effective October 31, 2012 and
neither Party has any liability to the other Party thereunder. 
 5. MISCELLANEOUS. 

(a) References. All references to Cypress in the Agreement shall be deemed references to Royalty Pharma. 

(b) Full Force and Effect; Entire Agreement. This Amendment amends the terms of the Agreement as expressly provided above, and the
Agreement, as so amended and including all of its other terms and provisions that are not amended, remains in full force and effect and sets forth the complete, final and exclusive agreement and all the covenants, promises, agreements, warranties,
representations, conditions and understandings between the Parties hereto with respect to the subject matter of the Agreement and supersedes, as of the Amendment Effective Date, all prior and contemporaneous agreements and understandings between the
parties with respect to the subject matter of the Agreement. 
 (c) Capitalized Terms. Capitalized terms used but not
defined herein shall have the meanings set forth in the Agreement. For clarity, the term “Agreement” in the Agreement means the Agreement as amended. 
 (d) Severability. In the event any provision of this Amendment should be held invalid, illegal or unenforceable in any jurisdiction or shall render this Amendment or the entire Agreement to be
invalid, illegal or unenforceable, the Parties shall negotiate in good faith and enter into a valid, legal and enforceable substitute provision that most nearly reflects the original intent of the Parties. All other provisions of this Agreement
shall remain in full force and effect in such jurisdiction. Such invalidity, illegality or unenforceability shall not affect the validity, legality or enforceability of such provision in any other jurisdiction. 

(e) Governing Law. This Agreement and all questions regarding the existence, validity, interpretation, breach or performance of
this Amendment, shall be governed by, and construed and enforced in accordance with, the laws of the State of California, without reference to its conflicts of law principles 
 (f) Counterparts. This Amendment may be executed in any number of counterparts each of which shall be deemed an original, and all of which together shall constitute one and the same instrument.
Signatures provided by facsimile transmission or in AdobeTM Portable Document Format (PDF) sent by electronic mail shall be deemed to be original signatures. 
 [Signature Page Follows] 

  
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 IN WITNESS WHEREOF, the Parties have executed this Amendment to License &
Development Agreement as of the Amendment Effective Date. 
  

									
	ALEXZA PHARMACEUTICALS, INC.	 		 	ROYALTY PHARMA
					
	By:	 	 /s/ Thomas B. King
	 		 	By:	 	 /s/ PABLO LEGORRETA

					
	Name:	 	 Thomas B. King
	 		 	Name:	 	 PABLO LEGORRETA

					
	Title:	 	 President & CEO
	 		 	Title:

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