Document:

EX-10.1

 Exhibit 10.1 
 EXCHANGE AGREEMENT 

                (the “Undersigned”), for
itself and on behalf of the beneficial owners listed on Exhibit A hereto (“Accounts”) for whom the Undersigned holds contractual and investment authority (each Account, as well as the Undersigned if it is exchanging Existing
Notes (as defined below) hereunder, a “Holder”), enters into this Exchange Agreement (the “Agreement”) with Hologic, Inc. (the “Company”) on February 15, 2013 whereby the Holder will exchange
(the “Exchange”) the Company’s 2.00% Convertible Senior Notes due 2037 (the “Existing Notes”) for the Company’s new 2.00% Convertible Senior Notes due 2043 (the “New Notes”) that will be
issued pursuant to the provisions of an Indenture dated as of December 10, 2007 (the “Base Indenture”) between the Company and Wilmington Trust Company, as Trustee (the “Trustee”), as supplemented by the Fourth
Supplemental Indenture thereto, to be dated as of February 21, 2013 (the “Supplement,” and, together with the Base Indenture and all other supplements thereto, the “Indenture”) between the Company and the
Trustee. 
 On and subject to the terms hereof, the parties hereto agree as follows: 

Article I: Exchange of the Existing Notes for New Notes 

Subject to the terms set forth in this Agreement, at the Closing (as defined herein), the Undersigned hereby agrees to cause the Holders
to exchange and deliver to the Company the following Existing Notes, and in exchange therefor the Company hereby agrees to issue to the Holders the principal amount of New Notes described below and to pay in cash the following accrued but unpaid
interest on such Existing Notes: 
  

							
	 Principal Amount of Existing Notes to be Exchanged:
	  	$	 	  	 	  

		  				 	(the “Exchanged Notes”).                    

			
	 Principal Amount of New Notes to be Issued in the Exchange:
	  	$	 	  	 	  

		  				 	(the “Holders’ New Notes”).                
			
	 Cash Payment of Accrued but Unpaid Interest on Exchanged Notes:
	  	$	 	  	 	  

		  				 	(the “Cash Payment”).            

 The closing of the Exchange (the “Closing”) shall occur on a date (the “Closing
Date”) no later than three business days after the date of this Agreement. At the Closing, (a) each Holder shall deliver or cause to be delivered to the Company all right, title and interest in and to its Exchanged Notes (and no other
consideration) free and clear of any mortgage, lien, pledge, charge, security interest, encumbrance, title retention agreement, option, equity or other adverse claim thereto (collectively, “Liens”), together with any documents of
conveyance or transfer that the Company may deem necessary or desirable to transfer to and confirm in the Company all right, title and interest in and to the Exchanged Notes free and clear of any Liens, and (b) the Company shall deliver to each
Holder the principal amount of Holders’ New Notes and the portion of the Cash Payment specified on Exhibit A hereto (or, if there are no Accounts, the Company shall deliver to the Undersigned, as the sole Holder, the Holders’ New
Notes and the Cash Payment specified above); provided, however, that the parties acknowledge that the delivery of the Holders’ New Notes to the Holder may be delayed due to procedures and mechanics within the system of the Depository Trust
Company and that such delay will not be a default under this Agreement so long as (i) the Company is using its best efforts to effect the issuance of one or more global notes representing the New Notes, (ii) such delay is no longer than
three business days, and (iii) interest shall accrue on such New Notes from the Closing Date. Simultaneously with or after the Closing, the Company may issue New Notes to one or more other holders of outstanding Existing Notes or to other
investors, subject to the terms of the Indenture. 

 Article II: Covenants, Representations and Warranties of the Holders

 Each Holder (and, where specified below, the Undersigned) hereby covenants (solely as to itself), as follows, and makes
the following representations and warranties (solely as to itself), each of which is and shall be true and correct on the date hereof and at the Closing, to the Company, Lazard Frères & Co. LLC and Lazard Capital Markets LLC, and all
such covenants, representations and warranties shall survive the Closing. 
 Section 2.1 Power and
Authorization. The Holder is duly organized, validly existing and in good standing, and has the power, authority and capacity to execute and deliver this Agreement, to perform its obligations hereunder, and to consummate the Exchange
contemplated hereby. If the Undersigned is executing this Agreement on behalf of Accounts, (a) the Undersigned has all requisite discretionary and contractual authority to enter into this Agreement on behalf of, and bind, each Account, and
(b) Exhibit A hereto is a true, correct and complete list of (i) the name of each Account, (ii) the principal amount of such Account’s Exchanged Notes, (iii) the principal amount of Holders’ New Notes to be
issued to such Account in respect of its Exchanged Notes, and (iv) the portion of the Cash Payment to be made to such Account in respect of the accrued interest on its Exchanged Notes. 

Section 2.2 Valid and Enforceable Agreement; No Violations. This Agreement has been duly executed and delivered by the
Undersigned and the Holder and constitutes a legal, valid and binding obligation of the Undersigned and the Holder, enforceable against the Undersigned and the Holder in accordance with its terms, except that such enforcement may be subject to
(a) bankruptcy, insolvency, fraudulent transfer, reorganization, moratorium or other similar laws affecting or relating to enforcement of creditors’ rights generally, and (b) general principles of equity, whether such enforceability
is considered in a proceeding at law or in equity (the “Enforceability Exceptions”). This Agreement and consummation of the Exchange will not violate, conflict with or result in a breach of or default under (i) the
Undersigned’s or the Holder’s organizational documents, (ii) any agreement or instrument to which the Undersigned or the Holder is a party or by which the Undersigned or the Holder or any of their respective assets are bound, or
(iii) any laws, regulations or governmental or judicial decrees, injunctions or orders applicable to the Undersigned or the Holder. 
 Section 2.3 Title to the Exchanged Notes. The Holder is the sole legal and beneficial owner of the Exchanged Notes set forth opposite its name on Exhibit A hereto (or, if there
are no Accounts, the Undersigned is the sole legal and beneficial owner of all such Exchanged Notes). The Holder has good, valid and marketable title to its Exchanged Notes, free and clear of any Liens (other than pledges or security interests that
the Holder may have created in favor of a prime broker under and in accordance with its prime brokerage agreement with such broker). The Holder has not, in whole or in part, except as described in the preceding sentence, (a) assigned,
transferred, hypothecated, pledged, exchanged or otherwise disposed of any of its Exchanged Notes or its rights in its Exchanged Notes, or (b) given any person or entity any transfer order, power of attorney or other authority of any nature
whatsoever with respect to its Exchanged Notes. Upon the Holder’s delivery of its Exchanged Notes to the Company pursuant to the Exchange, such Exchanged Notes shall be free and clear of all Liens created by the Holder. 

Section 2.4 Accredited Investor and Qualified Institutional Buyer. The Holder is (i) an “accredited
investor” within the meaning of Rule 501 of Regulation D (“Regulation D”) promulgated under the Securities Act of 1933, as amended (the “Securities Act”) and (ii) a “qualified institutional
buyer” within the meaning of Rule 144A promulgated under the Securities Act. 
 Section 2.5 No Affiliate
Status. The Holder is not, and has not been during the consecutive three month period preceding the date hereof, a director, officer or “affiliate” within the meaning of Rule 144 promulgated under the Securities Act (an
“Affiliate”) of the Company. To its knowledge, the Holder did not acquire any of the Exchanged Notes, directly or indirectly, from an Affiliate of the Company. 

  
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 Section 2.6 No Illegal Transactions. Each of the Undersigned and the
Holder has not, directly or indirectly, and no person acting on behalf of or pursuant to any understanding with it has, engaged in any transactions in the securities of the Company (including, without limitation, any Short Sales (as defined below)
involving any of the Company’s securities) since the time that the Undersigned was first contacted by either the Company, Lazard Frères & Co. LLC or Lazard Capital Markets LLC or any other person regarding the Exchange, this
Agreement or an investment in the New Notes or the Company. Each of the Undersigned and the Holder covenants that neither it nor any person acting on its behalf or pursuant to any understanding with it will engage, directly or indirectly, in any
transactions in the securities of the Company (including Short Sales) prior to the time the transactions contemplated by this Agreement are publicly disclosed. “Short Sales” include, without limitation, all “short sales”
as defined in Rule 200 of Regulation SHO promulgated under the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and all types of direct and indirect stock pledges, forward sale contracts, options, puts, calls, short
sales, swaps, derivatives and similar arrangements (including on a total return basis), and sales and other transactions through non-U.S. broker-dealers or foreign regulated brokers. Solely for purposes of this Section 2.6, subject to the
Undersigned’s and the Holder’s compliance with their respective obligations under the U.S. federal securities laws and the Undersigned’s and the Holder’s respective internal policies, (a) “Undersigned” and
“Holder” shall not be deemed to include any employees, subsidiaries or affiliates of the Undersigned or the Holder that are effectively walled off by appropriate “Chinese Wall” information barriers approved by the
Undersigned’s or the Holder’s respective legal or compliance department (and thus have not been privy to any information concerning the Exchange), and (b) the foregoing representations of this Section 2.6 shall not apply to any
transaction by or on behalf of an Account that was effected without the advice or participation of, or such Account’s receipt of information regarding the Exchange provided by, the Undersigned. 

Section 2.7 Adequate Information; No Reliance. The Holder acknowledges and agrees that (a) the Holder has been
furnished with all materials it considers relevant to making an investment decision to enter into the Exchange and has had the opportunity to review the Company’s filings and submissions with the Securities and Exchange Commission (the
“SEC”), including, without limitation, all information filed or furnished pursuant to the Exchange Act, (b) the Holder has had a full opportunity to ask questions of the Company concerning the Company, its business, operations,
financial performance, financial condition and prospects, and the terms and conditions of the Exchange, (c) the Holder has had the opportunity to consult with its accounting, tax, financial and legal advisors to be able to evaluate the risks
involved in the Exchange and to make an informed investment decision with respect to such Exchange and (d) the Holder is not relying, and has not relied, upon any statement, advice (whether accounting, tax, financial, legal or other),
representation or warranty made by the Company or any of its affiliates or representatives including, without limitation, Lazard Frères & Co. LLC and Lazard Capital Markets LLC, except for (A) the publicly available filings and
submissions made by the Company with the SEC under the Exchange Act, and (B) the representations and warranties made by the Company in this Agreement. 
 Section 2.8 No Public Market. The Holder understands that no public market exists for the New Notes and that there is no assurance that a public market will ever develop for the New
Notes. 
 Article III: Covenants, Representations and Warranties of the Company 

The Company hereby covenants as follows, and makes the following representations and warranties, each of which is and shall be true and
correct on the date hereof and at the Closing, to the Holders, Lazard Frères & Co. LLC and Lazard Capital Markets LLC, and all such covenants, representations and warranties shall survive the Closing. 

Section 3.1 Power and Authorization. The Company is duly incorporated, validly existing and in good standing under the
laws of its state of incorporation, and has the power, authority and capacity to execute and deliver this Agreement and the Supplement, to perform its obligations hereunder and thereunder, and to consummate the Exchange contemplated hereby.

  
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 Section 3.2 Valid and Enforceable Agreements; No Violations. This
Agreement has been duly executed and delivered by the Company and constitutes a legal, valid and binding obligation of the Company, enforceable against the Company in accordance with its terms, except that such enforcement may be subject to the
Enforceability Exceptions. At the Closing, the Supplement, substantially in the form of Exhibit B hereto, will have been duly executed and delivered by the Company and will govern the terms of the New Notes, and the Indenture will
constitute a legal, valid and binding obligation of the Company, enforceable against the Company in accordance with its terms, except that such enforcement may be subject to the Enforceability Exceptions. This Agreement, the Indenture and
consummation of the Exchange will not violate, conflict with or result in a breach of or default under (i) the charter, bylaws or other organizational documents of the Company, (ii) any agreement or instrument to which the Company is a
party or by which the Company or any of its assets are bound, or (iii) any laws, regulations or governmental or judicial decrees, injunctions or orders applicable to the Company. 

Section 3.3 Validity of the Holders’ New Notes. The Holders’ New Notes have been duly authorized by the
Company and, when executed and authenticated in accordance with the provisions of the Indenture and delivered to the Holder pursuant to the Exchange against delivery of the Exchanged Notes in accordance with the terms of this Agreement, the
Holders’ New Notes will be valid and binding obligations of the Company, enforceable in accordance with their terms, except that such enforcement may be subject to the Enforceability Exceptions, and the Holders’ New Notes will not be
subject to any preemptive, participation, rights of first refusal or other similar rights. Assuming the accuracy of each Holder’s representations and warranties hereunder, the Holders’ New Notes (a) will be issued in the Exchange
exempt from the registration requirements of the Securities Act pursuant to Section 4(2) of the Securities Act and/or Rule 506 of Regulation D, (b) will, at the Closing, be free of any restrictions on resale by such Holder pursuant to
Rule 144 promulgated under the Securities Act and (c) will be issued in compliance with all applicable state and federal laws concerning the issuance of the Holders’ New Notes. 

Section 3.4 Validity of Underlying Common Stock. The Holders’ New Notes will at the Closing be convertible into
shares of Common Stock, par value $0.01 per share, of the Company (the “Conversion Shares”) in accordance with the terms of the Supplement. The Conversion Shares have been duly authorized and reserved by the Company for issuance
upon conversion of the Holders’ New Notes and, when issued upon conversion of the Holders’ New Notes in accordance with the terms of the Holders’ New Notes and the Indenture, will be validly issued, fully paid and non-assessable, and
the issuance of the Conversion Shares will not be subject to any preemptive, participation, rights of first refusal or other similar rights. 
 Section 3.5 Listing Approval. At the Closing, the Conversion Shares shall be listed on the NASDAQ Global Select Market. 

Section 3.6 Disclosure. On or before the first business day following the date of this Agreement, the Company shall
issue a publicly available press release or file with the SEC a Current Report on Form 8-K disclosing all material terms of the Exchange and certain other matters concerning the Company (to the extent not previously publicly disclosed).

 Article IV: Miscellaneous 
 Section 4.1 Entire Agreement. This Agreement and any documents and agreements executed in connection with the Exchange embody the entire agreement and understanding of the parties
hereto with respect to the subject matter hereof and supersede all prior and contemporaneous oral or written agreements, representations, warranties, contracts, correspondence, conversations, memoranda and understandings between or among the parties
or any of their agents, representatives or affiliates relative to such subject matter, including, without limitation, any term sheets, emails or draft documents. 
 Section 4.2 Construction. References in the singular shall include the plural, and vice versa, unless the context otherwise requires. References in the masculine shall include the
feminine and neuter, and vice versa, unless the context otherwise requires. Headings in this Agreement are for convenience of reference only and shall not limit or otherwise affect the meanings of the provisions hereof. Neither party, nor its
respective counsel, shall be deemed the drafter of this Agreement for purposes of construing the provisions of this Agreement, and all language in all parts of this Agreement shall be construed in accordance with its fair meaning, and not strictly
for or against either party. 

  
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 Section 4.3 Governing Law. This Agreement shall in all respects be
construed in accordance with and governed by the substantive laws of the State of New York, without reference to its choice of law rules. 
 Section 4.4 Counterparts. This Agreement may be executed in counterparts, each of which shall be deemed an original, but all of which taken together shall constitute one and the same
instrument. Any counterpart or other signature hereon delivered by facsimile shall be deemed for all purposes as constituting good and valid execution and delivery of this Agreement by such party. 

[Signature Page Follow] 

  
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 IN WITNESS WHEREOF, each of the parties hereto has caused this Agreement to be executed as
of the date first above written. 
  

					
	“UNDERSIGNED”:	  	
		
	  
	  	
	(in its capacities described in the first paragraph hereof)	  	
			
	By:	  	  
	  	
			
	Name:	  	  
	  	
			
	Title:	  	  
	  	
	  
 “COMPANY”:

 
 HOLOGIC, INC.
	  	
			
	By:	  	  
	  	
			
	Name:	  	  
	  	
			
	Title:	  	  
	  	

 Signature Page to Exchange Agreement 

Hologic, Inc. 2.00% Convertible Senior Notes due 2043 Exchange 

 EXHIBIT A 
 Exchanging Beneficial Owners 
  

							
	 Name of
Beneficial Owner
	 	 Principal Amount of

Exchanged Notes
	 	 Principal Amount of

Holders’ New Notes
	  	Cash Payment

 EXHIBIT B 
 Form of Fourth Supplemental IndentureEX-10.16

 Exhibit 10.16 
 CYMER, INC. 
 AMENDMENT NO. 1 TO 

RESTRICTED STOCK UNIT AGREEMENTS AND 
 PERFORMANCE RESTRICTED STOCK UNIT AGREEMENTS 
 This
AMENDMENT NO. 1 (the “Amendment”) is effective as of December     , 2012, by and between CYMER, INC., a Nevada corporation
(the “Company”), and                     (“Holder”). 

RECITALS 
 A. The Company and Holder have entered into one or more Performance Restricted Stock Unit Agreements (Cymer Nos.     ,     ) and Restricted Stock Unit Agreements
(Cymer Nos.     ,     , and     ) (each, an “Original Agreement”) pursuant to which a number of shares of Common Stock are to be issued to the Holder during 2012.
Each Original Agreement was subject to Company’s 2005 Equity Incentive Plan (the “Plan”). Capitalized terms not otherwise defined herein shall have the meanings given in each Original Agreement and the Plan. 

B. The Company and Holder wish to amend certain terms set forth in each Original Agreement. 

AGREEMENT 
 The parties agree as follows: 
 1. Section 1 of each Original Agreement shall
be amended to add the following provision to the end thereof, which shall read as follows: 
 “Notwithstanding the
forgoing, with respect to any shares subject to your Award that vested between (and including) January 1, 2012 and December 13, 2012 (the “2012 Tranche”), the Company will deliver to you a number of shares of Common
Stock equal to the 2012 Tranche on December 13, 2012. 
 2. Section 10 of each Original Agreement shall be amended to
add a new subsection 10(c) to the end thereof, which shall read as follows: 
 “(c) With respect to shares of the
Company’s Common Stock that are issued to you between (and including) December 1, 2012 and December 31, 2012, if, on the applicable date on which shares are to be delivered to you in accordance with Section 1, you are precluded
under the Company’s policy regarding insider trading from engaging in market transactions involving the Company’s Common Stock, the Company shall satisfy its tax withholding obligation by withholding shares of Common Stock from the shares
of Common Stock issued or otherwise issuable to you in connection with your Restricted Stock Units with a Fair Market Value (measured as of the date shares of Common Stock are issued to you) equal to, but not exceeding, the amount of such tax
withholding obligation. Any fractional shares will be rounded down to the next whole share and you will be required to pay the Company via check an amount equal to 

 
any tax withholding shortfall. With respect to the portion of the tax withholding obligation that is satisfied by withholding in shares of Common Stock, for tax purposes, you are deemed to have
been issued the full number of vested shares of Common Stock subject to the Original Agreements, notwithstanding that a number of the shares of Common Stock are held back solely for the purpose of satisfying the tax withholding obligation.”

 3. Except as expressly set forth herein, each Original Agreement and all other documents referred to therein shall remain in
full force and effect and shall not be modified or altered in any other way. 
 4. This Amendment and all acts and transactions
pursuant hereto and the rights and obligations of the parties hereto shall be governed, construed and interpreted in accordance with the laws of the State of California, without giving effect to principles of conflicts of law. 

5. This Amendment may be executed in two counterparts, each of which shall be deemed an original and all of which together shall
constitute one instrument. 
 [SIGNATURE PAGE FOLLOW] 

  
 2 

 The parties hereto have executed this AMENDMENT NO. 1
TO RESTRICTED STOCK UNIT AGREEMENTS AND PERFORMANCE RESTRICTED STOCK UNIT AGREEMENTS
as of the date first written above. 
  

			
	COMPANY:
	
	CYMER, INC.
		
	By:	 	  

	
	HOLDER:
	
	  

  
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