Document:

EX-10.3

ADVENTRX PHARMACEUTICALS, INC.

RESTRICTED STOCK UNITS AGREEMENT

ADVENTRX Pharmaceuticals, Inc. has granted to the Participant named in the Notice of Grant of
Restricted Stock Units (the “Grant Notice”) to which this Restricted Stock Units Agreement (this
“Agreement”) is attached an Award consisting of Restricted Stock Units (the “Units”) subject to the
terms and conditions set forth in the Grant Notice and this Agreement. The Award has been granted
pursuant to and shall in all respects be subject to the terms conditions of the ADVENTRX
Pharmaceuticals, Inc. 2008 Omnibus Incentive Plan (the “Plan”), as amended to the Grant Date, the
provisions of which are incorporated herein by reference. By signing the Grant Notice, the
Participant: (a) acknowledges receipt of and represents that the Participant has read and is
familiar with the Grant Notice, this Agreement, the Plan and a prospectus for the Plan prepared in
connection with the registration with the Securities and Exchange Commission of the shares issuable
pursuant to the Award (the “Plan Prospectus”), (b) accepts the Award subject to all of the terms
and conditions of the Grant Notice, this Agreement and the Plan and (c) agrees to accept as
binding, conclusive and final all decisions or interpretations of the Committee upon any questions
arising under the Grant Notice, this Agreement or the Plan.

1. Definitions and Construction.

1.1 Definitions. Unless otherwise defined herein, capitalized terms shall have the meanings
assigned in the Grant Notice or the Plan. The term “Company” shall mean ADVENTRX Pharmaceuticals,
Inc., a Delaware corporation, and any successor company (or a subsidiary or parent thereof),
including any Acquiror (as defined in Section 8).

1.2 Construction. Captions and titles contained herein are for convenience only and shall not
affect the meaning or interpretation of any provision of this Agreement. Except when otherwise
indicated by the context, the singular shall include the plural and the plural shall include the
singular. Use of the term “or” is not intended to be exclusive, unless the context clearly
requires otherwise.

2. Administration.

All questions of interpretation concerning the Grant Notice, this Agreement and the Plan shall
be determined by the Committee. All determinations by the Committee shall be final and binding
upon all persons having an interest in the Award as provided by the Plan. Any officer of the
Company shall have the authority to act on behalf of the Company with respect to any matter, right,
obligation, or election which is the responsibility of or which is allocated to the Company herein,
provided such officer has apparent authority with respect to such matter, right, obligation, or
election.

3. The Award.

3.1 Grant of Units. On the Grant Date, the Participant shall acquire, subject to the
provisions of this Agreement, the Number of Restricted Stock Units set forth in the Grant Notice,
subject to adjustment as provided in Section 9. Each Unit represents a right to receive on a date
determined in accordance with the Grant Notice and this Agreement one (1) Share.

3.2 No Monetary Payment Required. The Participant is not required to make any monetary
payment (other than applicable tax withholding, if any) as a condition to receiving the Units or
Shares issued upon settlement of the Units, the consideration for which shall be past services
actually rendered and/or future services to be rendered to the Company or for its benefit.
Notwithstanding the foregoing, if required by applicable state corporate law, the Participant shall
furnish consideration in the form of cash or past services rendered to the Company or for its
benefit having a value not less than the par value of the Shares issued upon settlement of the
Units.

4. Vesting of Units; Timing of Settlement.

The Units shall vest and become “Vested Units” as provided in the Grant Notice. In the event
that the Vesting Date as provided by the Grant Notice (the “Original Settlement Date”) would occur
on a date on which a sale by the Participant of the Shares to be issued in settlement of the Units
becoming Vested Units on the Original Settlement Date would violate any insider trading or similar
policy or program of the Company (collectively, the “Insider Trading Policies”) or any federal,
state or foreign law or any contractual obligation to which the Participant is subject (such as a
“lock-up” or “market stand-off” agreement) (each, a “Contractual Obligation”), the settlement of
such Vested Units shall be deferred until the first to occur of (a) the next business day on which
a sale by the Participant of such Shares would not violate the Insider Trading Policies or any
Contractual Obligation and (b) the 15th day of the third month following the later of (i) the last
day of the calendar year in which the Original Settlement Date occurred and (ii) the last day of
the Company’s taxable year in which the Original Settlement Date occurred.

5. Company Reacquisition Right.

Except to the extent otherwise provided in an agreement between the Company and the
Participant, in the event that the Participant’s Services terminate for any reason or no reason,
with or without cause, the Participant shall forfeit and the Company shall automatically reacquire
all Units which are not, as of the time of such termination, Vested Units (“Unvested Units”), and
the Participant shall not be entitled to any payment therefor (the “Company Reacquisition Right”).

6. Settlement of the Award.

6.1 Issuance of Shares. Subject to the provisions of Section 4 and 6.3 below, the Company
shall issue to the Participant on the Settlement Date (as described in the Grant Notice) with
respect to each Vested Unit to be settled on such date one (1) Share. Shares issued in settlement
of the Units shall not be subject to any restriction on transfer other than any such restriction as
may be required pursuant to Section 6.3, Section 7, the Insider Trading Policies and any
Contractual Restrictions.

6.2 Beneficial Ownership of Shares; Registration of Shares. The Participant hereby
authorizes the Company, in its sole discretion, to deposit for the benefit of the Participant with
any broker with which the Participant has an account relationship of which the Company has notice
any or all Shares acquired by the Participant pursuant to the settlement of the Units. Except as
provided by the preceding sentence and subject to Section 11, the Shares issued upon settlement of
the Units shall be registered in the name of the Participant, or, if applicable, in the names of
the heirs of the Participant.

6.3 Restrictions on Grant of the Award and Issuance of Shares. The grant of the Award and
issuance of Shares upon settlement of the Units shall be subject to compliance with all applicable
requirements of federal, state or foreign law with respect to such securities. No Shares may be
issued hereunder if the issuance of such Shares would constitute a violation of any applicable
federal, state or foreign securities laws or other law or regulations or the requirements of any
stock exchange or market system upon which the Shares may then be listed. The inability of the
Company to obtain from any regulatory body having jurisdiction the authority, if any, deemed by the
Company’s legal counsel to be necessary for the lawful issuance of any Shares subject to the Award
shall relieve the Company of any liability in respect of the failure to issue such Shares as to
which such requisite authority shall not have been obtained. As a condition to the settlement of
the Award, the Company may require the Participant to satisfy any qualifications that may be
necessary or appropriate to evidence compliance with any applicable law or regulation and to make
any representation or warranty with respect thereto as may be requested by the Company.

6.4 Fractional Shares. The Company shall not be required to issue fractional Shares upon the
settlement of the Units.

7. Tax Withholding.

7.1 In General. At the time the Grant Notice is executed, or at any time thereafter as
requested by the Company, the Participant hereby authorizes withholding from payroll and any other
amounts payable to the Participant, and otherwise agrees to make adequate provision for, any sums
required to satisfy the federal, state, local and foreign tax (including any social insurance)
withholding obligations of the Company, if any, which arise in connection with the Award, the
vesting of Units or the issuance of Shares in settlement thereof. The Company shall have no
obligation to deliver Shares until the tax withholding obligations of the Company have been
satisfied by the Participant.

7.2 Assignment of Sale Proceeds; Payment of Tax Withholding by Check. Subject to compliance
with applicable law and the Insider Trading Policies, the Company may permit the Participant to
satisfy the Company’s tax withholding obligations in accordance with procedures established by the
Company providing for either (i) delivery by the Participant to the Company or a broker approved by
the Company of properly executed instructions, in a form approved by the Company, providing for the
assignment to the Company of the proceeds of a sale with respect to some or all of the Shares being
acquired upon settlement of Units, (ii) payment by check or such other procedure established by the
Committee pursuant to Section 13.2 of the Plan. The Participant shall deliver written notice of
any such permitted election to the Company on a form specified by the Company for this purpose at
least thirty (30) days (or such other period established by the Company) prior to a Settlement
Date. If the Participant elects payment by check, the Participant agrees to deliver a check for
the full amount of the required tax withholding to the Company on or before the third business day
following the Settlement Date. If the Participant elects payment by check but fails to make such
payment as required by the preceding sentence, the Company is hereby authorized, at its discretion,
to satisfy the tax withholding obligations through any means authorized by this Section 7,
including by directing a sale for the account of the Participant of some or all of the Shares being
acquired upon settlement of Units from which the required taxes shall be withheld, by withholding
from payroll and any other amounts payable to the Participant or by withholding Shares in
accordance with Section 7.3.

7.3 Withholding in Shares. The Company may require the Participant to satisfy all or any
portion of the Company’s tax withholding obligations by deducting from the Shares otherwise
deliverable to the Participant in settlement of the Units a number of whole Shares having a fair
market value, as determined by the Company as of the date on which the tax withholding obligations
arise, not in excess of the amount of such tax withholding obligations determined by the applicable
minimum statutory withholding rates.

8. Effect of Change in Control on Award.

In the event of a Change in Control, the surviving, continuing, successor, or purchasing
corporation or other business entity or subsidiary or parent thereof, as the case may be (the
“Acquiror”), may, without the consent of the Participant, assume or continue the Company’s rights
and obligations with respect to all or any portion of the outstanding Units or substitute for all
or any portion of the outstanding Units substantially equivalent rights with respect to the
Acquiror’s stock.

9. Adjustments for Changes in Capital Structure.

Subject to any required action by the stockholders of the Company and the requirements of
Section 409A of the Code to the extent applicable, in the event of any change in the Shares
effected without receipt of consideration by the Company, whether through merger, consolidation,
reorganization, reincorporation, recapitalization, reclassification, stock dividend, stock split,
reverse stock split, split-up, split-off, spin-off, combination of Shares, exchange of Shares, or
similar change in the capital structure of the Company, or in the event of payment of a dividend or
distribution to the stockholders of the Company in a form other than Shares (excepting normal cash
dividends) that has a material effect on the Fair Market Value of Shares, appropriate and
proportionate adjustments shall be made in the number of Units subject to the Award and/or the
number and kind of shares to be issued in settlement of the Units, in order to prevent dilution or
enlargement of the Participant’s rights under the Award. For purposes of the foregoing, conversion
of any convertible securities of the Company shall not be treated as “effected without receipt of
consideration by the Company.” Any fractional share resulting from an adjustment pursuant to this
Section shall be rounded down to the nearest whole number. Such adjustments shall be determined by
the Committee as contemplated in Section 12.2 of the Plan, and its determination shall be final,
binding and conclusive.

10. Rights as a Stockholder or Employee.

The Participant shall have no rights as a stockholder with respect to any Shares which may be
issued in settlement of the Units until the date of the issuance of such Shares (as evidenced by
the appropriate entry on the books of the Company or of a duly authorized transfer agent of the
Company). No adjustment shall be made for dividends, distributions or other rights for which the
record date is prior to the date such certificate is issued, except as provided in Section 9. If
the Participant is an Employee, the Participant understands and acknowledges that, except as
otherwise provided in a separate, written employment agreement between the Company and the
Participant, the Participant’s employment is “at will” and is for no specified term. Nothing in
this Agreement shall confer upon the Participant any right to continue providing Services or
interfere in any way with any right of the Company to terminate the Participant’s Services at any
time.

11. Legends.

The Company may at any time determine to issue certificates representing the Shares issued
pursuant to this Agreement rather than issue uncertificated Shares and the Company may at any time
place legends referencing any applicable federal, state or foreign securities law or Contractual
Obligation restrictions on all certificates representing Shares issued pursuant to this Agreement.
The Participant shall, at the request of the Company, promptly present to the Company any and all
certificates representing Shares acquired pursuant to settlement of the Units in the possession of
the Participant in order to carry out the provisions of this Section.

12. Miscellaneous Provisions.

12.1 Termination or Amendment. The Committee may terminate or amend the Plan or this
Agreement at any time; provided, however, that no such termination or amendment may adversely
affect the Participant’s rights under this Agreement without the consent of the Participant unless
such termination or amendment is necessary to comply with applicable law or government regulation,
including, but not limited to, Section 409A. No amendment or addition to this Agreement shall be
effective unless in writing.

12.2 Nontransferability of the Award. Prior to the issuance of Shares on the applicable
Settlement Date, neither the Award nor any Units subject to the Award shall be subject in any
manner to anticipation, alienation, sale, exchange, transfer, assignment, pledge, encumbrance, or
garnishment by creditors of the Participant or the Participant’s beneficiary, except transfer by
will or by the laws of descent and distribution. All rights with respect to the Award shall be
exercisable during the Participant’s lifetime only by the Participant or the Participant’s guardian
or legal representative.

12.3 Further Instruments. The parties hereto agree to execute such further instruments and to
take such further action as may reasonably be necessary to carry out the intent of this Agreement.

12.4 Binding Effect. This Agreement shall inure to the benefit of the successors and assigns
of the Company and, subject to the restrictions on transfer set forth herein, be binding upon the
Participant and the Participant’s heirs, executors, administrators, successors and assigns.

12.5 Delivery of Documents and Notices. Any document relating to participation in the Plan or
any notice required or permitted hereunder shall be given in writing and shall be deemed
effectively given (except to the extent that this Agreement provides for effectiveness only upon
actual receipt of such notice) upon personal delivery, electronic delivery at the e-mail address,
if any, provided by the Participant to the Company, or upon deposit in the U.S. Post Office or
foreign postal service, by registered or certified mail, or with a nationally recognized overnight
courier service, with postage and fees prepaid, addressed to the other party at the address shown
below that party’s signature to the Grant Notice or at such other address as such party may
designate in writing from time to time to the other party.

(a) Description of Electronic Delivery. The Plan documents, which may include but do not
necessarily include: the Plan, the Grant Notice, this Agreement, the Plan Prospectus, and any
reports of the Company provided generally to the Company’s stockholders, may be delivered to the
Participant electronically. In addition, the Participant may deliver electronically the Grant
Notice to the Company or to such third party involved in administering the Plan as the Company may
designate from time to time. Such means of electronic delivery may include but do not necessarily
include the delivery of a link to a Company intranet or the Internet site of a third party involved
in administering the Plan, the delivery of the document via e-mail or such other means of
electronic delivery specified by the Company.

(b) Consent to Electronic Delivery. The Participant acknowledges that the Participant has
read Section 12.5(a) of this Agreement and consents to the electronic delivery of the Plan
documents and Grant Notice, as described in Section 12.5(a). The Participant acknowledges that he
or she may receive from the Company a paper copy of any documents delivered electronically at no
cost to the Participant by contacting the Company in writing. The Participant further acknowledges
that the Participant will be provided with a paper copy of any documents if the attempted
electronic delivery of such documents fails. Similarly, the Participant understands that the
Participant must provide the Company or any designated third party administrator with a paper copy
of any documents if the attempted electronic delivery of such documents fails. The Participant may
revoke his or her consent to the electronic delivery of documents described in Section 12.5(a) or
may change the electronic mail address to which such documents are to be delivered (if Participant
has provided an electronic mail address) at any time by notifying the Company in writing of such
revoked consent or revised e-mail address. Finally, the Participant understands that he or she is
not required to consent to electronic delivery of documents described in Section 12.5(a).

12.6 Integrated Agreement. The Grant Notice, this Agreement and the Plan, together with any
employment, service or other agreement between the Participant and the Company referring to the
Award, shall constitute the entire understanding and agreement of the Participant and the Company
with respect to the subject matter contained herein or therein and supersede any prior agreements,
understandings, restrictions, representations, or warranties among the Participant and the Company
with respect to such subject matter other than those as set forth or provided for herein or
therein. To the extent contemplated herein or therein, the provisions of the Grant Notice, this
Agreement and the Plan shall survive any settlement of the Award and shall remain in full force and
effect.

12.7 Applicable Law. This Agreement shall be governed by the laws of the State of California
as such laws are applied to agreements between California residents entered into and to be
performed entirely within the State of California.

12.8 Counterparts. The Grant Notice may be executed in counterparts, each of which shall be
deemed an original, but all of which together shall constitute one and the same instrument.EX-10.1

EXHIBIT 10.1

THIRD SUPPLEMENTAL INDENTURE

THIRD SUPPLEMENTAL INDENTURE (this “Third Supplemental Indenture”) dated as of January 27,
2009 (the “Effective Date”), between THE KANSAS CITY SOUTHERN RAILWAY COMPANY, a corporation duly
organized and existing under the laws of the State of Missouri, and the successor by merger to each
of Mid-South Microwave, Inc. and Rice-Carden Corporation (the “Company”), KANSAS CITY SOUTHERN
(formerly known as Kansas City Southern Industries, Inc.) (the “Parent”), and GATEWAY EASTERN
RAILWAY COMPANY, PABTEX GP, LLC, PABTEX I, L.P. (f/k/a PABTEX L.P.), SIS BULK HOLDING, INC.,
SOUTHERN DEVELOPMENT COMPANY, SOUTHERN INDUSTRIAL SERVICES, INC., and TRANS-SERVE, INC. (together
with the Parent, the “Note Guarantors”), and U.S. BANK NATIONAL ASSOCIATION, as trustee under the
indenture referred to below (the “Trustee”).

W I T N E S S E T H :

WHEREAS, the Company and the Note Guarantors have heretofore executed and delivered to the
Trustee an Indenture (the “Indenture”) dated as of June 12, 2002, a First Supplemental Indenture
dated as of June 10, 2005 (the “First Supplemental Indenture”) and a Second Supplemental Indenture
dated as of February 5, 2007 (the “Second Supplemental Indenture”), providing for the issuance of
an aggregate principal amount of up to $200,000,000 of 71/2% Senior Notes due 2009 (the
“Securities”);

WHEREAS, the Company, the Note Guarantors and the Trustee desire to further amend the
Indenture to delete and amend certain provisions contained therein and in the Securities;

WHEREAS, Section 9.02 of the Indenture provides that, with the written consent of the Holders
of a majority in aggregate principal amount of the outstanding Securities (the “Requisite
Consents”), the Company, the Note Guarantors and the Trustee may amend the Indenture;

WHEREAS, pursuant to an Offer to Purchase and Related Solicitation of Consents dated January
14, 2009 (the “Offer to Purchase”), the Company offered to purchase all outstanding Securities and
solicited consents to the amendments to the Indenture and the Securities described herein (the
“Amendments”);

WHEREAS, Holders of at least a majority in principal amount of the Securities outstanding have
consented to the Amendments by tendering and not withdrawing their Securities and by delivering the
related consents pursuant to the terms of the Offer to Purchase;

WHEREAS, the Company, the Note Guarantors, and the Trustee are entering into this Third
Supplemental Indenture in order to set forth the Amendments; and

WHEREAS, this Third Supplemental Indenture has been duly authorized by all necessary corporate
action on the part of the Company, the Note Guarantors and the Trustee.

NOW THEREFORE, in consideration of the foregoing and for other good and valuable
consideration, the receipt of which is hereby acknowledged, the Company, the Note Guarantors and
the Trustee mutually covenant and agree for the equal and ratable benefit of the Holders as
follows:

ARTICLE 1

AMENDMENT OF THE INDENTURE

1.01. Amendments to the Indenture. Effective as of the Effective Date, the Indenture
is amended as set forth herein.

(a) Section 1.01 of the Indenture is hereby amended to delete the following definitions in
their entirety:

	 	 	 
	Additional Assets

	 	Grupo TFM Investment
	Asset Disposition

	 	Hedging Obligation
	Attributable Debt

	 	Interest Rate Agreement
	Capitalized Lease Obligations

	 	Investment Grade Rating
	Change of Control

	 	Net Available Cash
	Consolidated Coverage Ratio

	 	Net Cash Proceeds
	Consolidated Current Liabilities

	 	Permitted Business
	Consolidated Interest Expense

	 	Permitted Investment
	Consolidated Net Income

	 	Permitted Liens
	Consolidated Net Tangible Assets

	 	Purchase Money Indebtedness
	Consolidated Net Worth

	 	Rating Agency
	Designated Sale/Leaseback Transaction

	 	Refinancing Indebtedness
	Disqualified Stock

	 	Sale/Leaseback Transaction
	EBITDA

	 	Secured Indebtedness
	Equity Offering

	 	Securities Act
	Exchange Act

	 	Senior Indebtedness
	Excluded Contributions

	 	Stock Purchase Loans
	Foreign Equity Investment

	 	Subordinated Obligation
	Grupo TFM

	 	Temporary Cash Investments
	Grupo TFM Disposition

	 	TFM

(b) Each of the following Sections of the Indenture is hereby deleted in its entirety and
replaced in lieu thereof with the words “[Intentionally Deleted]”:

Section 4.02 SEC Reports.

Section 4.03 Limitation on Indebtedness.

Section 4.04 Limitation on Restricted Payments.

Section 4.05 Limitation on Restrictions on Distributions from Restricted
Subsidiaries.

Section 4.06 Limitation on Sales of Assets and Capital Stock.

Section 4.07 Limitation on Transactions with Affiliates.

Section 4.08 Change of Control.

Section 4.09 Compliance Certificate.

Section 4.10 Further Instruments and Acts.

Section 4.11 Future Note Guarantors.

Section 4.12 Limitation on Lines of Business.

Section 4.13 Limitation on Liens.

Section 4.14 Limitation of Sale/Leaseback Transactions.

Section 4.15 Covenant Suspension.

(c) Section 5.01 of the Indenture is hereby deleted in its entirety and replaced with the
following:

“SECTION 5.01. (a) When Company May Merge or Transfer Assets. The Company will not
consolidate with or merge with or into, or convey, transfer or lease all or substantially
all /its assets to, any Person, unless:

(i) the resulting, surviving or transferee Person (the “Successor Company”) shall be a
corporation organized and existing under the laws of the United States of America, any State
thereof or the District of Columbia and the Successor Company (if not the Company) shall
expressly assume, by a supplemental indenture hereto, executed and delivered to the Trustee,
in form satisfactory to the Trustee, all the obligations of the Company under the
Securities and this Indenture;

(ii) immediately after giving effect to such transaction (and treating any Indebtedness
which becomes an obligation of the Successor Company, the Parent or any Restricted
Subsidiary as a result of such transaction as having been Incurred by the Successor Company,
the Parent or such Restricted Subsidiary at the time of such transaction), no Default shall
have occurred and be continuing;

(iii) the Company shall have delivered to the Trustee an Officers’ Certificate and an
Opinion of Counsel, each stating that such consolidation, merger or transfer and such
supplemental indenture (if any) comply with this Indenture; and

The Successor Company will succeed to, and be substituted for, and may exercise every right
and power of, the Company under this Indenture, but the predecessor Company in the case of a
conveyance, transfer or lease of all or substantially all its assets shall not be released from the
obligation to pay the principal of and interest on the Securities.

(b) The Note Guarantors will not consolidate with or merge with or into, or convey,
transfer or lease all or substantially all of its assets to any Person unless: (i) the
resulting, surviving or transferee Person (the “Successor Guarantor”) will be a corporation
organized and existing under the laws of the United States of America, any State thereof or
the District of Columbia, and such Person (if not such Note Guarantor) shall expressly
assume, by a supplemental indenture, executed and delivered to the Trustee, in form
satisfactory to the Trustee, all the obligations of such Note Guarantor under its Note
Guarantee; (ii) immediately after giving effect to such transaction (and treating any
Indebtedness which becomes an obligation of the Successor Guarantor or any Restricted
Subsidiary as a result of such transaction as having been Incurred by the Successor
Guarantor or such Restricted Subsidiary at the time of such transaction), no Default shall
have occurred and be continuing; and (iii) the Parent shall have delivered to the Trustee an
Officers’ Certificate and an Opinion of Counsel, each stating that such consolidation,
merger or transfer and such supplemental indenture (if any) comply with this Indenture.

(c) Notwithstanding the foregoing, (i) any Restricted Subsidiary may consolidate with,
merge into or transfer all or part of its properties and assets to the Company or any Note
Guarantor; (ii) the Parent or the Company may merge with an Affiliate incorporated solely
for the purpose of reincorporating the Parent or the Company, as the case may be, in another
jurisdiction to realize tax or other benefits; and (iii) the Parent and the Company may
merge.”

(d) Section 6.01(d) is hereby deleted in its entirety and replaced in lieu thereof
with the words “(d) [Intentionally Deleted]”.

(e) The penultimate paragraph in Section 6.01 is hereby deleted in its entirety and
replaced with the following:

“A default under clauses (e) or (f) will not constitute an Event of Default until the
Trustee notifies the Company or the Holders of at least 25% in principal amount of the
outstanding Securities notify the Company and the Trustee of the Default and the Company or
the Note Guarantor, as applicable, does not cure such Default within the time specified in
clauses (e) or (f) hereof after receipt of such notice. Such notice must specify the
Default, demand that it be remedied and state that such notice is a “Notice of Default”.”

(f) Section 6.12 Waiver of Stay or Extension Laws. is hereby deleted in its entirety
and replaced in lieu thereof with the words “Section 6.12 [Intentionally Deleted]”.

(g) Sections 8.02(a)(iii), (vi) and (vii) are hereby deleted in their entirety and
replaced in lieu thereof with the words “[Intentionally Deleted]”.

(h) Section 9.04 Revocation and Effect of Consents and Waivers. is hereby deleted in
its entirety and replaced with the following:

“SECTION 9.04. Revocation and Effect of Consents and Waivers. (a) A consent
to an amendment or a waiver by a Holder of a Security shall bind the Holder and every
subsequent Holder of that Security or portion of the Security that evidences the same debt
as the consenting Holder’s Security, even if notation of the consent or waiver is not made
on the Security. After an amendment or waiver becomes effective, it shall bind every
Holder. An amendment or waiver becomes effective upon the (i) receipt by the Company or the
Trustee of the requisite number of consents, (ii) satisfaction of conditions to
effectiveness as set forth in this Indenture and any indenture supplemental hereto
containing such amendment or waiver and (iii) execution of such amendment or waiver (or
supplemental indenture) by the Company and the Trustee.”

(i) Section 10.06 is hereby deleted in its entirety and replaced in lieu thereof with
the words “Section 10.06 [Intentionally Deleted]”.

ARTICLE 2

MISCELLANEOUS

2.01. Ratification of Indenture, Supplemental Indentures Part of Indenture. Except as
expressly amended hereby, the Indenture, the First Supplemental Indenture and the Second
Supplemental Indenture are in all respects ratified and confirmed and all the terms, conditions and
provisions thereof shall remain in full force and effect. Upon the execution and delivery of this
Third Supplemental Indenture by the Company, the Note Guarantors and the Trustee, the Indenture
shall be supplemented in accordance herewith, this Third Supplemental Indenture shall form a part
of the Indenture for all purposes, and every Holder of Securities heretofore or hereafter
authenticated and delivered shall be bound hereby, and the respective rights, limitation of rights,
obligations, duties and immunities under the Indenture of the Company, the Note Guarantors, the
Trustee, and the Holders of the Securities shall thereafter be determined, exercised and enforced
thereunder, subject in all respects to such modifications and amendments, and all the terms and
conditions of this Third Supplemental Indenture shall be deemed to be part of the terms and
conditions of the Indenture and the Securities theretofore issued for any and all purposes.

2.02. Governing Law. THIS THIRD SUPPLEMENTAL INDENTURE SHALL BE GOVERNED BY, AND
CONSTRUED IN ACCORDANCE WITH, THE LAWS OF THE STATE OF NEW YORK BUT WITHOUT GIVING EFFECT TO
APPLICABLE PRINCIPLES OF CONFLICTS OF LAW TO THE EXTENT THAT THE APPLICATION OF THE LAWS OF ANOTHER
JURISDICTION WOULD BE REQUIRED THEREBY.

2.03. Trustee Acceptance. The Trustee accepts the amendment of the Indenture effected
by this Third Supplemental Indenture, but only upon the terms and conditions set forth in the
Indenture, as hereby amended, including the terms and provisions defining and limiting the
liabilities and responsibilities of the Trustee in the performance of its duties and obligations
under the Indenture, as hereby amended. Without limiting the generality of the foregoing, the
Trustee has no responsibility for the correctness of the recitals of fact herein contained which
shall be taken as the statements of the Company, and makes no representations as to the validity or
sufficiency of this Third Supplemental Indenture.

2.04. Severability Clause. In case any provision of this Third Supplemental Indenture
shall be invalid, illegal or unenforceable, the validity, legality and enforceability of the
remaining provisions shall not in any way be affected or impaired thereby.

2.05. Counterparts. The parties may sign any number of copies of this Third
Supplemental Indenture. Each signed copy shall be an original, but all of them together represent
the same agreement.

2.06. Definitions, Effect of Headings. All capitalized terms not otherwise defined
herein shall have the meanings ascribed to them in the Indenture. The section headings herein are
for convenience only and shall not effect the construction thereof.

[signature page following]

1

IN WITNESS WHEREOF, the parties hereto have caused this Third Supplemental Indenture to be
duly executed as of the date first above written.

THE KANSAS CITY SOUTHERN RAILWAY COMPANY

	 
	By /s/ Paul J. Weyandt

	 

	Name: Paul J. Weyandt

	 	 	Title: Senior Vice President – Finance and

Treasurer

KANSAS CITY SOUTHERN

	 
	By /s/ Paul J. Weyandt

	 

	Name: Paul J. Weyandt

	 	 	Title: Senior Vice President – Finance and

Treasurer

GATEWAY EASTERN RAILWAY COMPANY

	 
	By /s/ Paul J. Weyandt

	 

	Name: Paul J. Weyandt

	 	 	Title: Senior Vice President – Finance and

Treasurer

	 
	PABTEX GP, LLC

By /s/ Michael W. Upchurch

	 

	Name: Michael W. Upchurch

	 	 	Title: Vice President and Chief Financial Officer
of Southern Industrial Services, the sole
member of PABTEX GP, LLC

PABTEX I, L.P.

	 
	By /s/ Michael W. Upchurch

	 

	Name: Michael W. Upchurch

	 	 	Title: Vice President and Chief Financial Officer
of Southern Industrial Services, the sole
member of PABTEX GP, LLC, the general
partner of PABTEX I, L.P

2

	 
	SIS BULK HOLDING, INC.

By /s/ Michael W. Upchurch

	 

	Name: Michael W. Upchurch

	 	 	Title: Vice President and Chief Financial Officer

	 
	SOUTHERN DEVELOPMENT COMPANY

By /s/ Michael W. Upchurch

	 

	Name: Michael W. Upchurch

	 	 	Title: Vice President and Chief Financial Officer

	 
	SOUTHERN INDUSTRIAL SERVICES, INC.

By /s/ Michael W. Upchurch

	 

	Name: Michael W. Upchurch

	 	 	Title: Vice President and Chief Financial Officer

	 
	TRANS-SERVE, INC.

By /s/ Michael W. Upchurch

	 

	Name: Michael W. Upchurch

	 	 	Title: Vice President and Chief Financial

Officer

U.S. BANK NATIONAL ASSOCIATION.

By   /s/ Richard Prokosch

Name: Richard Prokosch

Title: Vice President

3

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