Source: s3://data.kl3m.ai/documents/govinfo/USCOURTS/USCOURTS-cand-5_02-cv-05946/USCOURTS-cand-5_02-cv-05946-1/pdf.json

Nature of Suit Code: 830
Nature of Suit: Patent
Cause of Action: 35:271 Patent Infringement

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United States District Court

For the Northern District of California

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United States District Court

For the Northern District of California

IN THE UNITED STATES DISTRICT COURT

FOR THE NORTHERN DISTRICT OF CALIFORNIA

SAN JOSE DIVISION

Bio-Rad Laboratories, Inc.,

Plaintiff,

 v.

Applera Corporation, et al.,

Defendants.

 /

NO. C 02-05946 JW 

ORDER GRANTING PARTIAL

SUMMARY JUDGMENT

I. INTRODUCTION

This is a patent dispute. Plaintiff, Bio-Rad Laboratories, Inc. (“Bio-Rad”), owns United States

Patent No. 5,089,111 (“’111 patent”) and asserts that certain products made by Defendant, Applera

Corporation (“Applera”), infringe one or more claims of the ’111 patent. 

The motion presently before the Court is for partial summary judgment. Applera requests partial

summary judgment that the chemical, polyacrylamide, is not an equivalent to “a substantially linear polymer

selected from the group consisting of methyl cellulose, hydroxypropyl methyl cellulose, hydroxyethyl methyl

cellulose, and hydroxybutyl methyl cellulose.” ’111 patent, 12:22-25. Applera argues that Bio-Rad, is

estopped from asserting infringement by the doctrine of equivalents because Bio-Rad made a narrowing

amendment to its claims in response to a rejection based on patentability. Bio-Rad disputes Applera’s

Motion and maintains that its amendment does not preclude it from asserting infringement by the doctrine of

equivalents. 

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The Court held oral argument on November 29, 2004. The parties, with this Court’s approval,

stipulated to multiple stays proceedings, including staying a decision on Applera’s Motion for Partial

Summary Judgment. On March 2, 2005, the Court conducted a case management conference. The

parties then informed the Court that they were no longer in settlement negotiations, and thus, requested the

Court to proceed with its decision on the pending motion. Based on all of the submissions and arguments

to date, the Court GRANTS Applera’s Motion for Partial Summary Judgement. 

II. BACKGROUND

Bio-Rad filed U.S. Patent Application No. 07/303,174 (“’174 application”) with the United States

Patent and Trademark Office ( the “PTO”) on January 27, 1989. The ’174 application initially contained

27 claims and was entitled, “Electrophoretic Sieving in Gel-Free Media with Dissolved Polymers.” Initially

filed claims 1 and 27 were the only independent claims. Of these 27 initially filed claims, initially filed claim

1 and initially filed claim 27 are relevant to this discussion. 

Initially filed claim 1 of the ’174 application read as follows:

1. A method of separating a mixture of sample ions of varying molecular weights in

a sample into components, said method comprising electrophoretically passing said sample

through a separation column containing a gel-free aqueous solution of a substantially linear

polymer having a molecular weight of about 10,000 to about 2,000,000, said molecular

weight being within a range of about 0.1 to about 200 times the average molecular weight

of said macromolecular species in said mixture, the concentration of said polymer in said

solution being sufficient to retard the flow of said species through said separation column to

degrees which vary with the molecular weights of said species.

Garber Decl., Exh. 1, ABBR065864. Initially filed claim 27 of the ’174 application read as follows:

27. A method of separating a mixture of polynucleotide chains in a sample, said

polynucleotide chains each containing from about 10 to 10,000 base pairs, said method

comprising electrophoretically passing said sample through a capillary column containing a

gel-free aqueous solution of a substantially linear polymer selected from the group

consisting of methyl cellulose, hydroxypropyl methyl cellulose, hydroxyethyl methyl

cellulose, and hydroxybutyl methyl cellulose, said polymer characterized in terms of the

viscosity of a 2% aqueous solution thereof being within a range of about 1,000 centipoise

to about 10,000 centipoise at 25NC, and the concentration of said polymer in said solution

is from about 0.1% to about 0.5% by weight.

Id. at ABBR065868.

The PTO examiner rejected initially filed claims 1-13 of the ’174 application as obvious under 35

U.S.C. § 103 in light of the Tietz, et al., Electrophoresis in Uncrosslinked Polyacrylamide Molecular

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Sieving and its Potential Applications, Electrophoresis, 7 1986, 217-220 (“Tietz”) and Bode, SDSPolyethyleneglycol Electrophoresis: A Possible Alternative to SDS- Polyacrylamide Ge Electrophoresis,

FEBS Lettes, 65(1) (1976) at 56-58 (“Bode”). The examiner stated that because Tietz “successfully

performed molecular sieving experiments using non-crosslinked linear polyacrylamide” claims 1-13 would

be obvious to the person having ordinary skill in the art. Id. at ABBR065889. In the same office action,

the examiner allowed initially filed claim 27 without comment.

In response to the office action, Bio-Rad amended initially filed claim 1 to read:

1. A method of separating a mixture of sample ions of varying molecular weights in

a sample into components, said method comprising electrophoretically passing said sample

through a separation column containing a gel-free aqueous solution of a substantially linear

water-soluble cellulose derivative polymer having a molecular weight of about 10,000 to

about 2,000,000, said molecular weight being within a range of about 0.1 to about 200

times the average molecular weight of said sample ions [macromolecular species] in said

mixture, the concentration of said polymer in said solution being sufficient to retard the flow

of said species through said separation column to degrees which vary with the molecular

weights of said species.

Id. at ABBR065894-95 (double underlined text indicates addition; bracketed text indicates deletion)

(amendment indicia in original). Initially filed claim 27 was unchanged. After Bio-Rad’s amendment to

initially filed claim 1, the PTO examiner issued a Notice of Allowability. 

Following the Notice of Allowability Bio-Rad abandoned the ’174 application in favor of a

Continuation-in-Part application (“CIP”). Notably, the CIP retained the title of the ’174 application, an

amended version of initially filed claim 1, and the original version of initially filed claim 27. The CIP issued

as the ’111 patent on February 18, 1992.

Amended claim 1 of the abandoned ’174 application was again altered in the newly filed CIP. 

Claim 1 of the CIP read:

1. A method of separating a mixture of sample ions of varying molecular weights in

a sample into components, said method comprising electrophoretically passing said sample

through a separation column containing a gel-free aqueous solution of a water-soluble

polymer selected from the group consisting of cellulose derivatives, saccharide-based and

substituted saccharide-based polymers, polysilanes, polyvinylalcohol and

polyvinylpyrrolidone, said polymer having a molecular weight of about 10,000 to about

2,000,000, said molecular weight being within a range of about 0.1 to about 200 times the

average molecular weight of said sample ions in said mixture, the concentration of said

polymer in said solution being sufficient to retard the flow of said species through said

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separation column to degrees which vary with the molecular weights of said species.

Id. at ABBR065950. Initially filed claim 27 from the ’174 application was retained, unchanged, as claim

16 of the CIP. The PTO issued a Notice of Allowability for the CIP without any rejections.

However, the PTO included a Statement of Reasons with its Notice of Allowability. The Statement

of Reasons recognized that no prior art taught or fairly suggested practicing the method of separating a

mixture of sample ions described in claim 1 or claim 16 of the CIP application. Garber Decl., Exh. 3,

ABBR065974-75. The examiner recited claims 1 and 16 of the CIP application and underlined the (1)

“electrophoretically passing” and (2) “said molecular weight being within a range of about 0.1 to about 200

times the average molecular weight of said sample ions in said mixture” language of claim 1. Id. The

examiner also underlined the (1)“the group consisting of methyl cellulose, hydroxypropyl methyl,

hydroxyethel methyl cellulose, and hydroxybutyl methyl cellulose,” (2) “the viscosity of a 2% aqueous

solution thereof being within a range of about 1,000 centipoise to about 10,000 centipoise at 25NC,” and

(3) “the concentration of said polymer in said solution is from about 0.1% to about 0.5% by weight”

language of claim 16. Id. Bio-Rad made no comment on the examiner’s Statement of Reasons and the

’111 patent issued from the CIP application.

Bio-Rad filed the present lawsuit against Applera on December 26, 2002. Applera manufactures

various performance optimized polymers (“POP”) that are used for molecular sieving. Applera’s POP

products contain polydimethylacrylamide (“PDMA”) and combinations of PDMA and polyacrylamide. 

Bio-Rad claims that the polyacrylamide and PDMA in Applera’s POP products represent equivalents to

claim 16 of the ’111 patent. Thus, according to Bio-Rad, Applera’s POP products infringe claim 16 of the

’111 patent.

Applera counters that prosecution history estoppel precludes Bio-Rad from asserting the doctrine

of equivalents against Applera’s polyacrylamide-containing POP products. Applera asserts that Bio-Rad’s

amendment to initially filed claim 1 in the ’174 application was to overcome a rejection related to

patentability. Applera notes that initially filed claim 27 contained the same objectionable limitation as

initially filed claim 1, that is, “a gel-free aqueous solution of a substantially linear polymer.” Applera argues,

however, that the PTO allowed initially filed claim 27 without amendment because initially filed claim 27

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was limited on its face to a discrete group of chemicals not including polyacrylamide. Thus, Applera asks

the Court to find that Bio-Rad’s amendment to initially filed claim 1 should also preclude the assertion of

infringement against Applera’s polyacrylamide-containing POP products by doctrine of equivalents as to

initially filed claim 27, now claim 16 of the ’111 patent. 

III. STANDARDS

Summary judgment is proper “if the pleadings, depositions, answers to interrogatories, and

admissions on file, together with the affidavits, if any, show that there is no genuine issue as to any material

fact and that the moving party is entitled to judgment as a matter of law.” Fed. R. Civ. P. 56(c). The

non-moving party “must set forth specific facts showing that there is a genuine issue for trial.” Fed. R. Civ.

P. 56(e). To preclude the entry of summary judgment, the non-moving party must bring forth material facts, 

i.e., “facts that might affect the outcome of the suit under the governing law . . . Factual disputes that are

irrelevant or unnecessary will not be counted.” Anderson v. Liberty Lobby, Inc., 477 U.S. 242, 247-48

(1986).

The construction of patent claims is a question of law for the Court. See Markman v. Westview

Instruments, Inc., 517 U.S. 370, 384 (1996). Likewise, the question of whether prosecution history

estoppel applies is a matter of law for the Court to decide. Glaxo Wellcome, Inc. v. Impax Laboratories,

Inc., 356 F.3d 1348, 1351 (Fed. Cir. 2004). As such, a question of prosecution history estoppel is

properly decided on a motion for summary judgment. Id. The moving party “is entitled to summary

judgment [on prosecution history estoppel] only if the facts and inferences, when viewed in the light most

favorable to [the non-moving party], would not persuade a reasonable jury to return a verdict for . . . the

nonmoving party.” Id. (citing Anderson, 477 U.S. at 255).

“According to the Supreme Court in Festo, ‘a narrowing amendment made to satisfy any

requirement of the Patent Act may give rise to an estoppel.’” Glaxo, 356 F.3d at 1351-52 (quoting Festo

Corp. v. Shoketsu Kinzoku Kogyo Kabushiki Co., 535 U.S. 722, 736 (2002) (Festo VIII )). The

estoppel is presumptive and may be rebutted if the patentee can show “[1] that the alleged equivalent could

not reasonably have been described at the time the amendment was made, or [2] that the alleged equivalent

was tangential to the purpose of the amendment, or [3] that the equivalent was not foreseeable (and thus

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1

 Applera contends that the examiner rejected initially filed claim 1 and not initially filed claim 27

because claim 27 was limited to the members of its Markush group, none of which are polyacrylamide. 

Whereas initially filed claim 1 was limited only by a general description of the attributes of the claimed

“substantially linear polymer.” Applera cites the examiner’s Statement of Reasons that issued with the

Notice of Allowability for support of its position. Applera notes that the examiner drew particular attention

to the Markush group in initially filed claim 27, now claim 16 and stated that even unamended, the claim

avoided prior art references. Applera argues that the examiner’s statements imply that the absence of

polyacrylamide in the Markush group was the reason it avoided the prior art. The Court notes that initially

filed claim 27 appears, on its face, more specific than initially filed claim 1. 

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not claimable) at the time of the amendment.” Glaxo, 356 F.3d at 1532 (citing Festo VIII, 535 U.S. at

740-41). An equivalent is foreseeable if the patentee can “show that at the time of the amendment one

skilled in the art could not reasonably have been expected to have drafted a claim that would have literally

encompassed the alleged equivalent.” Festo VIII, 535 U.S. at 733.

An amendment to one claim may “infect” another claim with estoppel. Glaxo, 356 F.3d at 1356. 

The Federal Circuit Court of Appeals (“FCCA”) has recognized “that subject matter surrendered via claim

amendments during prosecution is also relinquished for other claims containing the same limitation.” Id.

The “rule [ensures] consistent interpretation of the same claim terms in the same patent.” Id.

IV. DISCUSSION

Applera argues that Bio-Rad’s amendment to the ’174 application in response to the PTO’s

rejection of initially filed claims 1-13 triggers prosecution history estoppel as to claim 16 of the ’111 patent. 

Bio-Rad counters that prosecution history estoppel should not apply to claim 16 of the ’111 patent for

several reasons. First, Bio-Rad argues that it overcomes any presumptive estoppel because the use of

polyacrylamide would have been unforeseeable at the time of the amendment. Second, Bio-Rad argues

that claim 16 of the ’111 patent does not contain the same limitation as initially filed claim 1 and thus should

not be infected by any estoppel applied to initially filed claim 1. Finally, Bio-Rad argues that amending

initially filed claim 1, without more, does not link claim 16 of the ’111 patent to initially filed claim 1 such

that claim 16 should be subject to prosecution history estoppel.

A. Presumptive Prosecution History Estoppel

Bio-Rad amended the ’174 application in response to the PTO examiner’s obviousness rejection.1

Obviousness, under 35 U.S.C. § 103, is a rejection based on patentability under the Patent Act. See

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Indeed, Bio-Rad does not assert that claim 1 of the ’111 patent is infringed by Applera’s

polyacrylamide-containing POP products.

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Festo VIII, 535 U.S. at 736. Bio-Rad’s amendment to initially filed claim 1 changed the limitation “gel-free

aqueous solution of a substantially linear polymer” to “gel-free aqueous solution of a substantially linear

water-soluble cellulose derivative polymer.” In both Warner-Jenkinson and Festo VIII the Supreme

Court made “clear that a narrowing amendment may occur when either (1) a preexisting claim limitation is

narrowed by amendment or (2) a new claim limitation is added by amendment.” Honeywell Intern. Inc. v.

Hamilton Sundstrand Corp., 370 F.3d 1131, 1140 (Fed. Cir. 2004)(citing Warner-Jenkinson Co. v. Hilton

Davis Chemical Co., 520 U.S. 17, 30 (1997), and Festo VIII, 535 U.S. at 728). The addition of “watersoluble cellulose derivative” narrowed initially filed claim 1. Thus, Bio-Rad’s amendment of initially filed

claim 1 was “a narrowing amendment made to satisfy [the non-obviousness] requirement of the Patent Act

[and] may give rise to an estoppel.” Id. 

Before determining whether Bio-Rad’s amendment to initially filed claim 1 infects claim 16 of the

’111 patent with prosecution history estoppel, the Court must determine whether prosecution history

estoppel applies to initially filed claim 1 and whether Bio-Rad can overcome the presumption.

The effect of finding prosecution history estoppel is that the patentee presumptively surrenders his

or her right to use the doctrine of equivalents to recapture “subject matter conceded during prosecution.” 

Honeywell, 370 F.3d at 1141; Glaxo, 356 F.3d at 1351-52. Here, the PTO examiner rejected initially

filed claim 1 because of prior art that “successfully performed molecular sieving experiments using noncrosslinked linear polyacrylamide.” Garber Decl., Exh. 1, ABBR065889. In response, Bio-Rad gave up

the more general limitation “gel-free aqueous solution of a substantially linear polymer,” which includes

polyacrylamide, for the more restrictive limitation “gel-free aqueous solution of a substantially linear water

soluble cellulose derivative polymer,” that does not include polyacrylamide. Thus, unless Bio-Rad can

rebut the presumption, it is estopped from asserting that Applera’s POP products infringe claim 1 of the

’111 patent by way of the doctrine of equivalents.2

Bio-Rad argues that it overcomes any presumption of estoppel with regard to polyacrylamide

because the use of polyacrylamide and PDMA, as it is used in the allegedly infringing products, was

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unforeseeable at the time of Bio-Rad’s amendment. If an “equivalent [was] unforeseeable at the time of the

application . . . the patentee can overcome the presumption that prosecution history estoppel bars a finding

of equivalence.” Festo VIII, 535 U.S. at 740-41. The FCCA has explained that:

if the alleged equivalent represents later-developed technology (e.g. transistors in relation to

vacuum tubes, or Velcro® in relation to fasteners) or technology that was not known in the

relevant art, then it would not have been foreseeable. In contrast, old technology, while not

always foreseeable, would more likely have been foreseeable. Indeed, if the alleged

equivalent were known in the prior art in the field of the invention, it certainly should have

been foreseeable at the time of the amendment. 

Festo Corp. v. Shoketsu Kinzoku Kogyo Kabushiki Co., 344 F.3d 1359, 1369 (Fed. Cir. 2003) (Festo

IX). 

Bio-Rad argues that PDMA and polyacrylamide were not used in combination to

electrophoretically separate ions until years after the ’174 application was amended. Blanch Decl. ¶ 6. 

Bio-Rad also argues that the possibility of foreseeability is reduced because there were “well-known

problems with using [polyacrylamide] in general as well as the inability to create the proper range of

molecular weights for PDMA and mixtures of PDMA and polyacrylamide.” Opposition, 18. Furthermore,

Bio-Rad offers a list of mechanical problems, purity problems, manufacturing problems, toxicity problems,

and implementation problems that it asserts would have made the use of PDMA or a combination of

PDMA and polyacrylamide unforeseeable when initially filed claim 1 was amended. 

This Court disagrees, however, that the use of PDMA or a combination of PDMA and

polyacrylamide was sufficiently unforeseeable at the time of the amendment to overcome the presumption of

estoppel. First, Bio-Rad’s recitation of “well-known” problems with the use of polyacrylamide and PDMA

does not necessarily suggest that it would have been unforeseeable at the time of the amendment that

PDMA could represent an equivalent to the subject matter claimed in initially filed clam 1. Indeed, the fact

that a chemical is difficult to manufacture or had not yet been used for the purpose claimed does not make it

unforeseeable. Cf. Festo IX, 344 F.3d at 1369 (stating that transistors, in relation to vacuum tubes,

represent an unforeseeable technology). 

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 The Court ordered supplemental briefing on the issue of whether the accused polymers and

Tietz’s polyacrylamide are different. After reviewing the parties’ submissions the Court is satisfied that the

accused polymers are sufficiently similar to Tietz’s. Accordingly, the rejection based on Tietz suggests that

at the time of the amendment the drafter of the ’111 patent could have drafted a claim that would have

literally encompassed the accused products.

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Second, the PTO examiner made his rejection based on prior art that used polyacrylamide in

molecular sieving.3 Thus indicating that in drafting initially filed claim 1 with broad coverage of a “gel-free

aqueous solution of a substantially linear polymer,” coverage of acrylamides was not only foreseeable, but

accomplished. Thus, the Court finds that “at the time of the amendment one skilled in the art could . . .

reasonably have been expected to have drafted a claim that would have literally encompassed the alleged

equivalent.” Festo VIII, 535 U.S. at 733. Accordingly, the amendment to initially filed claim 1 imposes a

presumption of prosecution history estoppel, which Bio-Rad is unable to overcome on grounds of

unforseeability.

B. Infectious Estoppel

Applera argues that the amendment to initially filed claim 1 creates an estoppel that should be

applied to initially filed claim 27, now claim 16 of the ’111 patent. Bio-Rad contends that the estoppel

should not be applied because the two claims do not contain the same limitation and there was no action by

Bio-Rad in the course of the amendment that linked the claims in a way that requires the estoppel to be

imposed on claim 16 of the ’111 patent. 

Although Bio-Rad only amended initially filed claim 1, the same limitation, “gel-free aqueous

solution of a substantially linear polymer,” was contained in initially filed claim 27. Garber Decl., Exh. 1,

ABBR065864, ABBR065868. Bio-Rad argues that because initially filed claim 1 and initially filed claim

27 each claim different ionic separations the amendment to “claim 1 did not add the same limitation . . . that

is present in unamended claim 16.” Opposition, 8. This argument, however, misses the point. Infectious

estoppel is a mechanism employed to maintain the consistency of terms and limitations throughout a patent. 

Glaxo, 356 F.3d at 1356 (stating that infectious estoppel is a “quest for consistency” among claim terms). 

Both claims as initially filed and at the time of the amendment shared identical language. Insofar as the

terms shared by the claims present identical limitations, this Court sees no reason why the terms of the

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limitations would not have been construed alike. The two claims, although to different ionic separations,

contained the same limitation. Thus, initially filed claim 27, now claim 16 of the ’111 patent does “recite the

amended term” and is subject to the same estoppel. Id.

Bio-Rad also argues that the estoppel does not apply to claim 16 of the ’111 patent unless there

exists “some additional basis in combination with the narrowing amendment that justifie[s] infecting the

unamended claim with the same estoppel and Festo presumption as the [claim] that [was] amended to

include the same limitation.” Opposition, 12. Bio-Rad cites Builders Concrete, Inc. v. Bremerton

Concrete Prods. Co., 757 F.2d 255 (Fed. Cir. 1985), for the proposition that prosecution history estoppel

is not limited to amendment based estoppel, but may arise in other ways, like argument based estoppel. 

Bio-Rad then argues that the court in Glaxo relied on Builders and allowed the infectious estoppel because

the patentee failed to respond to the examiner’s argument that the amended limitation was critical to all

claims. Id. (citing Glaxo, 356 F.3d at 1356.) Thus, according to Bio-Rad, both the amendment and the

argument were necessary bases for applying the infectious estoppel. 

This Court does not read Glaxo to require an additional basis in combination with a narrowing

amendment before infecting an unamended claim with estoppel. Instead, it appears that the FCCA was

more concerned with the consistent interpretation of claim limitations than adding prerequisites to the

doctrine of prosecution history estoppel. See Glaxo, 356 F.3d at 1356 (“Thus, this court directs consistent

interpretation of claim terms within a patent in view of the prosecution history.”); see also Am. Permahedge,

Inc. v. Barcana, Inc., 105 F.3d 1441, 1446 (Fed.Cir.1997) (stating that “identical claim terms used in

different claims must be interpreted consistently” and “under the doctrine of equivalents, we see no reason

to assign different ranges of equivalents for the identical term used in different claims in the same patent”). 

Although argument accompanying an amendment may indicate precisely what subject matter is

surrendered, argument is not a necessary basis for applying estoppel to an unamended claim. 

The Court finds that Bio-Rad is estopped from asserting that Applera’s POP products containing

polyacrylamide or PDMA are equivalents to, and thereby infringe, initially filed claim 27, now claim 16 of

the ’111 patent. Bio-Rad may not use claim 16 of the ’111 patent to recover the subject matter it

surrendered by amending initially filed claim 1. 

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V. CONCLUSION

For the reasons stated above the Court GRANTS Applera’s Motion for Partial Summary

Judgment.

Dated: August 12, 2005 /s/ James Ware 

JAMES WARE

United States District Judge

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THIS IS TO CERTIFY THAT COPIES OF THIS ORDER HAVE BEEN DELIVERED TO:

Alice Garber alice.garber@weil.com

Bobby A. Ghajar ghajarb@howrey.com

David Leon Bilsker bilskerd@howrey.com

Eugene Y. Mar eugene.mar@weil.com

Eugene Y. Mar eugene.mar@weil.com

Matthew D. Powers matthew.powers@weil.com

Thomas C. Mavrakakis mavrakakist@howrey.com

Tracy Jolles Holland hollandt&#064;howrey.com

Vernon M. Winters vern.winters@weil.com

Wallace W. Wu wuw@howrey.com

Dated: August 12, 2005 Richard W. Wieking, Clerk

By: /s/ JW Chambers 

Ronald L. Davis

Courtroom Deputy

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