UNITED STATES DISTRICT COURT 

FOR THE DISTRICT OF COLUMBIA 

NIPPON SHINYAKU COMPANY, LIMITED, 

Plaintiff, 

v. 

ANDREI IANCU,1 Under Secretary of 

Commerce for Intellectual Property 

and Director of the United States 

Patent and Trademark Office, 

Defendant. 

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 Civil Action No. 10-1142 

 

MEMORANDUM OPINION 

I. Introduction 

Nippon Shinyaku Company, Limited (“Nippon”) owns United 

States Patent Nos. 7,205,302 and 7,494,997 (respectively, 

“ ‘302 patent” and “ ‘997 patent”). The United States Patent and 

Trademark Office (“USPTO”) issued the ‘302 patent in 2007 with a 

patent term adjustment (“PTA”) of 344 days, and the ‘997 patent 

in 2009 with a PTA of ninety-nine days. In 2010, the USPTO 

adopted new methods for calculating PTAs necessitated by the 

United States Court of Appeals for the Federal Circuit’s 

(“Federal Circuit”) decision in Wyeth v. Kappos, 591 F.3d 1364 

(Fed. Cir. 2010). Prior to adopting the final procedure for such 

calculations, the USPTO established an Interim Procedure for 

 

1 Andrei Iancu has been automatically substituted as the 

defendant in this case. See Fed. R. Civ. P. 25(d). 
2 

patentees seeking a recalculation of their PTAs subject to 

certain time restrictions. Given its untimely requests, however, 

Nippon was ineligible for a recalculation. Nippon brings this 

action under the Administrative Procedure Act (“APA”), 5 U.S.C. 

§§ 701 et seq., against the Under Secretary of Commerce for 

Intellectual Property and Director of the USPTO. Nippon 

challenges the USPTO’s Interim Procedure, alleging that the 

Interim Procedure arbitrarily ensures disparate treatment of two 

categories of patents and leaves it without a remedy to correct 

the improper calculations of the PTAs for the patents at issue. 

Pending before the Court are the parties’ cross-motions for 

summary judgment. Having carefully reviewed the motions, 

oppositions and replies, and the entire record herein, the Court 

concludes that the USPTO’s Interim Procedure was not arbitrary, 

capricious, an abuse of discretion, or otherwise not in 

accordance with law. Therefore, the Court DENIES Nippon’s motion 

for summary judgment and GRANTS the USPTO’s cross-motion for 

summary judgment. 

II. Background 

A. Statutory and Regulatory Framework 

A patent term begins “on the date on which the patent 

issues” and “end[s] 20 years from the date on which the 

application for the patent was filed in the United States[.]” 
3 

35 U.S.C. § 154(a)(2).2 Many patent terms became far shorter than 

Congress intended, however, due to the USPTO’s lengthy delays in 

examining patent applications and issuing patents. See Novartis 

AG v. Kappos (“Novartis I”), 904 F. Supp. 2d 58, 61 (D.D.C. 

2012), aff’d in part, rev’d in part sub nom. Novartis AG v. Lee 

(“Novartis II”), 740 F.3d 593 (Fed. Cir. 2014). To address this 

problem, Congress enacted the Patent Term Guarantee Act of 1999 

(“Act”), which provides a guarantee of prompt USPTO responses. 

See Pub. L. No. 106–113, §§ 4401–02, 113 Stat. 1501, 1501A–557 

(1999) (codified as amended at 35 U.S.C. § 154(b)); see also 

35 U.S.C. § 154(b)(1)(A). Section 154(b)(1) also provides a 

“[g]uarantee of no more than 3-year application pendency,” see 

35 U.S.C. § 154(b)(1)(B), and a guarantee of “1 day for each day 

of the pendency” of “deprivation proceedings, secrecy orders, 

and appeals.” See id. § 154(b)(1)(C). 

Since the prosecution of a patent application may take more 

than three years, and to give each patent a term of at least 

seventeen years, the Act allows the USPTO to adjust the terms of 

a patent for certain delays during the examination process. See 

 

2 In 1994, Congress replaced the seventeen-year patent term with 

a term ending twenty years after the filing of a patent 

application. See Wyeth, 591 F.3d at 1366 (citing Uruguay Round 

Agreements Act, Pub. L. No. 103-465, § 532, 108 Stat. 4809 

(1994) (codified as amended at 35 U.S.C. § 154)). A patent 

application filed on or after June 8, 1995 has a term of twenty 

years from the date the application was filed. Merck & Co. v. 

Kessler, 80 F.3d 1543, 1547-48 (Fed. Cir. 1996). 
4 

Daiichi Sankyo Co., Ltd. v. Rea (“Daiichi I”), 12 F. Supp. 3d 8, 

11-12 (D.D.C. 2013) (citations omitted), aff’d sub nom. Daiichi 

Sankyo Co. v. Lee (“Daiichi II”), 791 F.3d 1373 (Fed. Cir. 

2015), cert. denied, 136 S. Ct. 1491 (2016). The statute 

provides for the adjustment and calculation of patent terms 

caused by different categories of delay. Bristol-Myers Squibb 

Co. v. Kappos, 891 F. Supp. 2d 135, 137 (D.D.C. 2012). 

Nippon’s PTAs resulted from two of those categories: 

(1) “A Delay” and (2) “B Delay.” See generally Pl.’s Mot. for 

Summ. J. (“MSJ”), ECF No. 46; Def.’s Mot. for Summ. J. (“MSJ”) & 

Opp’n, ECF No. 48.3 The A Delay “is excluded from the calculation 

of the patent term” and “extend[s] the term of the patent one 

day for each day the [US]PTO does not meet certain examination 

deadlines[.]” Daiichi I, 12 F. Supp. 3d at 12 (citation 

omitted). The B Delay “extends the term of the patent one day 

for each day issuance is delayed due to the [US]PTO’s failure 

‘to issue a patent within 3 years after the actual filing date 

of the application in the United States.’” Wyeth, 591 F.3d at 

1367 (quoting 35 U.S.C. § 154(b)(1)(B)). 

1. The Wyeth Decision and its Implementation 

On April 22, 2004, the USPTO promulgated regulations 

 

3 When citing electronic filings throughout this Opinion, the 

Court cites to the ECF page number, not the page number of the 

filed document. 
5 

explaining the methodology for calculating the “A/B Overlap.” 

See Daiichi I, 12 F. Supp. 3d at 12 (citing Revision of Patent 

Term Extension and PTA Provisions, 69 Fed. Reg. 21704–01 (Apr. 

22, 2004)). Interpreting 35 U.S.C. § 154(b), the USPTO used the 

greater of the A Delay or B Delay to determine the proper PTA 

rather than combining the two delays. See Wyeth v. Dudas, 

580 F. Supp. 2d 138, 140 (D.D.C. 2008), aff’d sub nom. Wyeth, 

591 F.3d at 1368. In Wyeth, the district court rejected this 

interpretation because the USPTO’s “construction [could not] be 

squared with the language of § 154(b)(1)(B), which applies ‘if 

the issue of an original patent is delayed due to the failure of 

the [USPTO] to issue a patent within 3 years.’” 580 F. Supp. 2d 

at 142 (emphasis in original) (quoting 35 U.S.C. 

§ 154(b)(1)(B)). The court explained that B Delay “begins when 

the [US]PTO has failed to issue a patent within three years, not 

before.” Id. (emphasis added). The Federal Circuit upheld the 

district court’s determination that the USPTO’s methodology in 

calculating the A and B Delay overlap was contrary to the plain 

language in Section 154(b) because “it effectively counts B 

delay before it occurs.” Wyeth, 591 F.3d at 1375. 

Consistent with the Wyeth decision, after the USPTO decides 

that a patent application will be granted, it issues a written 

notice of allowance of the application. See 35 U.S.C. § 151(a). 

This notice includes the USPTO’s initial determination of the 
6 

PTA, if applicable. 35 U.S.C. § 154(b)(3)(B)(i) (requiring the 

USPTO to “make a determination of the period of any [PTA]” and 

“transmit a notice of that determination no later than the date 

of issuance of the patent[.]”). The PTA reflected in the notice 

of allowance does not include the B Delay. See Bristol-Myers 

Squibb Co., 891 F. Supp. 2d at 137. 

The USPTO determines the proper amount of the A Delay when 

it issues notice to the patent applicant and before the patent 

is granted. Daiichi I, 12 F. Supp. 3d at 12. The USPTO does not 

determine the proper amount of the B Delay until the patent is 

granted because the B Delay continues to accrue until the patent 

is granted. Id. After determining the proper amounts for the A 

Delay and the B Delay, the USPTO determines “the extent of any 

overlap between the two types of delay.” Id. (citation omitted). 

“To the extent that periods of [A Delay and B Delay] overlap, 

any [PTA] shall not exceed the actual number of days the 

issuance of the patent was delayed.” Id. (quoting 35 U.S.C. 

§ 154(b)(2)(A)). “Because the overlap determination depends on 

the amount of B Delay, it is also done at the time the patent is 

granted.” Id. (citation omitted). “The final determination of 

PTA—which factors in A Delay, B Delay, and A/B Overlap—is done 

at the time the patent is granted.” Id. (citation omitted). 

2. Administrative and Judicial Review of PTAs 

A patent applicant dissatisfied with PTA determinations may 
7 

seek administrative and judicial review. Id. at 12-13. The 

patent applicant may “request reconsideration of any [PTA] 

determination made by the Director,” 35 U.S.C. 

§ 154(b)(3)(B)(ii), “within two months of the date the patent 

issued,” 37 C.F.R. § 1.705(d) (2012) (“Rule 1.705(d)”). Daiichi 

I, 12 F. Supp. 3d at 13. A patentee dissatisfied with the 

USPTO’s response to the request for reconsideration may seek 

further administrative review of the USPTO’s decision under Rule 

1.705(d) by submitting a petition under 37 C.F.R. § 1.181(f) 

(“Rule 1.181(f)”) “within two months of the mailing date of the 

action or notice from which relief is requested[.]” 37 C.F.R. 

§ 1.181(f) (2012). “[O]n petition of the interested party,” the 

two-month limitation “may be suspended or waived by the Director 

or the Director’s designee” in “an extraordinary situation, when 

justice requires[.]” 37 C.F.R. § 1.183 (2013). 

Finally, the patent applicant may seek judicial review in 

federal district court. 35 U.S.C. § 154(b)(4)(A). At the time 

that Nippon’s patents were issued, a civil action for judicial 

review of a PTA determination had to be “filed in the United 

States District Court for the District of Columbia within 180 

days after the grant of the patent.” Id.4

 

4 In 2011, Congress amended the venue provisions in certain 

patent statutes, including Section 154, such that suits under 

Section 154(b) must be filed in the United States District Court 

for the Eastern District of Virginia within 180 days after the 
8 

3. The Interim Procedure 

Following the Wyeth decision, on February 1, 2010, the 

USPTO published notice of an Interim Procedure to “provid[e] 

patentees with the ability to request a recalculation of their 

[PTA] [consistent with the Wyeth decision] without a fee as an 

alternative to the petition and fee required by 37 CFR 

1.705(d).” Interim Procedure for Patentees To Request a 

Recalculation of the PTA To Comply With the Federal Circuit 

Decision in Wyeth v. Kappos Regarding the Overlapping Delay 

Provision of 35 U.S.C. 154(b)(2)(A) (“Interim Procedure” or 

“procedure”), 75 Fed. Reg. 5043–01, 5043 (Feb. 1, 2010). 

According to the USPTO, this procedure would be in effect until 

March 2, 2010, at which time the modifications to the computer 

program used to calculate PTAs necessitated by the Wyeth

decision would be complete. Id. at 5043. This procedure was 

available for only two types of PTA requests for reconsideration 

based on the Wyeth decision: (1) requests that could have been 

timely made within 180 days of the patent decision as set forth 

in 35 U.S.C. § 154(b)(4); or (2) requests that could have been 

timely made within the two-month time period set forth in Rule 

 

date of the Director’s decision on the applicant’s request for 

reconsideration. See Hyatt v. Iancu, 332 F. Supp. 3d 83, 89 n.4 

(D.D.C. 2018) (citing Leahy-Smith America Invents Act, Pub. L. 

112-29, § 9 (Sept. 16, 2011)); see also Def.’s MSJ, ECF No. 48 

at 4 n.1. 
9 

1.181(f). Id. at 5043-44. The USPTO explained that the statutory 

and regulatory framework provides that requests for 

reconsideration by the USPTO of the PTA must be filed within two 

months of the date the patent was issued pursuant to Rule 

1.705(d), and that applicants dissatisfied with a determination 

made by the Director of the USPTO could file a civil action 

within 180 days after the grant of the patent pursuant to 35 

U.S.C. § 154(b)(4). Id. The USPTO also cited the two-month 

deadline for reconsideration of a Rule 1.705(d) decision 

pursuant to Rule 1.181(f). Id. at 5044. The Interim Procedure 

therefore provided patentees who could timely challenge the preWyeth PTA determinations to the USPTO pursuant to Rule 1.181(f) 

or the district court pursuant to 35 U.S.C. § 154(b) with the 

opportunity to request reconsideration from the USPTO. Id. As a 

practical matter, the Interim Procedure was available for 

patents that had been issued between August 5, 2009 and March 1, 

2010 and for patentees who received the USPTO’s decision on a 

Rule 1.705(d) request for reconsideration on December 1, 2009 or 

later. See Daiichi II, 791 F.3d at 1375-76. Any petitions filed 

outside of these windows would be denied as untimely by the 

USPTO. 75 Fed. Reg. at 5043-44. 

B. Factual and Procedural Background 

The material facts in this case are undisputed. See Pl.’s 

MSJ, ECF No. 46 at 16-18, 20; see also Def.’s MSJ, ECF No. 48 at 
10 

1, 10-11. Nippon is a foreign corporation with its principal 

place of business in Kyoto, Japan. Second Am. Compl., ECF No. 24 

¶ 4. Nippon is the owner of the ‘302 patent, entitled 

“Heterocyclic Compound Derivatives and Medicines,” and the ‘997 

patent, entitled “Amide Derivative.” Pl.’s MSJ, ECF No. 46 at 

16. The ‘302 patent was issued on April 17, 2007 with a notice 

that its term would be extended or adjusted by 344 days under 35 

U.S.C. § 154(b). Administrative Record (“A.R.”), ECF No. 45-3 at 

90. The ‘997 patent was issued on February 24, 2009 with a 

notice that its term would be extended or adjusted by ninetynine days under 35 U.S.C. § 154(b). Id. at 3. 

On July 6, 2010, before seeking administrative relief, 

Nippon filed the initial complaint in this Court, alleging, 

inter alia, that the USPTO’s pre-Wyeth determinations and 

calculations “of the [PTAs] for the ‘302 and ‘997 patents were 

arbitrary, capricious, an abuse of discretion, or otherwise not 

in accordance with law under 5 U.S.C. § 706(2)(A).” Compl., ECF 

No. 1 ¶ 18. Nippon filed this civil action more than three years 

(1,176 days) after the issuance of the ‘302 patent and more than 

a year (497 days) after the issuance of the ‘997 patent. See, 

e.g., id. ¶ 7; Def.’s MSJ, ECF No. 48 at 10. 

Beginning in August 2010, Nippon also sought administrative 

review of the USPTO’s PTA determinations in light of the Wyeth

decision. See A.R., ECF No. 45-3 at 142-43. On October 12, 2010, 
11 

the USPTO denied Nippon’s August 30, 2010 request for the ‘302 

patent, treating it as a “request for reconsideration of [PTA]” 

under Rule 1.705(d). Id. at 151. Because this request was 

submitted outside of the “two months after the date of issuance 

of the [‘302] patent,” the USPTO dismissed it as untimely under 

Rule 1.705(d). Id. The record does not include the USPTO’s 

decision for Nippon’s second request, dated September 10, 2010, 

for the ‘302 patent. See generally A.R., ECF No. 45-3. 

On June 10, 2016, the USPTO mailed its decision on Nippon’s 

request as to the ‘997 patent, stating that it considered the 

request “for the issuance of a Certificate of Correction under 

the provisions of 37 CFR 1.322 and/or 37 CFR 1.323.” Id. at 86 

(styled “Response to the Request for Certificate of 

Correction”).5 The USPTO denied the request because it was 

“improper” and “[t]he patent was printed in accordance with the 

information set forth on the Issue Notification dated [February 

24, 2009] which indicated the [PTA] is 99 day(s).” Id. The USPTO 

stated that “[a] petition to Recalculate the [PTA] is required 

 

5 Pursuant to 37 C.F.R. § 1.322, “[t]he Director may issue a 

certificate of correction pursuant to 35 U.S.C. 254 to correct a 

mistake in a patent, incurred through the fault of the Office, 

which mistake is clearly disclosed in the records of the Office” 

under certain conditions. 37 C.F.R. § 1.322(a)(1). Under 

37 C.F.R. § 1.323, “[t]he Office may issue a certificate of 

correction under the conditions specified in 35 U.S.C. 255 at 

the request of the patentee or the patentee’s assignee, upon 

payment of the fee set forth in § 1.20(a).” 37 C.F.R. § 1.323. 
12 

to be granted in order for a certificate of correction to be 

issued.” Id. 

Between 2011 and 2014, the Court issued a series of stays, 

at the parties’ requests, because several cases challenging the 

USPTO’s pre-Wyeth PTA calculations closely resembled the issues 

in this action. See generally docket for Civil Action No. 10-

1142. In 2015, Nippon filed a second amended complaint, bringing 

a single facial challenge to the Interim Procedure, and seeking 

declaratory relief pursuant to 28 U.S.C. § 2201 in the form of a 

declaratory judgment stating that the Interim Procedure is 

arbitrary, capricious, an abuse of discretion, or otherwise not 

in accordance with the APA, and requesting that the Court enter 

an injunction requiring the USPTO to rescind the procedure and 

correct patent terms. See Second Am. Compl., ECF No. 24 at 6-8; 

see also Pl.’s MSJ, ECF No. 46 at 8, 30. Thereafter, the parties 

filed cross-motions for summary judgment. Those motions are ripe 

and ready for adjudication. 

III. Legal Standard 

A. Motion for Summary Judgment 

Under Federal Rule of Civil Procedure 56, “[t]he court 

shall grant summary judgment if the movant shows that there is 

no genuine dispute as to any material fact and the movant is 

entitled to judgment as a matter of law.” Fed. R. Civ. P. 56(a). 
13 

In a case involving review of a final agency 

action under the APA, ... [the court has a] 

limited role of ... reviewing the 

administrative record. The function of the 

district court is to determine whether or not 

as a matter of law the evidence in the 

administrative record permitted the agency to 

make the decision it did. Summary judgment 

thus serves as the mechanism for deciding, as 

a matter of law, whether the agency action is 

supported by the administrative record and 

otherwise consistent with the APA standard of 

review. 

Daiichi I, 12 F. Supp. 3d at 14 (quoting Nat'l Parks 

Conservation Ass’n v. Jewell, 965 F. Supp. 2d 67, 73 (D.D.C. 

2013) (alterations, internal quotation marks, and citations 

omitted)). 

B. Standard of Review 

Under the APA, the Court shall “hold unlawful and set 

aside” the agency’s decision if it is “arbitrary, capricious, an 

abuse of discretion, or otherwise not in accordance with law.” 

5 U.S.C. § 706(2)(A). “[A]n agency acts arbitrarily or 

capriciously only if the decision was not based on the relevant 

factors or it fails to examine the relevant data and articulate 

a satisfactory explanation for its action including a rational 

connection between the facts found and the choice made.” 

Japanese Found. for Cancer Research v. Lee, 773 F.3d 1300, 1304 

(Fed. Cir. 2014) (citation and internal quotation marks 

omitted). The scope of review under this standard is narrow. 

Id.; see also Motor Vehicle Mfrs. Ass’n of U.S., Inc. v. State 
14 

Farm Mut. Auto. Ins. Co., 463 U.S. 29, 43 (1983) (reviewing 

court may not “substitute its judgment for that of the 

agency.”). 

In determining whether the Interim Procedure comports with 

law, it is necessary to determine the level of deference the 

USPTO is entitled to in promulgating that procedure. Guided by 

the limitations placed on the USPTO’s authority to promulgate 

regulations under Section 154(b), the Federal Circuit and courts 

in this Circuit have held that the USPTO’s PTA determinations 

are not owed deference under Chevron, U.S.A., Inc. v. Natural 

Resources Defense Council, Inc., 467 U.S. 837 (1984). See, e.g.,

Merck, 80 F.3d at 1550; Wyeth, 580 F. Supp. 2d at 141 (noting 

that the USPTO is not afforded Chevron deference because it only 

has the authority to issue “procedural regulations regarding the 

conduct of proceedings before the agency.”). Section 154(b) 

limits the USPTO’s authority to “prescrib[ing] regulations 

establishing procedures for the application for and 

determination of [PTAs] [.]” 35 U.S.C. § 154(b)(3)(A). The USPTO 

is, however, entitled to deference pursuant to Skidmore v. Swift 

& Co., 323 U.S. 134 (1944) based on “the thoroughness evident in 

its consideration, the validity of its reasoning, its 

consistency with earlier and later pronouncements, and all those 

factors which give it power to persuade, if lacking power to 

control.” Id. at 140; see also Novartis I, 904 F. Supp. 2d at 
15 

64. 

The parties disagree as to whether the USPTO is entitled to 

deference of its interpretation of its regulations. Compare 

Def.’s MSJ, ECF No. 48 at 12 (“The USPTO’s interpretation of its 

own regulations is also entitled to substantial deference.”), 

with Pl.’s Reply, ECF No. 50 at 8 (“The USPTO is not entitled to 

deference” because Nippon “is not challenging the USPTO’s 

‘interpretation of its own regulations.’”). The Court is not 

persuaded by Nippon’s argument because Nippon expressly 

challenges the USPTO’s implementation of the Interim Procedure 

that was based on the USPTO’s interpretation of 35 U.S.C. § 

154(b) and its own regulations. See Pl.’s MSJ, ECF No. 46 at 15, 

21; see also Second Am. Compl., ECF No. 24 ¶ 15-32. 

IV. Analysis 

It is undisputed that the PTAs for Nippon’s patents were 

determined using the pre-Wyeth method of calculating A and B 

Delay overlap. See Second Am. Compl., ECF No. 24 at ¶ 8. It is 

also undisputed that Nippon’s patents were issued before August 

5, 2009; Nippon did not request reconsideration of the PTAs 

within two months of the patents’ issuance dates; and Nippon did 

not file a claim for judicial relief within the 180-day window. 

See Pl.’s MSJ, ECF No. 46 at 14, 16-17; see also Def.’s MSJ, ECF 

No. 48 at 10-11. Nor does Nippon contend that it was entitled to 

reconsideration of the PTAs under the Interim Procedure. See
16 

Pl.’s MSJ, ECF No. 46 at 16. Nippon also acknowledges that it 

was ineligible for relief under the Interim Procedure. See Pl.’s 

MSJ, ECF No. 46 at 17; see also Second Am. Compl., ECF No. 24 

¶¶ 22, 24. Undeterred, Nippon seeks judicial review of the 

Interim Procedure. See generally Second Am. Compl., ECF No. 24. 

Nippon seeks a recalculation of the PTAs by the USPTO based 

on the post-Wyeth methodology, alleging that the Interim 

Procedure violated the APA. Pl.’s MSJ, ECF No. 46 at 8. 

According to Nippon, the “sole issue” is “whether the [temporal] 

limitations for recalculation of [PTAs] post-Wyeth, set by the 

USPTO in the Interim Procedure, were a valid exercise of agency 

discretion.” Id. at 19-20. 

A. Federal Circuit precedent does not foreclose Nippon’s 

arguments 

As an initial matter, the parties dispute whether the 

doctrine of stare decisis determines the outcome of this case. 

Nippon argues that Federal Circuit precedent does not determine 

the outcome of this case on stare decisis grounds,6 Pl.’s Reply, 

 

6 Nippon also argues that res judicata and collateral estoppel do 

not apply here, see Pl.’s MSJ, ECF No. 46 at 23, a proposition 

that the USPTO does not dispute, see generally Def.’s MSJ, ECF 

No. 48; Def.’s Reply, ECF No. 52. Although the USPTO has 

conceded the argument by not responding, see Campbell v. Nat’l 

R.R. Passenger, 311 F. Supp. 3d 281, 327 n.13 (D.D.C. 2018), the 

Court agrees that Nippon is not precluded from bringing this 

case since it was not a litigant in Daiichi II. See Cornish v. 

United States, 885 F. Supp. 2d 198, 209 (D.D.C. 2012) (holding 

that res judicata barred a plaintiff’s claims where he brought 

the same claims against the same agency in a prior suit). Courts 
17 

ECF No. 50 at 10, because Nippon’s arguments here were neither 

presented to nor considered by the Federal Circuit in two cases 

dealing with some of the same issues in this case. See Daiichi 

II, 791 F.3d at 1379-80 (holding that the USPTO did not abuse 

its discretion by only applying the Interim Procedure to patents 

issued in the 180-day window); see also Novartis II, 740 F.3d at 

600 (holding that plaintiff did not timely file suit within 180 

days of denial of reconsideration pursuant to Section 

154(b)(4)).7 The USPTO responds that the issues raised by Nippon 

here were decided in the USPTO’s favor in that precedent when 

the Federal Circuit affirmed two lower court decisions, Daiichi 

II and Actelion Pharmaceuticals Ltd. v. Lee (“Actelion II”), 

565 F. App’x 887 (Fed. Cir. 2014), holding that the Interim 

Procedure did not violate the APA. See Def.’s MSJ, ECF No. 48 at 

4-5, 5 n.2, 13-18, 20, 24; see also Actelion Pharm. Ltd. v. 

 

narrowly construe the doctrines of res judicata and collateral 

estoppel to reach the merits. Cf. Cent. Delta Water Agency v. 

United States, 306 F.3d 938, 953 (9th Cir. 2002) (“[W]hen 

considering whether a prior action involved the same ‘nucleus of 

facts’ for preclusion purposes, we must narrowly construe the 

scope of that earlier action.”). 

7 Federal Circuit precedent is binding on this Court because a 

suit under Section 154(b) may only be appealed to the Federal 

Circuit. See 28 U.S.C. § 1295(a)(4)(C) (Federal Circuit has 

“exclusive jurisdiction” over “an appeal from a decision of” a 

federal “district court to which a case was directed pursuant to 

section . . . 154(b) of title 35[.]”); cf. Kline v. Cisneros, 

76 F.3d 1236, 1239 (D.C. Cir. 1996) (holding that the court of 

appeals had no jurisdiction over an appeal from a district court 

decision where 28 U.S.C. § 1295(a)(2) gave exclusive 

jurisdiction to the Federal Circuit over the appeal). 
18 

Kappos (“Actelion I”), 972 F. Supp. 2d 51, 58 (D.D.C. 2013), 

aff’d sub nom. Actelion II, 565 F. App’x 887. However, the USPTO 

acknowledges that the doctrine of stare decisis may not apply to 

all of Nippon’s arguments. See Def.’s MSJ, ECF No. 48 at 14, 18. 

 “Stare decisis compels adherence to a prior factually 

indistinguishable decision of a controlling court.” Brewster v. 

Comm’r, 607 F.2d 1369, 1373 (D.C. Cir. 1979). 

The rule of stare decisis is never properly 

invoked unless in the decision put forward as 

precedent the judicial mind has been applied 

to and passed upon the precise question. 

Questions which merely lurk in the record, 

neither brought to the attention of the court 

nor ruled upon, are not to be considered as 

having been so decided as to constitute 

precedents. 

Nat’l R.R. Passenger v. ExpressTrak, LLC, Civil Action No. 02-

1773, 2006 WL 2947558 at *6 (D.D.C. Oct. 16, 2006) (citations 

omitted); see also Supernus Pharm., Inc. v. Iancu, 913 F.3d 

1351, 1357 (Fed. Cir. 2019) (finding that a prior decision with 

different facts and a different legal question was not 

controlling in that action). Here, Nippon has raised arguments 

in its challenge to the Interim Procedure that were not 

specifically raised in the prior cases. Therefore, the Court can 

consider the open question of whether the Interim Procedure 

violates the APA based on those arguments. 
19 

B. The Interim Procedure does not violate the APA, and is 

not arbitrary and capricious or otherwise contrary to 

law 

Nippon contends that the Interim Procedure violates the APA 

because it treats similarly-situated patentees differently in 

that it allows some, but not all, patentees to receive postWyeth PTA recalculations. See Pl.’s MSJ, ECF No. 46 at 1, 9-11, 

23-30. The USPTO responds that Nippon’s claims must be resolved 

in its favor based on the Federal Circuit’s decisions in 

Novartis II, Daiichi II, and the summary affirmance in Actelion 

II because in those decisions, the Federal Circuit concluded 

that the Interim Procedure is not arbitrary, capricious, or 

otherwise contrary to law under the APA. See Def.’s MSJ, ECF No. 

48 at 13-18. According to the USPTO, Nippon’s “challenge is just 

another collateral attack on the USPTO’s decision not to reopen 

all of the final [PTA] determinations in earlier patents for 

which the patent owners did not seek timely reconsideration 

either under 37 C.F.R. § 1.705(d) [2012] or 35 U.S.C. § 

154(b)(4)(A).” Id. at 19. 

1. Prior challenges to the Interim Procedure 

Novartis II involved a challenge to the PTA determinations 

for certain patents outside of the 180-day limitation period set 

forth in Section 154(b)(4) rather than, as here, a facial 

challenge to the Interim Procedure. 740 F.3d at 595, 599-600. 

There, the plaintiff argued, among other things, that the 
20 

limitation period should be equitably tolled because the Wyeth

decision had not been decided when the patents issued. Id. at 

600. The Federal Circuit “readily affirm[ed] the district 

court’s holding that [the plaintiff]’s claims as to fifteen 

patents were untimely asserted” since the plaintiff did not seek 

relief within the 180-day period, noting that “nothing stood in 

the way of Novartis’s timely pressing the very claim Wyeth 

pressed.” Id. 

The other two cases cited by the USPTO did involve 

challenges to the Interim Procedure itself. In Daiichi II, the 

Federal Circuit affirmed the district court’s grant of summary 

judgment in favor of the USPTO where the plaintiff there 

challenged the USPTO’s use of the 180-day period for 

administrative review under the APA and the USPTO’s “disparate 

treatment” of patents issued before August 5, 2009. 791 F.3d at 

1379-81. Two of the patents at issue there did not qualify for 

the USPTO’s Interim Procedure because they were issued before 

August 5, 2009. Id. at 1376. The plaintiff filed Rule 1.705(d) 

requests for reconsideration of the PTAs outside of the twomonth window and petitions under 37 C.F.R. § 1.183 to waive the 

two-month window in light of the Wyeth decision. Id. The USPTO 

denied the plaintiff’s requests and petitions because they were 

untimely. Id. The plaintiff later filed requests for 

reconsideration of the USPTO’s denials, but the USPTO also 
21 

denied those requests because the USPTO’s Interim Procedure only 

allowed requests for recalculation of the PTAs within 180 days 

after the grant of the patent. Id. The USPTO explained, among 

other things, that the USPTO would not accept any requests for 

PTA recalculations outside of the 180-day window because “the 

judicial-review provision of 35 U.S.C. § 154(b)(4) evidenced 

congressional intent that PTA issues be resolved soon after 

issuance.” Id. (citation and internal quotation marks omitted). 

Accepting the USPTO’s reasoning for only considering 

requests filed within the 180—day window, the Federal Circuit 

held that the USPTO “acted within its discretion under the 

statute to ‘prescribe regulations establishing procedures for 

the . . . determination of [PTAs]’ . . . in adopting the 180-day 

period as part of the Interim Procedure.” Id. at 1379-80 

(quoting 35 U.S.C. § 154(b)(3)). The Federal Circuit also held 

that “the [US]PTO acted within its discretion in denying 

Daiichi’s requests for reconsideration of the [PTA] 

determinations.” Id. at 1380. The Federal Circuit accepted the 

USPTO’s “ample reasoning” that “this brief [180-day] period for 

judicial review indicates Congress’ intent that [the USPTO] 

resolve [PTA] issues more expeditiously than allowed under the 

full administrative challenge period.” Id. In doing so, the 

Federal Circuit found that the USPTO did not abuse its 

discretion in fashioning regulations for the procedures of PTA 
22 

reconsiderations that rejected petitions for administrative 

review outside of the 180-day window. Id. 

The Federal Circuit in Daiichi II also rejected the 

disparate treatment argument the plaintiff made there. See id.

at 1380-81. The Federal Circuit found that the USPTO’s decision 

to grant extensions of the administrative review period for some 

patents to match the 180-day judicial review period for all 

patents was not arbitrary and capricious. Id. at 1381. The 

Federal Circuit determined that the plaintiff “was treated 

identically to all other patentees whose patents had issued more 

than 180-days prior to the deadline for filing a petition and 

who were unable to show extraordinary circumstances.” Id. The 

Federal Circuit made clear that “[c]hoosing an administrative 

filing deadline that mirrors the judicial filing deadline, 

especially when it lengthens that deadline for some patentees, 

is neither arbitrary nor capricious.” Id. 

The USPTO also cites the Federal Circuit’s summary 

affirmance of Actelion I, in which the district court held that 

the Interim Procedure did not violate the APA. Actelion II, 565 

F. App’x 887 (affirming the district court’s decision without an 

opinion under Federal Circuit Rule 36). However, the grounds 

upon which the district court relied—that the plaintiff was 

“foreclosed from using an APA claim to circumvent 

§ 154(b)(4)(A)’s 180–day time limit to attain a PTA 
23 

recalculation” because Section 154(b)(4)(A) “expressly waives 

sovereign immunity for appeals of PTA determinations and makes 

them reviewable under the APA’s judicial review provisions”—is 

not an argument advanced by the USPTO here. Id. at 58 n.9. 

2. The Rule 1.181(f) Challengers were not treated 

differently

Nippon argues that the Interim Procedure violates the APA 

because it treats two categories8 of similarly-situated patentees 

differently without providing a rationale. Pl.’s MSJ, ECF No. 46 

at 23. The first category of similarly-situated patentees are 

 

8 The USPTO points out that Nippon does not fall into the 

categories of patents that the USPTO purportedly treated 

differently under the Interim Procedure because Nippon did not 

seek judicial relief within the prescribed time limits. See 

Def.’s MSJ, ECF No. 48 at 19-20. Nippon could not seek 

administrative relief under the Interim Procedure because it did 

not file a timely request for reconsideration under Rule 

1.705(d), and none of Nippon’s patents were issued between July 

15, 2009 and August 5, 2009. See id. at 19, n.8. In its reply 

brief, the USPTO states for the first time that the APA’s 

“harmless error” rule weighs against Nippon’s APA challenge 

because “[i]f the agency’s mistake did not affect the outcome, 

if it did not prejudice the petitioner, it would be senseless to 

vacate and remand for reconsideration.” Def.’s Reply, ECF No. 52 

at 6 (citation omitted). Although the USPTO pointed out the 

underlying factual issue in its cross motion, it did not make 

the legal argument until its reply brief. See generally Def.’s 

MSJ, ECF No. 48; Def.’s Reply, ECF No. 52. Arguments raised for 

the first time in a reply brief are waived. Lindsey v. District 

of Columbia, 879 F. Supp. 2d. 87, 95 (D.D.C. 2012). Even if the 

Court were to consider it, the Court doubts it would be 

meritorious because the relief Nippon seeks should the Court 

find the procedure to violate the APA is for the Court to enter 

an injunction requiring the USPTO to rescind the procedure and 

correct patent terms affected by the Wyeth decision, which would 

give Nippon the relief it seeks. See Second Am. Compl., ECF No. 

24 at 8; see also Pl.’s MSJ, ECF No. 46 at 8, 30. 
24 

those who could timely challenge the pre-Wyeth determinations to 

the USPTO pursuant to Rule 1.181(f) (“Rule 1.181(f) 

Challengers”). Id. at 23-24. Nippon argues that the Interim 

Procedure created an “exception” to allow patentees in this 

category to seek relief pursuant to the Interim Procedure and 

that the exception is arbitrary because a patentee’s ability to 

timely seek relief depends upon the date the USPTO’s response to 

the request for reconsideration was mailed pursuant to Rule 

1.705(d). Id. at 23-25. As a result, two patentees who received 

a patent on the same day are being treated differently due to 

the date the USPTO’s response was mailed. Id. at 25. 

Specifically, if one patentee timely requested reconsideration 

pursuant to Rule 1.705(d) and that request was denied within two 

months of February 1, 2010, the patentee could seek a post-Wyeth

adjustment. Id. If, however, the patentee’s request for 

reconsideration was denied more than two months prior to 

February 1, 2010, the patentee could not seek a post-Wyeth

adjustment. Id. Nippon argues that this is arbitrary and 

capricious because: (1) the two-month window from December 1, 

2009 to February 1, 2010 was arbitrary in part because the 

patentee has no control over the date triggering that window; 

and (2) no rationale was provided in the Interim Procedure for 

allowing this category of patentees to challenge the PTA 

determinations within two months rather than 180 days. Id. at 
25 

25-28. Nippon concludes that it is illogical to limit the 

availability of post-Wyeth relief for the Rule 1.181(f) 

Challengers because the reason for implementing the Interim 

Procedure was to expand administrative relief. Id. at 27; see 

also Pl.’s Reply, ECF No. 50 at 14. 

The USPTO responds that this aspect of the procedure is not 

arbitrary for at least two reasons. First, because the patentees 

in this category could seek review of the PTAs pursuant to 

existing regulations, their inclusion in the Interim Procedure 

was merely a recognition of this fact rather than an “exception” 

to the procedure. Def.’s MSJ, ECF No. 48 at 20-21. Second, “the 

Interim Procedure grouped patentees into two categories: those 

who could still timely challenge their pre-Wyeth PTA 

determination (either administratively or judicially) and those 

who could not.” Id. at 21. Patentees in the former category 

could use the Interim Procedure and those in the latter category 

could not. Id. The USPTO concludes that patentees who could 

still timely administratively challenge the PTA determination as 

of the date the Interim Procedure was published were similarly 

situated with those who could challenge it judicially and were 

treated alike, so there is no disparate treatment. Id. The USPTO 

also disputes that the two-month window was arbitrary and that 

no rationale was provided because the two-month window was 

dictated by existing USPTO regulations and the Interim Procedure 
26 

specifically cited 37 C.F.R. § 1.181(f). Id. at 22-24. 

The Court is not persuaded by Nippon’s arguments regarding 

the Rule 1.181(f) Challengers. Patentees who were able to timely 

seek post-Wyeth relief pursuant to Rule 1.181(f) were able to do 

so pursuant to long-standing USPTO regulations. See 37 C.F.R. 

§ 1.181(f) (A patentee dissatisfied with the response to the 

request for reconsideration may seek further administrative 

review of the USPTO’s decision under Rule 1.705(d) by submitting 

a petition under 37 C.F.R. § 1.181(f) “within two months of the 

mailing date of the action or notice from which relief is 

requested.”). Although the date of a USPTO decision responding 

to a Rule 1.705 request for reconsideration is not within the 

patentee’s control, “[f]iling deadlines, like statutes of 

limitations, necessarily operate harshly and arbitrarily with 

respect to individuals who fall just on the other side of them, 

but if the concept of a filing deadline is to have any content, 

the deadline must be enforced.” United States v. Locke, 471 U.S. 

84, 101 (1985). Moreover, this deadline exists in long-standing 

USPTO regulations. Cf. Sec. Univ. v. Acosta, 317 F. Supp. 3d 

343, 348 (D.D.C. 2018) (“Although there is no set timeframe for 

determining what is or is not arbitrary and capricious, these 

timeframes are consistent with analogous circumstances.”). The 

Court therefore finds that the two-month window is neither 

arbitrary nor capricious. See Daiichi II, 791 F.3d at 1380-81 
27 

(Section 154(b)(3)(A) expressly authorizes the USPTO to make 

regulations, including administrative filing deadlines, 

governing the procedures of PTA reconsiderations); cf. Novartis 

II, 740 F.3d at 600 (noting a plaintiff’s failure to comply with 

the USPTO’s “reasonable filing deadlines[.]”). 

Despite Nippon’s contention that no rationale was provided 

for allowing the Rule 1.181(f) challenges, the Interim Procedure 

itself cited Rule 1.181(f). See 75 Fed. Reg. at 5044. Finally, 

the Rule 1.181(f) Challengers were treated identically to all 

other patentees who could still timely challenge their PTA 

determinations under the Interim Procedure. See Daiichi II, 

791 F.3d at 1381. And patentees who could not timely challenge 

their PTA determinations were treated the same since they were 

excluded from the Interim Procedure. See 75 Fed. Reg. at 5043-

44. The USPTO’s grouping of challengers into those who could 

still timely challenge their PTA determinations and those who 

could not is a reasonable and valid exercise of agency 

discretion and firmly rooted in long-standing USPTO regulations. 

Nippon’s remaining arguments are without merit. Nippon 

argues that the “arbitrary nature of the two-month window for . 

. . a renewed request for reconsideration as provided in the 

Interim Procedure is further evidenced by the fact that the 

concept of the Interim Procedure was . . . to . . . essentially 

replac[e] the two month deadline with 180 days.” Pl.’s MSJ, ECF 
28 

No. 46 at 27. But as the USPTO points out, “[t]he Interim 

Procedure waived the two-month period set forth in Rule 1.705(d) 

. . . and ‘replaced’ it with the 180-day period set forth in 

Section 154(b)(4)(A) . . . because such timely judicial 

challenges would eventually return to the USPTO through remands 

from the court.” Def.’s MSJ, ECF No. 48 at 26. A similar 

replacement for the Rule 1.181(f) Challengers did not make sense 

because they already filed timely requests for reconsideration 

under Rule 1.705(d). 

Nippon also contends that the Interim Procedure was “simply 

arbitrary and capricious” for “provid[ing] no comment period.” 

Pl.’s MSJ, ECF No. 46 at 26-27; see also id. at 9 (“[T]he USPTO 

did not provide a period for public comment and articulated no 

rationale for its position”). The court in Actelion I rejected 

the plaintiff’s argument that the Interim Procedure violated the 

APA because it “was not promulgated via notice-and-comment 

rulemaking pursuant to 5 U.S.C. § 553.” 972 F. Supp. 2d at 58 

n.9. The court found that the “USPTO was not required to use 

notice-and-comment rulemaking to devise the Interim Procedure 

because it is a procedural rule, not a substantive rule.” Id. 

(citing 5 U.S.C. § 553(b)(A); Chamber of Commerce of U.S. v. 

U.S. Dep’t of Labor, 174 F.3d 206, 211 (D.C. Cir. 1999)). For 

the same reasons, this Court rejects Nippon’s suggestion that a 

comment period was required prior to the publication of the 
29 

Interim Procedure. 

3. The July patents were not treated differently 

The second category of allegedly similarly-situated 

patentees who Nippon asserts were treated differently as a 

result of the Interim Procedure are those whose patents issued 

between July 15, 2009 and August 5, 2009 (the “July patents”). 

See Pl.’s MSJ, ECF No. 46 at 28-30; see also Pl.’s Reply, ECF 

No. 50 at 7, 13, 19. Patents issued during this timeframe 

“reached 180 days post-issuance between the Wyeth decision and 

the establishment of the Interim Procedure.” Pl.’s MSJ, ECF No. 

46 at 28. Thus, these patentees could have filed judicial 

challenges to their PTA calculations in light of the Wyeth

decision, but no longer could once the Interim Procedure was 

published. Id. Nippon argues that these patentees were treated 

differently than patentees whose patents had issued more than 

180 days prior to the deadline and that they were “misled” by 

the USPTO’s announcements about forthcoming guidance to 

implement the Wyeth decision into thinking that they would have 

an administrative remedy. Id. at 28-30. Nippon maintains that it 

was “logical” for these patentees not to file a judicial 

challenge in light of the USPTO’s announcements. Id. at 28. 

The USPTO responds that the Federal Circuit decided this 

issue in Daiichi II when it held that the USPTO “did not abuse 

its discretion by determining not to accept petitions for 
30 

administrative review filed more than 180 days after the patent 

grant.” Def.’s MSJ, ECF No. 48 at 27 (quoting Daiichi II, 791 

F.3d at 1380). Even if this decision does not control, the USPTO 

alternatively maintains that the July patents were treated the 

same as patents issued before August 5, 2009, and the July 

patents are actually not a separate category because they belong 

to the same category of patent holders who fell outside of the 

180-day period under the Interim Procedure. See id. at 28. The 

USPTO disputes Nippon’s argument that it was “logical” for this 

group of patentees not to seek judicial relief because the 

USPTO’s announcements expressly reminded patentees that they 

needed to comply with the 180-day period to seek judicial 

relief. Id. at 28-29. 

The Court is not persuaded by Nippon’s arguments regarding 

the July patents. First, as the USPTO points out, it is 

undisputed that the July patents issued prior to August 5, 2009. 

See id. at 27. In Daiichi II, in rejecting the disparate 

treatment argument advanced there, the Federal Circuit 

determined that the plaintiff there “was treated identically to 

all other patentees whose patents had issued more than 180-days 

prior to the deadline for filing a petition and who were unable 

to show extraordinary circumstances.” 791 F.3d at 1380. In other 

words, the Daiichi II plaintiff was treated identically to all 

other patentees whose patents issued prior to August 5, 2009. 
31 

See id. 

Nippon maintains that the July patents were treated 

differently from other patentees whose patents issued prior to 

August 5, 2009 because they could have sought judicial review of 

their PTAs after the Wyeth decision, but they were “misled” by 

the USPTO in its announcements. Pl.’s MSJ, ECF No. 46 at 29. 

Assuming a filing deadline is a proper basis for determining 

whether parties are similarly-situated, the Court disagrees that 

the July patents were treated differently because nothing 

prevented those patentees from filing judicial challenges either 

pre- or post-Wyeth. See Novartis II, 740 F.3d at 600 (“At a 

minimum, nothing stood in the way of Novartis’s timely pressing 

the very claim Wyeth pressed.”). 

Finally, the record does not support Nippon’s contention 

that the July patents were “misled” by the USPTO. Four days 

after the Wyeth decision was issued on January 7, 2010, the 

USPTO posted a two-paragraph notice stating that pending a 

determination of whether to seek further review of the decision, 

“the USPTO is in the process of changing the manner it will 

calculate [PTAs] under Section 154(b) to conform to the Federal 

Circuit’s decision.” Pl.’s MSJ, Ex. B, ECF No. 46-3 at 2. The 

second paragraph reminded interested parties of the deadline for 

seeking judicial review: “Applicants and Patent Owners 

dissatisfied with a [PTA] determination by the agency are 
32 

reminded of the requirement to seek review of that determination 

within 180 days of patent issuance and the time periods set in 

the implementing regulations. See 35 USC 154(b)(4) and 37 CFR 

1.705.” Id. Later, on January 20, 2010, the USPTO issued a twoparagraph announcement stating that it and the Department of 

Justice would not seek further review of the Wyeth decision and 

that “[t]he USPTO [was] preparing guidance for expediting 

requests for recalculation of [PTA] by the USPTO in light of the 

Wyeth decision. This guidance will be issued as soon as 

possible.” Pl.’s MSJ, Ex. A, ECF No. 46-2 at 2. The announcement 

included the exact same reminder of the deadline for seeking 

judicial review that had been in the January 11, 2010 notice. 

Id. Therefore, rather than it being “reasonable” for the July 

patents “to believe that the USPTO was going to implement a 

process to correct its mistake that would not require judicial 

review” and “[t]here was no reason for these patentees to 

believe that the USPTO’s upcoming guidance would not apply to 

them[,]” Pl.’s MSJ, ECF No. 46 at 29-30, the USPTO expressly 

reminded patent applicants and owners of the deadline for 

seeking judicial review. Since Nippon has failed to show that 

the Interim Procedure treated similarly-situated patentees – 

i.e., those whose patents issued prior to August 5, 2009 – 

differently, and since the record does not support its 

contention that the July patents were misled by the USPTO, its 
33 

APA challenge fails.9 

V. Conclusion 

For the reasons set forth above, and in view of the narrow 

scope of review and deference appropriately due, the Court finds 

that the Interim Procedure is not arbitrary, capricious, an 

abuse of discretion, or otherwise not in accordance with law. 

Accordingly, the Court DENIES Nippon’s motion for summary 

judgment and GRANTS USPTO’s cross-motion for summary judgment. A 

separate Order accompanies this Memorandum Opinion. 

SO ORDERED 

Signed: Emmet G. Sullivan 

United States District Judge 

February 27, 2019 

 

9 Nippon argues that the USPTO treated it disparately when it 

denied its requests as untimely on different grounds. See Pl.’s 

MSJ, ECF No. 46 at 25-26. But the USPTO maintains that its 

denials of Nippon’s requests, which were improperly submitted as 

requests for certificates of correction, did not constitute 

“impermissible arbitrary and capricious treatment under the APA” 

because it specifically identified the procedural infirmities in 

Nippon’s requests in different responses—Nippon filed the 

request for the ‘302 patent outside of the two-month deadline 

and Nippon’s request for the ‘997 patent incorrectly used the 

general provisions of 35 U.S.C. § 254 instead of the regulations 

promulgated under 35 U.S.C. § 154(b)(4). Def.’s MSJ, ECF No. 48 

at 27. The Court agrees.