DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Office Action: Notice
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 12/11/2025 has been entered.
Claim Status
Claim 1 has been amended (12/11/2025). No new matter was added. Claims 1-5, 8-10, 12-13 and 15 are under examination on the merits.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-3, 8-10, 12-13 and 15 are rejected under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by Bostick et al., (WO 2017/048993 A1, published 3/23/2017, from IDS 4/13/2021). This rejection is modified, as necessitated by Applicants' amendments.
Regarding claim 1 Bostick teaches a library preparation and analysis (Figure 1; Abstract).
Regarding claim 1 step a, Bostick teaches an RNA sample (pg. 2).
Regarding claim 1 step b, Bostick teaches fragmenting RNA (pg. 12). Specifically, Bostick teaches chemical fragmentation (pg.12, line 16).
Regarding claim 1 step c Bostick teaches adenylating fragmented RNA (pg. 12), specifically Bostick teaches (poly)adenylating precursor RNA using any convenient approach (pg. 12, line 29).
Regarding claim 1 step d, Bostick teaches a cDNA primer may include a domain that hybridizes to the template RNA. Bostick teaches the sequence of the first and second domains may be independently defined or arbitrary (pgs. 14 and 15).
Regarding claim 1 step e, Bostick teaches the first strand cDNA primer includes a barcode domain for identification of the sample. In certain aspects the cDNA primer may include a unique molecular identifier (UMI) or other barcode to mark each RNA molecule converted to cDNA individually (pg. 15, lines 22-24). After first strand synthesis the cDNA is amplified via PCR to generate product double strand cDNA to produce a second strand DNA complementary to the first strand cDNA (pg.19, line 19, Bostick further teaches a unique molecular identifier (UMI) on Oligo dT primers (pg. 14 and 15). Additionally, Bostick teaches that solid phase amplification of these polynucleotides is typically performed by first ligating known adapter sequences or a template switch oligonucleotide under first strand cDNA synthesis conditions, as previously described, to each end of a targeted polynucleotide (i.e., aRNA) (p. 1, lines 1-15; p. 2, lines 1-5; p. 8 lines 10-20). Bostick also teaches that synthesis of cDNA from template nucleic acid mRNA in the methods described above are performed directly on cell lysates allowing purification or depletion of RNA via release from cells, to reduce mitochondrial and ribosomal contamination (p. 32, lines 10-15).
Regarding claim 2 Bostick teaches sample RNA is isolated from a single cell (pg.11 line 10).
Regarding claim 3 Bostick teaches RNA may be microRNA, small nucleolar RNA, and small nuclear RNA (pg.10).
Regarding claim 8, step k Bostick teaches PCR amplification conditions, sufficient to produce a product double stranded cDNA (pg. 20 line 27- 33). Bostick teaches primer binding sites (domains) which may be on the end of double stranded cDNA. Bostick teaches amplification primer binding site can be randomly attached to fragment ends of double-stranded cDNA library (pg. 8 line 25).
Regarding claim 9, it is noted that step (h) remains optional, and thus, the teachings of Bostick anticipate claim 9 for the same reasons they anticipate claim 8. Further, Bostick teaches the sequencing platform adapter may include adapter sequences, indexing sequences, sources barcode sequences, and UMI (unique molecular identification sequences) (pg.35, line 29).
Claim 10 further limits claim 8 optional step m, but does not require the practice of optional step m, therefore by meeting step k, claim 10 is also anticipated.
Regarding claim 12 Bostick teaches preparing a sequencing library, pooling one or more sequencing libraires (pg. 25, line 33), furthermore Bostick teaches deep sequencing the sequencing library (pgs. 32-34).
Regarding claim 13 Bostick teaches cDNA library and first strand cDNA primers include a unique molecular identifier or other barcode to mark each RNA molecule converted to cDNA individually (pg. 15 lines 21-24 and pg. 32-33).
Regarding claim 15, Bostick teaches PCR amplification conditions, sufficient to produce a product double stranded cDNA (pg. 20 line 27- 33). Bostick teaches primer binding sites (domains) which may be on the end of double stranded cDNA, and are randomly attached to fragment ends of double-stranded cDNA library (pg. 8 line 25). Specifically, Bostik teaches that following ligation of adapter sequences, unused adapter molecules must be separated from the ligated polynucleotides before proceeding to the amplification, so as to avoid unwanted amplification of adapters that have not been attached to the target polynucleotides (p.1, lines 20-25).
Bostick teaches each and every limitation of claims 1-3, 8-10, 12-13 and 15, and therefore Bostick anticipates claim 1-3, 8-10, 12-13 and 15.
Applicant’s Arguments: The Applicant argues that claim 1 has been amended, to specify a specific sequence in which fragmented RNA undergoes end-repair immediately followed by polyadenylation without intervening adapter ligation, which the Applicant contends is fundamentally different from Bostick’s adapter-ligation and template-switching approaches. The Applicant also asserts that Bostick’s disclosure of adenylation occurs in a different context and does not teach or suggest the claimed sequential end-repair and polyadenylation of fragmented RNA. The Applicant therefore maintains that Bostick fails to disclose all claim limitations arranged as required and cannot anticipate the amended claims.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully considered but are not found persuasive, as discussed below.
As set forth in MPEP 2131, a claim is anticipated if a single prior art reference discloses, expressly or inherently, each and every limitation of the claim, arranged as in the claim, and exact duplication of claim language or terminology as required (In re Gleave, 560 F.3d 1331 (Fed. Cir. 2009)).
Specifically, Bostick teaches preparing sequencing libraries from RNA, including fragmenting RNA (p. 12), followed by polyadenylating RNA using polyA polymerase (p. 12, line 29), and subsequently priming and synthesizing cDNA using oligo-dT primers (p. 14-15). Bostick further teaches that barcode and/or UMI sequences may be incorporated into primers used during cDNA synthesis (p. 15, lines 21-24; p. 32-33), and that cDNA may be amplified and converted to double-stranded cDNA for sequencing (p. 20, lines 27-33).
Applicant’s amendment specifying that end-repair is “immediately followed by polyadenylation without intervening adapter ligation” does not confer patentable distinction, because Bostick does not require adapter ligation prior to polyadenylation, and expressly teaches polyadenylating RNA prior to downstream priming and cDNA synthesis (p. 12, lines 16-29). Further, the Applicant’s arguments improperly limit Bostick to embodiments involving adapter ligation or template switching. However, anticipation is not avoided by focusing on preferred or downstream embodiments when the reference as a whole discloses the claimed limitations. Specifically, Bostick’s disclosure of adapter ligation occurs in separate contexts and downstream processing steps (i.e., p. 1, lines 15-25; p. 8, lines 10-25; p. 32, lines 32-34) and does not negate the express teaching of polyadenylating RNA prior to those steps.
Anticipation is not avoided by focusing on particular embodiments (i.e., adapter ligation or template switching) when the reference as a whole discloses the claimed subject matter. See MPEP 2131.01, citing In re Petering, 301 F.2d 676 (CCPA 1962). Further, a reference anticipates if it discloses all limitations arranges as in the claim, even if it does not expressly state the absence of an optional step, such as adapter ligation. See MPEP 2131; In re Schreiber, 128 F.3d 1473 (Fed. Cir. 1997). Because Bostick teaches polyadenylation of RNA fragments and does not require adapter ligation before that polyadenylation, the claimed limitation “without intervening adapter ligation” is inherently met.
Therefore, contrary to the Applicant’s assertions, Bostick teaches and anticipates all elements of amended claim 1. Therefore, the 35 U.S.C. 102“(a)(1)” and “(a)(2)” over Bostick is maintained.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 4-5 are rejected under 35 U.S.C. 103 as being unpatentable over Bostick et al., (WO 2017/048993 A1, published 3/23/2017, from IDS 4/13/2021), in view of Allen et al. (PGPub US 2020/0102586 A1, published 4/2/2020, filed 9/28/2018). This rejection is modified, as necessitated by Applicants' amendments.
The teachings of Bostick as they relate to claim(s) 1 and 7, from which claim 4-6 and 11 depends are given previously in this Office action and are fully incorporated here.
Claim 4, Bostick does not teach or suggest fragmentation by exposure to a divalent metal-cation at a temperature between 55-110 °C.
Regarding claim 5 Bostick does not teach or suggest that the metal cation is Mg2+.
Allen teaches a method to create a cDNA library, Allen teaches fragmenting mRNA, polyadenylating RNA fragments followed by oligo-dt primed reverse transcription.
Regarding claim(s) 4 and 5, Allen teaches fragmenting mRNA at 60 °C in the presence of a divalent cation e.g., Mg2+ (pg. 4 col. 2).
It would have been obvious to have modified the Bostick method of fragmenting mRNA for reverse transcription to include Allen’s step of treatment (end repair) under suitable conditions. One would have been motivated to do so because as stated by Allen treatment of the 5’ Hydroxyl and 3’ Phosphate may be required before moving on to the polyadenylation step.
It would have been obvious to have modified Bostick’s method of attaching adapters to RNA to include Allen’s step of ligating an adapter to RNA because Bostick teaches ligation-based strategies as an alternative method for adding nucleotides to precursor RNA (p. 13, lines 6-8) and Allen specifically teaches ligating an adapter to various strand locations throughout the previously described method. One of ordinary skill in the art would have been motivated to combine Allen’s adapter ligation with Bostick’s method because Allen teaches that adapter ligation can be used for quantitative determination of specified sequences within an RNA or DNA sample (p. 8, col. 2).
Applicant’s Arguments: The Applicant argues that amended claim 1 is allowable because Bostick in view of Allen does not teach performing end-repair and polyadenylation directly after RNA fragmentation, as previously described. Applicant further asserts that Allen’s disclosure of fragmentation conditions does not cure the alleged deficiencies of Bostick because neither reference teaches performing end-repair immediately after fragmentation and before polyadenylation, as claimed. The Applicant further asserts that the claimed sequence produces unexpected results and therefore would not have been obvious.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully considered but are not found persuasive, as discussed below.
As set forth in MPEP 2141, a claim is unpatentable under USC 103 if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious to one of ordinary skill in the art at the time of the invention.
Specifically, as discussed above, Bostick teaches preparing RNA sequencing libraries including RNA fragmentation, polyadenylation of RNA, priming, and cDNA synthesis (p. 12-15, 19-20). Allen teaches fragmenting RNA under conditions using a divalent metal cation (Mg), at elevated temperatures, and further teaches that treatment to address RNA end chemistry (i.e., 5’ hydroxyl and 3’ phosphate) may be required prior to downstream polyadenylation and reverse transcription (p. 4, col. 2; p. 8).
Therefore, the combination of Bostick and Allen establishes a prima facie case of obviousness. This combination would have been obvious because both references are directed to
methods of preparing nucleic acid libraries for sequencing, with Allen teaching a wider variety of adapter ligation within various steps of sequencing library formation. Specifically, it would have been obvious to modify Bostick’s RNA library preparation method to employ Allen’s well-known fragmentation conditions and end-treatment steps, as this represents the predictable use of prior art elements according to their established functions to achieve compatible RNA ends for downstream processing. The art demonstrates that adapter ligation and alternative methods are interchangeable techniques in sequencing workflows, and Allen provides direct motivation to employ adapter ligation for improved sequencing. See MPEP 2143, citing KSR Int’l Co. v. Teleflex Inc., 550 US 398 (2007). The Applicant’s argument that neither reference explicitly teaches the exact claimed sequence does not overcome obviousness, as 103 does not require an express teaching of the claimed combination so long as there is a reasonable motivation to combine with a reasonable expectation of success.
Accordingly, the rejection under USC 103 is maintained.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 2, 9 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1, 2, and 33 of copending Application No. 18020391 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because Claim 1 is anticipated by copending claim 2.
Regarding claim 2 in application 18020391 teaches fragmenting RNA (claim 1a, 33).
Regarding claim 1 step c, 18020391 teaches polyadenylation of RNA (claim 2).
Regarding step d, 18020391teaches cDNA synthesis with a poly-T primer hybridized to a polyA tag of RNA (claim 2). 391 further teaches reverse transcription to obtain cDNA sequencing library (claim1g).
Regarding step e, 18020391 teaches poly-T primer further comprising a UMI and/or barcode (claims 2,33).
Regarding claim 2, copending application teaches RNA from a single cell (claim 1).
Regarding claim 9, copending application teaches each cDNA in the cDNA sequencing library comprises a barcode and optionally a UMI (claim 33).
Claim(s) 1, 2, 3, 8, 9, 10, 12-13 and 15 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim(s) 1, 2, 15, and 33 of copending Application No. 18020391 in view of Bostick et al., (WO 2017/048993 A1, published 3/23/2017, from IDS 4/13/2021).
Regarding claim 2 copending application 18020391 teaches fragmenting RNA (claim 1a).
Regarding claim 1 step c, copending application teaches polyadenylation of RNA (claim 2).
Regarding step d, copending application teaches cDNA synthesis with a poly-T primer hybridized to a polyA tag of RNA (claim 2). 18020391 further teaches reverse transcription to obtain cDNA sequencing library (claim1g).
Regarding step e, copending application teaches poly-T primer further comprising a UMI and/or barcode (claims 2,33).
Regarding claim 2, copending application teaches RNA from a single cell (claim 1).
Regarding claim 9, copending application teaches each cDNA in the cDNA sequencing library comprises a barcode and optionally a UMI (claim 33).
The copending application does not teach the steps of claim(s) 3, 8, 10, 12-13 and 15.
Bostick teaches a method of preparing a sequencing library (Figure 1; Abstract).
Regarding claim 3 Bostick teaches RNA may be microRNA, small nucleolar RNA, and small nuclear RNA (pg.10).
Regarding claim 8, step k Bostick teaches PCR amplification conditions, sufficient to produce a product double stranded cDNA (pg. 20 line 27- 33). Bostick teaches primer binding sites (domains) which may be on the end of double stranded cDNA. Bostick teaches amplification primer binding site can be randomly attached to fragment ends of double-stranded cDNA library (pg. 8 line 25).
Claim 10 further limits claim 8 optional step m, but does not require the practice of optional step m, therefore by meeting step k, I am rejecting claim 10.
Regarding claim 12, Bostick teaches preparing a sequencing library, pooling one or more sequencing libraires (pg. 25, line 33), furthermore Bostick teaches deep sequencing the sequencing library (pgs. 32-34).
Regarding claim 13, Bostick teaches cDNA library and first strand cDNA primers include a unique molecular identifier or other barcode to mark each RNA molecule converted to cDNA individually (pg. 15 lines 21-24 and pg.32-33).
Regarding claim 15, Bostik teaches that following ligation of adapter sequences, unused adapter molecules must be separated from the ligated polynucleotides before proceeding to the amplification, so as to avoid unwanted amplification of adapters that have not been attached to the target polynucleotides (p.1, lines 20-25).
It would have been obvious to modify the method taught in the claims of copending application 18020391 to include Bostick’s method of creating a cDNA library. One would have been motivated to do so because this will create a cDNA library from RNA, wherein a next generation sequencing library are produced (Bostick pg.33).
This is a provisional nonstatutory double patenting rejection.
Claim(s) 1 and 4-6 is/are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim(s) 1, 2, 15, 17, 18 and 33 of copending Application No. 18020391 in view of Allen et al. (PGPub US 2020/0102586 A1, published 4/2/2020, filed 9/28/2018).
Regarding claim 1, copending application teaches the limitations of claim 1 as described above and is incorporated herein.
The copending application fails to teach the limitation of claim(s) 4-6 of the instant application.
Regarding claim(s) 4 and 5, Allen teaches fragmenting mRNA at 60 °C in the presence of a divalent cation e.g., Mg2+ (pg. 4 col. 2).
Regarding claim 6, Allen teaches some methods produce fragments that have 5’ Hydroxyl or 3’Phosphate and shall require treatment by phosphatase and/or kinase treatment before polyadenylation step (Allen pg. 10, col. 2).
It would have been obvious to have modified the copending application method of fragmenting to include Allen’s step of treatment (end repair) under suitable conditions. One would have been motivated to do so because as stated by Allen treatment of the 5’ Hydroxyl and 3’ Phosphate may be required before moving on to the polyadenylation step.
This is a provisional nonstatutory double patenting rejection.
Applicant’s Arguments: The Applicant argues that the provisional nonstatuatory double patenting rejection should be withdrawn because the instant application has an earlier effective filing date (10/29/2019) than the cited copending application (8/18/2021), and therefore the claims are not obvious over the copending claims. Applicant further contends that, pursuant to MPEP 1490 (VI)(D)(2)(a), where a provisional nonstatuatory double patenting rejection is the only remaining rejection in an application having the earlier patent term filing date, the rejection should be withdrawn and the application permitted to issue.
Examiner’s Response to Traversal: The Applicant’s arguments regarding withdrawal of the provisional nonstatuatory double patenting rejection have been fully considered, but are not persuasive at this time. As a rejection under both USC 102 and 103 remain outstanding, the provisional nonstatuatory double patenting rejection is maintained. Applicant’s arguments will be reconsidered if and when double patenting is the sole remaining issue. therefore, these rejections are maintained, as set forth above.
Conclusions
No claim is allowed.
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/ELIZABETH ROSE LAFAVE/
Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684