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 .
The claims filed 1/16/2026 are under consideration.
Election/Restrictions
Applicant’s election without traverse of Group II (claims 2-7, 26-34 and 38-39) in the reply filed on 1/16/2026 is acknowledged.
Claims 1 and 16-17 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 1/16/2026.
Applicant’s election without traverse of the species of claim 26 in the reply filed on 1/16/2026 is acknowledged.
Information Disclosure Statement
The listing of references in the specification or the citation of references throughout the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. The embedded hyperlink appears as an email address in para. 15.
The use of terms, such as Anticalin®, SMIPs™ and Adnectin®, which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claim 6 is objected to because of the following informalities: the claim recites “selected from…therapy, or combinations thereof” rather than “selected from…therapy and combinations thereof”. Appropriate correction is required.
Claim 26 is objected to because of the following informalities: the claim recites a list of genes. Multiple genes are listed multiple times, such as CCL5 (at least four times), CD52 (at least four times) and CXCL11 (at least four times). It is suggested applicant review the list and recite a gene only once. Alternatively, applicant should explain why certain genes are recited multiple times, including at least 4 times.
Appropriate correction is required.
Claim 30 is objected to because of the following informalities: the claim recites “one gene each of the gene groups” rather than “one gene from each of the gene groups”. Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38 and 39 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract ideas without significantly more.
The claim sets forth a series of steps and thus is a method, one of the four statutory classes.
The claim(s) recite(s):
“assessing both: (i) subtype markers of a subtype selected from mesenchymal (M), mesenchymal stem-like (MSL), and combinations thereof, and (ii) status markers of immunomodulatory (IM) status”; and
“calculating…an IO score by weighting the subtype markers as likely to indicate non-responsiveness to immunomodulation therapy and the status markers as likely to indicate responsiveness to immunomodulation therapy”.
The step of “assessing” broadly encompasses the reviewing of expression data as described in the instant specification, where data as retrieved from public databases. The claim does not require any tangible assay or methodology. The claimed “assessing” broadly encompasses an abstract idea that can be performed in a purely mental manner or with the aid of pen and paper.
The step of “calculating” also broadly encompasses an abstract idea as it broadly encompasses the analysis and calculation of an “IO score” based on data for two subtype markers and two status markers (i.e., the analysis of 4 data points). This limited amount of data may be processed in the human mind, but for the recitation of “by means of a computer” in the “calculating” steps. That is, other than reciting “by means of a computer” nothing in the steps preclude the steps from practically being performed in the human mind. For example, but for the “by means of a computer” language, “calculating” in the context of the claim encompasses the user mentally analyzing data organized in a table. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer steps, i.e., “by means of a computer”, then it falls within the “Mental Processes” grouping of abstract ideas. Accordingly, these steps recites an abstract idea. See MPEP 2106.04(a)(2)III.C.
The judicial exceptions are not integrated into a practical application because the claims do not involve:
improvements to the functioning of a computer or to any other technology or technical field;
applying or using the judicial exceptions to effect a particular treatment or prophylaxis for a disease or medical condition;
applying the judicial exception with, or by use of, a particular machine; or
effecting a transformation or reduction of a particular article to a different state or thing.
The claimed limitations add insignificant extra-solution activity to the judicial exceptions. The are no additional steps or elements that are not judicial exceptions.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims only set forth steps that fall within the mental processes grouping of abstract ideas.
Regarding claim 3, the administering step is conditioned on a set of criteria being met. The claim encompasses embodiments in which the IO score is not above the threshold. In those embodiments, the “administering step” is not performed because the criteria for performing are not met. Those embodiments do not integrate any of the abstract ideas because no practical application is carried out.
Claims 5 and 6 depend from claim 3 and do not add any practical applications either.
Regarding claim 4, the administering step is conditioned on a set of criteria being met. The claim encompasses embodiments in which the IO score is above a certain threshold. In those embodiments, the “administering step” is not performed because the criteria for performing it are not met. Those embodiments do not integrate any of the abstract ideas because no practical application is carried out.
Claims 7, 38 and 39 depend from claim 4 and does not add any practical application.
Regarding claim 32, the administering step is conditioned on a set of criteria being met. The claim encompasses embodiments in which the IO score is above a certain threshold. In those embodiments, the “administering step” is not performed because the criteria for performing it are not met. Those embodiments do not integrate any of the abstract ideas because no practical application is carried out.
Claim 33 depends from claim 32 and does not add any practical application.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38 and 39 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Regarding claim 2, the claim requires “assessing…subtype markers of a subtype selected from mesenchymal (M), mesenchymal stem-like (MSL), and combinations thereof”. The claim does not identify or define what is an “subtype marker”. The instant specification does not define the term. The instant specification does not identify any “subtype markers”. While the specification lists a number of genes, none of the genes are identified as any type of marker or which ones are correlated with a mesenchymal subtype versus a mesenchymal stem-like subtype. The ordinary artisan is provided no guidance as to which genes are and are not “subtype markers” because no representative species are provided.
The claim also requires “assessing…status markers of immunomodulatory (IM) status”. The claim does not identify or define what is an “status marker”. The instant specification does not define the term. The instant specification does not identify any “status markers”. While the specification lists a number of genes and gene groups, none of the genes or groups are identified as any type of marker or which ones are correlated with “immunomodulatory status”. The ordinary artisan is provided no guidance as to which genes or gene groups are and are not “status markers” because no representative species are provided.
The scope of the “assessing” step is not adequately described because it is unclear what markers are and are not encompassed by the step.
The claim requires “calculating, by means of a computer, an IO score by weighting the subtype markers as likely to indicate non-responsiveness to immunomodulation therapy and the status markers as likely to indicate responsiveness to immunomodulation therapy”. The claims do not identify how any “subtype marker” is to be “weighted”. Are they all weighted equally as “indicative” of non-responsiveness to immunomodulation therapy? Are they weighted differently? Are they weighted based on the level of expression? There is no guidance in the instant specification which genes are to be weighted or assessed, e.g., upregulation, downregulation, etc., and how they are relevant to calculating an IO score.
The same issue applies to the “weighting” of the “status” markers.
The scope of the “calculating” step is not adequately described because it is unclear what markers are being used as part of the calculations and how they are to be weighted.
The instant specification is an invitation to the user to identify which genes are and are not “subtype markers” and/or “status markers” that are relevant to assessing a tumor’s likely responsiveness to immunomodulation therapy.
Claims 26 and 27 list genes and groups of genes, but there is no indication which genes are “subtype markers”, which types of “subtype markers”, and “status markers”.
There is no guidance as to how one is to use these genes within the context of the claimed methods.
Claim 33 states “the additional therapy is selected to target gene pathways associated with negative IO scores”. The instant specification provides no representative examples of an IO score and which “additional therapy” should be selected based on the “negative score”. For example, there is no guidance as to how a “negative IO score” is associated with one type of additional therapy while a different “negative IO score” is associated with a different type of additional therapy.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 4, 5, 26, 27, 28 29, 30 31, 32 and 39 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claim 4, the claim recites “a certain threshold”. It is unclear what distinguishes a “certain” threshold from any other threshold, for example “a threshold” of claim 3.
Regarding claim 4, the claim is incomplete because the claim does not require any active step that determines an IO score is above a threshold. The claim does not require making an comparison between an IO score and a threshold.
Regarding claim 5, the claim recites “a certain threshold”. It is unclear what distinguishes a “certain” threshold from any other threshold, for example “a threshold” of claim 3.
Regarding claim 5, claim 3 requires administering the immunomodulation therapy to a subject whose tumor has been determined to have an IO score above a threshold established to correlate with responsiveness to the immunomodulation therapy. Claim 5 depends from claim 3 and requires the immunomodulation therapy to be “selectively” administered to subjects whose tumors have been determined to have IO scores above a certain threshold. It is unclear how the administering step of claim 5 is performed in addition to the one of claim 3.
Regarding claim 5, the claim is incomplete because the claim does not require any active step that determines an IO score is above a certain threshold. The claim does not require making an comparison between an IO score and a certain threshold.
Regarding claim 26, it is unclear which genes in the list are “subtype markers” and which are “status markers”.
Regarding claim 27, it is unclear which genes in the list are “subtype markers” and which are “status markers”.
Regarding claim 28, it is unclear if the subtype markers comprise at least one gene from five or more of the gene groups and the status markers also comprise at least one gene from five or more of the gene groups.
It is also unclear whether a combination of CCL5 and CD52 satisfies the claim because CCL5 is part of 4 gene groups and CD52 is part of 4 gene groups, and thus, are reasonably “markers” that comprise at least one gene from five or more of the gene groups.
Regarding claim 29, it is unclear if the subtype markers comprise at least one gene from ten or more of the gene groups and the status markers comprise at least one gene from ten or more of the gene groups.
It is also unclear whether a combination of CCL5, CD52 and ZCCHC24 satisfies the claim because CCL5 is part of 4 gene groups, CD52 is part of 4 gene groups and ZCCHC24 is part of 2 gene groups and thus, are arguably “markers” that comprise at least one gene from 10 or more of the gene groups.
Regarding claim 30, it is unclear if a subtype markers include a gene from each of the gene groups and the status markers include a gene from each of the gene groups. Additionally, it is unclear if a gene like CCL5 qualifies as a gene from each of Group A, Group B1, Group C5 and Group D1.
Regarding claim 31, it is unclear if a subtype markers include a gene from each of the recited gene groups and the status markers include a gene from each of the recited gene groups. Additionally, it is unclear if a gene like CCL5 qualifies as a gene from each of Group A, Group B1, Group C5 and Group D1.
Regarding claim 32, the claim recites “a certain threshold”. It is unclear what distinguishes a “certain” threshold from any other threshold, for example “a threshold” of claim 3.
Regarding claim 32, the claim recites “administering an additional therapy”. It is unclear if the term “additional” implicitly requires the administration of a “therapy” and an “additional therapy”.
Regarding claim 39, the claim states “the IO score is determined after alternative therapy administration”. Based on the use of the passive voice, it is unclear if the claim is setting forth an active method step of “determining an IO score after the alternative therapy administration.
Regarding claim 39, the claim specifies “the IO score is determined after alternative therapy administration”, presumably further limiting when the calculating IO score of claim 2 is performed. It is unclear how one is to determine if an IO score is changed when only one IO score is calculated.
Improper Markush Grouping Rejection
Claims 26 and 27 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984).
A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of claims 26 and 27 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: the alternatives are genes. The genes have different structures based on nucleic acid encoding sequences and amino acid sequences. The genes have different uses as they are involved in distinct pathways.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
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.
Claim(s) 2 is/are rejected under 35 U.S.C. 103 as being unpatentable over Shields (Scientific Reports. 2017. 7:807, 12 pages).
Regarding claim 2, Shields assesses both subtype markers, ILK, LIMS1, CREB1, PIGR and MYLK (p. 5-6) and status markers, E-cadherin, CD63, CXCL4 and CXCL12 (p. 6).
Shields calculates an “IO score” by using a computer to generate a heat map or non-metric multidimensional scaling ordination (p. 10; and Fig. 2c and Fig. 2d). Subtype markers like ILK were linked to or “weighted” to non-responsiveness in tumors (p. 5-6) and status markers such as CD63 and CXCL4 and CXCL12 were linked to or “weighted” to responsiveness in tumors.
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.
Claim(s) 3, 4, 5, 6, 7, 32 and 33 is/are rejected under 35 U.S.C. 103 as being unpatentable over Shields (Scientific Reports. 2017. 7:807, 12 pages).
Regarding claims 3, 4, 5, 6, 7, 32 and 33, Shields assesses both subtype markers, ILK, LIMS1, CREB1, PIGR and MYLK (p. 5-6) and status markers, E-cadherin, CD63, CXCL4 and CXCL12 (p. 6).
Shields calculates an “IO score” by using a computer to generate a heat map or non-metric multidimensional scaling ordination (p. 10; and Fig. 2c and Fig. 2d). Subtype markers like ILK were linked to or “weighted” to non-responsiveness in tumors (p. 5-6) and status markers such as CD63 and CXCL4 and CXCL12 were linked to or “weighted” to responsiveness in tumors.
Regarding claims 3, 5 and 6, Shields teaches administering ICI therapies to the subjects. It would have been obvious to have treated or not treated patients with ICI therapies based on their assessment and calculated scores.
Regarding claims 4 and 32, it would have been prima facie obvious to have administered a non-ICI therapy to a patient whose assessment and calculated scores indicates non-responsiveness.
Regarding claims 7 and 33, it would have been prima facie obvious to have administered an drug that targets EZH2, because it relates to non-responsiveness to ICI therapies (p. 8).
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 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38 and 39 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 60-79 of copending Application No. 18/835,307 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because the claims are nearly identical or substantially similar.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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/JOSEPH G. DAUNER/ Primary Examiner, Art Unit 1682