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 .
DETAILED ACTION
Continued Examination Under 37 CFR 1.114
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 12/29/2025 has been entered.
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-8, 10-11, 14-16, 20-21, 24-36, 38 and species: CH2CH3 domain, IgG1, antibody light chain and antibody heavy chain, human IL-15Ra (sushi + domain), serine protease, matriptase and uPa, SEQ ID NO: 326, in the reply filed 12/09/2024 is acknowledged.
Claims 24, 78, and 82-83 are withdrawn from consideration pursuant to 37 CFR1.142(b) as being drawn to nonelected inventions and species, there being no allowable generic or linking claims. Election was made in the reply filed 12/09/2024.
Claims 1, 10-11, 14, 16. 21, 25, 29-36, and 38 are now under consideration in the instant Office Action.
Withdrawn Rejections
Rejections of claims 1, 10-11, 14, 16, 20-21, 25, 29-36, and 38 under 35 U.S.C. 103 as being unpatentable over Modernatx (in IDS filed 12/06/2021 under “Modernatx, Inc.”), in view of CytomX (in IDS filed 12/06/2021 under “Stagliano et al.”), Vamosi (in IDS filed 12/06/2021), in further view of Friis et al. (in PTO-892 filed 02/26/2025) are hereby withdrawn in view of amendments to the claims which obviate the prior art.
Modified Rejections Necessitated by Amendment
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 1, 10-11, 14, 16, 21, 25, 29-36, and 38 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.
The MPEP states that the purpose of the written description requirement is to ensure that the inventor had possession, as of the filing date of the application, of the specific subject matter later claimed. The MPEP lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the application. These include “level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention.”
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, disclosure of drawings, or by disclosure of relevant identifying characteristics, for example, structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the Applicants were in possession of the claimed genus.
The instant claims are directed to an activatable homodimeric proprotein that retains IL-15 biological activity. The IL-15 polypeptide is a protein comprising the amino acid sequence of SEQ ID NO: 320, 326, or 332 and the instant claims recite any variant of the aforementioned sequences so long as it retains at least 90% identity to the claimed sequences. The modifications to the sequences can be up to 10% of the overall sequence, and can occur in any position of the larger polypeptide with any amino acid being substituted at any residue. The IL-15 variants are required to have specific functions, including having biological activity upon activation of the proprotein once cleaved by a protease.
The specification discloses IL-15 variants of SEQ ID NOs: 320, 326, 332, as well as a list of at least 30 representative species that fall within the scope of the claims and retain the required functions. However, the claims encompass a far broader genus of proteins than is supported in the instant specification. The instant claims recite proproteins having up to 10% variability in the identity of the sequence, although not all of the possible substitutions or modifications may be capable of the required functions. The variation of up to 10% of the identity of the proprotein sequence could yield thousands of possible proteins, and picking from 20 amino acids for each of the potential mutation sites would generate millions of possible variant proteins. The genus is even broader, because the protein can be varied more than 40 amino acids. These proteins have no correlation between their structure and function. The claims require that the protein exhibit specific functional characteristics, but the specification provides no guidance regarding which variants are capable of the required function. Additionally, Applicant has not recited a variant sequence that comprises all the potential variants that can arise from such levels of modification. Therefore, the specification provides insufficient written description to support the genus encompassed by the claim. Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, makes clear that "applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now claimed." (See page 1117.) The specification does not "clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed." (See Vas-Cath at page 1116.)
The skilled artisan cannot envision the detailed chemical structure of the encompassed polypeptides, regardless of the complexity or simplicity of the method of isolation. Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method for isolating it. The nucleic acid and/or protein itself is required. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993) and Amgen Inc. V. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016. In Fiddes v. Baird, 30 USPQ2d 1481, 1483, claims directed to mammalian FGF's were found unpatentable due to lack of written description for the broad class.
University of California v. Eli Lilly and Co., 43 USPQ2d 1398, 1404. 1405 held that:
...To fulfill the written description requirement, a patent specification must describe an invention and does so in sufficient detail that one skilled in the art can clearly conclude that "the inventor invented the claimed invention." Lockwood v. American Airlines Inc. , 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (1997); In re Gosteli , 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989) (" [T]he description must clearly allow persons of ordinary skill in the art to recognize that [the inventor] invented what is claimed."). Thus, an applicant complies with the written description requirement "by describing the invention, with all its claimed limitations, not that which makes it obvious," and by using "such descriptive means as words, structures, figures, diagrams, formulas, etc., that set forth the claimed invention." Lockwood, 107 F.3d at 1572, 41 USPQ2datl966.
Protein chemistry is one of the most unpredictable areas of biotechnology. This unpredictability prevents prediction of the effects that a given number or location of mutation will have on a protein (such as TNF or a cytokine) As taught by Skolnick et al (Trends Biotechnol. 2000 Jan;18(1):34-9, in instant PTO-892), sequence based methods for predicting protein function are inadequate because of the multifunctional nature of proteins (see e.g. abstract). Further, just knowing the structure of the protein is also insufficient for prediction of functional sites (see e.g. abstract). Sequence to function methods cannot specifically identify complexities for proteins, such as gain and loss of function during evolution, or multiple functions possible within a cells (see e.g. page 34, right column). Skolnick advocates determining the structure of the protein, then identifying the functionally important residues since using the chemical structure to identify functional sites is more in line with how a protein actually works (see e.g. page 34, right column).
The sensitivity of proteins to alterations of even a single amino acid in a sequence are exemplified by Burgess et al. (J. Cell Biol. 111:2129-2138, 1990, in instant PTO-892) who teach that replacement of a single lysine reside at position 118 of acidic fibroblast growth factor by glutamic acid led to the substantial loss of heparin binding, receptor binding and biological activity of the protein and by Lazar et al. (Mol. Cell. Biol., 8:1247-1252, 1988, in instant PTO-892) who teach that in transforming growth factor alpha, replacement of aspartic acid at position 47 with alanine or asparagine did not affect biological activity while replacement with serine or glutamic acid sharply reduced the biological activity of the mitogen. These references demonstrate that even a single amino acid substitution will often dramatically affect the biological activity and characteristics of a protein.
Further, Miosge (Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):E5189-98, in instant PTO-892) teach that short of mutational studies of all possible amino acid substitutions for a protein, coupled with comprehensive functional assays, the sheer number and diversity of missense mutations that are possible for proteins means that their functional importance must presently be addressed primarily by computational inference (see e.g. page E5189, left column). However, in a study examining some of these methods, Miosge shows that there is potential for incorrect calling of mutations (see e.g. page E5196, left column, top paragraph). The authors conclude that the discordance between predicted and actual effect of missense mutations creates the potential for many false conclusions in clinical settings where sequencing is performed to detect disease-causing mutations (see e.g. page E5195, right column, last paragraph). The findings in their study show underscore the importance of interpreting variation by direct experimental measurement of the consequences of a candidate mutation, using as sensitive and specific an assay as possible (see e.g. page E5197, left column, top paragraph). Additionally, Bork (Genome Research, 2000,10:398-400, in instant PTO-892) clearly teaches the pitfalls associated with comparative sequence analysis for predicting protein function because of the known error margins for high-throughput computational methods. Bork specifically teaches that computational sequence analysis is far from perfect, despite the fact that sequencing itself is highly automated and accurate (p. 398, column 1). One of the reasons for the inaccuracy is that the quality of data in public sequence databases is still insufficient. This is particularly true for data on protein function. Protein function is context dependent, and both molecular and cellular aspects have to be considered (p. 398, column 2). Conclusions from the comparison analysis are often stretched with regard to protein products (p. 398, column 3). Further, although gene annotation via sequence database searches is already a routine job, even here the error rate is considerable (p. 399, column 2). Most features predicted with an accuracy of greater than 70% are of structural nature and, at best, only indirectly imply a certain functionality (see legend for table 1, page 399). As more sequences are added and as errors accumulate and propagate it becomes more difficult to infer correct function from the many possibilities revealed by database search (p. 399, paragraph bridging columns 2 and 3). The reference finally cautions that although the current methods seem to capture important features and explain general trends, 30% of those features are missing or predicted wrongly. This has to be kept in mind when processing the results further (p. 400, paragraph bridging cols 1 and 2).
One key issue is the prediction of protein function based on sequence similarity, which could be one way to identify the functional proteins that are useful in the instant claims. Kulmanov et al (Bioinformatics, 34(4), 2018, 660–668, in instant PTO-892), teach that there are key challenges for protein function prediction methods (see e.g. page 661, left column). These challenges arise from the difficulty identifying and accounting for the complex relationship between protein sequence structure and function (see e.g. page 661, left column). Despite significant progress in the past years in protein structure prediction, it still requires large efforts to predict protein structure with sufficient quality to be useful in function prediction (see e.g. page 661, left column). Another challenge is that proteins do not function in isolation. In particular higher level physiological functions that go beyond simple molecular interactions will require other proteins and cannot usually be predicted by considering a single protein in isolation (see e.g. page 661, left column). Due to these challenges it is not obvious what kinds of features should be used to predict the functions of a protein and whether they can be generated efficiently for a large number of proteins, such as the vast genus of proteins encompassed by the instant claims (see e.g. page 661, left column).
Additionally, Fenton (Rheostat positions: A new classification of protein positions relevant to pharmacogenomics, 2020, Medicinal Chemistry Research, Volume 29, Pages 1133-1146, in instant PTO-892) teaches that while it is well known that most substitutions at conserved amino acid positions (which they call “toggle” switches) abolish function, it is also true that substitutions at non-conserved positions (which they call “rheostat” positions) are equally capable of affecting protein function [see Abstract]. Fenton further concludes that substitutions at some positions have highly unpredictable outcomes on the activities and specificities of protein-based drugs [see page 1144, left column, third paragraph]. Furthermore, when multiple mutations are introduced, there is even less predictability. For evidence thereof, see Guo (Protein tolerance to random amino acid change, 2004, PNAS, Volume 101, Number 25, Pages 9205-9210, in instant PTO-892), who teaches that the effects of mutations on protein function are largely additive [page 9207, left column, full paragraph 2]. Fenton, as cited above, also acknowledges this [see Abstract]. Further, changes in the primary amino acid sequence of a mammalian protein can have unpredictable effects on the ability of the resulting variant protein to fold properly after recombinant expression. See Domingues (U.S. 7,112,660 B2, in instant PTO-892) and Sailer (US 2003/0045474 A1, in instant PTO-892). This is further evidence of the lack of correlation between structure and function in the cytokine protein families. Thus, it is clear that the structure of variants of IL-15 do not predictably correlate with the function thereof.
Given the teachings of these references that point out the limitations and pitfalls of using sequence to predict functions, and the lack of a representative number of species across the breadth of the genus, one of skill in the art would reasonably conclude that only the IL-15 variants of SEQ ID NO: 320, 326, and 332 and listed proproteins in instant specification, but not the full breadth of the claims, meet the written description provision of 35 USC 112(a).
MPEP § 2163.02 states, “[a]n objective standard for determining compliance with the written description requirement is, 'does the description clearly allow person of ordinary skill in the art to recognize that he or she invented what is claimed’”. The courts have decided: the purpose of the "written description" requirement is broader than to merely explain how to "make and use"; the Applicant must convey with reasonable clarity to those skilled in the art, that as of the filing date sought, he or she was in possession of the invention. The invention is for purposes of the “written description” inquiry, whatever is now claimed. See Vas-Cath, Inc v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Federal Circuit, 1991).
Furthermore, the written description provision of 35 USC §112 is severable from its enablement provision; and adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method for isolating it. Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993). And Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016. Moreover, an adequate written description of the claimed invention must include sufficient description of at least a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics sufficient to show that Applicant was in possession of the claimed genus. However, factual evidence of an actual reduction to practice has not been disclosed by Applicant in the specification; nor has Applicant shown the invention was “ready for patenting” by disclosure of drawings or structural chemical formulas that show that the invention was complete; nor has the Applicant described distinguishing identifying characteristics sufficient to show that Applicant were in possession of the claimed invention at the time the application was filed.
Therefore for all these reasons the specification lacks adequate written description, and one of skill in the art cannot reasonably conclude that Applicant had possession of the claimed invention at the time the instant application was filed.
Response to Arguments
Applicant's arguments filed 12/29/2025 have been fully considered but they are not persuasive.
Applicant argues the amendments to the claims to define the amino acid sequence of the activatable proprotein as “having at least 90% identity to SEQ ID NO: 320, 326, or 332” is supported by a representative number of species and an art-recognized structure-function correlation regarding the claimed structures. This is not found persuasive.
While Applicant has amended the claims to now recite specific sequences which help to describe the structural components of the activatable proprotein, the claims still fail to satisfy the written description requirement. They fail to satisfy the written description requirement because the claim language as written allows for up to 10% of the claimed sequences to be modified, with no restrictions on where the modifications can occur or what they can be. Given the length of the amino acid of the proprotein, this allows for up to 40 amino acids that could be modified and still read on the instant claim language. Applicant has provided a list in the instant specification regarding the various proteins that have been identified as being modified from the base sequences of SEQ ID NO: 320, 326, or 326; however, the instant claims do not reflect this much narrower list as they encompass a much broader genus than is supported in the instant specification. Applicant is encouraged to recite the identified proproteins from the specification in the instant claims to obviate the instant rejection.
Thus, the rejection has been modified to address the remaining deficiencies of the newly amended claims.
New Rejections
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 1, 10-11, 14, 16, 21, 25, 29-36, and 38 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the IL-15 polypeptides comprising SEQ ID NO: 320, 326, 332 and identified proproteins in the instant specification, does not reasonably provide enablement for all IL-15 polypeptide variants with the claimed percentage modifications. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
MPEP § 2164.01 states:
The standard for determining whether the specification meets the enablement requirement was cast in the Supreme Court decision of Mineral Separation v. Hyde, 242 U.S. 261, 270 (1916) which postured the question: is the experimentation needed to practice the invention undue or unreasonable? That standard is still the one to be applied. In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988). Accordingly, even though the statute does not use the term “undue experimentation,” it has been interpreted to require that the claimed invention be enabled so that any person skilled in the art can make and use the invention without undue experimentation. In re Wands, 858 F.2d at 737, 8 USPQ2d at 1404 (Fed. Cir. 1988).
There are many factors to be considered when determining whether there is sufficient evidence to support a determination that a disclosure does not satisfy the enablement requirement and whether any necessary experimentation is “undue.” These factors include but are not limited to:
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The breadth of the claims;
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The nature of the invention;
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The state of the prior art;
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The level of one of ordinary skill;
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The level of predictability in the art;
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The amount of direction provided by the inventor;
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The existence of working examples; and
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The quantity of experimentation needed to make or use the invention based on the content of the disclosure.
In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988). The factors most relevant to this rejection are 1) the amount of direction provided by the inventor, 2) the existence of working examples, and 3) undue experimentation. In the instant case, the amount of direction provided by the inventor, undue experimentation, and existence of working examples disclosed in the specification, as filed, would not be sufficient to enable the skilled artisan to make and/or use the claimed invention at the time the application was filed without undue experimentation.
(1) The amount of direction provided by the inventor - The amount of guidance or direction needed to enable an invention is inversely related to the amount of knowledge in the state of the art as well as the predictability in the art. In re Fisher, 427 F.2d 833, 839, 166 USPQ 18, 24 (CCPA 1970). The “amount of guidance or direction” refers to that information in the application, as originally filed, that teaches exactly how to make or use the invention. The more that is known in the prior art about the nature of the invention, how to make, and how to use the invention, and the more predictable the art is, the less information needs to be explicitly stated in the specification. In contrast if little is known in the prior art about the nature of the invention and the art is unpredictable, the specification would need more detail as to how to make and use the invention in order to be enabling. See, e.g., Chiron Corp. v. Genentech Inc., 363 F.3d 1247, 1254, 70 USPQ2d 1321, 1326 (Fed. Cir. 2004). Due to the high level of unpredictability in treating polypeptide binding and functions, the skilled artisan would need significant guidance in preparing an activatable proprotein with a specific, targeted function. The skilled artisan recognizes that protein binding and cancer treatments are a wildly unpredictable endeavor that requires specificity in structure when targeting antigens or proteins. Without a proper structure provided by the Applicant for the invention(s), it is nearly impossible to envision and recognize all the potential structures amongst all potential possibilities of variant proproteins that would have a structure capable of binding, in addition to possessing the functionality needed to access it as a treatment.
(2) The existence of working examples - As stated above the specification reasonably provides enablement for proprotein that are defined by various sequences and names, such as those in SEQ ID NO: 320, 326, 332, or explicitly named proteins such as P1393, P1394, P1395, etc.; however, there is no showing in the specification of any means by which one skilled in the art could prepare any variant proprotein with 90% sequence identity to the reference sequence of a proprotein against IL-15. Applicant provides some description and examples in the instant specification of sequences with the claimed embodiments SEQ ID NO: 320, 326, and 332, but falls short to provide support for the sheer number of polypeptides that are encompassed by the broad language of the instant claims that can achieve the claimed function given that their structures have not been defined. Therefore, one skilled in the art would be subject to undue experimentation to practice the instant invention as it is currently claimed.
(3) Undue experimentation – The instant claims cover a large number of unknown and undefined variant proproteins specific for IL-15 as long as they are capable of performing the claimed function. Further, these claimed variant polypeptide encompass any possible future discoveries of any factors and variants with the claimed functions. When claims depend on a recited property (reducing binding to particular domain(s)), a fact situation comparable to Hyatt is possible, where the claim covers every conceivable structure (means) for achieving the stated property (result) while the specification discloses at most only those known to the inventor. See also Fiers v. Sugano, 984 F.2d 164, 25 USPQ2d 1601 (Fed. Cir. 1993) and MPEP §2164.08(a). Therefore, the specification fails to provide enough guidance for one skilled in the art on how to practice the instant method except for the instant Examples, thereby requiring trial and error experimentation to identify polypeptides meeting the functional limitations of the claims.
As set forth above, inadequate guidance is presented in the specification to overcome the obstacles in practicing the claimed invention in its full scope. The test of enablement is not whether any experimentation is necessary, but whether, if experimentation is necessary, it is undue. Given the tremendous breath of scope involving the instant claims, it would require undue experimentation for one of skill in the art to practice the claimed invention in its full scope. Therefore, the specification fails to provide enough guidance for one skilled in the art on how to practice the instant method, thereby requiring trial and error experimentation to identify antibodies or recombinant proteins meeting the functional limitations of the claims. The general knowledge and level of skill in the art do not supplement the omitted description because specific, not general, guidance is what is needed.
In conclusion upon careful consideration of the Wands factors that are used to determine whether undue experimentation is required to practice an invention, the amount of direction provided by the inventor, undue experimentation, and the working examples provided, as filed, is not deemed sufficient to enable the skilled artisan to make and/or use the invention commensurate in scope with the instant claims at the time the application was filed without undue experimentation.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SELAM BERHANE whose telephone number is (571)272-6138. The examiner can normally be reached Monday - Friday, 9-5.
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/SELAM BERHANE/Examiner, Art Unit 1675
/AURORA M FONTAINHAS/Primary Examiner, Art Unit 1675