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 .
Election/Restrictions
Applicant's election with traverse of Group I in the reply filed on 09 July 2026 is acknowledged. The traversal is on the ground(s) that:
(1) claims 1 and 16 are overlapping in scope and fall under a single inventive concept of preparing compositions for amelioration of skin-associated autoimmune inflammatory diseases and a composition for microbiome-based amelioration (Applicant’s remarks at pg. 19, para. 4 to 8);
(2) amended claim 16 comprises similar scope and similar technical features as claim 1, which require the technical feature of a composition comprising microbes, compounds, anti-sense RNA sequences, or antimicrobials (Applicant’s remarks at pg. 20, para. 1); and
(3) amended claim 16 includes a special technical feature of “The first composition is configured to perform one or more of: promoting growth…., reducing the abundance…, or managing an amplified state…” and “the second composition is configured to perform one or more of: promoting the growth…”, and “the third composition is configured to perform one or more of: managing the amplified state…” (Applicant’s remarks at pg. 20, para. 2 to pg. 22, para. 5).
This is not found persuasive because: claims 1 and 16 lack unity of invention because they do not share a corresponding technical feature. Claim 1 does not require the first, second, or third composition because each of these limitations are contingent upon a ratio being more than one, which is not required by the claims. See MPEP 2111.04 II. Furthermore, even if the first, second, or third composition was required, this shared technical feature between claim 1 and 16 is known in the art. Regardless, while Applicant states the technical feature of claim 16 is the first, second, and third compositions, claim 16 only requires “the composition comprises one…of a first composition, a second composition or a third composition”, but not all three compositions. Balato discloses antibiotics that target S. aureus used for topical inflammatory disease treatment (i.e. an antimicrobial configured to reduce the abundance of salvage microbes through antibiotics that target a salving microbe from the third list) (pg. 11, col. 1, para. 2; pg. 12, col. 1, para. 2, e.g. most common treatment against S. aureus infections is topical and oral antibiotics; Table 2). Furthermore, Abelson et al. (MRSA: It’s Not Just Resistant to Methicillin, 2008, Review of Opthalmology, pg. 1-6) also discloses various antibiotics that inhibit Staphylococcus aureus (pg. 1, para. 1; pg. 4, para. 5-7), which shows the first composition as claimed.
Therefore, at least the first composition is not a special technical feature.
The requirement is still deemed proper and is therefore made FINAL.
Claims 16 and 18-22 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. Applicant timely traversed the restriction (election) requirement in the reply filed on 09 July 2026.
Status of Claims
Claims 4, 15, 17, and 23-25 are cancelled.
Claims 1-3, 5-14, 16, and 18-22 are pending.
Claims 16 and 18-22 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.
Claims 1-3 and 5-14 are rejected.
Claims 1, 3, and 5 are objected to.
Priority
Applicant’s claim for the benefit of a prior-filed application, PCT/IB2021/050717 filed 29 Jan. 2021, under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Acknowledgment is made of applicant’s claim for foreign priority to IN202021004025 filed 29 Jan. 2020 under 35 U.S.C. 119 (a)-(d). Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Accordingly, the effective filing date of the claimed invention is 29 Jan. 2020
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because it does not contain a "Sequence Listing" as a separate part of the disclosure or a CRF of the “Sequence Listing.”. The application contains an amino acid sequence requiring a sequence listing in the specification in at least para. [0055] and [0069] as published.
Required response - Applicant must provide:
A "Sequence Listing" part of the disclosure; together with
An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(a)(2);
A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.821(a)(4); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(a)(3).
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
If the "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, applicant must also provide:
A CRF in accordance with 37 CFR 1.821(e)(1) or 1.821(e)(2) as required by 1.825(a)(5); and
A statement according to item 2) a) or b) above.
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification at para. [0055] and [0069] as published are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Drawings
The drawings filed 29 July 2022 are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: #300 in FIG. 2B
Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
Applicant is reminded of the proper content of an abstract of the disclosure.
A patent abstract is a concise statement of the technical disclosure of the patent and should include that which is new in the art to which the invention pertains. The abstract should not refer to purported merits or speculative applications of the invention and should not compare the invention with the prior art.
If the patent is of a basic nature, the entire technical disclosure may be new in the art, and the abstract should be directed to the entire disclosure. If the patent is in the nature of an improvement in an old apparatus, process, product, or composition, the abstract should include the technical disclosure of the improvement. The abstract should also mention by way of example any preferred modifications or alternatives.
Where applicable, the abstract should include the following: (1) if a machine or apparatus, its organization and operation; (2) if an article, its method of making; (3) if a chemical compound, its identity and use; (4) if a mixture, its ingredients; (5) if a process, the steps.
Extensive mechanical and design details of an apparatus should not be included in the abstract. The abstract should be in narrative form and generally limited to a single paragraph within the range of 50 to 150 words in length.
See MPEP § 608.01(b) for guidelines for the preparation of patent abstracts.
The abstract of the disclosure is objected to because:
The abstract refers to the purported merits of the invention in the first sentence of the abstract, which should be removed.
A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Claim Objections
Claims 1, 3, and 5 are objected to because of the following informalities:
Claim 1 recites “obtaining microbial sequencing data by performing microbiome sequencing of: the extracted microbial DNA…, or the extracted microbial DNA…”. Where a claim sets forth a plurality of elements or steps, each element or step of the claim should be separated by a line indentation, 37 CFR 1.75(i). There may be plural indentations to further segregate subcombinations or related steps. See MPEP 608.01(m). The limitations of “the extracted microbial DNA…, or the extracted microbial DNA…” should be indented further relative to the “obtaining microbial sequence data” step to increase readability.
Claim 1 recites “computing…a third ratio…from healthy skin site…from lesion skin site”, which is a grammatical error because an article is missing from each skin site, and the claim should be amended to recite “the healthy skin site” and “the lesion skin site”.
Claim 3 recites “enlisting…the plurality of skin inhabiting microbes and microbes capable of inhabiting skin are determined using…”, which is nonsensical, and should be amended to recite “…enlisting.. inhabiting skin using one or more of…”.
Claim 3 recites “deriving…a specific pathway…constituting the pathway…”, which should be amended to recite “…constituting the specific pathway” to increase clarity and use consistent language.
Claim 5 recites “wherein the first composition, the second composition and the third composition is applied”, which is a grammatical error and should recite “are applied”.
Appropriate correction is required.
Claim Interpretation
Claim 1 recites “administering a first composition to the person if the first ratio is less than one..; administering a second composition if the second ratio is more than one…; and administering a third composition if the third ratio is less than 1…”, which are contingent limitations. Each administering step is contingent upon a condition being met (i.e. the first ratio being less than one, the second ratio being more than one, or the third ratio being less than one), and the claims do not require that any of these condition precedents are met. Therefore, under the broadest reasonable interpretation of the claims, none of the administration steps are required by the claims. See MPEP 2111.04 II.
Claim 3 recites “wherein the microbes enlisted in the first list, the second list…, and the sixth list are identified through following steps: enlisting…”. The process in which the microbes were enlisted in the various lists is interpreted as a product by process limitation. However, the claim does not require a step of enlisting the microbes into the various lists. See MPEP 2113 I. [E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process." In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985) (citations omitted)
Claim Rejections - 35 USC § 112(b)
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.
Claims 1-3 and 5-14 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “the extracted microbial DNA corresponding to the subset of the plurality of microbes harboring one or more of pathways which are involved in biosynthesis of lipoic acid and upregulation…”. There is insufficient antecedent basis for “the subset of the plurality of microbes harboring one or more of pathways…” because claim 1 previously only recites “the extracted microbial DNA corresponds to genetic material extracted from… a subset of the plurality of microbes inhabiting on the skin of the person”, but does not require the subset harbors the recited one or more pathways.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “wherein the subset of the plurality of microbes mentioned in a first list, a second list…, and a sixth list”. Due to a grammatical error in the claims, it is not clear if the claim is intended to recite “wherein the subset… is mentioned in a first list…, and a sixth list…”, or if the claim intends to be referring to some other subset of the plurality of microbes mentioned in a first through sixth list (in which case there is a lack of antecedent basis for this subset in the claims). If Applicant intends the former, the limiting effect of the wherein clause on the subset of the plurality of microbes is further unclear because it is not clear if the limitation is merely defining the process in which the subset of microbes were previously determined (i.e. being obtained from the lists) or if the limitation intends to impart some physical requirement or characteristic of the microbes. Clarification is requested via claim amendment. For purpose of examination, the limitation regarding the subset of microbes being “mentioned” in the recited lists, is interpreted to define the process in which the subset was previously determined. Dependent claims 2 and 10-14 further limit the various lists. However, these claims only serve to further limit the lists for which the subset of microbes is also mentioned in, but these claims do not require that the subset of microbes themselves contain any of the microbes in the lists. If Applicant intends for the subset of microbes to be specific microbes in the list, the claims should be amended accordingly (e.g. “wherein the subset of the plurality of microbes are selected from…”, or a similar limitation).
Claim 1, and claims dependent therefrom, are indefinite for recitation of “the one or more hardware processors…” in the last limitation on pg. 2 of the claims. There is insufficient antecedent basis for this limitation in the claim because claim 1 does not previously recite any hardware processor(s).
Claim 1, and claims dependent therefrom, are indefinite for recitation of “generating…microbiome taxonomic profiles….wherein the microbiome taxonomic profiles indicate….a relative abundance of each of the plurality of microbes inhabiting the lesional skin site or the healthy skin site…”. However, claim 1 had previously recited “extracting microbial DNA…., wherein the extracted microbial DNA corresponds to genetic material extracted from a plurality of microbes or a subset of the plurality of microbes inhabiting on the skin of the person”. The sequencing data of claim 1 also recites that the sequencing data is for the plurality of microbes or the subset. As a result, it is not clear if claim 1 intends to require that microbial DNA of the plurality of microbes is extracted and analyzed (as suggested by the generating microbiome taxonomic profiles limitation) or if claim 1 can only analyze a subset of the plurality. If Applicant intends the latter, it is further not clear if the microbiome profile can include abundances for each microbe of the subset of microbes. Clarification is requested.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “computing a…a first ratio…of the subset of the plurality of microbes within the microbiome taxonomic profile from the lesional skin site harboring one or more pathways involved in lipoic acid biosynthesis…” and “the subset of the plurality of microbes within the microbiome taxonomic profile from the lesional skin site harboring one or more pathways involved in upregulation of lipoic acid salvage” in the first limitation on pg. 3. There is insufficient antecedent basis for these limitations in the claim because claim 1 previously recites “the extracted microbial DNA corresponding to the subset of the plurality of microbes harboring one or more pathways which are involved in biosynthesis of lipoic acid and upregulation of lipoid acid salvage” (i.e. a single subset of microbes harboring a pathway(s) for both lipoid acid biosynthesis and the upregulation from the plurality of microbes). However, claim 1 does not recite two separate subsets of the plurality of microbes, one being a subset comprising pathway(s) involved in lipoic acid biosynthesis and another being a subset comprising pathway(s) involved in upregulation of lipoid acid salvage. Therefore, it is not clear if these are supposed to be the same or different subsets. If Applicant intends for these subsets to all be the same, it is further unclear in what way a comparison between subsets can be performed because all microbes of the subset having pathways for lipoid acid biosynthesis would also have pathways for lipoic acid salvage, and thus the comparison would be with itself.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “computing…a second ratio…of the subset of the plurality of microbes within the microbiome taxonomic profile from the healthy skin site harboring one or more pathways involved in lipoic acid biosynthesis…” and “the subset of the plurality of microbes within the microbiome taxonomic profile from the lesional skin site harboring the same pathways in lipoid acid biosynthesis” in the second limitation on pg. 3 for the same reasons discussed above. That is, there is insufficient antecedent basis for these limitations in the claim because claim 1 previously recites “the extracted microbial DNA corresponding to the subset of the plurality of microbes harboring one or more pathways which are involved in biosynthesis of lipoic acid and upregulation of lipoid acid salvage” (i.e. a single subset of microbes harboring a pathway(s) for both lipoid acid biosynthesis and the upregulation from the plurality of microbes). So its not clear if these are the same or different subsets. Furthermore, it is not clear what pathways “the same pathways” in lipoic acid synthesis are referring to, given the claim does not specify what the pathways are the same as.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “…computing…a third ratio of relative abundances of subset of the plurality of microbes within the microbiome taxonomic profile from healthy skin site harboring one or more pathways in upregulation of lipoic acid salvage” and “subset of the plurality of microbes within the microbiome taxonomic profile from lesion skin site harboring the same pathways in upregulation of lipoic acid salvage”. First, due to a grammatical error in the claims, this limitation is missing an article before each recitation of “subset”, and therefore it is not clear if this is intended to be a new subset (i.e. a subset…) or refer to a previously recited subset (i.e. the subset). Furthermore, there is insufficient antecedent basis for these limitations in the claim because claim 1 previously recites “the extracted microbial DNA corresponding to the subset of the plurality of microbes harboring one or more pathways which are involved in biosynthesis of lipoic acid and upregulation of lipoid acid salvage” (i.e. a single subset of microbes harboring a pathway(s) for both lipoid acid biosynthesis and the upregulation from the plurality of microbes). So it is not clear if these are the same or different subsets. Furthermore, it is not clear what pathways “the same pathways” in upregulation of lipoic acid salvage are referring to, given the claim does not specify what the pathways are the same as.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “to decide whether the microbe synthesizes…” in the last two lines of the third limitation on pg. 3. Claim 1 previously recites “the plurality of microbes” and therefore it is not clear which microbe “the microbe” is referring to.
Claims 1, and claims dependent therefrom, are indefinite because the metes and bounds of each of the first and third compositions are not clear. A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 1 recites the broad recitation “wherein the first composition comprises one or more of: one or more microbes…; one or more compounds inducing favorable physical and chemical factors, anti-sense RNA sequences, or antimicrobials, and the claim then later recites (1) “wherein the first composition is configured to perform one or more of: promoting growth…through favorable physical factors and by administration of one or more probiotic non-pathogenic microbes…” (i.e. compounds inducing favorable factors and microbes) and (2) “reducing the abundance…through competing microbes and antibiotics…” (i.e. both microbes and antibiotics) which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. For example, it is not clear if the first composition may comprise only antimicrobials, or if the first composition is required to include both antimicrobials and microbes (as suggested by the “reducing the abundance…” limitation). Furthermore, due to the claims further limiting the first composition using functional language, rather than describing what the composition is (i.e. “configured to perform one or more of:”, it is not clear of the limitations “through favorable physical factors and by administration of one or more probiotic…microbes” and “through competing microbes and antibiotics” is intended to (1) require the composition itself comprises these elements (e.g. both compounds and microbes or both microbes and antibiotics, respectively), or (2) if the composition is merely required to affect “competing microbes” but is not required to include competing microbes, for example. The third composition similarly broadly recites the composition may comprise microbes, compounds, or antimicrobials, but then later recites the third composition is configured to perform various functions of “managing the amplified state…through competing microbes and antibiotics…”. Overall, the metes and bounds of the first and third compositions are not clear. For purpose of examination, the first and third compositions are required to include only one (or more) of the recited elements of the composition that are configured to perform the recited functions (e.g. antibiotics that reduce the abundance of salvage microbes reads on the composition of claim 1).
Claim 1, and claims dependent therefrom, are indefinite for recitation of “favorable physical and chemical factors” at the third from last line on pg. 3 and line 5 of pg. 5, and “favorable physical factors” in line 3 of pg. 4 and the 4th from the last line on pg. 4. The term “favorable” in claim 1 is a relative term which renders the claim indefinite. The term favorable is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “the salvage pathway as enlisted in the first list and the second list”. There is insufficient antecedent basis for this limitation in the claim because claim 1 does not previously recite a salvage pathway enlisted in the first and second list.
Claim 1, and claims dependent therefrom, recite “wherein the inhibiting factors ensure…” on line 13 of pg. 5. Claim 1 previously recites “inhibiting factors” in the fifth limitation on pg. 4 and on the 6th limitation of pg. 5. Therefore it is not clear which inhibiting factors “the inhibiting factors” on line 13 of pg. 5 is referring to, or if these are all intended to be the same inhibiting factors.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “competing microbes against microbes enlisted” regarding the third composition…”. The term “competing” is a relative term which renders the claim indefinite. The term is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. As a result, it is not clear what microbes would be considered to “compete” against the enlisted microbes. For example, given any microbe require water for survival, any microbe could be considered to “compete” with another microbe. As a result, it is not clear what level of competition is required for a microbe to be considered a “competing microbe”. Clarification is requested via claim amendment.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “one or more of microbes enlisted in the first list and the second list as probiotic”, “microbes harboring lipoid acid biosynthetic pathways enlisted in the first and second list”, “microbes involved in upregulation of lipoic acid salvage as enlisted in the third list”, “inhibiting factors enlisted in a seventh list”, “microbes enlisted in the fourth list and the fifth list and the sixth list..”, “microbes harboring lipoic acid pathway and lacking the salvage pathway as enlisted in the first and second list”, “promoting the abundance of microbes enlisted in the first list and the second list”, “microbes against microbes enlisted in the third list, the fourth list, and the fifth list”, “target salvaging microbes enlisted in the third list”. Overall claim 1 attempts to further limit various microbes based on their enlistment in various lists. However, claim 1 had only previously recited “the subset of the plurality of microbes [is] mentioned in a first list, a second list, a third list, a fourth list, a fifth list, and a sixth list”, but provides no indications what these lists pertain to and/or the microbes contained in each list. As a result, it is unclear what microbes are being referenced when reference “microbes…enlisted in the…list”. For example, does “microbes against microbes enlisted in the third list” encompass any microbe that can target another microbe, or does “microbes enlisted in the third list” further limit what type of microbes are being targeted in some way. Overall, the metes and bounds of the claim are unclear because the contents of the lists are not described in the claim, and as a result, one of ordinary skill in the art cannot ascertain which microbes may be a part of any given list and resultingly, it is further unclear what the various first, second, and third compositions actually are, given they are functionally defined with respect to these lists. Claim 2 does serve to further clarify what microbes are part of the various lists, and therefore is not indefinite for the reason set forth above pertaining to claim 1. However, it is noted that even claim 2 is indefinite for the reasons set forth below.
Claim 2 is indefinite for recitation of “non-pathogenic microbes capable of thriving on skin…”. The term “thriving” is a relative term which renders the claim indefinite. The term “thriving” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. As a result, it is not clear which microbes would be considered “thriving” versus merely growing or surviving.
Claim 2 is indefinite for recitation of “the third list is a set of pathogenic salvage microbes which can be targeted by antibiotics…”. Notwithstanding the permissible instances, the use of functional language in a claim may fail "to provide a clear-cut indication of the scope of the subject matter embraced by the claim" and thus be indefinite. In re Swinehart, 439 F.2d 210, 213 (CCPA 1971). The metes and bounds of what microbes are intended to be encompassed by the third list is unclear because the metes and bounds of which microbes can versus cannot be targeted by antibiotics is not clear. First, the scope of which microbes with antibiotics that target them varies with time. For example, if at the time of the effective filing date, an antibiotic for a given microbe does not exist, but later an antibiotic is developed, it is unclear if this microbe could be included in the third list or not. Furthermore, theoretically, every microbe could be targeted by an antibiotic, even if antibiotics to particular strains have yet to be developed by humans. This further raises confusion regarding the limiting effect of “can be targeted by antibiotics” and which microbes are intended to be encompassed by the claim.
Claim 3 is indefinite for recitation of “the plurality of skin inhabiting microbes and microbes capable of inhabiting skin”. There is insufficient antecedent basis for this limitation in the claim because claim 1 does not previously recite a plurality of skin inhabiting microbes and microbes capable of inhabiting skin.
Claim 3 is indefinite for recitation of “the enlisted plurality of microbes”. Claim 1, from which claim 3 depends, recites various microbes enlisted in different lists as outlined above for claim 1, including “one or more of microbes enlisted in the first list and the second list as probiotic”, “microbes harboring lipoid acid biosynthetic pathways enlisted in the first and second list”, etc. Claim 3 also recites “enlisting…the plurality of skin inhabiting microbes”. As a result it is unclear which set of enlisted microbes, “the enlisted plurality of microbes” is referring to.
Claim 3 is indefinite for recitation of “the enlisted genome”. Claim 3 previously recites “individual enlisted genomes” and therefore it is not clear which enlisted genome is being referenced.
Claim 3 is indefinite for recitation of “the microbes which are involved in different branch points of lipoic acid metabolism…”. There is insufficient antecedent basis for this limitation in the claim because claim 3 does not previously recite microbes which are involved in different branch points.
Claim 3 is indefinite for recitation of “…wherein the mentioned branch point definitions refer to a capability…capability…capability…”. Due to a grammatical error in the claims, it is not clear if the claim should read, “capability…capability…or capability” or “capability…capability…and capability”.
Claim 3 is indefinite for recitation of “the lipoic acid pathway” and “ the pathway” in the last limitation. Claim 1, from which claim 3 depends recites “one or more pathways involved in lipoic acid biosynthesis and upregulation of lipoic acid salvage”, “one or more pathways involved in lipoic acid biosynthesis” and “one or more pathways involved in upregulation of lipoic acid salvage”, and therefore it is not clear which lipoic acid pathway or pathway is being referenced.
Claim 5, and claims dependent therefrom, are indefinite for recitation of “wherein the plurality of skin-patches is employed for targeted delivery of the composition”. Claim 5 previously recites “wherein the first composition, the second composition and the third composition is applied in the form of…skin-patches”. Therefore it is not clear if “the composition” is referring to the first, second, or third composition, or if “the composition” is referring to all of the first, second, and third composition. For purpose of examination, the limitation is interpreted to mean “for targeted delivery of a composition”.
Claim 7 is indefinite for recitation of “the mosaic patch”. There is insufficient antecedent basis for this limitation in the claim because claim 5, from which claim 7 depends, does not recite a mosaic patch. It is noted that claim 6 does recite a mosaic patch.
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 1-3 and 5-14 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claim 1 being representative) is directed a method of preparing compositions. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claim 1 recites the following steps which fall under the mathematical concepts and/or mental processes groupings of abstract ideas:
wherein the subset of the plurality of microbes mentioned in a first list, a second list, a third list, a fourth list, a fifth list, and a sixth list;
generating…microbiome taxonomic profiles from the obtained microbial sequencing data, wherein the microbiome taxonomic profiles indicate one of an absolute abundance and a relative abundance of each of the plurality of microbes inhabiting the lesional skin site or the healthy skin site samples respectively;
computing… a first ratio of relative abundances of the subset of the plurality of microbes within the microbiome taxonomic profile from the lesional skin site harboring one or more pathways involved in lipoic acid biosynthesis to that of the subset of the plurality of microbes within the microbiome taxonomic profile from the lesional skin site harboring one or more pathways involved in upregulation of lipoic acid salvage;
computing….a second ratio of relative abundances of the subset of the plurality of microbes within the microbiome taxonomic profile from the healthy skin site harboring one or more pathways involved in lipoic acid biosynthesis to relative abundances of subset of the plurality of microbes within the microbiome taxonomic profile from the lesional skin site harboring the same pathways in lipoic acid biosynthesis;
computing….a third ratio of relative abundances of subset of the plurality of microbes within the microbiome taxonomic profile from healthy skin site harboring one or more pathways in upregulation of lipoic acid salvage to relative abundances of subset of the plurality of microbes within the microbiome taxonomic profile from lesion skin site harboring the same pathways in upregulation of lipoic acid salvage, wherein the subsets of the plurality of microbes for the first ratio, the second ratio and the third ratio are derived using a decision making system containing decisions defined by a unique combination of protein domains comprising one or more of LIAS_N, BPLplA_lipB, Lipprot_ligC and GCV (Glycine Cleavage Domain) protein domain to decide whether the microbe synthesizes, salvages or performs both salvage and synthesis functions;
The identified claim limitations falls into one of the groups of abstract ideas of mathematical concepts and/or mental processes, for the following reasons. First, assigning microbes to lists is a mental process of organizing information. Generating microbiome taxonomic profiles comprising absolute abundance and a relative abundance of each of the plurality of microbes can be practically performed in the mind by analyzing the sequencing data to determine read counts corresponding to particular microbes. The limitation further recites a mathematical concept because it amounts to a textual equivalent to performing mathematical calculations of division (e.g. determining a relative abundance). Furthermore, the steps of computing a first ratio, second ratio, and third ratio each recite a mental process and a mathematical concept because the human mind is practically able to divide two numbers and performing division is a mathematical calculation, respectively. That is, other than reciting the steps are carried out by a processor, nothing in the claims precludes the step from being practically performed in the mind. See MPEP 2106.04(a)(2) I and III.
Dependent claims 2-3 and 9-14 further recite an abstract idea and/or are part of the abstract idea identified above. Dependent claims 2 and 9-14 further limit the organizing of various microbes into lists, and thus is part of the abstract idea. Dependent claim 3 defines the process in which the microbes were previously enlisted into lists, and thus is part of the abstract idea of microbes assigned to lists in claim 1.
Claims 1-3 and 5-14 further recite the law of nature of the presence of various microbes on the skin of a person and a response to a composition (e.g. including antibiotics), analogous to the natural relationship between a patient’s CYP2D6 metabolizer genotype and the risk that the patient will suffer QTc prolongation after administration of a medication called iloperidone, Vanda Pharmaceuticals Inc. v. West-Ward Pharmaceuticals, 887 F.3d 1117, 1135-36, 126 USPQ2d 1266, 1281 (Fed. Cir. 2018).
Therefore, claims 1-3 and 5-14 recite an abstract idea and law of nature. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
Dependent claims 2-3 and 9-14 do not recite any elements in addition to the judicial exception and therefore are part of the judicial exception.
The additional elements of claim 1 further include:
one or more hardware processors;
collecting sample from a lesional skin site of the person;
collecting sample from a healthy skin site of the person; extracting microbial DNA from the collected healthy skin site and lesional skin site samples, wherein the extracted microbial DNA corresponds to genetic material extracted from a plurality of microbes or a subset of the plurality of microbes inhabiting on the skin of the person;
obtaining microbial sequence data by performing microbiome sequencing of: the extracted microbial DNA corresponding to the plurality of microbes of the person, or the extracted microbial DNA corresponding to the subset of the plurality of microbes harboring one or more of pathways which are involved in biosynthesis of lipoic acid and upregulation of lipoic acid salvage;
First, the additional element of the processors is a generic computer component that is merely used to carry out the abstract idea identified above. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See MPEP 2106.05(f).
The additional elements of collecting samples from a lesional and healthy skin site, and obtaining sequencing data by sequencing extracted microbial DNA from the samples only serves to collect information for use by the abstract idea, and therefore, amounts to insignificant extra-solution activity that does not provide integration. See MPEP 2106.05(g). Dependent claim 8 only serves to further limit the lesional skin site of the person to be from a person with atopic dermatitis, psoriasis, or eczema, and therefore is part of the data gathering of claim 1.
The additional elements of claim 1 further include:
administering a first composition to the person if the first ratio is less than one (including all wherein clauses further limiting the first composition);
administering a second composition if the second ratio is more than one (including all wherein clauses further limiting the second composition); and
administering a third composition if the third ratio is less than 1 (including all wherein clauses further limiting the third composition).
The additional elements of claims 5-7 include:
wherein the first composition, the second composition and the third composition is applied in the form of one or a plurality of skin- patches, wherein the plurality of skin-patches is employed for targeted delivery of the composition;
wherein a first patch out of the plurality of patches is a mosaic patch comprises of a synthetic acid mantle, lipoic acid based ointment and a chelating agent; and
wherein a second patch out of the plurality of patches is the mosaic patch comprises lipoic acid based ointment and an allosteric specific inhibitor, antisense-RNA placed on opposite corners of a square of the second patch.
The above additional elements of administering the first, the second, and the third composition, including dependent claims 5-7 which further limit the composition, is not sufficient to integrate the recited judicial exception into a practical application because the administration of a composition is not required by the claims. Each administering step is contingent upon a condition being met (i.e. the first ratio being less than one, the second ratio being more than one, or the third ratio being less than one), and the claims do not require that any of these condition precedents are met. Therefore the subsequent administering step is not required. See MPEP 2106.04(d)(2), stating Examiners should keep in mind that in order to qualify as a "treatment" or "prophylaxis" limitation for purposes of this consideration, the claim limitation in question must affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition. For example, a step of "prescribing a topical steroid to a patient with eczema" is not a positive limitation because it does not require that the steroid actually be used by or on the patient.
Therefore, the additionally recited elements amount to insignificant extra-solution activity and, as such, the claims as a whole do no integrate the abstract idea into practical application. Thus, claims 1-3 and 5-14 are directed to an abstract idea. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception for the following reasons.
Dependent claims 2-3 and 9-14 do not recite any elements in addition to the judicial exception and therefore are part of the judicial exception.
The additional elements of claims 1 and 5-8 are outlined above.
First, the additional element of the processors is a conventional computer component that is merely used to carry out the abstract idea identified above. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit).
The additional elements of collecting samples from a lesional and healthy skin site of a person with atopic dermatitis, psoriasis, or eczema, and obtaining sequencing data by sequencing extracted microbial DNA form the samples is well-understood, routine, and conventional. This position is supported by Applicant’s own specification and Bjerre et al. (The role of the skin microbiome in atopic dermatitis: a systematic review: 2017, British Journal of Dermatology, 177, pg. 1272-1278). First, Applicant’s own specification at para. [0028] discloses that any known technique for sample collection is within the scope of the disclosure. Furthermore, Bjerre reviews the role of the skin microbiome in patients with atopic dermatitis (pg. 1272 Summary), and discloses numerous case-control studies that analyze the microbiome composition of affected skin sites (i.e. a lesional skin site) compared to nonaffected skin sites (i.e. a healthy skin site) (pg. 1273, col. 2, para. 6). Bjerre further discloses that in these studies, the microbiome composition of skin samples was determined by sequencing extracted DNA from skin swabs, including 16S rRNA sequencing (pg. 1274, col. 1, para. 2).
Last, the additional element relating to administering the first, second, and third composition cannot provide significantly more because it is not required under the broadest reasonable interpretation of the claims.
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself. [Step 2B: NO]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea and/or law of nature without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
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.
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 1-3 and 5-14 are rejected under 35 U.S.C. 103 as being unpatentable over Apte (2017) in view of Bjerre (2017).
Cited references:
Apte et al., US 2017/022851 A1; cited on IDS filed 29 July 2022; and
Bjerre et al. (The role of the skin microbiome in atopic dermatitis: a systematic review: 2017, British Journal of Dermatology, 177, pg. 1272-1278).
Regarding claim 1, Apte discloses a method of characterizing skin conditions (Abstract), including eczema, psoriasis, or atopic dermatitis (Abstract; [0021]), comprising the following steps:
Apte discloses receiving a biological skin sample from a skin lesion of a user, using a sample kit ([0029, e.g. skin-fluids from a skin lesion]; [0091]; Figure 2).
Apte discloses collecting biological samples from a skin lesion from a population of users, which includes healthy users (i.e. samples from a healthy skin site) (Figure 1B; [0054])
Apte discloses performing sample processing on the biological sample by purifying DNA in the sample and then sequencing the DNA into microbiome datasets (i.e. extracting microbial DNA and obtaining microbial sequence data as claimed) ([0026]; [0037]).
Apte discloses determining microbiome composition and functional diversity features from the sequencing data ([0025]; Figure 2). Apte discloses a set of features for characterizations of eczema and/or other skin-related conditions can include features including and/or otherwise derived from one or more of the following taxa: Streptococcus genus (i.e. lipoic acid salvaging microbes, as evidenced by Applicant’s specification at [0046] and [0049]) and Corynebacterium genus (i.e. lipoic acid synthesis microbes, as evidenced by Applicant’s specification at ([0047]-[0048]), and/or any other suitable taxa ([0071];[0078]), which demonstrates the sequencing data includes sequencing data of a subset of microbes harboring pathways involved in biosynthesis of lipoic caid and upregulation of lipoic acid salvage).
Apte discloses Apte discloses determining microbiome composition and functional diversity features from the sequencing data (i.e. a microbiome profile) ([0025]; Figure 2), which comprises relative abundances of each group of taxa (i.e. each of the plurality of microbes inhabiting the lesional skin site and healthy samples) ([0036]).
Apte further discloses generating microbiome features describing the presence or absence of certain taxonomic groups of microorganisms and/or ratios between exhibited taxonomic groups in the lesion sample collected from the person ([0044]). Apte discloses these taxonomic groups include Streptococcus genus (i.e. lipoic acid salvaging microbes), Corynebacterium, and/or any other suitable taxa ([0071]; [0078]), demonstrating a ratio between Streptococcus genus (i.e. lipoic acid salvaging microbes) and Corynebacterium (i.e. lipoic acid synthesis microbes) in the lesion sample may be used as a feature.
Apte further discloses computing a ratio of the abundance of taxa in a sick user vs healthy user (i.e. ratios of the same taxa between a lesion and healthy subject) ([0054]). Apte discloses these taxa include Streptococcus genus (i.e. lipoic acid salvaging microbes), Corynebacterium, and/or any other suitable taxa ([0071]; [0078]), thus demonstrating a ratio of Streptococcus genus (i.e. lipoic acid salvaging microbes) between a lesion and healthy sample and a ratio of Corynebacterium (i.e. lipoic acid synthesis microbes) between a lesion and healthy sample can be determined.
Regarding the steps of administering a first composition, a second composition, and a third composition, these limitations are not required under the broadest reasonable interpretation of the claim because they are contingent limitations and the condition precedents are not met by the claims, as discussed in claim interpretation above.
Further regarding claim 1, Apte does not disclose the following limitations:
Apte does not disclose the sample of the healthy skin site is from the person for which the sample from the lesional skin site was collected, and instead discloses using DNA from skin samples of healthy subjects, as discussed above.
However, Bjerre reviews the role of the skin microbiome in patients with atopic dermatitis (pg. 1272 Summary), and discloses numerous case-control studies that either analyze the microbiome composition of affected skin sites (i.e. a lesional skin site) compared to nonaffected skin sites (i.e. a healthy skin site) or analyze the microbiome between affected individuals and control individuals (pg. 1273, col. 2, para. 6).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Apte to have collected a heathy skin sample from the person with the lesion, rather than using a healthy control user, as shown by Bjerre above. One of ordinary skill in the art would have been motivated to combine the methods of Apte and Bjerre based on the simple substitution of the healthy control user sample of Apte with the sample from the healthy skin site of the person with the lesion of Bjerre. One of ordinary skill in the art would have recognized that a healthy control from the same person could be used as the healthy reference and performed the same function of a control as the healthy control from a different user in Apte, particular given Bjerre discloses studies that use other separate people as healthy controls or healthy controls collected from the same diseased person, as discussed above.
Regarding claim 3, the wherein clause defining the process in which the microbes were enlisted in the various lists is a product by process limitation. However, the claim does not require a step of enlisting the microbes into the various lists. See MPEP 2113 I. [E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process." In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985) (citations omitted). Because the subset of microbes of Apte reads on the subset of microbes in claim 1, as presently interpreted in view of the 112(b) rejections, the product (microbes) of Apte are the same as those in claim 3.
Regarding claims 2 and 9-14, the claims only serve to further limit the first, second, third, fourth, fifth, sixth, and seventh lists. The process in which the subset of microbes was previously obtained (e.g. from the first through sixth lists) is a product by process limitation that only defines the process in which the subset of microbes was previously determined (e.g. being obtained from the recited lists. See the interpretation in the 112(b) rejection above Therefore, the subset of microbes of Apte is the same as the product of the subset of microbes of the claim, and thus Apte discloses these limitations for the first through sixth list. Further regarding the 7th list, this limitation only further limits the administered compositions, which is not required by the claims as discussed above.
Regarding claims 5-7, the claims further limit the administration steps, which are not required under the broadest reasonable interpretation of the claims as discussed above. Therefore, Apte discloses claims 5-7 for the same reasons as applied to claim 1 above.
Regarding claim 8, Apte discloses the skin associated auto-immune disease is eczema ([0059]).
Therefore the invention is prima facie obvious.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAITLYN L MINCHELLA whose telephone number is (571)272-6485. The examiner can normally be reached 7:00 - 4:00 M-Th.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685