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 .
Claims status
The amendment filed 04/17/2026 has been entered.
Claims 10, 11, and 18 remain withdrawn pursuant to a restriction requirement.
Claims 4 and 13 are cancelled.
Claim 19 is new.
Claims 2, 3, and 12 are amended.
Claims 2 and 3 are objected to.
Claims 5-9, 12, 14-17, and 19 are rejected.
Response to Amendment
Withdrawn Objections/Rejections
Claim Rejections - 35 USC § 112(b)
The previous rejections of claims 2 and 3 under 35 USC § 112(b) are withdrawn in response to Applicant’s amendments to the claims. The amendments removed the indefinite limitation.
Claim Rejections - 35 USC § 112(a) – Written Description
The previous rejections of claims 2 and 3 under 35 USC § 112(a) are withdrawn in response to Applicant’s amendments to the claims. The amendments removed the limitation without written description support.
Claim Rejections - 35 USC § 112(a) – Enablement – Biological Deposit
The previous rejections of claims 2 and 3 under 35 USC § 112(a) regarding the biological deposit are withdrawn in response to Applicant’s submission of the Declaration Regarding Biological Culture Deposits, filed 04/17/2026.
Maintained Objections/Rejections
Claim Objections
Applicant is advised that should claim 9 be found allowable, claim 14 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 4-9, 12, 14-17 are rejected under 35 U.S.C. 103 as being unpatentable over Ghannoum et al (WO2019173763A1, filed 03/08/2019, published 09/12/2019) as evidenced by Rupp et al (The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms, J Biotechnol. 2015 Oct 10;211:20-30, published 2015), in view of Ceugniez et al (Anti-Salmonella activity and probiotic trends of Kluyveromyces marxianus S-2-05 and Kluyveromyces lactis S-3-05 isolated from a French cheese, Tomme d' Orchies, Research in Microbiology 168 (2017) 575-582, published 2017).
Ghannoum et al teaches a method of treating and/or preventing (paragraph 193, treat is defined to include prevent) gastrointestinal inflammation and/or a disease, disorder or condition associated with gastrointestinal inflammation in a subject in need thereof, comprising administering a composition comprising an effective amount of non-pathogenic fungal strains to the subject ((IX) Method of Treating Gut Inflammation, (VI) Methods of disrupting biofilm and treatment, and Table 4), wherein exemplary fungal strains include Kluyveromyces lactis and Pichia jadinii (which is an older and synonymous name for Cyberlindnera jadinii, as evidenced by Rupp et al (Introduction paragraph 1)) (paragraphs 16 and 92), as is relevant to claim 12.
Claims 4-6 and 14-17 depend on claim 12. The teachings of the prior art regarding claim 12 are incorporated in its entirety here and further described below.
Ghannoum et al teaches the fungal strain in the composition is present at about 1 x 10^9 CFU/g to about 5 x 10^10 CFU/g of composition (Table 5 and Table 7), as is relevant to claim 4.
Ghannoum et al teaches the composition is a probiotic (Abstract, Table 4), as is relevant to claim 5.
Ghannoum et al teaches the composition is a pharmaceutical composition and further comprises at least one pharmaceutically acceptable carrier and/or excipient (paragraphs 146-150, 159), as is relevant to claim 6.
Ghannoum et al teaches the composition is formulated for oral administration (paragraphs 142-158) or topical administration (paragraphs 159-167), as is relevant to claim 7.
Ghannoum et al teaches the composition is a food product, food ingredient, dietary supplement, or medicament (e.g. (IV) Cooked Food Products, Table 4), as is relevant to claim 8.
Ghannoum et al teaches the disease, disorder, or condition is IBD, IBS, cancer, chemotherapy-induced gastrointestinal inflammation, radiation-induced gastrointestinal inflammation, immunotherapy-induced gastrointestinal inflammation, bacterial infection, viral infection, fungal infection, antibiotic use, aging, dysbiosis, obesity, type 2 diabetes, metabolic syndrome, asthma, atherosclerosis, non- alcoholic fatty liver disease, multiple sclerosis, or skin inflammation (e.g. paragraphs 25, 29, 192), as is relevant to claims 9 and 14; and specifically IBD (e.g. paragraphs 29, 192), as is relevant to claim 15; and specifically ulcerative colitis or Crohn's disease (e.g. paragraphs 29, 192), as is relevant to claim 16; and specifically dysbiosis (e.g. paragraph 25), as is relevant to claim 17.
However, Ghannoum et al teaches Saccharomyces boulardii as a heavily used and studied yeast in probiotics, and uses Saccharomyces boulardii in their example compositions. Although Ghannoum et al does teach exemplary fungal strains in the compositions include Kluyveromyces lactis and Cyberlindnera jadinii, it does not explicitly teach Cyberlindnera jadinii or Kluyveromyces lactis in the exemplary embodiments disclosed, as is relevant to claim 12 and its dependent claims.
However, Ceugniez et al teaches that Kluyveromyces lactis is safe (Introduction paragraph 3; section 2.4. Safe Properties), has potential as a probiotic, and displayed inhibitory activities against human bacterial infection (Abstract), and compared it to Saccharomyces boulardii, as is relevant to reference Ghannoum et al, and differentiated it from the pathogenic Candida albicans, as is relevant to the instant specification. Ceugniez et al further teaches Kluyveromyces lactis' capacity to survive in vitro gastrointestinal conditions (Discussion paragraph 4), has antagonistic activity against bacterial and fungal human pathogens (Discussion paragraph 1).
It would have been obvious to one skilled in the art, before the effective filing date of the instant application, to substitute the Saccharomyces boulardii explicitly taught in the methods of Ghannoum et al with Cyberlindnera jadinii, as taught in Ghannoum et al, or Kluyveromyces lactis, in light of the teachings of Ghannoum et al and Ceugniez et al. Although Ghannoum et al teaches an extensive list of exemplary non-pathogenic fungal strain that could be appropriate for their method in their specification (e.g. paragraphs 16 and 92), they explicitly claim the non-pathogenic fungal strain in the method is selected from a narrower list comprising of Cyberlindnera jadinii and Saccharomyces boulardii in Claim 20 of Ghannoum et al. As such, it would have been obvious to one skilled in the art, before the effective filing date of the instant application, that Ghannoum et al explicitly teaches Cyberlindnera jadinii as an alternative to Saccharomyces boulardii. Ghannoum et al further teaches that Saccharomyces boulardii was chosen for its ability to reduce virulence of the human pathogenic Candida fungus, which can invade the gastrointestinal epithelial mucosa (paragraph 234). Ceugniez et al teaches they corroborated Kluyveromyces lactis antagonistic properties against Candida albicans (Discussion paragraph 1). Additionally in light of the Ghannoum et al already teaching Kluyveromyces lactis as an exemplary non-pathogenic fungus for their methods, it would have been obvious to one skilled in the art, before the effective filing date of the instant application, that Kluyveromyces lactis could be a suitable substitute for Saccharomyces boulardii.
Ceugniez et al further teaches that recent research regarding non-Saccharomyces yeasts have expanded interest in developing these yeast as probiotic candidates. In light of these interests and teachings of the suitability of Cyberlindnera jadinii and Kluyveromyces lactis as substitutes for a commonly known fungal strain in probiotics and food additives for gastrointestinal health, Saccharomyces boulardii, one skilled in the art, before the effective filing date of the instant application, would be motivated to also develop these beneficial fungal strains to treat gastrointestinal infection and inflammation.
One skilled in the art, before the effective filing date of the instant application, would have reasonable expectation of success because these Cyberlindnera jadinii and Kluyveromyces lactis have already been taught as alternatives to Saccharomyces boulardii in methods for treating gastrointestinal inflammation, disease, disorders, or conditions in a subject in need thereof, comprising of administering this yeast to the subject.
KSR International Co. v. Teleflex Inc. (KSR), 550 U.S. 398, (2007), discloses that a simple substitution of one known element for another to obtain predictable results is obvious. In this case, the prior art contained a method which differed from the claimed method by the fungus used in the method, Saccharomyces boulardii instead of the instantly claimed Cyberlindnera jadinii and Kluyveromyces lactis. However, the prior art also teaches the instantly claimed fungi as suitable alternatives to Saccharomyces boulardii, arriving at the claimed invention. The prior art teaches the motivation to focus on Cyberlindnera jadinii and Kluyveromyces lactis. The prior art teaches that the substituted fungus and their functions were known in the art relative to Saccharomyces boulardii. One skilled in the art, before the effective filing date of the instant application, could have substituted one fungus for another and the results of the substitution would have been predictable in light of teachings that Cyberlindnera jadinii is a suitable alternative for Saccharomyces boulardii and that Kluyveromyces lactis has the same functions that underlies the motivation for using Saccharomyces boulardii.
New Objections/Rejections
Claim Objections
Claims 2 and 3 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims, i.e. the specifically deposited strains. Note: The withdrawn groups of invention also comprise the genus of Cyberlindnera jadinii or Kluyveromyces lactis and could benefit from the same recitation of the specifically deposited strains.
Claim Rejections - 35 USC § 103
New claim(s) 19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ghannoum et al (WO2019173763A1, filed 03/08/2019, published 09/12/2019) as evidenced by Rupp et al (The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms, J Biotechnol. 2015 Oct 10;211:20-30, published 2015), in view of Ceugniez et al (Anti-Salmonella activity and probiotic trends of Kluyveromyces marxianus S-2-05 and Kluyveromyces lactis S-3-05 isolated from a French cheese, Tomme d' Orchies, Research in Microbiology 168 (2017) 575-582, published 2017).
New claim 19 depends on claim 12. The teachings of the prior art regarding claim 12 are incorporated in its entirety here and further described below.
Regarding claim 12, it follows that if a method reduces symptoms of gastrointestinal inflammation, it would reduce the disease activity index (DAI) of the associated disease since the DAI accounts for symptoms of the disease.
Response to Arguments
Claim Rejections - 35 USC § 103
Applicant’s argument:
As a preliminary matter, the Applicant argues that amended claim 12 requires:
Administration of a fungal species alone (either C. jadinii or K. lactis)
A therapeutic effect on gastrointestinal inflammation or a disease, disorder or
condition associated with gastrointestinal inflammation
No requirement for probiotic bacteria, enzymes, or additional components; and
an effective amount of at least 1 x 109 Colony-Forming Units; and
administration of the composition reduces at least one symptom of gastrointestinal inflammation in the subject
Applicant further argues that the prior art reference Ghannoum lacks these core features.
The argument is not commensurate with the scope of the claim. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
The claimed method is recited as “comprising: administering a composition comprising an effective amount of Cyberlindnera jadinii or Kluyveromyces lactis to the subject”. The transitional word “comprising” is inclusive or open-ended and does not exclude additional, unrecited elements or method steps. See MPEP 2111.03. Therefore, claim 12 does not require administration of a fungal species alone, as the Applicant argues, and does not exclude probiotic bacteria, enzymes, or additional components, as the Applicant alludes to.
Furthermore, the claims recite a “method of treating or preventing gastrointestinal inflammation or a disease, disorder or condition associated with gastrointestinal inflammation” meaning that it does not require only therapeutic effects, i.e. treating the disease, disorder, or condition, but also preventive effects would fall under the claim, as written.
Finally, the argument that the prior art reference Ghannoum lacks these features is moot since the claim did not require all these discussed. The other limitations will be discussed below, as they relate to subsequent arguments.
Applicant’s argument:
Applicant argues that amended claim 12 requires a specific therapeutic result, which Ghannoum lacks.
Applicant further argues that Ceugniez does not cure Ghannoum’s deficiencies because it lacks in vivo anti-inflammatory teachings, and lacks administration to any subjects, instead focusing primarily on anti-Salmonella antagonism and virulence gene effects, survival in gastrointestinal fluids, and in vitro cell adhesion. Applicant argues that Ceugniez teaches these traits only enhance K. lactis’s potential as probiotic strains, and does not say for certain whether they are usable probiotic strains. Applicant argues that Ceugniez focuses only on microbiological and probiotic characterization, not medical treatment.
Regarding the argument that neither Ghannoum nor Ceugniez teach the reduction of at least one symptom of gastrointestinal inflammation in the subject, the following points are reiterated or presented to emphasize the previous rejection in light of the specific arguments made:
Ghannoum teaches “a method of treating gut inflammation in a subject in need thereof with high Proteobacteria and low Candida levels relative to a subject without gut inflammation… by administration to the subject of super greens blend 1” and “a method of treating gut inflammation in a subject in need thereof with elevated Proteobacteria and Candida levels relative to a subject without gut inflammation… by administration to the subject of super greens blend 4” (p. 57, para. 0210-0211). Super greens blend 1 is accordingly “useful for treating or reducing gut inflammation and/or dysbiosis in a subject with high level of Proteobacteria and low level of Candida relative to a subject without gut inflammation and/or dysbiosis” and super greens blend 4 is accordingly “useful for treating or reducing gut inflammation and/or dysbiosis in a subject with high levels of Proteobacteria and Candida relative to a subject without gut inflammation and/or dysbiosis”. As such, the pathogenic Candida fungus is understood to be associated with gut inflammation.
Ghannoum teaches super greens blend 1 and 4 both comprise of one non-pathogenic fungi, S. boulardii (p. 37, Table 4).
Ghannoum teaches the probiotic strains comprised in super greens blend 1 and 4 are able to reduce the virulence of Candida, preventing them from invading the epithelial mucosa and causing gut inflammation (p. 62, para. 0234). As such, Ghannoum provides evidence for the actual mechanism by which super greens blend 1 and 4 would reduce gut inflammation in a subject and, as stated previously, envisions this treatment or preventive method in a subject.
Ghannoum teaches a list of potential alternatives for S. boulardii including Kluyveromyces lactis. In combination with the teachings by Ceugniez, which teach Kluyveromyces lactis’s agonistic properties towards Candida albicans also, and further its anti-Salmonella enterica Typhimurium activity, Kluyveromyces lactis becomes a prime substitution candidate because it shares therapeutic properties with S. boulardii and has an additional beneficial property. The anti-Salmonella enterica Typhimurium activity is not unrelated to gastrointestinal inflammation as Applicant suggests. Salmonella enterica Typhimurium infections and biofilm formation in the gastrointestinal tract lead to inflammation. Further, Kluyveromyces lactis’s ability to survive in the gastrointestinal tract is an important trait for compositions targeting the harsh environment of the gastrointestinal tract. Ceugniez also specifically links why Kluyveromyces lactis is being studied as an alternative to S. boulardii (p. 576, col. 1, para. 3-4).
MPEP 2143.02 teaches that obviousness does not require absolute predictability, but only a reasonable expectation of success is required. In vivo data or actual administration to a subject is not required to provide reasonable expectation of success if other teachings provide one skilled in the art sufficient information that the in vitro data providing the mechanism of actions would, more likely than not, translate to its linked effects in vivo. Although Ghannoum and Ceugniez may not actualize the administration of these compositions to a subject, the microbiological and probiotic characterizations they are provide are the underlying physiological mechanism for therapeutic or preventive effects and are clearly conducted to provide evidence supporting the use of these fungi for such purposes. Their ability to survive and persist in the gastrointestinal tract, reduce virulence of pathogenic microbes, such as Candida, and modulate the microbiome composition in favor of symbiotic microbes, sets them apart from other candidates, and these effects are what enable anti-inflammatory effects specifically in the gastrointestinal tract.
Further, as Applicant notes, Ceunguiz, with sound scientific integrity, would not claim probiotic function with absolute certainty until the results of human trials are known. However. Absolute certainty is not required, only reasonable expectation of success. Ceunguiz not only claim the potential of Kluyveromyces lactis as a probiotic but also provides the pertinent evidence regarding the mechanism of action and traits that would lead one skilled in the art to reasonably expect this probiotic function more likely than not.
Applicant’s argument:
Applicant argues that the rejection is not commensurate with the BRI of the amended claim 12 that explicitly requires reduction of at least one symptom of gastrointestinal inflammation in the subject. Applicant argues that claim 12 cannot encompass the in vitro screening or probiotic potential provided by the cited references.
However, as explained in the above response, the rejection does not stop at mere probiotic potential or in vitro screening but provides the rationale for why it translate to the claimed function as these in vitro screenings are done to support the function in subjects.
Applicant’s argument:
Applicant further argues that KSR Predictability Analysis for “Simple Substitution” is not supported because (A) the disclosure shows species-dependent outcomes amounting to unpredictability in the results and (B) claimed function is not addressed by the substitution rationale and further that the laundry list of fungal species does not provide motivation to select the claimed fungal species.
The Applicant further asserts unpredictability between species and even a level of unpredictability even within the same species, i.e. Saccharomyces cerevisiae var. boulardii (i.e. Saccharomyces boulardii) and Saccharomyces cerevisiae.
Related to this, Applicant argues that Ghannoum does not teach the claimed method, as properly construed, because Ghannoum does not exemplify use of the claimed species for the claimed result and no predictable results are possible from the substituted species, and further that the results of the prior art teaching cannot reasonably be used to predict the claimed function.
First, in response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). The motivation to combine does not stop with the mere list of alternative fungal species from Ghannoum. The motivation to combine Ghannoum with the teachings of Ceunguiz was provided, related to the first set of arguments, and discusses how Ceunguiz teaches the claimed species and their use for the claimed result.
The rejection does not rely on solely a list of potential alternative fungi. The asserted unpredictability of species variation in probiotic functions does not take into account the teachings of the combined references, such as Ghannoum in view of Ceunguiz, that explain the mechanism of action of specific species that would push them forward as candidates with a reasonable expectation of success, and teachings of the art, like the Applicant provides, that would deter one from selecting a known pathogenic fungal species. The foundational teaching regarding alternative fungal species is provided by Ghannoum and built upon further by Ceunguiz.
Applicant admits that there is a level of unpredictability even within the same species, and implies that this unpredictability unequivocally disables one skilled in the art to ever arrive at a reasonable expectation of success short of explicit reduction to practice or screening of reducing particular disease symptoms in vivo. However, this is contradictory to the scope of Applicant’s own disclosure, as the Applicant only reduces to practice the use of one specific strain of Kluyveromyces lactis but claims these results using the entire species of Kluyveromyces lactis. Clearly, some level of unpredictability is tolerated. Even though Kluyveromyces lactis and Saccharomyces boulardii are of two different genera, the teachings of the prior art provide a level of predictability by directly showing the functions of Kluyveromyces lactis overlapping with the functions of Saccharomyces boulardii, and that these functions are linked to the reduction of gastrointestinal inflammation in human subjects.
Applicant’s argument:
Applicant argues that Ghannoum teaches away from using any fungi alone and asserts that teaches away from fungal-only therapies.
The argument is not commensurate with the scope of the claims. The claims, under BRI, is properly construed to encompasses a method that comprises of the claimed fungal species, and does not exclude other components, for reasons provided in the preliminary matters regarding the term “comprising”. Therefore, the compositions taught by the combination of the prior art are encompassed by the scope of the claim.
Applicant’s argument:
Applicant argues overbroad interpretation of “treating” when using in vitro probiotic generalizations to establish reasonable expectation of success for the claimed in vivo anti-inflammatory method.
First, it should be noted that claim 12 recites a “method for treating or preventing gastrointestinal inflammation or a disease, disorder, or condition associated with gastrointestinal inflammation … wherein administration of the composition reduces at least one symptom of gastrointestinal inflammation in the subject” (emphasis in italics added).
Second, Applicant’s own Specification defines “treat” broadly (para. 00271): “As used herein, the terms "treat" or "treatment" includes inhibition or postponement of the development of the symptoms associated with a disorder and/or a reduction in the severity of the symptoms of such disorder. The terms further include ameliorating existing uncontrolled or unwanted symptoms, preventing additional symptoms, and ameliorating or preventing the underlying causes of such symptoms” (emphasis in italics added).
Treatment is therefore defined by the Applicant’s specification to include preventing the underlying causes of symptoms, even if they, by definition, may not have manifested as symptoms yet. Therefore, the teachings of the prior art references regarding how Kluyveromyces lactis is able to combat the underlying causes of gut inflammation and dysbiosis, such as by antagonizing pathogenic Candida albicans and Salmonella enterica Typhimurium already directly falls within the Applicant’s own definition of treating. The likelihood that Kluyveromyces lactis would reasonably reduce manifested symptoms is provided earlier as is relevant to previous arguments about expected success.
Conclusion
Claims 2 and 3 are objected to for depending on a rejected claim but containing allowable subject matter. Claims 5-9, 12, 14-17, and 19 are rejected.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/BONIRATH CHHAY/
Examiner, Art Unit 1645
Thursday, September 10, 2026
/BAO-THUY L NGUYEN/Supervisory Patent Examiner, Art Unit 1677 September 15, 2026