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
Summary
This is the Final Office Action based on application 16/469337 response filed 07/27/2026.
Claims 1, 11, 14, 20, 27, & 30-39, 41 have been examined and fully considered.
Claims 2-10, 12-13, 21-26, 28-29 & 40 are cancelled.
Claim Rejections - 35 USC § 102
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 11, 20, 27 & 32 are rejected under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by STUART in AU 2007340265.
With respect to Claim 1, STUART teaches of a method for detection of biomarkers (abstract, Page 6, first-2nd paragraph), and further of detection of gene expression or of the expression of the proteins the genes encode for (Page 1, last paragraph, Page 8, last paragraph and page 9, first two paragraphs). STUART teaches that the gene detected can be MAP4(Page 82, line/row labeled 1163), and GDI1 (Page 71, row labeled 781). STUART further teaches that the detection can be by any appropriate method, including for example, detecting the quantity of mRNA transcribed from the gene or the quantity of cDNA produced from the reverse transcription of the mRNA transcribed from the gene or the quantity of the polypeptide or protein encoded by the gene (Page 298, last paragraph). STUART teaches of determining the gene expression or protein from a biological sample of a patient (Page 6, paragraph 1). Through broadest reasonable interpretation, this sample and patient is one which “may,” “suffer from Parkinson’s disease,” since any patient or sample “may,” suffer from Parkinson’s.
With respect to Claim 11, STUART teaches of detecting NPM1 (Page 88, line/row marked as 1378), and ADAR (Page 50, line marked as 33) among other biomarkers.
With respect to Claims 20 & 32, STUART teaches of the sample being a blood sample (Page 296, paragraph 2).
With respect to Claim 27, STUART teaches that the gene detected can be MAP4(Page 82, line/row labeled 1163), and GDI1 (Page 71, row labeled 781). STUART teaches of detecting NPM1 (Page 88, line/row marked as 1378), and ADAR (Page 50, line marked as 33) among other biomarkers.
Claim Rejections - 35 USC § 103
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.
Claims 33, 36-38 & 41 are rejected under 35 U.S.C. 103 as being obvious over STUART in AU 2007340265.
With respect to Claim 33, STUART teaches of a method for detection of biomarkers (abstract, Page 6, first-2nd paragraph), and further of detection of gene expression or of the expression of the proteins the genes encode for (Page 1, last paragraph, Page 8, last paragraph and page 9, first two paragraphs). STUART teaches that the gene detected can be MAP4(Page 82, line/row labeled 1163), and GDI1 (Page 71, row labeled 781). STUART further teaches that the detection can be by any appropriate method, including for example, detecting the quantity of mRNA transcribed from the gene or the quantity of cDNA produced from the reverse transcription of the mRNA transcribed from the gene or the quantity of the polypeptide or protein encoded by the gene (Page 298, last paragraph). STUART teaches of determining the gene expression or protein from a biological sample of a patient (Page 6, paragraph 1). Through broadest reasonable interpretation, this sample and patient is one which “may,” “suffer from Parkinson’s disease.”
STUART further teaches of comparing the expression signature of gene or protein to a normal (which means healthy) “relevant” or control sample (Page 10, 3rd paragraph, halfway through starting with “A differentially expressed…” (Page 18, 2nd paragraph from bottom, halfway through, Page 19, last paragraph 5 & 4 lines from bottom).
STUART does not call out specifically finding decreased levels of MAP4, NPM1, or GDI1 though STUART does overall teach of monitoring for the biomarkers which are “differentially expressed,” meaning above or below, when compared to the reference. This teaching makes the claimed act of taking a sample and if the sample has a decreased level in comparison to a reference, detecting it obvious to one of ordinary skill in the art (Page 18, 2nd paragraph from bottom, halfway through, Page 19, last paragraph 5 & 4 lines from bottom). Further, detecting decreased levels of the biomarkers MAP4, NPM1, or GDI1 will depend on the sample taken.
With respect to Claim 36, STUART teaches of detecting NPM1 (Page 88, line/row marked as 1378), and ADAR (Page 50, line marked as 33) among other biomarkers.
With respect to Claims 37 & 38, STUART teaches of the sample being a blood sample (Page 296, paragraph 2).
With respect to Claim 41, STUART teaches that the gene detected can be MAP4(Page 82, line/row labeled 1163), and GDI1 (Page 71, row labeled 781). STUART teaches of detecting NPM1 (Page 88, line/row marked as 1378), and ADAR (Page 50, line marked as 33) among other biomarkers.
Claims 30-31 & 34-35 are rejected under 35 U.S.C. 103 as being obvious over STUART in AU 2007340265 in view of in view of POTASHKIN in US 20160244833.
With respect to Claims 30 & 34, STUART teaches of the claimed invention as shown above for Claims 1 & 33. STUART does not teach of the sample being taken from a patient who is aged 52 to 69 years.
POTASHKIN is used to remedy this. POTASHKIN further teaches of a method of detecting Alzheimer’s (abstract and paragraph 0003) wherein the Parkinson’s disease patient is around an age of 60 years old (paragraph 0003, & 0058-0059), which falls into the claimed range. It would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention to use a patient and sample from a patient who is in a range of years around 60 years of age since Parkinson’s disease is known to affect people over the age of 60 and there is a need in the art to better diagnose during the early stages of the disease (POTASHKIN, paragraph 0003).
With respect to Claim 31 & 35, STUART teaches of the claimed invention as shown above. STUART does not teach of the Parkinson’s being sporadic Parkinson’s disease.
POTASHKIN et al. teach of methods and kits for diagnosing, prognosing, and monitoring Parkinson’s disease (title). More specifically, POTASHKIN et al. teach of methods of diagnosing Parkinson’s Disease (PD), and also of diagnosing sporadic PD (paragraphs 0007-0009, & 0003). POTASHKIN et al. further teach of identifying a common transcriptional signature in blood of PD patients, four microarray studies (Table 1) were analyzed using INMEX, a web interface for the integrative meta-analysis.
POTASHKIN et al. further teach of determining the expression levels of all the markers on Table III which include MAP4 (paragraph 0035), and performing a meta-analysis on it (paragraph 0056), and of comparison of the samples to a control to see if they are above or below the control (paragraph 0008-0012, 0025). Further, POTASHKIN et al. teach of monitoring" refers to determining the regression, progression, course and/or onset of, and/or prognoses of PD before any treatment or during treatment in order to assess the PD patient's improvement or lack thereof over time (paragraph 0046). POTASHKIN et al. also teach of comparison of the samples to control thresholds (paragraph 0008-0012, 0025, 0070).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention to diagnose sporadic Parkinson’s as is done in POTASHKIN in the method of PAWLOWSKI due to the need in the art for a method which can help diagnose sporadic Parkinson’s disease (POTASHKIN, paragraphs 0003-0006).
Claims 14 & 39 are rejected under 35 U.S.C. 103 as being obvious over STUART in AU 2007340265 in view of in view of PAWLOWSKI in US 20150152474.
With respect to Claims 14 & 39, STUART teaches of the invention as shown above. STUART does not teach of detection by mass spectrometry and of using antibodies.
PAWLOWSKI is used to remedy this. PAWLOWSKI teaches of a method of detecting diagnostic biomarkers and of identifying phenotypes for stage or progression of disease (abstract).
PAWLOWSKI teaches that the phenotype detected can be Parkinson’s disease (paragraph 0080, 0335).
PAWLOWSKI further teaches of taking a sample from the patient who can be suspected of having a disease including Parkinson’s (Table 0001). It is noted though through broadest reasonable interpretation (BRI) any sample from any patient can be considered a subject who “may suffer from Parkinson’s disease,” “with or without,” diagnosis.
PAWLOWSKI further teaches of detecting biomarkers NPM1 and GDI1 (Table 5), and of detecting biomarker MAP4(Table 5), of monitoring the protein expression level (paragraph 0459, 0479, 0333-0335). Table 5 identifies the biomarkers, and paragraph 0479 says that the protein expression of the biomarkers can be detected/analyzed. PAWLOWSKI further teaches of monitoring the phenotype by detecting the biomarkers relative to a reference level and of looking for decreased levels of the biomarkers (paragraph 0246). PAWLOWSKI further teaches that the reference value can be from the same subject who is assessed or from a representative or healthy population not suffering from the diseases (paragraph 0247).
PAWLOWSKI even further teaches of detecting the expression by mass spectrometry and also of using ELISA and antibodies (paragraph 0444, 0445).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention to use mass spectrometry and antibody detection for gene or protein expression as is done in PAWLOWSKI in the method of STUART due to the advantage it offers for both qualitatively and quantitatively detecting the level of the biomarker/s (PAWLOWSKI, paragraph 0444, 0452, 0458-0459, 0478).
Response to Arguments
Applicant's arguments filed 07/27/2026 have been fully considered but they are not persuasive.
Applicant argues with respect to the 102 rejection that STUART does not teach of detecting MAP4 (Page 82 of Stuart) and GDI1 (Page 71 of Stuart), because STUARTS teaching of their detection is only found in a large tabular listing of 7,343 genes within STUART. The examiner disagrees and maintains that the large tabular listing in STUART specifically notates what genes (and products thereof) are detected.
Applicant further argues that STUART does not teach of detecting BOTH MAP4 and GDI1 in combination. With respect to this, the examiner does not understand applicant’s argument about this. What is actually claimed is that MAP4 is detected and also GDI1 is detected, and STUART does in fact teach of this.
Applicant further argues that STUAT does not teach of detecting protein expression of the genes as is instantly claimed. The examiner disagrees.
Specifically- STUART notes that the genes in all of the tables IV-XX are of interest (tables which MAP4 and GDI1 are present on and specifically MAP4 (Page 82 of Stuart and GDI1 Page 71 of Stuart).
The examiner further notes that in the last paragraph on Page 298 of STUART it is stated that “ Detection (of the genes of interest) can be by any appropriate method, including for example, detecting the quantity of mRNA transcribed from the gene or the quantity of cDNA produced from the reverse transcription of the mRNA transcribed from the gene or the quantity of the polypeptide or protein encoded by the gene.” The examiner notes that this applies to all of the genes in the instant tables of STUART.
Therefore, STUART does teach of detecting both the protein expression levels of the genes detected, as is instantly claimed.
Applicant further argues that STUART does not teach of detecting protein expression of GDI1 and MAP4 as a diagnostic approach for Parkinson’s disease. With respect to this, the examiner notes that this argument is not commensurate in scope with the claims as no diagnostic step is claimed.
What applicant does claim is that the sample is obtained from a subject who “may” suffer from Parkinson’s disease. With respect to this, this examiner notes that through broadest reasonable interpretation any subject “may,” suffer from Parkinson’s. Therefore, the prior art of STUART reads on the instant claims, especially as broadly claimed.
Applicant further argues that the examiner’s characterization of STUART is relying on “picking and choosing,” from multiple teachings. The examiner disagrees--- though as the teachings of STUART are broad and vast, they do in fact read on the instant claims and especially claim as it is broadly claimed without picking and choosing. If applicant means something more specific, then they should amend the claims and claim it.
Applicant further argues that the nature of the STUART reference, is an mRNA expression study and not a protein expression method, as instantly claimed and that it bears no relationship to Parkinson’s disease.
With respect to this, the examiner again notes that on Page 298 of STUART it is stated that “ Detection (of the genes of interest) can be by any appropriate method, including for example, detecting the quantity of mRNA transcribed from the gene or the quantity of cDNA produced from the reverse transcription of the mRNA transcribed from the gene or the quantity of the polypeptide or protein encoded by the gene ,” which is protein expression. Further- again the examiner notes that the claims do not really require a relationship of anything claimed with Parkinson’s as no diagnosis is claimed and any sample “may,” have Parkinson’s, which is really all that is claimed with respect to Parkinson’s through broadest reasonable interpretation.
Applicant argues that MPEP 2131 requires that for anticipation the reference must disclose the specific claimed combination with the same level of specificity of the claim itself. The examiner maintains that this is the case with respect to Stuarts and again notes that the claims are very very broad.
Applicant further argues that the office actions broadest reasonable interpretation of the patient limitation is unsupportable. Again the examiner disagrees. With respect to this, applicant further argues that STUART does not mention Parkinson’s anywhere. The examiner again emphasizes that no diagnosis is being claimed and that the patient or subject applicant is referring to can be one that only “may suffer from Parkinsons.” The examiner maintains that any subject anywhere “may,” suffer from Parkinsons and not know it yet. Though not clearly, applicant seems to argue that Stuarts teachings focus on using mice samples and not human samples and that this is reason that the patients in Stuart do not “may,” have Parkinsons. The examiner is not stretching, “so far as to read the PD-specific patient limitation out of the claim entirely,” but instead is looking and examining the claims within the broadest reasonable interpretation (BRI). There is a difference. Even if this patient and sample is a mouse, mice are genetically modified all the times for case studies to having Alzheimers and plaques. The examiner notes that especially in the independent claim, it is not even specified if the patient is human or not. Again, if applicant means something more specific, then they should claim it.
Applicant further argues that the claimed biomarkers of GDI1 and MAP4 were identified through a study of human Parkinsons disease patients. The examiner understands this, but it does not change the fact that the STUART reference reads on the instantly very broad claims.
Applicant argues that the office actions interpretation is unreasonable because it ignores the context provided by the specification as well as the context of the cited art. Again the examiner disagrees, and maintains that the office action is instead reasonable. The examiner further notes that they have not “ignored,” the context of the instant specification and that of the prior art, but has instead read the claims in light of their broadest reasonable interpretation. The examiner notes that the claims are not limited by what is found in the specification.
With respect to Claims 11, 20, 27 and 32, applicant argues similarly to Claims 1 that the additional biomarkers claimed, as taught by STUART only appear in a large tabular list. The examiner maintains that this large tabular listing along with the other teachings from STUART highlighted in response to the Claim 1 arguments adequately teach of the claims as broadly claimed.
Applicant further argues about a specific combinatorial detection strategy and a specific three way co-detection for Claims 11, 20, 27 & 32 and argues that STUART does not teach of this. With respect to this, the examiner again notes that it is unclear what applicant means by co-detection. STUART does in fact teach of detection of the three compound in Claim 27, and therefore reads on the claim. What applicant seems to mean with respect to the codetection, is that the combination of the 3 analytes, when detected together give a specific result. The examiner notes that the specific result is not claimed, so therefore is not limiting in the claims. Therefore, the claims are considered taught by STUART and the rejections are maintained.
With respect to Claims 33, 36-38 and 41, applicant argues that they are not obvious of Stuart. Applicant argues that STUART does not teach specifically of detecting decreased protein expression for the claimed markers. The examiner disagrees.
STUART teaches of detection of the markers and protein expression thereof as shown above. With respect to the decrease, STUART does not call out specifically finding decreased levels of MAP4, NPM1, or GDI1 though STUART does overall teach of monitoring for the biomarkers which are “differentially expressed,” meaning above or below (or increased or decreased), when compared to the reference. This teaching makes the claimed act of taking a sample and if the sample has a decreased level in comparison to a reference, detecting it obvious to one of ordinary skill in the art (Page 18, 2nd paragraph from bottom, halfway through, Page 19, last paragraph 5 & 4 lines from bottom). Further, detecting decreased levels of the biomarkers MAP4, NPM1, or GDI1 will depend on the sample taken. Again, this makes the instant claims obvious.
Applicant further argues again with respect to the instant specification for these claims with respect to arguments about the “relevant control,” in Claim 33. The examiner notes that for Claim 33 applicant is attempting to both claim the comparison to a control, and not claim it, since there could be 101 issues with respect to this. The examiner notes that as instantly claimed with the comparison to a control read into the claims this reads on patent-inelligible subject matter. Without it being read into the claims, it is unclear what a decrease is with respect to. In any event, the teaching by STUART of detecting differentially expressed levels or the markers including MAP4, NPM1, or GDI1 though STUART does overall teach of monitoring for the biomarkers which are “differentially expressed,” meaning above or below (or increased or decreased), when compared to the reference, makes the claimed detecting of a decreased level in comparison to a reference, obvious to one of ordinary skill in the art (Page 18, 2nd paragraph from bottom, halfway through, Page 19, last paragraph 5 & 4 lines from bottom). Therefore, the claims are still properly rejected.
With respect to Claims 36-41, applicant does not add any further substantive arguments. Applicant argues that these claims are allowable. The examiner disagrees.
With respect to claims 30-31 and 34-35, applicant argues that they are not obvious over STUART and POTASKIN.
Applicant goes through a plethora of arguments restating that POTASHKIN does not teach of the biomarkers already taught by STUART. With respect to this, the examiner notes that a 103 rejection was made, so one reference does not need to teach of everything and notes that STUART already taught of the claimed biomarkers.
POTASKHIN was used specifically to teach of STUART does not teach of the sample being taken from a patient who is aged 52 to 69 years.
POTASHKIN is used to remedy this. POTASHKIN further teaches of a method of detecting Alzheimer’s (abstract and paragraph 0003) wherein the Parkinson’s disease patient is around an age of 60 years old (paragraph 0003, & 0058-0059), which falls into the claimed range. POTASHKIN also teaches that the patients can have or be diagnosed with sporadic PD (paragraphs 0007-0009, & 0003). Further- with respect to this, the examiner notes that it does not matter if the markers in POTASHKIN and STUART match, as what is claimed for the patient population is still only a subject who “may, “ have parkinsons or sporadic parkinsons. The examiner further notes that there is in fact reason for combination of patients of the age claimed from Potashkin with STUART, for the reasons shown above and due to the fact too that an older population is more likely to have a plethora of conditions so need for genetic screening.
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).
Applicant even further argues that there are further issues with respect to the rejections of Claim 31 and 35, however again applicant is focused on the claiming of sporadic parkisons and the lack of teaching of the claimed biomarkers in POTASHKIN and the claiming of the decrease of the claimed biomarkers. The examiner has already responded to these arguments as shown above, so therefore the examiner will not be repetitive.
With respect to Claims 14 and 19 applicant argues that the claims are not obvious over STUART an PAWLOWSKI. The examiner disagrees.
Applicant specifically argues that there is a “technical and subject matter mismatch,” between PAWLOWSKI and the claimed invention, and specifically that the PAWLOWSKI reference is specific to cancer and vesicle detection while the instant claims are drawn towards markers for Parkinson’s disease. Again, the examiner notes that as broadly claimed, this argument is not convincing as the subject is not required to have parkinson’s as claimed, and also as claimed it is not claimed if the sample is cells or vesicles or anything else. As broadly claimed, the instant claims read as a broad detection claim, and therefore the detection method of PAWLOWSKI is in fact applicable. Though this is the case, the examiner does not that PAWLOWSKI does indicate that Parkinson’s disease can be related to their methods (paragraph 0080, 0335).
Applicant argues that PAWLOWSSKI does not teach of the claimed biomarkers of GDI1 or MAP4. Again, the examiner notes that a 103 rejection was made, and the primary reference STUART already taught of these markers, so PAWLOWSKI does not need it.
Applicant further argues that the examiners reliance on PAWLOWSKI table 5 for the biomarker teaching is legally insufficient. With respect to this--- the examiner notes that the rejection does not even need this teaching from STUART, since the biomarkers on Table 5 of PAWLOWSKI, NPM1 GDI1 and MAP4 were already taught by STUART. Therefore, applicants arguments with respect to this are unconvincing.
Applicant further argues that Pawlowski teaches mass spectrometry and antibody detection in the context of vesicle based cancer biomarker detection, not protein expression analysis for PD.
The examiner again notes that applicant is seemingly arguing that Pawlowski needs to teach everything claimed, which is not required as a 103 rejection was made. With respect to this, the examiner notes that since STUART already taught of detection of the claimed biomarkers in a sample (of which any sample “may,” have Parkinson’s,) and PAWLOWSKI is merely showing that these same biomarker are/would be obvious to detect by mass spectrometry as claimed. Therefore, this makes the instant claims obvious.
Applicant further argues that the claimed mass spectrometry techniques are targeted quantitative approaches and that they are distinct from the broad mass spectrometry techniques taught in PAWLOWSKI. That there is a difference between the claimed “targeted,” approaches and the broad techniques in PAWLOWSKI is not convincing, because they teach exactly the same detection.
Specifically, PAWLOWSKI teaches of detecting the expression by mass spectrometry and also of using ELISA and antibodies (so mass spectrometry including or in addition by antibody detection)(paragraph 0444, 0445).
Applicant argues that the claims require SRM, MRM, PRM, DDA, or DIA. The examiner notes that the claim as noted above, does not limit to these things, but instead also gives options for antibody detection and mass spectrometry. Therefore, applicant’s arguments are not commensurate in scope with the instant claims.
Applicant notes that the office action must still provide reason why a skilled artisan would apply PAWLOWSKIS antibody detection methodology to the claimed biomarkers. The examiner again notes that one reason for this is since Pawlowski does in fact teach of these biomarkers itself.
Applicant even further argues that there is no valid motivation for combination of STUART and PAWLOWSKI. The examiner disagrees.
Specifically, it would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention to use mass spectrometry and antibody detection for gene or protein expression as is done in PAWLOWSKI in the method of STUART due to the advantage it offers for both qualitatively and quantitatively detecting the level of the biomarker/s (PAWLOWSKI, paragraph 0444, 0452, 0458-0459, 0478).
Applicant argues that this motivation is not sufficient because it is generic and would not apply to combine STUARTS biomarker list with PAWLOWSKIS detection methods for vesicles. With respect to this, the examiner notes that this instant claims are pretty generic and in the very least, extremely broad. The examiner again notes that not specific type of sample, (vesicular or not) is claimed and therefore arguments with respect to this itself and the overall argument is not convincing. The combination does not require, “working across two distinct technical areas,” as argued by applicant but instead both references are applicable to the same technical area as is present in the instant broad claims of general chemical and analytical testing and detection.
All claims remain rejected.
Conclusion
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to REBECCA M FRITCHMAN whose telephone number is (303)297-4344. The examiner can normally be reached 9:30-4:30 MT Monday-Friday.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Maris Kessel can be reached on 571-270-7698. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/REBECCA M FRITCHMAN/Primary Examiner, Art Unit 1758