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 .
Applicant’s election without traverse of group IV and the species: liver disease progression, GPRIN3 and GSTA1, non-alcoholic liver disease, non-alcoholic steatohepatitis, fresh tissue, and GPRIN3 and GSTA1 in the reply filed on 9/3/25 is acknowledged.
Claims 1, 15-21, and 23-26 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 9/3/25.
Drawings
The drawings filed on 8/30/22 are objected to because Figures 1B, 4B, 4D, 6A, 7A, and 8A are not fully legible. A complete response to this office action must correct the defects cited above and a response to the action on the merits which follows.
The aforementioned instance of failure to comply is not intended as an exhaustive list of all such potential failures to comply in the instant application. Applicants are encouraged to thoroughly review the application to ensure that the entire application is in full compliance. This requirement will not be held in abeyance.
Improper Markush Rejection
Claims 22 and 27-37 are rejected on the judicially-created basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). The improper Markush grouping includes species of the claimed invention that do not share both a substantial structural feature and a common use that flows from the substantial structural feature. The members of the improper Markush grouping do not share a substantial feature and/or a common use that flows from the substantial structural feature for the following reasons: The claims are directed to a large multitude of possible combinations of marker genes. Each of the genes has a different sequence and activity. One cannot be substituted for another with expectation of identical activity.
In response to this rejection, Applicant should either amend the claim(s) to recite only individual species or grouping of species that share a substantial structural feature as well as a common use that flows from the substantial structural feature, or present a sufficient showing that the species recited in the alternative of the claims(s) in fact share a substantial structural feature as well as a common use that flows from the substantial structural feature. This is a rejection on the merits and may be appealed to the Board of Patent Appeals and Interferences in accordance with 35 U.S.C. 134 and 37 CFR 41.31(a)(1).
When the Markush grouping is for alternatives of chemical compounds, they shall be regarded as being of a similar nature where the following criteria are fulfilled:
(A) All alternatives have a common property or activity; and
(B) (1) A common structure is present, i.e., a significant structural element is shared by all of the alternatives; or
(B) (2) In cases where the common structure cannot be the unifying criteria, all alternatives belong to a recognized class of chemical compounds in the art to which the invention pertains.
In paragraph (B)(1), above, the words “significant structural element is shared by all of the alternatives” refer to cases where the compounds share a common chemical structure which occupies a large portion of their structures, or in case the compounds have in common only a small portion of their structures, the commonly shared structure constitutes a structurally distinctive portion in view of existing prior art, and the common structure is essential to the common property or activity. The structural element may be a single component or a combination of individual components linked together.
In paragraph (B)(2), above, the words “recognized class of chemical compounds” mean that there is an expectation from the knowledge in the art that members of the class will behave in the same way in the context of the claimed invention. In other words, each member could be substituted one for the other, with the expectation that the same intended result would be achieved.
In order for the members of the Markush group to belong to “recognized class of chemical compounds” there must be an expectation that the members of the class will behave in the same way in the context of the claimed invention. In other words, each member of the class could be substituted one for the other with the expectation that the same intended result would be achieved. In the instant case, activity of any specific gene is dependent upon the specific sequence of nucleotides. There is no expectation that any one of the genes as claimed can be substituted for any of the other with a completely different sequence with the expectation of the same activity.
As set forth in MPEP2117, “Note that where a Markush group includes only materials from a recognized scientific class of equivalent materials or from an art-recognized class, "the mere existence of such a group in an application tend[s] to prove the equivalence of its members and when one of them [is] anticipated the group [is] therefore rendered unpatentable, in the absence of some convincing evidence of some degree of non-equivalency of one or more of the remaining members." In re Ruff, 256 F.2d 590, 598-99, 118 USPQ 340, 348 (CCPA 1958)("[A]ctual equivalence is not enough to justify refusal of a patent on one member of a group when another member is in the prior art. The equivalence must be disclosed in the prior art or be obvious within the terms of Section 103." Id. at 599, 118 USPQ at 348).”
In the instant case, art against any one gene would not be evidence against any of the remaining members that have completely different sequences and do not have identical activity.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 22 and 27-37 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims recite administration of any preventative treatment to the subject. The specification discloses that the treatment may be an inhibitor of a chromatin reader or modifier, a regulator or reader-targeting or previously identified candidate compounds for treatment of advanced liver disease and HCC prevention (e.g., Nizatidine).
The species of the specification are not representative of the entire claimed genus, the genus being any preventative treatment. Without further description of the structure required for the function, one would not be able to readily recognize which agents are necessarily included or excluded from the instant genus of any preventative treatment.
Additionally, claim 27 recites that the liver disease is due to viral hepatitis. However, the specification does not describe the species representative of the entire claimed genus of liver diseases that are due to viral hepatitis.
Claim 28 recites that the liver disease is chronic hepatitis A, B, C, D, or E related. The specification does not describe species representative of the entire claimed genus of liver diseases that are related in any manner to chronic hepatitis A, B, C, D, or E.
The MPEP states that for a generic claim, the genus can be adequately described if the disclosure presents a sufficient number of representative species that encompass the genus. See MPEP § 2163. If the genus has a substantial variance, the disclosure must describe a sufficient variety of species to reflect the variation within that genus. See MPEP § 2163. Although the MPEP does not define what constitute a sufficient number of representative species, the courts have indicated what do not constitute a representative number of species to adequately describe a broad genus. In Gostelli, the courts determined that the disclosure of two chemical compounds within a subgenus did not describe that subgenus. In re Gostelli, 872, F.2d at 1012, 10 USPQ2d at 1618. Additionally, in Carnegie Mellon University v. Hoffman-La Roche Inc., Nos. 07-1266, -1267 (Fed. Cir. Sept. 8, 2008), the Federal Circuit affirmed that a claim to a genus described in functional terms was not supported by the specification’s disclosure of species that were not representative of the entire genus. Furthermore, for a broad generic claim, the specification must provide adequate written description to identify the genus of the claim. In Regents of the University of California v. Eli Lilly & Co. the court stated:
"A written description of an invention involving a chemical genus, like a description of a chemical species, 'requires a precise definition, such as by structure, formula, [or] chemical name,' of the claimed subject matter sufficient to distinguish it from other materials." Fiers, 984 F.2d at 1171, 25 USPQ2d 1601; In re Smythe, 480 F.2d 1376, 1383, 178 USPQ 279, 284985 (CCPA 1973) ("In other cases, particularly but not necessarily, chemical cases, where there is unpredictability in performance of certain species or subcombinations other than those specifically enumerated, one skilled in the art may be found not to have been placed in possession of a genus ...") Regents of the University of California v. Eli Lilly & Co., 43 USPQ2d 1398.
The Guidelines for Examination of Patent Applications under the 35 USC § 112, first paragraph, “Written Description” Requirement”, published at Federal Register, Vol. 66, No. 4, pp. 1099-1111 outline the method of analysis of claims to determine whether adequate written description is present. The first step is to determine what the claim as a whole covers, i.e., discussion of the full scope of the claim. Second, the application should be fully reviewed to understand how applicant provides support for the claimed invention including each element and/or step, i.e., compare the scope of the claim with the scope of the description. Third, determine whether the applicant was in possession of the claimed invention as a whole at the time of filing.
Thus, having analyzed the claims with regard to the Written Description guidelines, it is clear that the specification does not disclose a representative number of species of preventative treatments, liver diseases due to viral hepatitis, and liver diseases related to chronic hepatitis A, B, C, D, or E. Thus, one skilled in the art would be led to conclude that Applicant was not in possession of the claimed invention at the time the application was filed.
Claims 22 and 27-37 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a method of diagnosing NASH via detection of upregulation of specific genes and downregulation of specific genes, does not reasonably provide enablement for a method of diagnosing risk for progression of any possible liver disease via detection of any up or down regulation of any of the recited genes; or a method of prevention or delay of progression of any possible liver disease via detection of any up or down regulation of any of the recited genes followed by administration of any preventative treatment. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
Factors to be considered in a determination of lack of enablement include, but are not limited to:
(A) The breadth of the claims;
(B) The nature of the invention;
(C) The state of the prior art;
(D) The level of one of ordinary skill;
(E) The level of predictability in the art;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure.
In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988)
The instant claims are directed to a method of diagnosing risk for progression of any possible liver disease via detection of any up or down regulation of any of the recited genes; or a method of prevention or delay of progression of any possible liver disease via detection of any up or down regulation of any of the recited genes followed by administration of any preventative treatment.
The specification discloses that transcriptomic data for 72 NASH patients was derived from external expression dataset NCBI Gene Expression Omnibus database (page 35). The specification discloses epigenetic changes observed in NASH patients with advanced liver disease and HSC patients. The specification discloses identification of 1693 changed genes that was associated with significantly shorter survival and a significantly earlier HCC development than those with transcriptionally intact liver (page 41) (Table S3), with 25 genes with highest prediction of HCC or NASH (Table S4).
The specification is enabling for a method of diagnosing NASH via detection of upregulation of specific genes and downregulation of specific genes as demonstrated in Table S4, but does not reasonably provide enablement for a method of diagnosing risk for progression of any possible liver disease via detection of any up or down regulation of any of the recited genes; or a method of prevention or delay of progression of any possible liver disease via detection of any up or down regulation of any of the recited genes followed by administration of any preventative treatment.
The specification does not draw an adequate nexus between the data specific for NASH and any possible liver disease. Each condition has different etiologic considerations and gene signatures.
Even with regards to NASH and HCC, the species of liver diseases demonstrated in the specification to have a specific gene profile, the instant claims are directed to up or down regulation of any of the recited genes, which includes the opposite of what is demonstrated in Table S4 (i.e. the claims encompass up regulation of the genes required to be down regulated and down regulation of the genes that are required to be up regulated for diagnosis).
Instant claim 33 requires at least one gene selected from GPRIN3, COL1A2, SLC7A6, CHST11, LBH, TRPC1, IGF2BP2, ARRDC2, SELM, and TMED3 to be overexpressed and/or wherein at least one gene of GSTA1, GRB14, SERPINA5, CAT, SLC25A1, PKLR, ADH4, GLYAT, TTR, HPX, RARRES2, ACADSB, CFHR5, DCXR and GALK1 is under-expressed in the subject sample in comparison to the control sample. However, the claim encompasses one gene (i.e. GPRIN3) being upregulated whereas COL1A2 can still be downregulated. The claims are not directed to any specific static gene expression profile and the diagnosis of any specific liver disease. Claim 22 requires any significant difference in any of the recited genes and the diagnosis of risk of progression of any liver disease.
For example, Ying et al. (Clin Exp Pharmacol Physiol. 2017;44:1180–1191) teach that COL1A2 was significantly downregulated in NAFLD (page 1180), although instant claim 33 recites that COL1A2 is upregulated in the liver disease. Therefore, Ying et al. is evidence that COL1A2 overexpression would not be indicative of risk for progression of any possible liver disease.
Hennig et al. (J. Cell. Mol. Med. Vol 18, No 9, 2014 pp. 1762-1772) teach that GSTA1 is increased in NASH, although instant claim 33 recites that GSTA1 is under expressed in the liver disease. Therefore, Hennig et al. is evidence that GSTA1 under expression would not be indicative of risk for progression of any possible liver disease.
Cariou et al. (The FASEB Journal, 2004, 18, 9, 1-21) teach that Grb14 is increased in adipose tissue in insulin resistance (Title, abstract). Therefore, Grb14 under expression would not be indicative of risk for progression of any possible liver disease.
Zhang et al. (Frontiers in Oncology, 2021, 11, 652354, 1-18) teach that SERPINA5 is upregulated in liver metastatic cancer tissues (page 9). Therefore, SERPINA5 under expression would not be indicative of risk for progression of any possible liver disease.
With regards to prevention or delay, the specification does not draw an adequate nexus between a detection of any up or down regulation of any of the recited genes followed by administration of any preventative treatment and the predictable outcome of absolute prevention or delay of progression of any possible liver disease.
The scope of the claims in view of the specification as filed together do not reconcile the unpredictability in the art to enable one of skill in the art to make and/or use the claimed invention, namely a broad method of preventing or delaying the progression of any liver disease encompassing in vivo effects.
MPEP 2164.01
Any analysis of whether a particular claim is supported by the disclosure in an application requires a determination of whether that disclosure, when filed, contained sufficient information regarding the subject matter of the claims as to enable one skilled in the pertinent art to make and use the claimed invention.
Also, MPEP 2164.01(a)
A conclusion of lack of enablement means that, based on the evidence regarding each of
the above factors, the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed
invention without undue experimentation. In re Wright, 999 F.2d 1557,1562, 27
USPQ2d 1510, 1513 (Fed. Cir. 1993).
Given the teachings of the specification as discussed above, one skilled in the art could not predict a priori whether introduction of any possible type of preventative treatment in vivo by the broadly disclosed methodologies of the instantly claimed invention, would result in successful prevention or delay of the progression of any possible liver disease wherein any of the instantly recited genus have been up or down regulated by any significant difference. Without further guidance, one of skill in the art would have to practice a substantial amount of trial and error experimentation, an amount considered undue and not routine, to practice the instantly claimed invention.
A conclusion of lack of enablement means that, based on the evidence regarding each of the above factors, the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention without undue experimentation (see MPEP 2164.01(a)).
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 22 and 27-37 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception, a natural correlation, without significantly more.
The claims are directed to assaying for a gene or a plurality of genes and correlating the expression with risk for a liver disease. This is a natural correlation, and it existed in the body before people had discovered it (Step 2A, Prong One). It is a natural phenomenon. Therefore, the claims are directed to a judicial exception.
The claims are directed to the use of the recited markers or an assay to measure those markers. This is recited at a high level of generality, and methods of measuring gene expression were routine and conventional at the time of filing. The claim appears to pre-empt all uses of the correlation, because it encompasses all possible assays to gather the data that are necessary to make the correlation. Obtaining the genes to perform the test is well understood, routine, and conventional activity for those in the field of diagnostics. Mere data gathering is needed to use the correlation. Therefore the additional steps fail to add significantly more to the judicial exceptions, and the claims are not eligible (Step 2A, Prong Two).
Claim 22 recites administration of any preventative treatment to the subject, which is not considered to be significantly more than the judicial exception. Generally linking the use of the judicial exception to a particular technological field is not indicative of integration into practical application (see MPEP 2106.05(h)) (Step 2B). With regards to instant claim 29 limits the patient population rather than any specific unconventional treatment with a specific drug for a specific disease state.
For example, Ward et al. (WO 2015/071669 A2) describes a method for diagnosing, prognosticating or monitoring a liver tumor in an individual by means of the detection or quantification of one or more markers present in particular in the blood; the list of markers is extremely broad and includes, in particular, ADHIA, ADHIB, GSTA1, FABP1, ARG1, GPT1 (corresponding to 1ALT1), BHMT and ADH4 proteins. Ward is evidence that it was routine in the art to quantify gene expression of GSTA1 and correlate the expression with a liver disease. Ward et al. teach treatment after the method of diagnosis.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 22, 27, 31, 34, 36, and 37 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ward et al. (WO 2015/071669 A2), in view of Amato et al. (Cells 2020, 9, 832, 1-11).
Ward et al. teaches a method for diagnosing, prognosticating or monitoring a liver tumor in an individual by means of the detection or quantification of one or more markers present in particular in the blood; the list of markers is extremely broad and includes, in particular, ADHIA, ADHIB, GSTA1, FABP1, ARG1, GPT1 (corresponding to 1ALT1), BHMT and ADH4 proteins.
Ward et al. teaches that the detection of a liver injury can be demonstrated by the detection and / or quantification of seven biomarkers specifically namely ADH1 (ADHIB and / or (ADHIB and ADHIA)), ADH4, BHMT (variant 1 and / or a mixture of both variants 1 and 2), ARG1, FABP1, GSTA1 and ALT1.
Ward et al. teaches that such biomarkers of tumor cell lineage can provide an aid to earlier diagnosis, prognostic monitoring of disease, optimized treatment selection and may potentially identify new selective therapeutic targets for future drug development.
Therefore, it would have been obvious to administer a preventive treatment to the subject that has been diagnosed (instant claim 22).
Ward et al. teaches that GSTA1 is a protein differentiating peripheral cholangiocarcinoma from normal cholangiocytes and is downregulated in cholangiocarcinoma (Table 3, page 27).
Therefore, in view of Ward et al., it would have been obvious to detect downregulation of GSTA1 in cholangiocarcinoma and diagnose the subject as at risk of progression of cholangiocarcinoma, a liver disease (instant claims 22 and 31).
Cholangiocarcinoma meets the instant limitation of “a non-alcoholic or alcoholic liver disease” as recited in instant claim 27. This claim language is not limiting to any specific non-alcoholic or alcoholic liver disease.
Ward et al. teach that the term "liver tissue sample" include, but is not limited to, a specimen of liver tissue removed by resection or core needle biopsy (instant claim 34). Ward et al. teach that the tissue is a fresh liver specimen (instant claim 36).
It would have been obvious for the sample to be patient-derived spheroids by culturing fresh liver tissue in spheroid culture medium because Amato et al. teach that these spheroids are useful for cholangiocarcinoma disease modeling (title, abstract).
Claim(s) 22, 27-32, 35, and 36 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ward et al. (WO 2015/071669 A2), in view of Teratani et al. (Hepatology Communications, VOL. 3, NO. 8, 2019, 1098-1112).
Ward et al. teaches a method for diagnosing, prognosticating or monitoring a liver tumor in an individual by means of the detection or quantification of one or more markers present in particular in the blood; the list of markers is extremely broad and includes, in particular, ADHIA, ADHIB, GSTA1, FABP1, ARG1, GPT1 (corresponding to 1ALT1), BHMT and ADH4 proteins.
Ward et al. teaches that the detection of a liver injury can be demonstrated by the detection and / or quantification of seven biomarkers specifically namely ADH1 (ADHIB and / or (ADHIB and ADHIA)), ADH4, BHMT (variant 1 and / or a mixture of both variants 1 and 2), ARG1, FABP1, GSTA1 and ALT1.
Ward et al. teaches that such biomarkers of tumor cell lineage can provide an aid to earlier diagnosis, prognostic monitoring of disease, optimized treatment selection and may potentially identify new selective therapeutic targets for future drug development.
Therefore, it would have been obvious to administer a preventive treatment to the subject that has been diagnosed (instant claim 22).
Ward et al. teaches that GSTA1 is a protein differentiating peripheral cholangiocarcinoma from normal cholangiocytes and is downregulated in cholangiocarcinoma (Table 3, page 27).
Therefore, in view of Ward et al., it would have been obvious to detect downregulation of GSTA1 in cholangiocarcinoma and diagnose the subject as at risk of progression of cholangiocarcinoma, a liver disease (instant claims 22 and 31).
Ward et al. teach that the term "liver tissue sample" include, but is not limited to, a specimen of liver tissue removed by resection or core needle biopsy (instant claim 34). Ward et al. teach that the tissue is a fresh liver specimen (instant claim 36).
Ward et al. is evidence that it was routine to utilize biomarkers in blood for the detection of gene expression and correlation to a disease state in the liver.
Regarding non-tumorous liver tissue (instant claim 35), Teratani et al. teach that Col1a2 is increased significantly in NASH (page 1102). Teratani et al. teach that the LPL-mediated HSC activation pathway could be a promising therapeutic
target for treating liver fibrosis in NASH (page 1098).
Therefore, it would have been obvious to detect increased expression of COL1A2 to diagnose increased risk of progression of NASH (instant claims 22, 27, and 28).
Selection of a patient that has been previously treated as recited in instant claim 29 is a matter of design choice given that the intended objective is to treat any patient with NASH.
It would have been obvious to administer a preventative treatment because Teratani et al. teach the LPL-mediated HSC activation pathway could be a promising therapeutic target for treating liver fibrosis in NASH (instant claim 22).
Teratani et al. teach that different targets are increased or decreased in NASH (Figure 3). It would have been obvious to screen for a combination of targets that are known to have increased or decreased expression for the method of diagnosis as a matter of design choice (instant claims 29-32).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Amy R Hudson whose telephone number is (571)272-0755. The examiner can normally be reached M-F 8:00am-6:00pm.
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/AMY ROSE HUDSON/Primary Examiner, Art Unit 1636