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 arguments and amendments have been thoroughly reviewed and considered. Claims 8-10 and 16-21 are pending and are examined on the merits herein.
Response to Applicant’s Amendments
Drawing Objections
Figures 2-5 were objected to because they were not wholly legible. In light of Applicant’s amendments to the drawings submitted 9/23/2025, these objections have been withdrawn.
Claim Objections
Claims 8 and 20 were objected to for minor informalities. In light of Applicant’s amendments to the claims submitted 9/23/2025, these objections have been withdrawn. However, see new grounds of objection below.
35 USC 112(b) Rejections
Claims 8-10 and 16-21 were rejected due to various indefiniteness issues associated with claim 8. In light of Applicant’s Remarks and amendments to the claims submitted 9/23/2025, these rejections have been withdrawn. However, see new grounds of rejection below.
35 USC 102 Rejections
Claims 8-10 and 16-21 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kharti et al. (WO 2017/214061 A1; cited in Applicant’s IDS). In light of Applicant’s amendments to the claims submitted 9/23/2025, these rejections have been maintained. See “Response to Applicant’s Arguments” and the 35 USC 112(b) Rejections below.
Double Patenting Rejections
Claims 8-10, 16-18, and 21 were provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 163-169 and 173-176 of copending Application No. 17/736,495 in view of Kharti et al. (WO 2017/214061 A1). In light of Applicant’s amendments to the claims submitted 9/23/2025, these rejections have been maintained. See “Response to Applicant’s Arguments” and the 35 USC 112(b) Rejections below.
Response to Applicant’s Arguments
Regarding the 35 USC 102 Rejections, Applicant argues that Kharti, the reference used in the prior art rejections, does not teach providing a report indicating whether a subject has a viral or intracellular/extracellular bacterial infection and treating the subject accordingly (Remarks, page 29).
In the Non-Final Rejection, the Examiner provided a “Claim Interpretation” section indicating how the word “report,” which appears in claim 8, was being interpreted in light of the instant specification. It concluded, “The “report” of the instant claims will therefore be interpreted to be any presentation of results that can be used by the ordinary artisan to identify whether a subject has a bacterial or viral infection,” (para. 13 of the Non-Final Rejection). Applicant has not provided any arguments against this interpretation. Thus, the analyzing of expression levels to determine if a patient has a viral or bacterial infection in Kharti (pages 17-18 joining para.) would be encompassed by the claimed term “report.”
It is noted that Kharti does not distinguish between intracellular and extracellular bacterial infections. However, as stated in the 35 USC 112(b) Rejections below, the newly amended language of claim 8 concerning the infection types is unclear. Specifically, it is unclear if the claim is intending to compare viral versus intracellular/extracellular bacterial infections (i.e. comparing a viral infection to any type of bacterial infection) or if the claim is intending to compare viral versus intracellular versus extracellular bacterial infections (i.e. comparing all three potential types of infections to one another). The first scenario does not require a distinction between intracellular and extracellular bacteria, and thus, is similar in scope to the previous version of the claim. This is the basis for maintaining the prior art rejections and double patenting rejections below.
Claim Objections
Claim 8 is objected to because of the following informalities: “a pair of genes listed in the following table:” should read “a pair of genes listed in the following table in a sample from the subject:” rather than stating “in a sample from the subject” after the colon and table. Additionally, in step (c), “as having intracellular or extracellular” should read “as having an intracellular or extracellular”. Appropriate correction is required.
Claim 16 is objected to because of the following informalities: the preamble of the claim should state “wherein the method further comprises”. Appropriate correction is required.
Claim Interpretation
It is noted that the word “report” as used in the instant claims has no specific definition in the instant specification. Page 6 notes that the report can be in electronic form (para. 3), but this is not a limiting definition. The “report” of the instant claims will therefore be interpreted to be any presentation of results that can be used by the ordinary artisan to identify whether a subject has a bacterial or viral infection.
In claim 19, it is specified that the measuring of the levels of the RNA transcripts must be done by sequencing. The instant specification provides no specific definition for sequencing. Prior art will be considered to teach this limitation if a measuring protocol involves the use of sequencing in any portion.
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 8-10 and 16-21 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 8 is rejected because the newly amended portions concerning infection types are unclear. Specifically, it is unclear if the claim is intending to compare viral versus intracellular/extracellular bacterial infections (i.e. comparing a viral infection to any type of bacterial infection) or if the claim is intending to compare viral versus intracellular versus extracellular bacterial infections (i.e. comparing all three potential types of infections to one another). The first scenario does not require a distinction between intracellular and extracellular bacteria, and is the basis for maintaining the prior art rejections below. The second scenario is addressed in the 35 USC 112(a) Rejections below.
Claims 9-10 and 16-21 are rejected based on their dependence on rejected claim 8.
Claim Rejections - 35 USC § 112(a) – New Matter
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 8-10 and 16-21 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.
As noted above in the 35 USC 112(b) Rejections, claim 8 may be interpreted as requiring the distinction between all three claimed infection types. However, in the instant specification, intracellular and extracellular bacterial infections are compared to one another. Figures 2-5 show plots comparing various bacterial infections to viral infections, but not comparing intracellular bacterial infections to extracellular bacterial infections. Though the working examples of the instant specification do note intracellular and extracellular bacterial infections (e.g. page 16, para 1), a report indicating the infection type utilizing at least a pair of genes, as required by the claim, is not disclosed. The genes of Table 1 are also grouped into general bacterial and viral categories, with no discrimination of bacterial infection type. These genes are then used in Table 2 with no further discrimination. Thus, claim 8 is considered to contain new matter, as the specification does not teach discriminating between intracellular and extracellular bacterial infections in the manner claimed.
Claims 9-10 and 16-21 are rejected based on their dependence on rejected claim 8.
Claim Rejections - 35 USC § 112(a) - Enablement
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 8-10 and 16-21 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 enablement requirement. The claims contain subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Specifically, the specification does not provide reasonable enablement for utilizing gene pairs to distinguish extracellular bacterial and intracellular bacterial infections. As noted above in the 35 USC 112(b) Rejections, claim 8 may be interpreted as requiring a distinction between viral infections, intracellular bacterial infections, and extracellular bacterial infections, and this interpretation is used in the following rejections.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 USC 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (CA FC 1988). These factors include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims. Each of these factors is discussed below.
Nature of the Invention
Claims 8-10 and 16-21 are drawn to a method for indicating whether a subject has a viral, extracellular bacterial, or intracellular bacterial infection by measuring at least one specific gene pair, and treating the subject based on the type of infection detected.
The claimed methods are classified in the unpredictable arts of molecular biology and biochemistry.
Breadth of the Claims
Claim 8 is very broad in scope because as few as a single pair of genes may be examined, with an upper limit of over one thousand pair of genes examined. None of the dependent claims (9-10 and 16-21) narrow this broad aspect of the claims.
Level of Skill in the Art
The ordinary artisan typically holds at least a master’s degree has several years of experience.
State of the Prior Art & Unpredictability
Concerning the claimed invention, what was (and is) unpredictable in the art is whether a particular claimed gene pair or set of gene pairs would be capable of distinguishing between extracellular bacterial and intracellular bacterial infections. Therefore, it is not possible to know a priori that a particular expression pattern for a gene pair is associated with a particular type of infection.
No prior art could be found that explicitly groups infections into viral, extracellular bacterial, and intracellular bacterial categories, nor that specifically compare intracellular and extracellular bacterial infections.
Herberg et al. (JAMA, 2016) does teach use of a 2-transcript signature that can distinguish generally between viral and bacterial infections (Abstract), but this reference does not determine if the transcripts can distinguish between extracellular/intracellular types of bacterial infections (see Figures 4 and 5 for example). This 2-transcript signature was also part of a larger 38-transcript signature (page 840, “Identification of Minimal Transcript Signatures”).
Similarly, Tang et al. (Eur Respir, 2017) teaches a single biomarker, IFI27 (cited in the current application), that can distinguish between influenza and bacterial infections (Abstract). However, the specific extracellular/intracellular type of bacterial infection is not determined with this biomarker (see Figure 6 for example).
Sampson et al. (Scientific Reports, 2017) teaches a four-biomarker signature for distinguishing viral from non-viral conditions (Abstract). Bacterial infections are taken into account here, but are not parsed out into extracellular and intracellular types (Figure 8).
There are also examples in the prior art in which viral and bacterial infections are distinguished from one another where the type of bacteria present is known, and so intracellular versus extracellular infection distinctions could be made. For instance, Sweeney et al. (Science Translational Medicine, 2016) derived a seven-gene signature for discrimination between viral and bacterial infections (Abstract). Tables 1 and 2 show the specific bacterial and viral infections in the samples of the validation datasets, and Figure 4a also details specific infection types. Generally however, the reference does not discriminate between intracellular and extracellular bacterial infections in terms of gene expression, and the lack of prior art which does make this discrimination indicates that this is not common practice, even when the specific type of bacterial infection is known.
Thus, while the use of a low number of biomarkers (i.e. 1-2) for distinguishing between viral and bacterial infections is known in the art, there is no evidence that such a low number of biomarkers can also distinguish between viral, extracellular bacterial, or intracellular bacterial infections.
Guidance in the Specification and Examples
Generally throughout the specification, the expression patterns associated with different infections are discussed, but these are in the context of comparing bacterial infections to viral infections. Page 2, paras. 1-3 discuss comparing viral infections with bacterial infections generally, as does page 5, para. 1, page 6, para. 2, and page 8, para. 2, for example.
In the working examples, though some of the datasets are noted to have all three claimed infection types (page 13, para. 3 and page 16, para. 1), it is unclear how these distinctions were made. There does not appear to be any discussion of using pairs of genes to distinguish between bacterial infection types. The pairs of genes in Table 1 only distinguish between viral and bacterial infections generally, with no notation of the type of bacterial infection presented (page 16). The claimed pairs of genes are then shown in Table 2, with no additional information provided about which pairs may distinguish between viral, extracellular bacterial, and intracellular bacterial infections.
As to the drawings, Figures 2-5 contain data regarding discriminating between viral infections to intracellular and extracellular bacterial infections, but none compare intracellular bacterial infections to extracellular bacterial infections.
In view of the unpredictability in the art discussed above, it is not clear that the results discussed by Applicant would extend over the full scope of the claimed invention. Namely, Applicant has not shown that a single gene pair, or any of their gene pairs generally, can be used to specifically distinguish between viral, intracellular, and extracellular bacterial infections. The specification appears to only discuss these pairs generally with regard to viral versus general bacterial infections.
Quantity of Experimentation
The ordinary artisan would have to conduct a very large quantity of highly unpredictable experimentation before being able to successfully practice the full scope of the claimed methods. Specifically, the ordinary artisan would have to determine that each pair of genes described by the claim is capable of functioning as a marker for distinguishing between a viral, extracellular bacterial, or intracellular bacterial infection. Based on the teachings in the art, this would be an inventive and unpredictable undertaking, requiring extensive experimentation in which there is no guarantee of success. The large quantity of experimentation and its unpredictability constitute undue experimentation.
Conclusion
In view of the foregoing, it is clear that the specification fails to enable the scope of the claimed methods, and claims 8-10 and 16-21 are rejected under 35 U.S.C. 112(a) for failing to comply with the enablement requirement.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(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.
Claims 8-10 and 16-21 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kharti et al. (WO 2017/214061 A1; cited in Applicant’s IDS).
Regarding claims 8-10 and 16, Kharti teaches obtaining a biological sample from a subject, measuring the levels of expression for at least two biomarkers, and analyzing the expression levels to determine if the patient has a viral or bacterial infection (pages 17-18 joining para.). For bacterial biomarkers, a higher expression level indicates a bacterial infection, and the same applies to viral biomarkers. The bacterial biomarkers include PGD, SORT1, ACAA1, SORL1, DYSF, PROS1, and STAT5B. The viral biomarkers include SAMD9, IFIT5, IFIT3, IFI44L, IFI27, RSAD2, IFI44, DNMT1, IFIT2, ISG20, IFIT1, LY6E, JUP, HESX1, OAS1, OAS2, MX1, RSAD2, ISG20, and GZMB. These biomarkers can be RNA transcripts (page 27, para. 5). Kharti states that after performing this method and obtaining a patient diagnosis, a therapeutically effective amount of an anti-viral agent or antibiotic can be administered depending on if the patient has a viral or bacterial infection, respectively (page 37, para. 4).
Regarding claim 17, Kharti teaches that the levels of the biomarkers can be measured using RT-PCR (page 4, para. 7).
Regarding claim 18, Kharti teaches that polynucleotides can be analyzed via isothermal amplification (page 49, para. 5). The biomarkers of the invention can be polynucleotides (page 27, para. 5).
Regarding claim 19, Kharti teaches that the levels of the biomarkers can be measured using serial analysis of gene expression (SAGE; page 4, para. 7). This method involves determining nucleotide sequences derived from amplification products that contain cDNA derived from a sample, and therefore includes sequencing (pages 51-52 joining para.).
Regarding claim 20, Kharti teaches that the levels of the biomarkers can be measured using microarrays. On such arrays, probes corresponding to each of the target biomarkers are hybridized to a solid support (page 41, para. 2 through page 42, para. 3). These probes are specifically noted as being capable of hybridizing to mRNA or cDNA (page 42, para. 3).
Regarding claim 21, Kharti teaches that in any embodiment, the biological sample can be whole blood or peripheral blood mononucleated cells (page 4, para. 2).
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 8-10, 16-18, and 21 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 163-169 and 173-176 of copending Application No. 17/736,495 in view of Kharti et al. (WO 2017/214061 A1).
Claim 163 of the ‘495 application teaches receiving a biological sample from a subject and measuring the expression level of at least two genes, and using this expression information to determine if a subject has a bacterial or viral infection. The genes that may be used are in Table 8 of the specification of the ‘495 application, and include many genes in common with the instant application, such as LY6E and OAS1. Though this application does not specifically state that a subject may be treated depending on their type of infection, it would be obvious to do so in view of Kharti. Kharti teaches a similar method in which biomarker expression level is used to determine if a subject has a viral or bacteria infection, and teaches that after making this determination, a subject may be treated with an anti-viral or antibacterial agent (pages 17-18 joining para. and page 37, para. 4). The ordinary artisan would be motivated to use the method of the ‘945 application in view of the teachings of Kharti to treat the subject so as to improve patient outcomes. It is noted that the ‘945 application also contains additional limitations not explicitly described in instant claim 8 (e.g. the ROC curve information), but as the method of instant claim 8 comprises the listed steps, additional limitations are not precluded.
Thus, claim 163 of the ‘945 application in view of Kharti reads on instant claims 8-10.
Claims 164-169 of the ‘945 application further specify genes that may be used in the method. None recite closed groups of genes, and so may include others listed in Table 8, such as those in common with the instant application. Therefore, claims 164-169 in view of Kharti also read on claims 8-10.
Regarding instant claim 16, claim 163 of the ‘945 application does not specify the type of material that may be used to measure the gene expression data (e.g. DNA or RNA). Kharti teaches that genes themselves or RNA transcripts of genes may be used to measure gene expression levels (page 27, para. 5), and so it would be obvious that either could be used in the method of claim 163. Thus, this claim in view of Kharti reads on instant claim 16.
Regarding instant claims 17-18, claim 175 of the ‘945 application states that expression levels may be measured with RT-PCR or isothermal amplification. Further regarding claim 18, claim 176 of the ‘945 application teaches a specific type of isothermal amplification.
Regarding instant claim 21, claims 173-174 of the ‘945 application teach that blood samples may be used, with claim 174 specifically stating whole blood. These claims thus overlap in scope with instant claim 21.
This is a provisional nonstatutory double patenting rejection.
Conclusion
No claims are currently allowable.
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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/F.F.G./Examiner, Art Unit 1681
/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681