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 .
New Examiner
The examiner assigned to your application in the USPTO has changed. To aid in correlating any papers for this application, all further correspondence regarding this application should be directed to James (Doug) Schultz, Supervisory Patent Examiner, Art Unit 1631.
Allowance Vacated
Applicant is advised that the Notice of Allowance mailed 16 April 2025 is vacated. The indicated allowability of claims 29-33, 35-36, 38, 40-41, 43, 45, 47-48, 52-53 and 56-71 is withdrawn in view of the newly discovered reference(s), considerations and rejections cited below.
If the issue fee has already been paid, applicant may request a refund or request that the fee be credited to a deposit account. However, applicant may wait until the application is either found allowable or held abandoned. If allowed, upon receipt of a new Notice of Allowance, applicant may request that the previously submitted issue fee be applied. If abandoned, applicant may request refund or credit to a specified Deposit Account.
Election/Restrictions
In view of the vacated notice of allowance discussed above, the restriction requirement mailed 16 December 2024 is reinstated. This is because rejoinder of non-elected methods was predicated on allowability of the elected compositions, and the allowability of the compositions has been withdrawn. Accordingly, applicant’s election of Group I, reading on originally presented claims 29-32, and further on claims 56-59 that were added subsequent to said restriction requirement mailed 16 December 2024, is acknowledged. All requirements to elect species have been withdrawn in full. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement in the response of 19 December 2024, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 33, 35, 36, 38, 40, 41, 43, 45, 47, 48, 52, 53, 60-71 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 19 December 2024.
Finally, the examiner reaffirms Applicant’s right to rejoinder of method claims that properly depend from an allowable composition claim and recite all limitations of such allowable composition claims, provided prosecution is open at that time.
Claims 29-32 and 56-59 are examiner on the merits herein.
Claim Interpretation of independent claim 29
Claim 29 is the sole independent claim under examination, and merits standalone discussion given the complexity of the subject matter and applicable patent law. Discussion of claim interpretation for all dependent claims has been provided as appropriate in the rejections below.
Claim 29 recites “[a] cell-containing composition comprising:
a population of anterior foregut endoderm (AFE) cells cultured in a medium containing bone morphogenetic protein 4 (BMP4), and retinoic acid (RA), wherein the medium is absent a transforming growth factor beta (TGFβ) inhibitor, and absent TGFβ; and
the composition further comprises at least one third pharyngeal pouch (TPP) cell.”
With regard to the claim interpretation of claim 29, it is first noted this claim reads on a composition comprising a cell (or cells) that have been subjected to a step of culturing in specific reagents recited in claim 29. Said cell composition is not construed as requiring the medium or any of the reagents recited in claim 29 per se, since reference to the medium and its reagents is made in the context of a “step” (i.e. a process) requiring AFE cells that have been “cultured in a medium” comprising the specified reagents. Note the use of the verb “cultured”. Accordingly, since the claims are drawn to a composition comprising AFE cells that have been treated according to a process step (i.e. cultured in a medium comprising the specified reagents), claim 29 is considered to read on a cell composition claimed as a product-by-process, specifically AFE cells that are induced by culturing in a medium comprising the specified reagents to result in TPP cells. It is well understood in the art that third pharyngeal pouch (TPP) cells are derived from AFE cells cultured in reagents such as those recited in claim 29 a (as evidenced by claim 33 for example).
It is well-accepted case law that product-by-process claims are not limited to the manipulations of the recited steps, only the structure implied by the steps. See M.P.E.P. § 2113(I). The cell composition of claim 29 is therefore interpreted as encompassing AFE cells (the input cell) that have been wholly or partially induced to TPP cells (the output cell). The composition therefore comprises at least TPP cells and optionally, AFE cells and/or cells that are induced along the pathway between AFE cells and TPP cells that have not yet been fully differentiated into TPP cells. In the de minimis sense, claim 29 reads on as little as a cell composition comprising TPP cells in the situation where induction of all AFE input cells into TPP output cells is complete.
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 30 and 57 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. This is a new matter rejection.
With regard to claim 30, it is noted that this claim was added after the initial filing date. Moreover, the instant specification appears not to disclose the term “D8” as a cell marker or any other type of protein that may be expressed in the recited AFE cells. While the instant specification recites the term “CD8”, it does not appear to do so in the context of AFE cells per se. Regardless “CD8”is not equivalent to “D8”. Finally, the prior art appears to be silent as to the use of this term, or its presence as a diagnostic agent for AFE cells. Accordingly, reference to D8 positive AFE cells is considered to comprise improper addition of new matter, and is rejected therefore.
With regard to claim 57, a review of the specification results in the finding that there is no explicit textual disclosure in the provided specification that a single, defined composition is prepared or formulated to include two cell types where one was incubated in TGFβ and the other was not. The examiner is unable to locate any explicit passage in the specification that states that a single cell-containing composition simultaneously includes two cell types where one was incubated in TGFβ and the other was not. While the specification does describe stage-specific presence/absence experiments with TGFβ and TGFβ inhibitors and reports little effect on certain markers. Relevant passages include:
“The present data indicate that the addition of TGFβ during the anterior foregut endoderm (AFG) to TEP or during the TPP to TEP stages had very little effect on the differentiation efficiency… Additionally, TGFβ addition has no effect on the induction of TPP markers HOXA3 and EYA1 (Fig. 8C).” [0119]
Differentiation conditions include an example with LY364947 (a TGFβ receptor inhibitor) during days 5–13 (Condition 4): “LY364947, 5 µM (d5–13).” [0116], [0120]These show that both TGFβ signaling and its inhibition were manipulated at different stages in vitro.
The data also show heterogeneity at specific time points, implying mixed populations within the same culture: “Quantification of the TPP marker HOXA3 protein revealed that approximately 40% of cells differentiated with the disclosed methods express this marker [at day 9].” See ¶¶ [0076], [0115–0117]. While this implies that non-HOXA3+ cells co-exist in the same culture, the specification does not expressly label those non-HOXA3+ cells as AFE, nor does it explicitly link their prior culture history to “no TGFβ,” while the HOXA3+ cells were “with TGFβ.”
Accordingly, the specification is considered to support that different stages of the differentiation protocol are performed under different TGFβ conditions and that cultures are heterogeneous at certain time points, which provides implicit support for mixed cell populations with differing TGFβ exposure histories. However, there does not appear to be explicit or implicit textual disclosure in the provided specification that a single, defined composition is prepared or formulated to include two cell types where one was incubated in TGFβ and the other was not. The subject matter of claim 57 is thus considered to comprise new matter therefore.
Claim Rejections - 35 USC § 112
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 30 and 32 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 32 recites “The cell-containing composition according to claim 29, wherein the population of AFE cells are derived from a population of induced pluripotent stem cells (iPSCs) comprising a population of hematopoietic stem cells (HSCs), lymphocytes, peripheral blood mononuclear cells (PBMCs), cells isolated from cord blood, or somatic cells or combination thereof.”
Claim 30 is indefinite for reciting D8 (D8+) positive AFE cells. Notwithstanding the rejection of claim 30 above for new matter relating to the introduction of reference to D8 positive AFE cells, it is noted that the instant specification fails to provide any definition for this marker or its relationship to the recited AFE cells. Moreover, the examiner is unable to locate after a review of the prior art examples of a D8 marker or protein expressed in AFE cells. Accordingly, claim 30 is indefinite for reciting an apparently unknown and presently undisclosed/undescribed marker of AFE cells.
Claim 32 is indefinite for vaguely reciting the relationship between the recited IPSCs and the remaining non-iPSC cells (i.e. HSCs, lymphocytes, PBMCs, cells isolated from cord blood, or somatic cells). If the intention is to recite that the population of IPSCs further comprises the other recited cells, then the claim should be amended to recite this. If the intention is to recite that the population of IPSCs is derived or generated from the non-IPSC cells, then the claim should be amended to recite this (as in claim 58, which clearly states the relationship between the non-IPSCs and IPSCs. Otherwise, the claim improperly suggests that the population of IPSCs is equivalent to the other recited cells.
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.
Claim 29, 31, 32 and 56-59 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a naturally occurring product without significantly more.
The most recent update to the Office’s patent eligibility requirements are the 2019 Revised Patent Subject Matter Eligibility Guidance (2019 PEG) published on January 7 and October 19, 2019 (84 Fed. Reg. 50), which provides the following analysis to determine patent eligibility, derived from the decisions rendered in Mayo Collaborative Svcs. v. Prometheus Labs., 566 U.S. __, 132 S. Ct. 1289, 101 U.S.P.Q.2d 1961 (2012) (hereinafter “Mayo”), and in Alice Corp. Pty. Ltd. v CLS Bank Int’l, 573 U.S. __, 134 S. Ct. 2347, 110 U.S.P.Q.2d 1976 (2014) and subsequent court cases:
Step 1 is to determine whether the claim is directed to a process, machine, manufacture, or composition of matter. If the claim is directed to a statutory category, proceed to Step 2.
Step 2 is the two-part analysis from Alice Corp. (also called the Mayo test).
Step 2A has been divided into 2 prongs.
Step 2A, prong 1 requires determining whether the claim is directed to the judicial exceptions of an abstract idea, a product of nature, or a law of nature or natural phenomenon other than a product of nature. To determine if the claim recites a nature-based product limitation, the markedly different characteristics analysis is used to evaluate whether the claim is directed to a “product of nature” that falls under the law of nature and natural phenomenon exceptions. In this analysis, markedly different characteristics can be expressed in terms of the product’s structure, function, and/or other properties. If YES, the claim is directed to a judicial exception, proceed to step 2A, prong 2.
Step 2A, prong 2 requires evaluating whether a judicial exception is integrated into a practical application (e.g. improving technology, effecting a particular treatment or prophylaxis, implementing with a particular machine, etc.) identified by the Supreme Court and the Federal Circuit, to ensure that the claim as a whole “integrates [the] judicial exception into a practical application [that] will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, such that the claim is more than a drafting effort designed to monopolize the judicial exception.” If NO, the claim does not integrate the judicial exception into a practical application, then proceed to step 2B.
Step 2B requires analyzing whether the claim as a whole amounts to significantly more than the exception by determining whether any element, or combination of elements, in the claim is sufficient to ensure that the claim as a whole amounts to significantly more than the judicial exception. To be patent-eligible, a claim that is directed to a judicial exception must include additional features to ensure that the claim describes a process or product that applies the exception in a meaningful way, such that it is more than a drafting effort designed to monopolize the exception. The Supreme Court has identified the following non-limiting considerations for determining whether a claim with additional elements amounts to significantly more than the judicial exception itself:
• Improvements to another technology or technical field;
• Improvements to the functioning of the computer itself;
• Applying the judicial exception with, or by use of, a particular machine;
• Effecting a transformation or reduction of a particular article to a different state or thing;
• Adding a specific limitation other than what is well-understood, routine and conventional in the field, or adding unconventional steps that confine the claim to a particular useful application; or
• Other meaningful limitations beyond generally linking the use of the judicial exception to a particular technological environment.
Claim 29 has been discussed above, and as stipulated therein, reads on as little as a cell composition comprising TPP cells. Regarding step 1 of the analysis above, the claims are drawn to a composition of matter. Regarding step 2A prong 1, the claims of been construed as reading on a cell composition comprising TPP cells. TPP cells are naturally occurring. For example, the instant specification as filed at paragraph 70 teaches that “The thymus is a glandular organ that is essential for the generation of a functional adaptive immune system by providing positive and negative selection of developing T-cells. The thymus is an endodermal derived tissue and originates from the third pharyngeal pouch (TPP) during embryonic development.” Regarding step 2A prong 2, the claims are not integrated into a practical application because claim 29 is a composition claim that recites no particular use. Even if a use were to be recited, it is well accepted case law that an intended use recited in a composition claim does not limit the claim unless it confers a structural or manipulative difference. See M.P.E.P. § 2111.02(II): “During examination, statements…reciting the purpose or intended use of the claimed invention must be evaluated to determine whether or not the recited purpose or intended use results in a structural difference…”. Regarding step 2B, the claims are not held to recite significantly more, since there is no disclosed structural or functional difference in either the instant specification or the prior art between the TPP cells of claim 29 and naturally occurring TPP cells. The claims thus recite ineligible patent subject matter since they are drawn to a product of nature.
Claim 30 recites the cell composition of claim 29 wherein the AFE cells comprise D8 positive AFE cells. To the extent that AFE cells may be positive for a D8 marker (notwithstanding the rejections above for new matter and indefiniteness regarding this term) and under the presumption /interpretation that this marker is otherwise inherent to AFE cells, claim 30 is rejected for the same reason claim 29 is, i.e. that the claimed cell composition is ultimately drawn in its de minimis form to a composition comprising TPP cells and nothing more, and additionally since there is no evidence of record that cells induced from AFE cells that may be positive for D8 are induced to TPP cells that are otherwise distinguishable from those found in nature as discussed above in claim 29.
Claim 31 requires the TPP cell to express either HOXA3 or EYA1, or both. TPP cells naturally express at least HOXA3. See Sultana et al. (Blood 2009;113:2976-2987), 2nd ¶ of introduction.
Claims 32 and 58 require that the AFE input cells are derived from IPSCs that comprise HSCs, lymphocytes, PBMCs, cells isolated from cord blood, or somatic cells. Notwithstanding the rejection of claim 32above for indefiniteness, neither the instant specification nor the prior art indicates that there is any marked difference (i.e. by structure or function) between TPP cells that are naturally occurring and those that are derived from IPSCs, and thus the cells of claim 32 are not distinguished from those of that are otherwise naturally occurring.
Claim 56 requires the TPP cells to comprise at least the expression of FOXN1. TPP cells naturally express at least FOXN1. See Sultana et al. (Blood 2009;113:2976-2987), 3rd ¶ of introduction.
Claims 57 and 59 require specific culture conditions leading to derivation of the recited TPP cells. Regardless of the means of derivation, the claim remain directed to TPP cells that are not markedly different from those that occur in nature (i.e. not differing in either structure or function).
Regarding step 2A prong 2, as with claim 29, claims 30-32 and 56-59 are not integrated into a practical application because they are drawn to a composition claim that recite no particular use. Even if a use were to be recited, it is well accepted case law that an intended use recited in a composition claim does not limit the claim unless it confers a structural or manipulative difference. See M.P.E.P. § 2111.02(II): “During examination, statements…reciting the purpose or intended use of the claimed invention must be evaluated to determine whether or not the recited purpose or intended use results in a structural difference…”. Regarding step 2B, the claims are not held to recite significantly more, since there is no disclosed structural or functional difference in either the instant specification or the prior art between the TPP cells of claims 30-32 and 56-59 and naturally occurring TPP cells. The composition claims lack additional elements that transform the nature-based products into patent-eligible subject matter. The recited culture conditions (BMP4 and RA, absence of TGFβ or TGFβ inhibitor) describe how a population of AFE cells is produced but do not change the claimed product from a naturally occurring cell type into something markedly different in structure or function. The claims thus recite ineligible patent subject matter since they are drawn to a product of nature.
Finally, it is noted that even if the claims are read to encompass the presence of both AFE and TPP cells, The mere presence of two naturally occurring cell types together in a composition (AFE and TPP) is analogous to mixing natural products; absent a recited change in properties or a functional interaction that is not naturally occurring, the co-presence alone does not supply “significantly more” and is akin to the Funk Brothers line of authority. The claims (composition and product-by-process recited cell composition claims) are rejected under 35 U.S.C. § 101 as directed to products of nature / natural phenomena without reciting additional features that amount to “significantly more.”
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.
(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.
Claim(s) 29-32 and 56-59 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Su et al. , M., Hu, R., Jin, J. et al. Efficient in vitro generation of functional thymic epithelial progenitors from human embryonic stem cells. Sci Rep 5, 9882 (2015) as evidenced by Sultana et al. (Blood 2009;113:2976-2987).
Regarding claim 29, Su teaches a differentiation protocol that results in the generation of cell -containing compositions comprising 3rd pharyngeal pouch cells. Figure 1 of Su presents a schematic of their differentiation protocol. hESCs were induced to generate DE that further developed into TEPs in the presence of BMP4 + FGF7 + FGF10 + EGF + RA (BFFER), rFOXN1 (100 ng/ml) and rHOXA3 (200 ng/ml).
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Su teaches that they first induced the differentiation of hESCs into DE that was further induced to develop into TEPs. Su teaches: “[a]lthough our protocol does not include separate steps that direct the differentiation of DE into the third PPE, or anterior foregut endoderm (AFE) and ventral pharyngeal endoderm (VPE) [references omitted], our kinetic analysis of the expression genes related to PPE and TEPs indicates that on days 9–11 the DE developed into the third PPE or VPE which then further developed into TEPs on day 14. (1st ¶ of discussion).
It is noted that Su does not teach the use of TGFβ or an inhibitor thereof. However, even if the conditions were not met by Su (a position not adopted), it is emphasized from the claim construction discussion above with regard to claim 29 that claim 29 does not require the actual presence or absence of the recited factors since these factors limit only the process (i.e. “cultured”) step, which does not limit a product claim if the product is otherwise indistinguishable. The claims are held to read on a cell composition comprising TPP cells and optionally AFE cells.
Claim 30 is included in the instant rejection notwithstanding the rejections above regarding the presence or absence of D8+ AFE cells, since AFE cells are not actually required to be present in the cell -containing composition, but are rather the “input” cell that is induced into a TPP cell. There is no evidence of record to suggest that the “output” (i.e. TPP) cell is any different in structure or function based upon its derivation from a D8+ or D8- AFE cell. Furthermore, even if the claims require the presence of D8+ AFE cells (again notwithstanding the rejections for new matter and indefiniteness presented above), this marker is presumed to be inherent to all AFE cells in the absence of evidence to the contrary.
Regarding claim 31, Sultana evidences that TPP cells express at least 1 of HOXA3 and EYA1. See 2nd ¶ of introduction of Sultana.
Regarding claims 32 and 57-59, it is noted that these limitations are directed to the method steps by which the AFE cells are derived. Since AFE cells are not held to be required in the claims as presently constructed, they are not limiting and are thus rejected for the same reasons that claim 29 is above. Furthermore, even if they were limiting (a position not adopted), AFE cells derived by any means remain AFE cells, and their methods of derivation are not held to structurally or functionally impact the AFE cells of the prior art and are included in the rejection for the same reasons that claim 29 is above.
Claim(s) 29-32 and 56-59 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Sun et al. (Cell Stem Cell, Volume 13, Issue 2, 2013, Pages 230-236), as evidenced by Sultana et al. (Blood 2009;113:2976-2987).
Regarding claim 29, Sun teaches a differentiation protocol that results in the generation of cell-containing compositions comprising 3rd pharyngeal pouch cells. Sun teaches Shows that DE goes to third PPE, which is equivalent to the instantly recited TPP cells. It is noted that Sun does not teach the use of TGFβ or an inhibitor thereof. However, even if the conditions were not met by Sun (a position not adopted), it is emphasized from the claim construction discussion above with regard to claim 29 that claim 29 does not require the actual presence or absence of the recited factors since these factors limit only the process (i.e. “cultured”) step, which does not limit a product claim if the product is otherwise indistinguishable. The claims are held to read on a cell composition comprising TPP cells and optionally AFE cells. See Sun, figure 1A for example.
Claim 30 is included in the instant rejection notwithstanding the rejections above regarding the presence or absence of D8+ AFE cells, since AFE cells are not actually required to be present in the cell -containing composition, but are rather the “input” cell that is induced into a TPP cell. There is no evidence of record to suggest that the “output” (i.e. TPP) cell is any different in structure or function based upon its derivation from a D8+ or D8- AFE cell. Furthermore, even if the claims require the presence of D8+ AFE cells (again notwithstanding the rejections for new matter and indefiniteness presented above), this marker is presumed to be inherent to all AFE cells in the absence of evidence to the contrary.
Regarding claim 31, Sultana evidences that TPP cells express at least 1 of HOXA3 and EYA1. See 2nd ¶ of introduction of Sultana.
Regarding claims 32 and 57-59, it is noted that these limitations are directed to the method steps by which the AFE cells are derived. Since AFE cells are not held to be required in the claims as presently constructed, they are not limiting and are thus rejected for the same reasons that claim 29 is above. Furthermore, even if they were limiting (a position not adopted), AFE cells derived by any means remain AFE cells, and their methods of derivation are not held to structurally or functionally impact the AFE cells of the prior art and are included in the rejection for the same reasons that claim 29 is above.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to J. Douglas Schultz whose telephone number is (571)272-0763. The examiner can normally be reached M-F 8-5 PST.
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J. Douglas SCHULTZ
Supervisory Patent Examiner
Art Unit 1631
/JAMES D SCHULTZ/Supervisory Patent Examiner, Art Unit 1631