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. Election/Restrictions Applicant’s 01/07/2026 election without traverse of Group IV (claims 32 and 33) is acknowledged . As listed below, claims 1, 3-8, 10, 12-15, 18, 25, and 27-30 are withdrawn as drawn to nonelected inventions pursuant to 37 CFR 1.142(b), and the remaining claims (claims 32 and 33) are under examination. The Group election of Group IV (claims 32 and 33) stands, however, the Species election in the 11/05/2025 Requirement for Restriction is canceled, such that examination is not bound by any Species election. Office Action Outline Claim Status Pending: 1, 3-8, 10, 12-15, 18, 25, 27-30, and 32-33 Withdrawn: 1, 3-8, 10, 12-15, 18, 25, and 27-30 Examined: 32 and 33 Canceled: 2, 9, 11, 16-17, 19-24, 26, 31, 34-56 Independent: 3, 27, and 32 Amended 1, 4-8, 10, 12-15, 18, 25, 28, and 30 New: none Allowable: none Objected to: 32 Rejections applied Abbreviations 112/b Indefiniteness PHOSITA "a Person Having Ordinary Skill In The Art before the effective filing date of the claimed invention" 112/b "Means for" BRI Broadest Reasonable Interpretation 112/a Enablement, Written description CRM "Computer-Readable Media" and equivalent language 112 Other IDS Information Disclosure Statement X 102, 103 JE Judicial Exception X 101 JE(s) 112/a 35 USC 112(a) and similarly for 112/b, etc. 101 Other N:N page:line X Double Patenting MM/DD/ YYYY date format Priority As detailed in the 12/12/2023 filing receipt, this application is a 371 of PCT/US2022/013449, filed 01/24/2022, which claims benefit to Provisional Application No. 63/140,574, filed 01/22/2021 . Drawings The 07/19/2023 drawings are objected to as failing to comply with 37 CFR 1.84(u) as follows: The drawings on pp.2/49, 5/49, 9/49, 11-13/49, 15-17/49, 19/49, 23/49, 46/49, and 48/49 respectively recite "FIG. 1 CONT.," "FIG. 3 CONT.," "FIG. 6 CONT.," "FIG. 7 CONT.," "FIG. 8 CONT.," "FIG. 9 CONT.," "FIG. 13 CONT.," "FIG. 66 CONT.," and "FIG. 67 CONT." Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter (see MPEP 608.02(V) and 37 C.F.R. 1.84(u)). The following suggestions are examples of amendments which may help overcome the objection : (Please note, below is not a complete list of amendments to be made to the drawings. Amendments should be applied to all drawings in the list in the preceding paragraph.) • Page 1/49 , amend " FIG. 1 " to recite "FIG.1A” • Page 2/ 49 , amend " FIG. 1 CONT. " to recite "FIG.1B” • Page 11/49, amend "FIG. 7" to recite "FIG.7A” • Page 12/49, amend "FIG. 7 CONT." to recite "FIG.7B” • Page 13/49, amend "FIG. 7 CONT." to recite "FIG.7C” • Page 14/49, amend " FIG. 7 CONT." to recite "FIG.7D” Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance. Specification The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code , e.g., at page 48:26, 48:32, 49:11, etc. Applicant is required to delete all instances of the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. Claim Objections Claim 32 is objected to because of the following informalities: A grammatical article appears to be missing from claim 32 step c), which sh ould be amended to either "characterizing a host-targeted antimicrobial or anticytokine signature" or to "characterizing host-targeted antimicrobial or anticytokine signature s ." Appropriate correction is required. 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 32-33 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. MPEP 2106 details the following framework to analyze Subject Matter Eligibility: • Step 1 : Are the claims directed to a category of statutory subject matter (a process, machine, manufacture, or composition of matter)? (see MPEP § 2106.03) • Step 2A, Prong One : Do the claims recite a judicially recognized exception, i.e. an abstract idea, a law of nature, or a natural phenomenon? (see MPEP § 2106.04(a)). Note, the MPEP at 2106.04(a)(2) & 2106.04(b) further explains that abstract ideas and laws of nature are defined as: • mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations); • certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or • mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information). • laws of nature and natural phenomena are naturally occurring principles/ relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature. • Step 2A, Prong Two : If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application? (see MPEP § 2106.04(d)) • Step 2B : If the claims do not integrate the judicial exception, do the claims provide an inventive concept? (see MPEP § 2106.05) Step 1 : Claims 32-33 are directed to a 101 process, here a method , and therefore to a category of statutory subject matter. (See MPEP § 2106.03). (Step 1: Yes.) Step 2A, Prong One : The claims recite abstract ideas as follows: Claim 32 recites mental processes and mathematical concepts of: • identifying differentially expressed genes ( DEGs ) • characterizing host-targeted antimicrobial or anticytokine signature • identifying compounds that stimulate the anti-microbial or -cytokine signature • evaluating known and predicted targets of compounds identified in step d • constructing an infection host response protein-protein interaction (PPI) network and modules, • prioritizing compounds based on network proximity analysis, • clustering of prioritized compounds associated with selected disease modules, • selecting representative compounds from each cluster for in vitro assays, and • analyzing the results of steps a- i to thereby identify the compound for treating or preventing the infection. Claim 33 further limits the infectious microbe of claim 32 step a) to a coronavirus. Step 2A Prong One Summary: Claim 32 and 33 recite judicial exceptions of abstract ideas (characterized as mental processes and mathematical concepts). Considering the broadest reasonable interpretation (BRI) of the claims, the mental processes recited in independent claim 32 (e.g., identifying DEGs , characterizing signatures, identifying compounds, evaluating targets, constructing a PPI, etc.) are directed to processes that may be performed in the human mind, or with pen and paper, because there are no limitations recited which would prevent the analysis and generating of results mentally. Additionally, at least the limitations for prioritizing compounds and clustering the prioritized compounds inherently recite mathematical concepts such as those disclosed in Specification [122:17-123:19]. Such analysis performed mentally, or with paper and pencil, may take considerable time and effort, and although a general-purpose computer can perform these calculations at a rate and accuracy that can far exceed the mental performance of a skilled artisan, the nature of the activity is essentially the same, and therefore constitutes an abstract idea. Therefore, the claims recite elements that constitute a judicial exception in the form of an abstract idea. ( Step 2A, Prong One: Yes.) Step 2A, Prong Two: In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions ( JEs ). Here at Step 2A, Prong Two, any remaining steps and/or elements not identified as JEs are therefore in addition to the identified JE(s), and are considered additional elements. Because the claims have been interpreted as being directed to judicial exceptions (abstract ideas in this instance) then Step 2A, Prong Two provides that the claims be examined further to determine whether the judicial exception is integrated into a practical application [see MPEP § 2106.04(d)]. A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. 20. MPEP § 2106.04(d)(I) lists the following five example considerations for evaluating whether a judicial exception is integrated into a practical application: (1) An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a). (2) Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2). (3) Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b). (4) Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c). (5) Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e). The claims recite additional elements as follows: Additional elements of data gathering : Claim 32 recite s the additional element of obtaining data. Data gathering steps are additional elements which perform functions of inputting, collecting, and outputting the data needed to carry out the abstract idea. These steps are considered insignificant extra-solution activity, and are not sufficient to integrate an abstract idea into a practical application as they do not impose any meaningful limitation on the abstract idea or how it is performed, nor do they provide an improvement to technology [see MPEP § 2106.04(d)(I)]. Step 2A Prong Two summary : The claims have been further analyzed with respect to Step 2A, Prong Two, and no additional elements have been found, alone or in combination, that would integrate the judicial exception into a practical application. ( Step 2A, Prong Two: No ). Step 2B: Because the additional claim elements do not integrate the judicial exceptions (i.e., the abstract ideas) into a practical application, the claims are further examined under Step 2B , which evaluates whether the additional elements, individually and in combination, amount to significantly more than the judicial exception itself by providing an inventive concept. An inventive concept is furnished by an element or combination of elements that is recited in the claim in addition to the judicial exception, and is sufficient to ensure that the claim, as a whole, amounts to significantly more than the judicial exception itself (see MPEP § 2106.05). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that are well-understood, routine, and conventional. Those additional elements are as follows: Additional elements of data gathering : The additional element of obtaining data in claim 32 does not cause the claims to rise to the level of significantly more than the judicial exception. The courts have recognized receiving or transmitting data over a network; storing and retrieving information in memory; using polymerase chain reaction to amplify and detect DNA; detecting DNA or enzymes in a sample; analyzing DNA to provide sequence information or detect allelic variants; and amplifying and sequencing nucleic acid sequences , [see MPEP§2106.05(d)(II)], as well-understood, routine, conventional activity when they are claimed in a merely generic manner (e.g., at a high level of generality) or as extra-solution activity. Therefore the additional elements of data gathering are shown to be routine, well-understood, and conventional in the art, and do not provide an inventive concept needed to amount to significantly more than the judicial exception. All limitations of claims 32-33 have been analyzed with respect to Step 2B, and none provides a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception, and thus do not transform the judicial exception into a patent eligible application of the exceptions. Step2B: NO . Therefore, claims 32 and 33 , when the limitations are considered individually and as a whole, are rejected under 35 U.S.C. § 101 as being directed to non patent -eligible subject matter. 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. This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention. Claims 32 and 33 are rejected under 35 U.S.C. 103 as being unpatentable over Zhou , (Cell discovery, vol. 6(1):14, pp. 1-18 (2020); cited in the 09/26/2023 IDS) . Regarding obtaining transcriptomic data from cell infected with an infectious microbe, and identifying differentially expressed genes ( DEGs ) of claim 32 steps a) and b ), and wherein the microbe is coronavirus of claim 33 , Zhou shows collecting three differential gene expression data sets of hosts infected by human coronaviruses ( HCoVs ), two transcriptome data sets were SARSCoV -infected samples from patient’s peripheral blood (GSE1739) and one from Calu-3 cells (GSE33267) (p.15, col.2, ¶2). Regarding characterizing host-targeted antimicrobial or anticytokine signatures , identifying compounds that stimulate those signatures, and evaluating targets of the identified compounds of claim 32 steps c) , d), and e) , Zhou shows the three datasets were used as HCoV –host signatures to evaluate the treatment effects of drugs. Regarding constructing an infection host response protein-protein interaction (PPI) network and modules, prioritizing compounds based on network proximity analysis, and clustering of prioritized compounds associated with selected disease modules of claim 32 steps f ) , g ), and h) Zhou shows the interplay between the virus–host interactome and drug targets in the human PPI network (p.3, fig.1); drug-target network analysis of the HCoV –host interactome (p.6, fig.3); and a discovered drug- HCoV network, including network proximity (Z-score) between drug targets and the HCoV -associated proteins in the human interactome network (p.7, fig.4). Additionally, it would have be en obvious to use clustering on prioritized compounds. Regarding selecting representative compounds from each cluster for in vitro assays, and analyzing the results of the previous steps to identify the compound for treating or preventing the infection of claim 32 step i ) and j) , Zhou shows based on comprehensive evaluation, the prioritization of 16 candidate repurposable drugs (see Fig. 5, p.8-9) and three potential drug combinations (see Fig. 6, p.12) for targeting 2019-nCoV/SARS-CoV-2 (p.13, col.1, ¶2). It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use the drug repurposing method of Zhou with clustering for the prioritized compounds, as clustering is a widely known statistical technique for grouping data. One of ordinary skill would have had a reasonable expectation of success, as Zhou shows a network-based methodology for systematic identification of putative repurposable drugs and drug combinations for potential treatment of 2019-nCoV/SARS-CoV-2, and based on comprehensive evaluation of Zhou, 16 candidate repurposable drugs were prioritized. 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. Instant c laims 32 and 33 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 7 of reference Application No. 18/686,925 (the '925 application) i n view of Gordon , (Nature, vol.583(7816), pp.459-468 (2020); cited in the 09/26/2023 IDS) . Although the claims at issue are not identical, they are not patentably distinct from each other because reference claims 1 and 7 of the '925 application recite a method similar to instant claims 32 and 33 for analyzing RNA-seq data (i.e., transcriptome data) ; identifying differentially expressed genes ( DEGs ); deriving gene expression signatures associated with disease states of the disease using the DEGs and the differentially enriched biological pathways; identifying drugs predicted to reverse a particular gene expression signature; prioritizing the drugs predicted to normalize the particular gene expression signature; testing a drug or combination of drugs selected from the drugs ( '925, claim 1) and using clustering ( '925, claim 7). Reference claims 1 and 7 of the '925 application do not recite a Protein Protein Interaction network (PPI) as in instant claim 32, nor coronavirus as in instant claim 33. Regarding the PPI of instant claim 32 , and coronavirus of instant claim 33, Gordon shows analysis of SARS-COV2-host protein interactions (p.460, and entire document), showing both PPI and a coronavirus. It would have been obvious to one of ordinary skill in the art to modify the method of reference claims 1 and 7 of the '925 application to include the PPI and coronavirus of Gordon , as the method of Gordon identified PPIs between SARS-CoV-2 protein and human protein, which further led to identification of compounds targeting the interactions. One would have had a reasonable expectation of success in combining, as both Gordon and the '925 application are drawn to related teachings of d rug r epurposing, and as such, the combination would have been obvious. Accordingly, instant claims 32 and 33 are not patentably distinct from reference claims 1 and 7 of the ‘925 application. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented. Conclusion No claims are allowed. This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this action. Any inquiry concerning this communication or earlier communications from the examiner should be directed to FILLIN "Examiner name" \* MERGEFORMAT Meredith A Vassell whose telephone number is FILLIN "Phone number" \* MERGEFORMAT (571)272-1771 . The examiner can normally be reached FILLIN "Work Schedule?" \* MERGEFORMAT 8:30 - 4:30 . Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. 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If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /M.A.V./ Examiner, Art Unit 1687 /G. STEVEN VANNI/ Primary patents examiner, Art Unit 1686