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Patent Application 17743367 - Data Processing Device and Method for the - Rejection

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Patent Application 17743367 - Data Processing Device and Method for the

Title: Data Processing Device and Method for the Evaluation of Mass Spectrometry Data

Application Information

  • Invention Title: Data Processing Device and Method for the Evaluation of Mass Spectrometry Data
  • Application Number: 17743367
  • Submission Date: 2025-04-09T00:00:00.000Z
  • Effective Filing Date: 2022-05-12T00:00:00.000Z
  • Filing Date: 2022-05-12T00:00:00.000Z
  • National Class: 702
  • National Sub-Class: 019000
  • Examiner Employee Number: 81580
  • Art Unit: 1635
  • Tech Center: 1600

Rejection Summary

  • 102 Rejections: 0
  • 103 Rejections: 1

Cited Patents

The following patents were cited in the rejection:

Office Action Text


    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 .

Information Disclosure Statement
The IDS filed 1/16/2023 has been considered by the Examiner.  

Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged.  Priority of US application 15/318,101 filed 12/12/2016  is acknowledged. Priority to provision application 62/012,228, or foreign applications GB1415273.o and GB1419699.2 is not granted because the claimed system and process steps performed by the system are not found in the provisional and foreign applications.

Status of Claims
Claims 1-20 are under examination.

Claim Rejections - 35 USC § 101
The following rejection is maintained for reasons in the Office Action of 8/1/2024 and modified in view of Amendments filed 10/31/2024.
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
Claims 1-20 are drawn to a system comprising a processor unit, storage and mass spectrometer (claim 20), so a machine.
Step 2A Prong One: Identification of an Abstract Idea
The claim(s) recite(s):
1. process a plurality of mass spectrometry data sets provided by a mass spectrometer from a plurality of samples introduced into the mass spectrometer, each mass spectrometry data set comprising: value pairs of measured intensity versus mass or mass over charge, a spectrum over a defined frequency range or a transient given over a defined time span.
This step reads on a process that can be performed by the human mind because processing mass spectrometry date sets reads on performing calculations or general analysis by human thinking. The limitation reciting that the data sets were “provided by a mass spectrometer from a plurality of samples introduced into the mass spectrometer,” only describes where the data originated but does not further limit the step of processing. The step is therefore an abstract idea.
2. processing being carried out in one, two or more processing steps and comprising: adjusting a mass scale, normalizing the intensity and/or identifying compound producing items of processed data comprising processed mass spectrometry data sets and/or identifications of compounds.
This limitation drawn to processing being carried out by a plurality of steps of adjusting a mass scale, normalizing the intensity and/or identifying compound producing items reads on a step that can be performed by the human mind. The recited “processing” reads on an analysis that can be performed as a mental process. Adjusting a mass scale, normalization or identifying compound producing items can be performed by the human mind. The step is therefore an abstract idea.
3. each saved item of additional data or each saved item of processed data and each saved item of additional data is connected to at least one saved mass spectrometry data set mass spectrometry data set to be retrievable as sets of corresponding data items.
This limitation describing connected data in a storage reads on an abstract idea because the limitation is broad with respect to how the data is connected. The connection reads on a data that is listed together in a list, table or a graph including a graph connected by pointers or arrows such as a tree or directed graph. Generally reciting connected data reads on an abstract idea because such connections can be made with a mental process or with the aid of paper/pen. The limitation is therefore an abstract idea.
4. group, select and/or modify mass spectrometry data and/or items of processed data according to one or more of the properties of the sample saved in the storage unit as saved items of additional data, the mass spectrometry data and/or items of processed data retrieved by the storage unit based on the one or more properties of the sample as set of corresponding data items.
The step of grouping, selecting or modifying mass spectrometry data or items of processed data according to properties of the sample can be performed by the human mind and is drawn to an abstract idea. The limitation reciting that the data items of processed data were “retrieved by the storage unit based on the one or more properties of the sample as set of corresponding data items” only describes the data’s origins. 
5. calculate intensity ratios of peaks from the first subset of data and peaks from the second subset of data.
This step reads on math and on a mental process and is therefore an abstract idea. Calculating intensity ratios of peaks can be performed by the human mind with math. 
Dependent claims 2-4, 7-9, 11-13 and 15 further recite limitations drawn to abstract ideas or descriptions of how the data originated. Claim 2 is drawn to the abstract idea of assigning an identifier and connecting data. Claims 3-4 are drawn to the abstract idea of defining dynamic tables. Claim 9 describes the type of sample used to collect the data which only characterizes the data. Claim 11 is drawn to the abstract idea of defining sequences. Claim 12-13 are drawn to the abstract idea of defining a workflow. Claim 15 is drawn to comparing processing steps which is an abstract idea. The claims are therefore also judicial exceptions.

Step 2A Prong Two: Consideration of Practical Application
The claims are drawn to steps of analyzing mass spectral data and resulting steps of grouping, selecting or modifying mass spectrometry data, calculating intensity ratio from peaks and providing a visualization of a comparison of a first subset and second subset of data The claims do not recite any additional elements that integrate the recited abstract idea into a practical application because providing a visualization of calculation results and organized information is an extra solution activity as described in MPEP 2106.05(g).
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field; 
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition; 
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses 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.

Step 2B: Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to: 
1. a processor adapted to process mass spectrometry data, as in claim 1.
2. a storage unit adapted to save, store and retrieve mass spectrometry data, as in claims 1, 14, and 16.
3. a data interface for defining dynamic data types, as in claim 1.
4. retrieve a first and second subset of processed data based on a first and second study variable, as in claim 1. 
5. provide a visualization of a comparison of data, as in claim 1.
6. the relational database comprises dynamic tables, as in claims 3 and 5-6.
7. module interface for adding dynamic modules, as in claim 10.
8. a visualization unit (i.e. computer monitor and printer), instrument interface and mass spectrometer, as in claims 17-20.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because processors and storage units (i.e. computer memories) are generic computer structures that perform well known computer functions. 
The newly amended step of retrieving data from a storage unit reads on transmission of data which is an extra solution activity. The newly amended limitation of providing a visualization of data comparison is also considered an extra solution activity. See MPEP 2106.05(g) discussion transmission of data and displaying data resulting from an abstract idea. Data or information must be received or collected in order to carryout an abstract idea. Such is nominal pre-solution or extra solution activity. Displaying results of calculations is also considered tangential and an extra solution activity. 
The recited data interface is also well known, routine and conventional. The specification (par. 0117) describes an embodiment of the interface as an object oriented mapper. O’Neil (Proceedings of the 2008 ACM SIGMOND international conference of Management of data, 2008) teach Microsoft’s Entity Data Model for .NET systems (Abstract) which is an object/relational mapper.  O’Neal teaches that the Entity Model maps for application objects to tables (page 1351, col. 2, par. 3) and contains database tables and relational tables (i.e. predefined and dynamic tables). Therefore O’Neil evidences that object oriented mappers as data interfaces are well known. The object oriented mapper is also analogous to that described in the specification (par. 0117) which is an “Entity Data Service,” or mapper that maps .NET classes to tables in a database file.
The claims do not include additional elements that are sufficient to amount of significantly more than the judicial exception because the recited additional elements are routine computer structures for storing, retrieving and processing data. The recited dynamic tables, module interface, visualization unit, instrument interface of claims 3, 5, 6, 9, and 16-19 are routine computer structures. The module interface reads on an input unit for entering programming instructions. The visualization unit is described in the specification (par. 0054) as a monitor or printer. The mass spectrometer recited in claim 20 is also a routine device that is routinely coupled with a computer by an instrument interface.
Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself.  Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter. 

Response to Arguments
Applicant's arguments filed 10/31/2024 have been fully considered but they are not persuasive. 
Applicants argue that the specification of the instant application states that the disclosed method improves the efficient use of computational resources by splitting  the processing workflow into constant and variable parts cut that the common results need not be recomputed. 
In response, Applicant’s arguments are not reflected in the claims. The claims do not include steps of splitting a processing workflow into constant and variable parts. Instead, the claims are drawn to storing and retrieving mass spectra data to arrive at calculating intensity ratios between a first and second subset of processing data and visualize a comparison of the two subsets. Furthermore, with respect to Applicant’s arguments, the instant claims are not directed to any kind of specialized data processing method where data is specifically “split” and specially allocated to processors to arrive at improved computational efficiency. Also, it is noted that merely filtering data is also not an improvement to a computer because the computer functionality does not change, i.e. data is simplified as a result of an abstract idea but, the processor functions as it would ordinarily. 
Applicants argue that here the claims recite concrete and specific steps implemented by various devices to accomplish the task of identifying compounds and assessing influence of study variables.
In response, specific steps that encompass processes performed by the human mind or with math, performed by a generic computer (involving specific parts ordinarily found in a routine computers) for processing efficiency are not sufficient to render claims patent eligible. The claims are directed to determining intensity ratios and providing a comparison of two subsets of data. The process as claimed involves routine storage units that save and retrieve the data that is calculated. These routine storage units are tangential to the process that the claims are directed to, which is analysis of mass spectrometry data. However, the recited analysis of the mass spectrometry data are recited as steps that can be performed by the human mind or with math.


Claim Rejections - 35 USC § 112-2nd paragraph
The instant rejections are maintained for reasons of record in the Office action of 8/1/2024.

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 4, 6, 8 and 9 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 pre-AIA  the applicant regards as the invention.
Claim 4 recites “wherein a storage form of an item of the defined dynamic data type is converted into a processing form when retrieving data from the storage unit, and the processing form of an item of the defined dynamic data type is converted into the storage form when saving data to the storage unit.” It is unclear how this limitation is intended to further limit the system of claim 1. Claim 1 is drawn to a processor configured to process mass spectrometry data and a storage unit adapted to store and retrieve mass spectrometry data. The system of claim 1 does not recite any active steps of retrieving data from the storage unit or saving data to the storage unit. It therefore not clear how this claim is intended to further limit the system of claim 1.
Claim 6 recites the system of claim 1, “wherein one dynamic table is created for each connection between two dynamic data types.” .” It is unclear how this limitation is intended to further limit the system of claim 1. Claim 1 is drawn to a processor and a storage unit comprising a data interface for defining dynamic data type (dynamic tables). It is not clear if claim 6 is attempting recite a process step of creating a dynamic table performed by the processor or if claim 6 further describes how the data interface is configured. 
Claim 8 recites “wherein the samples introduced in the mass spectrometer contain protein and/or peptides.” This limitation is drawn to a method step. It is unclear how this limitation is intended to further limit the system of claim 1. Claim 1 is a system comprising a processor, storage unit and data interface and does not recite any steps drawn to introducing samples into a mass spectrometer. 
Claim 9 also recites a limitation which is drawn to a method step wherein it is not clear how “wherein the samples introduced in the mass spectrometer contain a drug…” is intended to further limit the system of claim 1.
Claim 9 recites “and modification” wherein it is unclear what is meant by “modification” or if this is a typographical error. Clarification is needed.

Response to Arguments
Applicant's arguments filed 10/31/2024 have been fully considered but they are not persuasive. 
Regarding claim 4, the claims are directed to a system which is a product with parts. The parts are a processor and a storage unit. Claim 4 recites “wherein a storage form of an item of the defined dynamic data type is converted into a processing form when retrieving data from the storage unit, and the processing form of an item of the defined dynamic data type is converted into the storage form when saving data to the storage unit.” It is not clear how this limitation is further limiting the structure or functionality of the storage unit. The limitation is drawn to a process that acts on the data in the storage unit however the claims are not drawn to a system which includes data but only to a processor and storage unit for processing and saving/retrieving data. Furthermore, it is not clear what is performing these active steps of converting data into a processing form and storage form. The claims are drawn to a system of parts comprising a processor and storage. The claimed system does not include any instructions to covert data into processing and storage form.
Regarding claims 8 and 9, Applicants have not clarified the limitations in these claims. Claim 8 and 9 similarly recite process steps which further limit parts that are not part of the claimed system. Claims 8 and 9 describe the plurality of samples introduced into the mass spectrometer. However, the system of claim 1 does not recite a mass spectrometer, but only a processor and storage. Also, the hanging term “modification” in claim 9 has not been clarified.

Claim Rejections - 35 USC § 102
	The rejection of claims 1, 3, 5-14 and 16-20 under 35 U.S.C. 102(a) as being anticipated by Sharma et al. (Molecular and Cellular Proteomics vol. 11 (2012) pgs. 824-832; IDS filed 1/16/2024) is withdrawn in view of Applicant’s amendments filed 10/31/2024.  
	
Claim Rejections - 35 USC § 103
	The instant rejection is necessitated by Applicant’s amendments filed 10/31/2024.	
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains.  Patentability shall not be negatived by the manner in which the invention was made.

	This application currently names joint inventors.  In considering patentability of the claims under 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary.  Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
	Claims 1, 3, 5-14 and 16-20 are rejected under 35 U.S.C. 103(a) as being unpatentable over Sharma et al. (Molecular & Cellular Proteomics vol. 11 (2012) pgs. 824-832; IDS filed 1/16/2023) in view of Oda (US 2009/0148960).
	Sharma et al. teach software for searching and comparing results from mass spectrometry experiments (Abstract and Figure 1 “Data Acquisition, MS Scans”)(i.e. processor unit adapted to: process a plurality of mass spectrometry data sets provided by a mass spectrometer from a plurality of samples introduced into the mass spectrometer, each mass spectrometry data set comprising: value pairs of measured intensity versus mass or mass over charge,  a spectrum over a defined frequency range or  a transient given over a defined time span), as in claim 1.
	Sharma et al. teach computational data processing peptide serum matching, PEP and FDR analysis (which identifies peptides) and protein inference and outputting to a data file (Figure 1)(i.e. the processing being carried out in one, two or more processing steps and comprising identifying a compound producing items of processed data comprising processed mass spectrometry data sets and/or identifications of compounds), as in claim 1.
	Sharma et al. teach a relational database (Abstract), file systems, hard drives (page 824, col. 2,  par. 2)  and databases (page 825, col. 1-2)(i.e. a storage unit adapted to save and retrieve the mass spectrometry data sets and/or the items of processed data, and items of additional data, the items of additional data comprising properties of the sample introduced in the mass spectrometer that are study variables). It is noted that the limitation reciting properties of the sample introduced in the mass spectrometer and how the data was collected form a mass spectrometer does not serve to further limit the recited storage unit.
	Sharma et al. teach that the databases include a set of tables (i.e. dynamic data types) and include core attributes; wherein the tables are populated for every mass spectrometry run, peptide search, or protein inference result loaded into the database (page 825, col. 2)(i.e. wherein the storage unit is adapted to: store the mass spectrometry data, the items of processed data and/or the items of additional data in a relational database and  is comprising a data interface for defining dynamic data types in the relational database and/or modifying the relational database, so that the dynamic tables can be added and/or columns can be added to existing dynamic tables), as in claim 1.
	Sharma et al. teach that the core tables may be extended to encapsulate data specific to particular mass spectrometry analysis (page 825, col. 2, par.  4)(i.e. the dynamic tables can be added and/or columns can be added to existing dynamic tables), as in claim 1.

	Sharma et al. do not specifically teach a processor unit that instructs the storage unit to retrieve a first subset of data based on a first study variable and a second subset of processed data based on a second study variable to calculate intensity ratios of peaks from first and second subset, and provide a visualization of a comparison of the first subset and second subset of processed data.
	
	Oda et al teach fractionating a first group of proteins and a second group of proteins and analyzing the fractions with mass spectrometry (Abstract and par. 0009)(i.e. retrieve a first subset of data based on a first study variable and a second subset of processed data based on a second study variable), as in claim 1.
	Oda et al. teach obtaining an intensity ratio between a peak from a protein in fraction from a first group and a peak from a from a fraction in a second group (Abstract)(i.e.  calculate intensity ratios of peaks from first and second subset), as in claim 1.
	Oda et al. teach comparing binding ability of the proteins to a compound (Abstract)(i.e. provide a visualization of a comparison of the first subset and second subset of processed data), as in claim 1.
	It would have been obvious to one of ordinary skill in the art at the time the invention was made to have combined the searching and comparing of data from mass spectrometry experiments taught by Sharma et al. with the ratio of intensity peak calculations taught by Oda et al. Oda et al. provide motivation by teaching that their calculations are useful for analyzing binding ability of a protein to a compound (Abstract). One of skill in the art would have had a reasonable expectation of success at combining Sharma et al. and Oda et al. because both teach mass spectroscopy data management and analysis as applied to proteins. 

Regarding dependent claims 3, 5-14 and 16-20
	Sharma et al. teach core tables that can extend to support data generated from separate programs (Figure 3)(i.e. dynamic tables), as in claims 3, 5 and 6.
Sharma et al. teach a table that lists residue information, charge and peptide information (Figure 3, msRunSearchResult)(i.e. dynamic data types is adapted for the characterization of the sample or targeted compound), as in claim 7.
	Sharma et al. teach core tables (Figure 3) that store data identifying peptides, as in claim 8.
	Sharma et al. teach peptides and proteins as mass spectrometry data in the databases (page 825, col. 2, par. 3)(i.e. metabolites as user defined data types), as in claim 9.
	Sharma et al. teach a Web Interface and connected databases (Figure 2)(i.e. module interface which allows adding dynamic modules that can save or retrieve items of data), as in claim 10.  
	Sharma et al. teach a workflow management system that drives a workflow (page 825, col. 1, par. 1)(i.e a work flow interface for defining sequences and provides services to modules, defining workflow sequences wherein the workflow comprises processing steps), as in claims 11-13.
	Sharma et al. teach a workflow management system that drives a workflow (page 825, col. 1, par. 1), (i.e. system adapted to store a workflow of a sequence of processing steps in a workflow file); Sharma et al. teaches a Data Platform that archives data from workflows (page 825, col. 1, par. 1)(i.e. system adapted to store items of processed data from a workflow being carried out by the processor unit in result line), as in claim 14.
	Sharma et al. teach platforms and tables adapted to store processed data, as in claim 16.
	Sharma et al. teach a web interface (Figure 2) and application interface (Figure 4)(i.e. visualization means), as in claim 17.
	Sharma et al. teach a mass spectrometer that interfaces with software for storing and analyzing the data (Abstract), as in claims 18-20.

Response to Arguments
Applicant's arguments filed 10/31/2024 have been fully considered but they are not persuasive. 
	Applicants arguments are directed to the newly introduced amendments to claim 1 which are addressed by the additionally added reference of Oda et al.
E-mail communication Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.

Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action.  Accordingly, THIS ACTION IS MADE FINAL.  See MPEP § 706.07(a).  Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).  
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action.  In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee 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 date of this final action. 
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Anna Skibinsky whose telephone number is (571) 272-4373.  The examiner can normally be reached on 12 pm - 8:30 pm.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Ram Shukla can be reached on (571) 272-0735.  The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system.  Status information for published applications may be obtained from either Private PAIR or Public PAIR.  Status information for unpublished applications is available through Private PAIR only.  For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/Anna Skibinsky/
Primary Examiner, AU 1635
	
	


    
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
    


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