{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001139","ANALYSIS_ID":"AN001869","VERSION":"1","CREATED_ON":"02-08-2024"},

"PROJECT":{"PROJECT_TITLE":"P4HA1 knockdown in the breast cell line MDA231","PROJECT_SUMMARY":"Determine the effect of knocking down P4HA1 in the MDA231 cell line (including alterations to metabolic pathways).","INSTITUTE":"University of Kentucky","DEPARTMENT":"Markey Cancer Center","LAST_NAME":"Xu","FIRST_NAME":"Ren","ADDRESS":"BBSRC361, 741 South Limestone, Lexington, KY 40536, USA","EMAIL":"ren.xu2010@uky.edu","PHONE":"000-000-0000","DOI":"http://dx.doi.org/10.21228/M8T10P"},

"STUDY":{"STUDY_TITLE":"P4HA1 knockdown in the breast cell line MDA231 Gln metabolism (part VI)","STUDY_TYPE":"isotope tracer","STUDY_SUMMARY":"Determine the effect on glutamine metabolism of knocking down P4HA1 in the MDA231 cell line.","INSTITUTE":"University of Kentucky","DEPARTMENT":"Markey Cancer Center","LAST_NAME":"Xiong","FIRST_NAME":"Gaofeng","ADDRESS":"BBSRC361, 741 South Limestone, Lexington, KY 40536, USA","EMAIL":"gaofeng.xiong@uky.edu","PHONE":"000-000-0000","SUBMIT_DATE":"2019-02-15"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A",
"Factors":{"protocol.id":"13C15NGln_shCTL"},
"Additional sample data":{"lineage_1":"2_MDA231_13C15NGln_shCTL_rep1","cell_type":"MDA231","plate_with_media_weight":"19.66","plate_with_media_weight%units":"g","replicate":"1","lineage_2":"2_MDA231_13C15NGln_shCTL_rep1-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A","protocol.id":"['polar_extraction', 'NMR_file_storage2']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.28579888665166403","type":"polar","weight":"0.4825999999999999","weight%units":"g","lineage_4":"2_MDA231_13C15NGln_shCTL_rep1-cells-protein","dry_weight":"0.0008000000000000229","dry_weight%units":"g","protein_weight":"0.5884","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A",
"Factors":{"protocol.id":"13C15NGln_shCTL"},
"Additional sample data":{"lineage_1":"3_MDA231_13C15NGln_shCTL_rep2","cell_type":"MDA231","plate_with_media_weight":"19.65","plate_with_media_weight%units":"g","replicate":"2","lineage_2":"3_MDA231_13C15NGln_shCTL_rep2-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A","protocol.id":"['polar_extraction', 'NMR_file_storage3']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.25640876252621786","type":"polar","weight":"0.44010000000000016","weight%units":"g","lineage_4":"3_MDA231_13C15NGln_shCTL_rep2-cells-protein","dry_weight":"0.0006999999999999229","dry_weight%units":"g","protein_weight":"0.5808","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A",
"Factors":{"protocol.id":"13C15NGln_shCTL"},
"Additional sample data":{"lineage_1":"4_MDA231_13C15NGln_shCTL_rep3","cell_type":"MDA231","plate_with_media_weight":"19.17","plate_with_media_weight%units":"g","replicate":"3","lineage_2":"4_MDA231_13C15NGln_shCTL_rep3-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A","protocol.id":"['polar_extraction', 'NMR_file_storage4']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.2617664493183165","type":"polar","weight":"0.4416000000000002","weight%units":"g","lineage_4":"4_MDA231_13C15NGln_shCTL_rep3-cells-protein","dry_weight":"0.0007000000000000339","dry_weight%units":"g","protein_weight":"0.5344000000000001","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A",
"Factors":{"protocol.id":"13C15NGln_shP4HA1"},
"Additional sample data":{"lineage_1":"6_MDA231_13C15NGln_shP4HA1_rep1","cell_type":"MDA231","plate_with_media_weight":"19.13","plate_with_media_weight%units":"g","replicate":"1","lineage_2":"6_MDA231_13C15NGln_shP4HA1_rep1-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A","protocol.id":"['polar_extraction', 'NMR_file_storage6']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.2785457645697584","type":"polar","weight":"0.45740000000000025","weight%units":"g","lineage_4":"6_MDA231_13C15NGln_shP4HA1_rep1-cells-protein","dry_weight":"0.0009000000000000119","dry_weight%units":"g","protein_weight":"0.5952000000000001","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A",
"Factors":{"protocol.id":"13C15NGln_shP4HA1"},
"Additional sample data":{"lineage_1":"7_MDA231_13C15NGln_shP4HA1_rep2","cell_type":"MDA231","plate_with_media_weight":"19.66","plate_with_media_weight%units":"g","replicate":"2","lineage_2":"7_MDA231_13C15NGln_shP4HA1_rep2-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A","protocol.id":"['polar_extraction', 'NMR_file_storage7']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.2859185984148737","type":"polar","weight":"0.4797999999999998","weight%units":"g","lineage_4":"7_MDA231_13C15NGln_shP4HA1_rep2-cells-protein","dry_weight":"0.0010999999999999899","dry_weight%units":"g","protein_weight":"0.5852","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A",
"Factors":{"protocol.id":"13C15NGln_shP4HA1"},
"Additional sample data":{"lineage_1":"8_MDA231_13C15NGln_shP4HA1_rep3","cell_type":"MDA231","plate_with_media_weight":"19.3","plate_with_media_weight%units":"g","replicate":"3","lineage_2":"8_MDA231_13C15NGln_shP4HA1_rep3-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A","protocol.id":"['polar_extraction', 'NMR_file_storage8']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.2918280979912975","type":"polar","weight":"0.48960000000000004","weight%units":"g","lineage_4":"8_MDA231_13C15NGln_shP4HA1_rep3-cells-protein","dry_weight":"0.0008999999999999009","dry_weight%units":"g","protein_weight":"0.6532","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Collection and quench of cells in culture","COLLECTION_PROTOCOL_ID":"cell_quench_collection","COLLECTION_PROTOCOL_FILENAME":"3A_Cells_Quench_Cell_Fan_20170412.pdf","SAMPLE_TYPE":"cultured cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells grown in unlabeled glutamine and infected with empty vector. Cells grown in unlabeled glutamine and infected with shP4HA1 lentivirus. Cells grown in labeled glutamine and infected with empty vector. Cells grown in labeled glutamine and infected with shP4HA1 lentivirus.","TREATMENT_PROTOCOL_ID":"12C14NGln_shCTL 12C14NGln_shP4HA1 13C15NGln_shCTL 13C15NGln_shP4HA1"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Polar extraction from cells. Protein extraction and quantification.","SAMPLEPREP_PROTOCOL_ID":"polar_extraction protein_extraction","SAMPLEPREP_PROTOCOL_FILENAME":"4B_Extract_Polar_Lipid_Prot_Fan_070417.pdf;4D_17Jun4_Fan_Prot_Quant.pdf"},

"CHROMATOGRAPHY":[],

"ANALYSIS":{"ANALYSIS_TYPE":"NMR"},

"NM":{"INSTRUMENT_NAME":"Agilent 600","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"HC-HSQC","STANDARD_CONCENTRATION":"0.5 mM","SPECTROMETER_FREQUENCY":"600 MHz","NMR_PROBE":"cryogenic triple resonance HCN","NMR_SOLVENT":"D20","NMR_TUBE_SIZE":"1.7 mm","SHIMMING_METHOD":"gradient shimming","PULSE_SEQUENCE":"gHSQCAD","WATER_SUPPRESSION":"presaturation","CHEMICAL_SHIFT_REF_CPD":"DSS","TEMPERATURE":"15 celsius","ACQUISITION_TIME":"2 s","RELAXATION_DELAY":"4 s","BASELINE_CORRECTION_METHOD":"Bernstein Polynomial"},

"NMR_METABOLITE_DATA":{
"Units":"Peak area normalized",

"Data":[{"Metabolite":"Asp-3a_1","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"24.5423","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"29.7037","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"24.6903","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"30.2698","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"27.1926","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"39.0372"},{"Metabolite":"Asp-3a_2","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"31.1144","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"34.9874","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"35.4275","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"38.3173","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"18.8921"},{"Metabolite":"Asp-3b_1","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"16.0053","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"19.9233","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"17.7178","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"18.3136","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"26.2934","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"12.4482"},{"Metabolite":"Asp-3b_2","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"24.0222","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"20.4347","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"18.5852","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"21.5341","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"12.1033"},{"Metabolite":"DSS_1","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"3.7089","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"2.7599","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"3.5932","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"3.3434","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"2.8324","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"2.8002"},{"Metabolite":"Gln-3_1","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"228.3296","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"181.8510","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"245.8179","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"184.8079","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"182.7145","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"298.4413"},{"Metabolite":"Gln-3_2","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"201.0946","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"177.7722","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"304.1650","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"294.0866","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":""},{"Metabolite":"Gln-4_1","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"94.5777","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"51.5843","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"66.8797","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"75.2415","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"67.4374","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"106.0323"},{"Metabolite":"Gln-4_2","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"86.4081","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"53.6395","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"92.7602","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"84.8903","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"99.0015","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"88.7858"},{"Metabolite":"Gln+Glu-2_1","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"231.4167","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"200.0727","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"209.9923","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"175.1039","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"205.1693","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"197.4518"},{"Metabolite":"Glu-3-a_1","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"814.6414","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"592.3812","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"110.2269","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"700.7143","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"681.2972","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"116.9320"},{"Metabolite":"Glu-3-a_2","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"28.9067","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"16.8148","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"455.6918","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"7.3636","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"302.2954"},{"Metabolite":"Glu-3-a_3","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"30.3685","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"381.9717"},{"Metabolite":"Glu-3-a_4","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"36.1272"},{"Metabolite":"Glu-3-b_1","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"207.4967","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"622.2894","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"177.5475","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"258.9825","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"178.9555","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"278.1596"},{"Metabolite":"Glu-3-b_2","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"510.6707","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"342.3489","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"360.6655","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"451.9234","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"943.6137"},{"Metabolite":"Glu-4_1","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"261.1516","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"231.5831","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"221.2428","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"255.6909","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"231.9403","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"328.4375"},{"Metabolite":"GSH+GSSG-3_1","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"97.7528","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"183.3769","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"115.8869","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"89.3400","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"104.2341","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"44.2969"},{"Metabolite":"GSH+GSSG-3_2","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"65.8716","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":""},{"Metabolite":"GSH+GSSG-4_1","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"49.0177","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"35.5730","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"48.5555","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"53.6964","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"42.5425","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"42.1479"},{"Metabolite":"Lac-3_1","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_NMR_A":"8.3287","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_NMR_A":"4.6150","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_NMR_A":"7.1817","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_NMR_A":"8.2858","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_NMR_A":"8.7615","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_NMR_A":"10.2799"},{"Metabolite":"P-Cho 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}

}