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title	ts.xpt (trial summary, study level parameters)

• Assumption: The intent of this dataset is to provide a summary of trial (study) information. This is not subject-level data. 
• Assumption: A Trial (study) can have more than one assay type
• Assumption: ASSAYID value of ALL indicates that it applies to all assays in the study
• Sponsor should be "applicant", how do we represent this?
• TK6, human keratinocyte, is this "test system"?
• Can we draft a starting list of Study Types and Sub Types to submit to CT now?

Row

STUDYID

ASSAYID

DOMAIN

TSSEQ

TSGRPID

TSPARMCD

TSPARM

TSVAL

TSVALNF

1123NRUTS1GLPTYPGood Laboratory Practice TypeFDA2123NRUTS2GLPTYPGood Laboratory Practice TypeOECD3123NRUTS1STSTDTCStudy Start Date2022-05-254123NRUTS1STITLEStudy Title

Determination of the in vitro genotoxicity potential of 10 tobacco products in both the in vitro Micronucleus Assay and the in vitro Neutral Red Uptake

5123NRUTS1SNDIGVERSEND Implementation Guide VersionTOBACCO IMPLEMENTATION GUIDE VERSION 1.06123NRUTS1SNDCTVERSEND Controlled Terminology VersionSEND Terminology 2021-09-307123NRUTS1SSPONSORSponsor Applicant's OrganizationExample Applicant Inc.8123NRUTS1SPREFIDSponsor's Applicant's Study Reference IDNOT APPLICABLE9123NRUTS11TSTFNAMTest Facility NameExample Tox Testing Lab Name10123NRUTS11TSTFLOCTest Facility Location10 Somewhere Street, Montgomery, AL 1000011123NRUTS11TFCNTRYTest Facility CountryUSA12123NRUTS11STDIRStudy DirectorDr. R. Smith13123NRUTS1GLPFLGLP FlagY14123NRUTS1ASTDAssay StandardNIH Publication No. 07-451915123NRUTS1ASTDVAssay Standard Version2006-1116123NRUTS1SSTYPStudy TypeGENOTOXICITY IN VITRO17123NRUTS1SSSTYPStudy Sub TypeIn Vitro Neutral Red Uptake18123NRUTS1SPECIESSpeciesSalmonella enterica 19123NRUTS1??Test System??TK6 Normal Human Keratinocyte Expand

title	tx.xpt (trial sets)

• Assumption: The Trial Sets (TX) domain provides the list of distinct sets of subjects having different experimental factors, treatment factors, inherent characteristics, or distinct sponsor designations as specified in the trial design.
• During CT definition/reviews will decide appropriate TXPARM and TXVAL; Treatment duration may be controlled;  For now, we just include good example values based on our experience

RowSTUDYIDASSAYIDDOMAINSETCD

SET (what sponsor calls it)

TXSEQTXPARMCDTXPARMTXVAL1123NRUTX1-1-A

(plate-col-row in the 96-well plate)

CSC-10

(through SLS-200)

PLATENUM. (e.g., 1 or 2)

11 2123NRUTX1-1-ACSC-10

WELLNUM (e.g., 1-A through 10-H)

Number representing the location of the well in the 96-well plate1-A 3123NRUTX1-1-ACSC-10INTRVNname of the intervention articleCigarette Smoke Condensate4123NRUTX1-1-ACSC-10ITVTYPE

(CT e.g, Product, positive control, negative control)

type of intervention articlePRODUCT5123NRUTX1-1-ACSC-10ITVCONCintervention concentration106123NRUTX1-1-ACSC-10ITVCONCUintervention unitug/ml7123NRUTX1-1-ACSC-10STRAINStrain/SubstrainSalmonella enterica enterica8123NRUTX1-1-ACSC-10REGIMESmoking RegimeTraditional combustible 9123NRUTX1-1-ACSC-10RUN

Assay run number (how is this different from REPNUM)

1

10

123NRUTX1-1-ACSC-10PORTPort ID111123NRUTX1-1-ACSC-10SMPLIDSample ID03000112123NRUTX1-1-ACSC-10SMKFRCSmoke FractionA13123NRUTX1-1-ACSC-10REPNUMReplicate Number114123NRUTX1-1-BCSC-10ITVCONCintervention concentration1015123NRUTX1-1-BCSC-10ITVCONCUintervention unitug/ml......123NRUTX1-10-HSLS-10PLATENUMPlate number1  123NRUTX1-10-HSLS-10WELLNUMNumber representing the location of the well in the 96-well plate10-H123NRUTX1-10-HSLS-10INTRVNname of the intervention articlesodium laurel sulfate123NRUTX1-10-HSLS-10ITVTYPEtype of intervention articlePOSITIVE CONTROL123NRUTX1-10-HSLS-10ITVCONCintervention concentration200123NRUTX1-10-HSLS-10ITVCONCUintervention unitug/ml......123NRUTX2-10-HSLS-10PLATENUMPlate number2123NRUTX2-10-HSLS-10WELLNUMNumber representing the location of the well in the 96-well plate10-H123NRUTX2-10-HSLS-10INTRVNname of the intervention articlesodium laurel sulfate123NRUTX2-10-HSLS-10ITVTYPEtype of intervention articlePOSITIVE CONTROL

Dataset wrap

Rowcaps Rows 1-2: Show 2 records for TSPARMCD = "GLPTYP", using TSSEQ to indicate multiple records, since both GLP types apply for this example study.  Row 3: Shows that this study was conducted as a GLP study. Rows 4-5: Show the study start date and study title. Rows 6-7: Show the version of SEND Implementation Guide and version of Controlled Terminology used in this study. Row 8: Shows the applicant's organization. Row 9: Shows that the applicant's study reference ID is not applicable. Rows 10-13: Show that TSGRPID has been used to link records (name, location, country) related to the test facility (TSGRPID = 1). The study director is associated with the test facility. Rows 14-16: Show that TSGRPID (TSGRPID=4) has been used to link the information on the testing guideline followed on this study (TSTGDNAM, TSTGDORG, TSTGDVER). Row 17: Shows the study type for this study. Row 18: Shows that this study includes a Neutral Red Uptake Assay. Rows 19-20: Show that the species is human and the cell line is NHK in this study. Dataset2 Row STUDYID DOMAIN TSSEQ TSGRPID TSPARMCD TSPARM TSVAL TSVALNF 1 123 TS 1 GLPTYP Good Laboratory Practice Type FDA 2 123 TS 2 GLPTYP Good Laboratory Practice Type OECD 3 123 TS 1 GLPFL GLP Flag Y 4 123 TS 1 STSTDTC Study Start Date 2022-05-25 5 123 TS 1 STITLE Study Title Determination of the in vitro genotoxicity potential using the in vitro Neutral Red Uptake assay 6 123 TS 1 SNDIGVER SEND Implementation Guide Version TOBACCO IMPLEMENTATION GUIDE VERSION 1.0 7 123 TS 1 SNDCTVER SEND Controlled Terminology Version SEND Terminology 2021-09-30 8 123 TS 1 APPLCNT Applicant Example Applicant Inc. 9 123 TS 1 APREFID Applicant Study Reference ID NOT APPLICABLE 10 123 TS 1 1 TSTFNAM Test Facility Name Example Test Lab Name 11 123 TS 1 1 TSTFLOC Test Facility Location 10 Somewhere Street, Montgomery, AL 10000 12 123 TS 1 1 TFCNTRY Test Facility Country USA 13 123 TS 1 1 STDIR Study Director Dr. R. Smith 14 123 TS 1 4 TSTGDNAM Testing Guideline Name Publication No. 07-4519 15 123 TS 1 4 TSTGDORG Testing Guideline Organization NIH 16 123 TS 1 4 TSTGDVER Testing Guideline Version 2006-11 17 123 TS 1 SSTYP Study Type GENOTOXICITY IN VITRO 18 123 TS 1 GNTXAID Genetic Toxicology Assay Identifier NRU 19 123 TS 1 SPECIES Species HUMAN 20 123 TS 1 CELLLN Cell Line NHK

Dataset wrap

Rowcaps Rows 1-12: Show the test conditions for the set with a short name or SETCD value of NRU. The applicant chose this value to represent test conditions for the entire assay.  Rows 13-31: Show the test conditions for the set with a short name or SETCD value of CSC-50b. The applicant chose this value to represent plate number 1, well row A, well column 3, with a concentration of 50µg/mLof cigarette smoke condensate as shown in the report table for study 123.  The value for Cell Line (CELLLN) is not applicable because the well is a media-only well, having no NHK cells. Rows 32-50: Show the test conditions for the set with a short name or SETCD value of CSC-50. The applicant chose this value to represent plate number 1, well rows B-G, well column 3 and plate number 2, well rows A-H, well column 3. These all have the concentration of 50µg/mLof cigarette smoke condensate as shown in the report table for study 123. Rows 51-69: Show the test conditions for the set with a short name or SETCD value of SLS-110. The applicant chose this value to represent plate number 1, well rows B-G, well column 10, and plate number 2, well rows A-H, well column 10. These all have the concentration of 110µg/mLof sodium laurel sulfate as shown in the report table for study 123. Dataset2 ROW STUDYID DOMAIN SETCD SET TXSEQ TXPARMCD TXPARM TXVAL 1 123 TX NRU NRU_ASSAY 1 IVTDMIN In vitro Treatment Duration Minimum 47.5 2 123 TX NRU NRU_ASSAY 2 IVTDTRG In vitro Treatment Duration Target 48 3 123 TX NRU NRU_ASSAY 3 IVTDMAX In vitro Treatment Duration Maximum 48.5 4 123 TX NRU NRU_ASSAY 4 IVTDU In vitro Treatment Duration Unit HOURS 5 123 TX NRU NRU_ASSAY 5 INCBTMP Incubation Temperature 37 6 123 TX NRU NRU_ASSAY 6 INCBTMPU Incubation Temperature Unit C 7 123 TX NRU NRU_ASSAY 7 SWAVENM Spectrophotometer Wavelength 540 8 123 TX NRU NRU_ASSAY 8 ATMRHP Atmospheric Relative Humidity Percent 90 9 123 TX NRU NRU_ASSAY 9 ATMCO2P Atmospheric CO2 Percent 5 10 123 TX NRU NRU_ASSAY 10 SPDEVID applicant defined device identifier PUFFMASTER3k 11 123 TX NRU NRU_ASSAY 11 SMKRGM Smoking Regimen MEDIUM INTENSITY REGIMEN 12 123 TX NRU NRU_ASSAY 12 SPTOBID Applicant-defined tobacco identifier CIG01a 13 123 TX CSC-50b CSC-50-blank 13 IVTDMIN In vitro Treatment Duration Minimum 47.5 14 123 TX CSC-50b CSC-50-blank 14 IVTDTRG In vitro Treatment Duration Target 48 15 123 TX CSC-50b CSC-50-blank 15 IVTDMAX In vitro Treatment Duration Maximum 48.5 16 123 TX CSC-50b CSC-50-blank 16 IVTDU In vitro Treatment Duration Unit HOURS 17 123 TX CSC-50b CSC-50-blank 17 INCBTMP Incubation Temperature 37 18 123 TX CSC-50b CSC-50-blank 18 INCBTMPU Incubation Temperature Unit C 19 123 TX CSC-50b CSC-50-blank 19 SWAVENM Spectrophotometer Wavelength 540 20 123 TX CSC-50b CSC-50-blank 20 ATMRHP Atmospheric Relative Humidity Percent 90 21 123 TX CSC-50b CSC-50-blank 21 ATMCO2P Atmospheric CO2 Percent 5 22 123 TX CSC-50b CSC-50-blank 22 SPDEVID applicant defined device identifier PUFFMASTER3k 23 123 TX CSC-50b CSC-50-blank 23 SMKRGM Smoking Regimen MEDIUM INTENSITY REGIMEN 24 123 TX CSC-50b CSC-50-blank 24 SPTOBID Applicant-defined tobacco identifier CIG01a 25 123 TX CSC-50b CSC-50-blank 25 EXPTYP Exposure Type Air Liquid Interface 26 123 TX CSC-50b CSC-50-blank 26 SAMTYP Sample Type Whole Smoke Conditioned Media 27 123 TX CSC-50b CSC-50-blank 27 ITVNAM Name of the Intervention Article Tobacco ProdA 28 123 TX CSC-50b CSC-50-blank 28 ITVTYPE Intervention Article Type PRODUCT 29 123 TX CSC-50b CSC-50-blank 29 ITVCONC Intervention Article Concentration 50 30 123 TX CSC-50b CSC-50-blank 30 ITVCONCU Intervention Article Concentration Unit ug/ml 31 123 TX CSC-50b CSC-50-blank 31 CELLLN Cell Line NOT APPLICABLE 32 123 TX CSC-50 CSC-50 32 IVTDMIN In vitro Treatment Duration Minimum 47.5 33 123 TX CSC-50 CSC-50 33 IVTDTRG In vitro Treatment Duration Target 48 34 123 TX CSC-50 CSC-50 34 IVTDMAX In vitro Treatment Duration Maximum 48.5 35 123 TX CSC-50 CSC-50 35 IVTDU In vitro Treatment Duration Unit HOURS 36 123 TX CSC-50 CSC-50 36 INCBTMP Incubation Temperature 37 37 123 TX CSC-50 CSC-50 37 INCBTMPU Incubation Temperature Unit C 38 123 TX CSC-50 CSC-50 38 SWAVENM Spectrophotometer Wavelength 540 39 123 TX CSC-50 CSC-50 39 ATMRHP Atmospheric Relative Humidity Percent 90 40 123 TX CSC-50 CSC-50 40 ATMCO2P Atmospheric CO2 Percent 5 41 123 TX CSC-50 CSC-50 41 SPDEVID applicant defined device identifier PUFFMASTER3k 42 123 TX CSC-50 CSC-50 42 SMKRGM Smoking Regimen MEDIUM INTENSITY REGIMEN 43 123 TX CSC-50 CSC-50 43 SPTOBID Applicant-defined tobacco identifier CIG01a 44 123 TX CSC-50 CSC-50 44 EXPTYP Exposure Type Air Liquid Interface 45 123 TX CSC-50 CSC-50 45 SAMTYP Sample Type Whole Smoke Conditioned Media 46 123 TX CSC-50 CSC-50 46 ITVNAM Intervention Article Name Tobacco ProdA 47 123 TX CSC-50 CSC-50 47 ITVTYPE Intervention Article Type PRODUCT 48 123 TX CSC-50 CSC-50 48 ITVCONC Intervention Article Concentration 50 49 123 TX CSC-50 CSC-50 49 ITVCONCU Intervention Article Concentration Unit ug/ml 50 123 TX CSC-50 CSC-50 50 CELLLN Cell Line NHK 51 123 TX SLS-110 SLS-110 51 IVTDMIN In vitro Treatment Duration Minimum 47.5 52 123 TX SLS-110 SLS-110 52 IVTDTRG In vitro Treatment Duration Target 48 53 123 TX SLS-110 SLS-110 53 IVTDMAX In vitro Treatment Duration Maximum 48.5 54 123 TX SLS-110 SLS-110 54 IVTDU In vitro Treatment Duration Unit HOURS 55 123 TX SLS-110 SLS-110 55 INCBTMP Incubation Temperature 37 56 123 TX SLS-110 SLS-110 56 INCBTMPU Incubation Temperature Unit C 57 123 TX SLS-110 SLS-110 57 SWAVENM Spectrophotometer Wavelength 540 58 123 TX SLS-110 SLS-110 58 ATMRHP Atmospheric Relative Humidity Percent 90 59 123 TX SLS-110 SLS-110 59 ATMCO2P Atmospheric CO2 Percent 5 60 123 TX SLS-110 SLS-110 60 SPDEVID applicant defined device identifier PUFFMASTER3k 61 123 TX SLS-110 SLS-110 61 SMKRGM Smoking Regimen MEDIUM INTENSITY REGIMEN 62 123 TX SLS-110 SLS-110 62 SPTOBID Applicant-defined tobacco identifier CIG01a 63 123 TX SLS-110 SLS-110 63 EXPTYP Exposure Type Air Liquid Interface 64 123 TX SLS-110 SLS-110 64 SAMTYP Sample Type Liquid 65 123 TX SLS-110 SLS-110 65 ITVNAM Intervention Article Name Sodium Laurel Sulfate 66 123 TX SLS-110 SLS-110 66 ITVTYPE Intervention Article Type POSITIVE CONTROL 67 123 TX SLS-110 SLS-110 67 ITVCONC Intervention Article Concentration 110 68 123 TX SLS-110 SLS-110 68 ITVCONCU Intervention Article Concentration Unit ug/ml 69 123 TX SLS-110 SLS-110 69 CELLLN Cell Line NHK

Dataset wrap
Name relref
The applicant chose to define the REFID values to indicate the Plate, the Column, and the Row of the wells of the 96-well plate in use, such that the well on plate 2, column 10, row G would assigned a REFID of 2-10-G. Rowcaps Row 1: Shows the REFID of 123NRU that indicates the entire assay. Rows 2-4:  Show the REFIDs at the second level, all within the parent assay of 123NRU (REFID values of 1-3, 1-10, 2-10) which have LVLDESC of OBSERVATIONAL SUMMARY.  If this study had recorded summary statistics for an entire trial set (e.g., across both plates for the same dose level), there would be an additional REFID for the trial set (with a LVLDESC of TRIAL SET). Rows 5-6: Show the REFIDs 1-3-A and 1-3-H that indicate two experimental units that are also observational units within the SETCD of CSC-50b that have the parent REFID of 123NRU. Rows 7-8: Show the REFIDs 1-3-B and 1-3-C that indicate two experimental units that are also observational units within the SETCD of CSC-50 that have the parent REFID of 1-3. Row 9: Shows the REFID of 1-10-G that indicates the experimental unit that is also an observational unit within the SETCD of SLS-110 that has the parent REFID of 1-10. Row 10:  Shows the REFID of 2-10-G that indicates the experimental unit that is also an observational unit within the SETCD of SLS-110 that has the parent REFID of 2-10. Dataset2 tableid relref Row STUDYID SETCD REFID PARENT LEVEL LVLDESC 1 123 NRU 123NRU 1 ASSAY 2 123 CSC-50 1-3 123NRU 2 OBSERVATIONAL SUMMARY 3 123 SLS-110 1-10 123NRU 2 OBSERVATIONAL SUMMARY 4 123 SLS-110 2-10 123NRU 2 OBSERVATIONAL SUMMARY 5 123 CSC-50b 1-3-A 123NRU 2 EXPERIMENTAL UNIT/OBSERVATIONAL UNIT 6 123 CSC-50b 1-3-H 123NRU 2 EXPERIMENTAL UNIT/OBSERVATIONAL UNIT 7 123 CSC-50 1-3-B 1-3 3 EXPERIMENTAL UNIT/OBSERVATIONAL UNIT 8 123 CSC-50 1-3-C 1-3 3 EXPERIMENTAL UNIT/OBSERVATIONAL UNIT 9 123 SLS-110 1-10-G 1-10 3 EXPERIMENTAL UNIT/OBSERVATIONAL UNIT 10 123 SLS-110 2-10-G 2-10 3 EXPERIMENTAL UNIT/OBSERVATIONAL UNIT

0.780

Dataset wrap
Name gt
Certain data (Absorbance Reading and Background Corrected Absorbance Reading) are not shown in the sample report table above but are included here for completeness of the NRU assay. Rowcaps Rows 1-3: Show the experimental unit data for GTREFID 1-3-B.  Rows 4-6: Show the experimental unit data for GTREFID 1-3-C. Rows 7-9: Show the data for the entire trial set, GTREFID=1-3. Rows 10-12: Show the experimental unit data for GTREFID 1-10-G Rows 13-15: Show the data for the entire trial set, GTREFID=1-10 Rows 16-18: Show the experimental unit data for GTREFID 2-10-G.  Rows 19-21: Show the data for the entire trial set, GTREFID=2-10 Row 22: Shows the data for the entire assay, GTREFID=123NRU. Dataset2 Row STUDYID DOMAIN GTSEQ GTREFID GTTESTCD GTTEST GTORRES GTORRESU GTCOLSRT GTSTRESC GTSTRESN GTSTRESU 1 123 GT 1 1-3-B ABSORB Absorbance Reading 1.7 1.7 1.7 2 123 GT 2 1-3-B BKCABS Background Corrected Absorbance Reading 1.6 1.6 1.6 3 123 GT 3 1-3-B RELABS Relative Absorbance Reading 77.7 77.7 77.7 4 123 GT 4 1-3-C ABSORB Absorbance Reading 1.8 1.8 1.8 5 123 GT 5 1-3-C BKCABS Background Corrected Absorbance Reading 1.7 1.7 1.7 6 123 GT 6 1-3-C RELABS Relative Absorbance Reading 77.4 77.4 77.4 7 123 GT 7 1-3 RELABS Relative Absorbance Reading 78.2 % MEAN 78.2 78.2 % 8 123 GT 8 1-3 RELABS Relative Absorbance Reading 2.9 % STANDARD DEVIATION 2.9 2.9 % 9 123 GT 9 1-3 RELABS Relative Absorbance Reading 3.6 COEFFICIENT OF VARIANCE 3.6 3.6 10 123 GT 10 1-10-G ABSORB Absorbance Reading 0.7 0.7 0.7 11 123 GT 11 1-10-G BKCABS Background Corrected Absorbance Reading 0.6 0.6 0.6 12 123 GT 12 1-10-G RELABS Relative Absorbance Reading 8.57 8.57 8.57 13 123 GT 13 1-10 RELABS Relative Absorbance Reading 8.94 % MEAN 8.94 8.94 14 123 GT 14 1-10 RELABS Relative Absorbance Reading 2.72 % STANDARD DEVIATION 2.72 2.72 15 123 GT 15 1-10 RELABS Relative Absorbance Reading 30.5 COEFFICIENT OF VARIANCE 30.5 30.5 16 123 GT 16 2-10-G ABSORB Absorbance Reading 0.9 17 123 GT 17 2-10-G BKCABS Background Corrected Absorbance Reading 0.8 18 123 GT 18 2-10-G RELABS Relative Absorbance Reading 6.30 6.30 6.30 19 123 GT 19 2-10 RELABS Relative Absorbance Reading 5.91 % MEAN 5.91 5.91 20 123 GT 20 2-10 RELABS Relative Absorbance Reading 0.83 % STANDARD DEVIATION 0.83 0.83 21 123 GT 21 2-10 RELABS Relative Absorbance Reading 14.1 COEFFICIENT OF VARIANCE 14.1 14.1 22 123 GT 22 123NRU EC50CYTX Effective Concentration of 50 Percent Cytotoxicity 123 ug/ml 123 123
123	NRU	TX	2-10-H	SLS-10	ITVCONC	intervention concentration	200	123	NRU	TX	2-10-H	SLS-10	ITVCONCU	intervention unit	ug/ml
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title gt.xpt (similar to LB)
Image RemovedImage Removed
Row	STUDYID	ASSAYID	DOMAIN	TXCD	GTSEQ	GTTESTCD	GTTEST	GTORRES	GTORRESU	GTSTRESC	GTSTRESN	GTSTRESU
1	123	NRU	GT	1-1-A	1	RELABS	Relative Absorbance Reading	100	ug/ml	100	100	ug/ml
2	123	NRU	GT	1-1-B	1	RELABS	Relative Absorbance Reading	107	ug/ml	100	100	ug/ml
3	123	NRU	GT	1-1-C	1	RELABS	Relative Absorbance Reading	98.6	ug/ml	100	100	ug/ml
4	123	NRU	GT	1-1-D	1	RELABS	Relative Absorbance Reading	94.9	ug/ml	100	100	ug/ml
5	123	NRU	GT	1-1-E	1	RELABS	Relative Absorbance Reading	111	ug/ml	111	111	ug/ml
123	NRU	GT	1-1-F	1	RELABS	Relative Absorbance Reading	96.9	ug/ml	96.9	96.9	ug/ml	123	NRU	GT	1-1-G	1	RELABS	Relative Absorbance Reading	105	ug/ml	105	105	ug/ml	123	NRU	GT	1-1-H	1	RELABS	Relative Absorbance Reading	95.2	ug/ml	95.2	95.2	ug/ml
10	123	NRU	GT	1-2-A	1	RELABS	Relative Absorbance Reading	83.0	ug/ml	83.0	83.0	ug/ml
11	123	NRU	GT	1-2-B	1	RELABS	Relative Absorbance Reading	77.7	ug/ml	77.7	77.7	ug/ml
...	...
80	123	NRU	GT	1-10-H	1	RELABS	Relative Absorbance Reading	0.791	ug/ml	0.791	0.791	ug/ml
...	...	160	123	NRU	GT	2-10-H	1	RELABS	Relative Absorbance Reading	0.780	ug/ml	0.780

ug/ml