NMP_readme_zip_files
-Paul Schlosser, NCEA, U.S. EPA
-September 23, 2013

The .zip files, NMP_human_9-23-13.zip and NMP_rat_9-23-2013.zip, contain sets of files that constitute workspaces for the computation software, acslX (v. 3.0.2.1, The AEgis Technologies Group, Inc., Huntsville, AL).  Most of the files contained in each workspace are specific to acslX and a basic knowledge of this software is necessary to make use of them.

The workspaces can be used by unzipping the corresponding .zip files.  Once this is done the resulting folder will contain a workspace (.aws) file of the corresponding name (e.g., NMP_human_2013_2.aws) and a "Project 1" subfolder.  The .aws can be opened from within acslX, which will then display the primary acslX program (.csl) file and scripts (.m files) for reproducing the simulations and model fits shown in the QA report, n-Methylpyrrolidone PBPK QA Report 091613 V3.docx, or used and shown in the dose-response analysis.  A detailed list of scripts and their functions follow.

While various files within the acslX "Project 1" folders can be viewed outside of acslX, changing them can damage their functionality.  In particular .aps files set formatting for various plots and are created/edited by acslX when a user is manipulating a plot through the graphical user interface.  Please do not edit them directly.

** The file Residential.xlsx in the human "Project 1" folder should not be altered, as it contains inputs for the residential exposure scenario. 

In the primary model (.csl) files, all changes made by the U.S. EPA are noted in comments at the end of or just above or below the altered code.  Significant changes in script (.m) files are also noted with comments.  In order to avoid the possibility of having some parameters assigned different values for different simulations, all parameters other than those defining exposures/scenarios have been consolidated into one or two 'param.m' scripts.  Where values had been set in other scripts, these have been commented out, but there may not be explanatory commments on each instance.

The document, n-Methylpyrrolidone PBPK QA Report 091613 V3.docx, is referred to as "the QA report" below.


NMP_rat_9-23-2013 / NMP_rat_2013_2.aws

 > NMPpreg_rat.csl: model definition file

 > raparam.m: sets rat model parameters except pregnancy-specific values

 > preg_rat_params.m: calls ratparam.m and then sets pregnancy-specific values

 > Poet2010_Fig5_oral.m: plots in preface of QA report, reproducing Fig. 5 of Poet 
	et al. (2010)

 > Fig 1 IV plasma.m: plots shown in Figure 1 (p. 8) of the QA report.

 > Fig 2 Payan 2002 IV 5HNMP.m: plots shown in Fig. 2 (p. 9) of the QA report.
	The last plot is an expanded view of results for the lowest 3 doses.

 > Fig 3 Payan 2003 Dermal plasma.m: Updated version of Fig. 3 (p. 10) in the QA
	report. Results differ slightly from those in Fig. 3 of the QA report due 
	to changes noted in the preface of the report.

 > Poet2013_Fig1_gestation growth.m: recreates plot of BW and tissue changes for 
	rat pregnancy; these differ from Fig. 1A of Poet et al. (2010) but match 
	Poet (2013) (liver not shown). Not in QA report.

 > Poet2013_Fig3_Ghantous_1995.m: reproduces Fig. 3 of Poet (2013) report.
	Not in QA report.

 > Saillenfait_2002_gavage.m: calculates internal doses for Saillenfait et al.
	(2002) oral bioassay

 > Saillenfait_2003_inhalation.m: internal doses for Saillenfait et al. (2003)
	inhalation bioassay

 > Becci_1982_dermal.m: internal doses for Becci et al. (11982) dermal bioassay.


NMP_human_9-23-13 / NMP_human_2013_2.aws

 > HumPregRetreive Restored 1.csl: model definition file

 > human_params.m: physiological and biochemical parameter values for human model

 > Figs_4-5_Poet 2013 Fig 4.m: Figs. 4 & 5 in the QA report; Fig. 4 in Poet (2013)

 > Fig_6_Poet 2013 Fig 5 plasma.m: Fig. 6 in QA report; Fig. 5 in Poet (2013)

 > Fig_7_Poet 2013 Fig 8 plasma & urine.m: Fig. 7 in QA report; Fig. 8 in Poet (2013)

 > Fig_8_Poet 2013 Fig 9 plasma .m: Fig. 8 in QA report; Fig. 9 in Poet (2013)

 > Poet 2013 Fig 6 plasma.m: Fig. 6 in Poet (2013); not in QA report

 > spraywork.m: workplace exposure simulations; results written to spraywork.csv

 > residential.m: residential exposure simulations, written to Residential.csv