United States Environmental Monitoring EPA 600/8-91/043
Environmental Protection Systems Laboratory June 1991
Agency P.O. Box 93478 Preissue Copy
Las Vegas NV 89193-3478
Research and Development
&EPA Protein Adducts for
Exposure Monitoring:
A Computerized Database
Software and IJfter's Manual
0888mGR91
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USER'S MANUAL TO EPA'S PROTEIN ADDUCTS DATABASE
Software and Documentation by:
F. C Schnell
Lockheed Engineering and Sciences Company
Las Vegas, Nevada 89119
Contract No. 68-CO-0049
for
Work Assignment Manager
Charles H. Nauman
Exposure Assessment Division
Environmental Monitoring Systems Laboratory
Las Vegas, Nevada 89193
ENVIRONMENTAL MONITORING SYSTEMS LABORATORY
OFFICE OF RESEARCH AND DEVELOPMENT
U.S. ENVIRONMENTAL PROTECTION AGENCY
LAS VEGAS, NEVADA 89193
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NOTICE
The information in this document has been funded wholly or
in part by the United States Environmental Protection Agency
under contract 68-C0-0049 to Lockheed Engineering and Sciences
Company, Environmental Monitoring Systems Laboratory, Las Vegas,
Nevada. It has been subjected to the Agency's peer and
administrative review, and it has been approved for publication
as an EPA document. Mention of trade names or commercial
products does not constitute endorsement or recommendation for
use.
ii
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ABSTRACT
The Computerized Protein Adducts Database (CPAD) was created
to provide an efficient means of updating and disseminating
information on protein adducts relating to their utility as
dosimeters of exposure to environmental contaminants, especially
genotoxic and/or carcinogenic.compounds. The structure of the
database as well as its initial contents were derived primarily
from the document, "Protein Adduct-Forming Chemicals for Exposure
Monitoring: Chemicals for Further Study" (EPA/600/4-89/035).
The programs that enable the user to search, modify, or
update the database and display its contents were originally
written in the DBASE III PLUS™ programming language, then
converted, compiled and linked by DBASE IV™, version 1.1. The
final product is a user-friendly, menu-driven, stand-alone DBASE
application that requires little from the user beyond the ability
to read the screen and operate a keyboard. Even a "User's
Manual" is, to some extent, superfluous. The present document
largely represents a "hard" copy of documentation that is already
provided within the program itself. The CPAD diskette also
contains a copy of this document which may be viewed on screen or
printed out as a WORDPERFECT™ 5.0 document file .
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TABLE OF CONTENTS
NOTICE ii
ABSTRACT iii
FIGURES.. v
1. Introduction 1
Project Background 1
Installation and Startup 2
2. Searching the Database 4
The Main Menu 4
The Data Display Screens 4
Chemical Data Screens 6
Protein Adduct Data Screens 6
3. Modifying the Database. 16
The Add Record Screen 16
The Delete Record Screen 21
The Field Edit Screens 21
Single-Field Screens 23
Double-Field Screens 23
The CAS Number and Synonym Screens 26
The Reference Field Screen 26
References 29
Appendices:
A: Database Structure of CPAD. A-l
B: Chemicals in the Database as of September 1990 B-l
C: CPAD files: The Dbase III Plus version C-l
D: CPAD files: The Dbase IV version D-l
iv
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FIGURES
wnmiiAr Page
1. The Main Menu 5
2. The Main Field-Selection Menu 5
3. The Chemical Data Fields Menu 7
4. The CAS Number Screen 7
5. The Synonyms Screen 8
6. The Manufacturing Data Screen 8
7. The Major Uses Screen .... 9
*
8. The Exposure Data Screen 9
9. The Health Effects Screen 10
10. The Metabolism Data Screen 10
11. The Host Factors Screen 11
12. The Protein Adduct Fields Menu 11
13. The Reactive Metabolites Screen 13
14. The In Vitro Rate Constant Screen 13
15. The Major Adducts Screen 14
16. The Background Adduct Levels Screen 14
17. The Dose-Response Data Screen 15
18. The Adduct Detection Methods Screen 15
19. The References Screen 17
20. The Add/Delete Menu 17
21. The Add New Record Screen 18
22. The Duplicate Entry Protection Feature 18
23. The Save New Data Prompt 19
v
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Figures (Continued)
24. The More /Done Prompt 19
25. The Re-Sort Database Prompt 20
26. The Delete Record Screen ......20
27. The Locate Record Prompt 22
28. The Selection Confirmation Prompt 22
29. The Deletion Confirmation Prompt 24
30. The Major Adducts Edit Screen-Options Mode 24
31. The Edit-Help Screen 25
32. The Major Adducts Edit Screen-Edit Mode 25
33. The Exposure Data Edit Screen-Save Prompt 27
34. The CAS Number Edit Screen 27
35. The Synonyms Edit Screen 28
36. The References Edit Screen 28
vi
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INTRODUCTION
PROJECT BACKGROUND
The Environmental Protection Agency (EPA) has executed its
mandate to protect human health and the environment by placing
restrictions and regulations on the use of chemicals that have
been shown to be detrimental to human health or the environment.
In addition, the Agency has developed an initiative designed to
develop, refine and apply appropriate biomarkers for use in
conjunction with environmental monitoring data to provide better
estimates of exposure and risk to individuals and populations.
Only by relating biological measurements to environmental
monitoring measurements can the relationships between total
exposure, effective dose and disease be determined.
In a 1987 report entitled "Carcinogen-DNA Adducts:
Introduction, Literature Summary and Recommendations" (EPA/600/4-
87/005) , it was recognized that hemoglobin and serum albumin
adducts may be more advantageous than DNA adducts as biological
markers of exposure, because protein adducts are typically more
stable and more abundant than DNA adducts. A subsequent report
entitled "Protein Adduct-Forming Chemicals For Exposure
Monitoring: Literature Summary and Recommendations" (EPA 600/4-
90/007) summarized the literature regarding adducts formed by
xenobiotics with proteins, particularly hemoglobin and serum
albumin, and examined the feasibility of their use as dosimeters
of exposure. Those chemicals of interest to the EPA that were
recommended for further study were ranked according to their
potential utility in exposure monitoring by protein adduct-based
methods. These prioritized chemicals (22 in number) were
examined in greater detail in a report entitled "Protein Adduct-
Forming Chemicals For Exposure Monitoring: Chemicals Selected for
Further study" (EPA/600/4-89/035) .
It was anticipated that, due to rapid developments in the
field of molecular dosimetry, the information in the last-
mentioned protein adducts report, as well as the prioritized
chemicals list, itself, would require frequent amendments and
updates in the future. To facilitate that process, the
Computerized Protein Adducts Database (CPAD) was developed. The
structure of the database as well as its initial contents were
derived primarily from the above-mentioned document, "Protein
Adduct-Forming Chemicals for Exposure Monitoring: Chemicals
Selected for Further Study" (EPA/600/4-89/035). The database
includes entries on the following topics: manufacture and use,
sources and levels of exposure, known health effects, metabolism
1
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(detoxification and activation), host factors, reactive
metabolites, adduct characterization, rates of adduct formation
(i.e., second order rate constants), background adduct levels,
dose-response relationships, and methods of adduct detection.
INSTALLATION AND STARTUP OF CPAD
THE DBASE™ III PLUS VERSION
The database proper (i.e., SPADDUCTS.DBF) is a DBASE™ III
PLUS file. So that users unfamiliar with DBASE™ would have
ready access to the data in CPAD, some 32 program files were
written in the DBASE™ III PLUS programming language, then
compiled and linked into a single program file (PADDUCTS.PRG) to
create a user-friendly, menu-driven DBASE™ application. (Note:
in addition to PADDUCTS.PRG, this version requires thirteen
accompanying *.FRM files in order to run.) This version of CPAD
may be used with or without DBASE™ III PLUS.
IF YOUR COMPUTER DOES HAVE DBASE™ III PLUS INSTALLED, ONLY
THE FILES IN THE CPAD.DB3 DIRECTORY OF THE 3.5" CPAD DISKETTE
NEED BE COPIED TO A SEPARATE DATA SUBDIRECTORY ON YOUR HARD DRIVE
(e.g., c:\CPAD). These files will require approximately 270K of
memory on your hard disk. IF YOUR COMPUTER DOES NOT HAVE DBASE™
III PLUS INSTALLED, THEN THE THREE DBRUN FILES IN THE RUNTIME.DB3
DIRECTORY OF THE CPAD DISKETTE MUST ALSO BE COPIED INTO THE CPAD
DIRECTORY ON YOUR HARD DISK. These files will run CPAD in
exactly the same way that DBASE™ III PLUS would, but, unlike the
DBASE* system files, these DBRUN files can be legally copied and
distributed along with the CPAD files.
Other directories on the CPAD diskette contain the source
code (i.e., SRC files) and the object code (i.e., PRG files) that
were used in conjunction with the DBASE™ III PLUS utilities
dbc.com and dbl.com to generate the linked file padducts.prg.
These files are not required to run CPAD and are included only
for the information of users interested in the program's design.
THE DBASE™ IV. 1.1. VERSION
For the benefit of those who have DBASE™ IV, version 1.1,
installed on their computers, a compatible version of CPAD has
been included in the CPAD.411 directory of the CPAD diskette. In
this version of CPAD, all program and report form files from the
DBASE™ III PLUS version have been converted to DBASE™ IV version
1.1 format. The resulting files (44 in all) were then compiled
and linked to form the single file, MAINMENU.DBO. (Note: The
drivers IBMPR0_l.pr2 and PRNTFRM.PRF in the CPAD.411 directory
are required for the operation of the DBASE™ IV version of CPAD,
even though the printer itself, regardless of brand, is not used
by the program.)
2
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To install this version of CPAD, simply COPY at.t. THE FILES
FROM THE CPAD.411 DIRECTORY OF THE CPAD DISKETTE TO A SEPARATE
SUBDIRECTORY ON YOUR HARD DRIVE (e.g., c:\CPAD). You will need
only about 325K of disk space for the DBASE™ IV version, since
no Runtime files are required. However, THIS VERSION OF CPAD
ONLY WORKS IF DBASE™ IV, VERSION 1.1, IS INSTALLED ON YOUR
COMPUTER. Your DBASE™ IV directory must also be in the path
statement of your autoexec.bat file. A stand-alone (Runtime)
DBASE™ IV, 1.1, version of CPAD is not included. The stand-
alone (DBRUN) DBASE™ III PLUS application is the best choice for
computers without DBASE™ installed because (1) it requires a
million bytes less than would a DBASE™ IV, 1.1, Runtime version
and (2) it runs better than the DBASE™ IV version which
occasionally exibits some minor but irritating "quirks" during
data entry.
The directories SRCCODE.411 and OBJCODE.411, respectively,
contain source code (i.e., PGR and FRM files) and object code
(i.e., DBO and FRO files). The 44 object files were combined
into a single large file (Mainmenu.dbo) using the DBASE™ IV
(version .1.1) utility DBLINK.EXE. (See Appendix D.)
GETTING STARTED
To run either version of CPAD, simply enter "START" from
within the subdirectory that contains the CPAD files (and the
three DBRUN files, in the stand-alone version). Alternatively,
the compatible version of CPAD may be run from within DBASE™ III
PLUS or DBASE™ IV by entering "DO PADDUCTS" or "DO MAINMENU",
respectively, at the dot prompt, provided that (1) DBASE is
loaded from within your CPAD directory, thereby making it the
default directory, and (2) the DBASE directory is in your PATH
statement.' It would also be useful to write a batch file (e.g.,
CPAD.bat) that would allow you to load CPAD from the root
directory.
The internal documentation of CPAD should prove sufficient
for those users who like to jump right'in arid-play with a new
program. For those preferring a more structured approach, the
material that follows is provided. It leads the reader step-by-
step through all the screens of CPAD, briefly describes its
various features and reiterates certain hints and warnings
provided within the program, itself. All the illustrations in
this manual, including those on the cover and back page,
represent actual screens from CPAD. Any comments or questions
about CPAD should be directed to Charles Nauman at the following
address: United States Environmental Protection Agency,
Environmental Monitoring Systems Laboratory, Exposure Assessment
Research Division, P.O. Box 93478, Las Vegas, NV, 89193-3478.
3
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SEARCHING THE DATABASE
THE MAIN MENU
Pressing ESCAPE at the TITLE SCREEN loads the program file
PADDUCTS.PRG or MAINMENU.DBO, depending on the version of CPAD
(i.e., DBASE™ III PLUS or DBASE™ IV, ver.1.1). The total number
of records (i.e., chemicals) contained in the database is
determined and displayed on THE MAIN MENU (Figure 1), along with
the first seven chemicals in alphabetical order. As indicated by
the prompts at the top and bottom of the screen, the rest of the
alphabetical listing may be viewed in either of two ways:
1.) the user may scroll forward or backward a
"page" at a time by pressing the PGDN or PGUP
key, respectively, or
2.) if the user is searching for a specific
chemical record, he may skip to the
appropriate portion of the alphabetical
listing by entering the first letter in the
name of the chemical. (Note: any leading
numerals or greek letters in the chemical
name are placed at the end of the name so as
not to interfere with the alphabetical
sorting of records.)
Once the desired chemical record has been displayed on the
screen by one or a combination of the above methods, that record
is selected for viewing or editing by entering the corresponding
number (up to 3 digits). (Note: In the DBASE™ IV version, an
audible "beep" indicates the program is ready for user input.)
The name of the selected chemical will appear on all subsequent
screens. Other options available at the main menu are "Exit to
DOS" (F10) and "ADD/DELETE RECORD".
THE DATA DISPLAY SCREENS
Immediately after a selection is made, the name of the
selected chemical is displayed on THE MAIN FIELD-SELECTION MENU
(Figure 2) along with the following options:
1.) View fields containing information on the
selected chemical (enter 1),
2.) View fields containing information on protein
adducts formed by the chemical (enter 2), and
3.) View all fields in sequence (enter 3).
4
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Figure 1 The Main Menu
PGUP/PGDN = fiCROT.T. F8 = ADD/DELETE RECORD 510 ° EXIT TO DOS
(THERE ARE A TOTAL OF 22 RECORDS TO VIEW)
PROTEIN ADDUCT-FORMING CHEMICALS
1
ACRYLAMIDE
2
ACRYLONITRILE
3
AMINOBIPHENYL, 4-
4
BENZENE
5
BENZIDINE
6
BENZO[A]PYRENE
7
BENZYL CHLORIDE
Press 1st letter in chemical name to 'jump' through
listing or TYPE NUMBER of CHOICE (Press ENTER if
<3 characters)
Figure 2 The Main Field-Selection Menu
(F9)_PREVIOUS MENU (F10) QUIT
SELECT FIELDS
TO VIEW FOR AMINOBIPHENYL, 4-
1)
CHEMICAL INFORMATION
2)
PROTEIN ADDUCT DATA
3)
BROWSE (i.e., see all fields in
sequence)
CHOOSE ONE
5
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Other options available at this menu are: return to "PREVIOUS
MENU" (F9) and "QUIT" (F10). Throughout the program, "Quit" and
Exit to DOS" are synonymous.
CHEMICAL DATA SCREENS
Selecting 1 at the MAIN FIELD-SELECTION MENU will cause the
CHEMICAL DATA FIELDS MENU (Figure 3) to be displayed on the
screen. From this menu, one may select any of the following
database fields to view: CAS NUMBER, SYNONYMS, volume and method
of MANUFACTURE, major USES, sources and levels of EXPOSURE,
HEALTH EFFECTS, METABOLISM (Detoxification and Activation) and
HOST FACTORS relating to metabolism and susceptibility. A field
is selected by entering the letter (A-I) to the right of the
field name. The BROWSE option (I) allows the user to view all
the chemical data fields in sequence. Other options available at
the Chemical Fields Selection Menu are: return to the PREVIOUS
MENU (F9) and QUIT (F10).
Entering a letter (A-I) at the CHEMICAL DATA FIELDS MENU
causes one of the chemical data display screens (Figures 4-11) to
appear on the screen, along with the prompt " AFTER VIEWING DATA,
PRESS A FUNCTION KEY TO PROCEED". The function keys referred to
are those defined at the top of the screen, i.e., F8, F9 and F10.
If you wish to modify the data displayed on the screen, select F8
(EDIT SCREEN). If you wish to exit to DOS, press F10 (QUIT).
Pressing F9, the CONTINUE option, has two different effects,
depending upon what was selected at the CHEMICAL DATA FIELDS
MENU. If you choose the BROWSE mode (I), then pressing F9 will
produce the next data display screen in the sequence. If you
selected a specific data display screen (A-H), then pressing F9
will return you to the CHEMICAL DATA FIELDS MENU where you can
make another selection, return to earlier menus or exit to DOS.
Note that the MANUFACTURE, EXPOSURE and METABOLISM screens
(Figures 6, 8 and 10, respectively) each display two fields
rather than one as the others do. Although-the SYNONYMS screen
(Figure 5) displays up to six different synonyms for the selected
chemical name, all the synonyms for a chemical are stored in a
single field and separated by semicolons. As discussed in the
next chapter, "Modifying the Database", this fact becomes
important when editing data in the synonyms field.
PROTEIN ADDUCT DATA SCREENS
Selecting 2 at the MAIN FIELD-SELECTION MENU will cause the
PROTEIN ADDUCT FIELDS MENU (Figure 12) to be displayed on the
screen. From this menu, which operates the same way that the
CHEMICAL DATA FIELDS MENU does, one may select any of the
following database fields to view: REACTIVE METABOLITES,
(protein) ADDUCTS FORMED, (in vivo second order) RATE CONSTANT,
6
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Figure 3 The chemical Data Fields Menu
(F9\ PREVIOUS MENU
/FlOl QUIT
CHEMICAL INFORMATION FOR AMINOBIPHENYL, 4-
CAS NUMBER (A)
MANUFACTURER (B)
EXPOSURE (C)
METABOLISM (D)
BROWSE
SYNONYMS
USES
HEALTH EFFECTS.
HOST FACTORS...
(I)
(E)
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Figure 5 The synonym Screen
/F81 EDIT SCREEN
I F9l CONTINUE
f F10 > QUIT
SYNONYMS FOR AMINOBIPHENYL, 4-
1)
4-AMINOBIPHENYL
2)
p-BIPHENYLAMINE
3)
[1,1'-BIPHENYL]-4-AMINE
4)
p-AMINOBIPHENYL
5)
p-AMINODIPHENYL
6)
ANILINOBENZENE
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED.
Figure 6 The Manufacturing Data Screen
JF81 EDIT SCREEN tF9\ CONTINUE (F10) QUIT
MANUFACTURING DATA FOR AMINOBIPHENYL, 4-
VOLUME OF PRODUCTION IN U.S.
METHODS OF MANUFACTURE:
No longer manufacturer
No longer manufactured
in U.S.
in U.S.
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED.
8
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Figure 7 The Major Uses Screen
(F8l EDIT SCREEN 1F9^ CONTINUE
(FlOl QUIT
MAJOR USES FOR AMINOBIPHENYL, 4-
Formerly used as rubber anti-oxidant. Only current use
is as a research chemical and as an analytical reagent
for the detection of sulfates. 2-ABP, an intermediate
that contains 4-ABP as a contaminant, is used in the
manufacture of dyes. [1]
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED
Figure 8 The Exposure Data Screen
(F8) EDIT SCREEN JF9l CONTINUE fFlOl QUIT
EXPOSURE DATA FOR AMINOBIPHENYL, 4-
SOURCES OF EXPOSURE:
Cigarette smoke and other
combustion products.
Certain azo dyes contain
4-ABP as a contaminant
and may release more on
metabolism. [2]
LEVELS & ROUTES OF EXPOSURE:
Nanogram amounts in cigarette
smoke. Trace amounts in
certain azo dyes such as FD&C
Yellow #5 and #6. 4-ABP and
4-Nitrobiphenyl (which yields
4-ABP"upon enzymatic
nitroreduction) may occur in
a number of combustion
products. [2]
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED
9
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Figure 9 The Health Effects Screen
(F8) EDIT SCREEN (F9) CONTINUE
fFlOl QUIT
HEALTH EFFECTS OF AMINOBIPHENYL, 4-
Acute toxicity result of methemoglobinemia [2,3].
Symptoms include liver & kidney damage, bladder
irritation, corneal damage and CNS depression. An
established human bladder carcinogen. Only N-hydroxy
metabolite is mutagenic in Ames test. [2]
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED.
Figure 10 The Metabolism Data Screen
(F8 ) EDIT SCREEN (F9l CONTINUE fFlOl QUIT
METABOLISM DATA FOR AMINOBIPHENYL, 4-
DETOXIFICATION
ACTIVATION
Acetylation, a detoxification
route in Man, yields
4-acetamidobiphenyl as a
major urinary metabolite [2].
The N-hydroxy metabolite may
be detoxified by glucuronide
conjugation only to be re-
activated in the acidic
environment of the human
Arylamine-N-hydroxylase
converts 4-ABP to N-hydroxy>-
4-ABP, a procarcinogen that
can bind directly to DNA.
Further oxidation yields
highly reactive N-nitroso-
4-ABP which forms Hb adducts
[ 5^ 6 ].
N-sulfonyloxy-N-acetyl-4-ABP
binds to serum albumin [7].
bladder [4].
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED.
10
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Figure 11 The Host Factors Screen
(F8l EDIT SCREEN (F9l CONTINUE (FlOl QUIT
HOST FACTORS FOR AMINOBIPHENYL, 4-
Humans exhibit genetic polymorphism with regard to
acetylator status. Slow acetatylators are at higher
risk for arylamine-related bladder cancer compared
to fast acetylators [3,4,5,7].
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED.
Figure 12 The Protein Adduct Fields Menu
(F9l PREVIOUS MENU
(FlOl QUIT
PROTEIN ADDUCT DATA FOR AMINOBIPHENYL, 4-
REACTIVE METABOLITE (A)
RATE CONSTANT (B)
DOSE/RESPONSE DATA (C)
REFERENCES (D)
ADDUCTS FORMED (E)
BACKGROUND LEVELS (F)
MEfrHODS OF'DETECTION (G)
BROWSE (H)
CHOOSE ONE
11
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BACKGROUND LEVELS (of adducts), DOSE/RESPONSE DATA, METHODS OF
(adduct) DETECTION and REFERENCES. A field is selected by-
entering the letter (A-H) to the right of the field name. The
BROWSE option (H) allows the user to view all the protein adduct
data fields in sequence. Other options available at the PROTEIN
ADDUCT FIELDS MENU are: return to the PREVIOUS MENU (F9) and QUIT
(F10).
Entering a letter (A-H) at the PROTEIN ADDUCT FIELDS MENU
causes one of the protein adduct data display screens (Figures
13-19) to appear on the screen, along with the prompt "AFTER
VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED". The function
keys referred to are those defined at the top of the screen,
i.e., F8, F9 and F10. If you wish to modify the data displayed
on the screen, select F8 (EDIT SCREEN). If you wish to exit to
DOS, press F10 (QUIT) . As in the CHEMICAL DATA FIELDS MENU,
pressing F9, the CONTINUE option, has two different effects,
depending upon what was selected at the PROTEIN ADDUCT FIELDS
MENU. If you choose the BROWSE mode (H), then pressing F9 will
produce the next data display screen in the sequence. If you
selected a specific data display screen (A-G), then pressing F9
will return you to the PROTEIN ADDUCT FIELDS MENU where you can
make another selection, return to earlier menus or exit to DOS
(i.e., Quit).
Note that, with the exception of the REFERENCES screen (Figure
19), all of the protein adduct data display screens are single-
field displays. The REFERENCES screen, unlike the SYNONYMS
screen (Figure 5), displays seven separate fields, one for each
of a maximum of seven citations.
12
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Figure 13 The Reactive Metabolites screen
f F8 ) EDIT SCREEN (F9) CONTINUE
REACTIVE METABOLITES OF AMINOBIPHENYL, 4-
(F101 QUIT
N-Hydroxy-4-ABP, co-oxidized to the nitroao cmpd. by heme,
forms sulfanamide adducts at the beta-93 cysteine of Hb [5].
N-Sulfonyloxy-acetyl-4-ABP forms a unique tryptophan adduct
with serum albumin [7].
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED.
»
Figure 14 The in vitro Rate Constant Screen
-------
Figure 15 The Major Adducts Screen
l F8 EDIT SCREEN (F9l CONTINUE
ADDUCTS FORMED BY AMINOBIPHENYL, 4-
(F10) QUIT
(DNA): N-(deoxyguanosin-8-yl-ABP [2]. Sulfinamide adduct
at the beta-93 cysteine residue hemoglobin [5,6], and
3-Tryptophan-Nl-y1)-4-acetyl-ABP adduct at the Trp-214
residue of serum Albumin [7].
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED.
Figure 16 The Background Adduct Levels Screen
(F8 EDIT SCREEN (F9l CONTINUE (F10) QUIT
BACKGROUND ADDUCT LEVELS FOR AMINOBIPHENYL, 4-
In non-smoking humans, mean adduct levels around 28 pg/g Hb,
compared to 154 pg/g Hb for smokers [4].
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED.
14
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Figure 17 The Dose-Response Data screen
(F8) EDIT SCREEN =•5% of dose bound to Hb as the cysteine adduct [5].
After 60 days chronic dosing, adduct level reached
plateau 30 tiroes > that obtained after single dose [5].
Serum albumin adduct "0.02% of dose [7].
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED.
igure 18 The Adduct Detection Methods Screen
(F8 ) EDIT SCREEN (F9 \ CONTINUE . fFlOl QUIT
ADDUCT DETECTION METHODS FOR AMINOBIPHENYL 4-
GC-MS of free amine released into solution from Hb adduct by
mild hydrolysis (0.1N NaOH yields cleaner chromatogram than
does 0.1N HCl). NCIMS preferred over ECMS due to greater
selectivity of former (detection limit >10 pg 4-ABP/10 ml.
whole blood) [4].
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED.
15
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MODIFYING THE DATABASE
THE ADD RECORD SCREEN
The ADD/DELETE MENU (Figure 20) appears on the screen when
F8 is pressed while viewing the main menu. The ADD NEW RECORD
SCREEN (Figure 21) is accessed by pressing "A" at the Add/Delete
Menu. A new record is added to the database by entering a new
chemical name and CAS number at the ADD NEW RECORD SCREEN. The
new entry will not be alphabetized correctly unless the first
character in the chemical name is a capital letter because, when
DBASE™ sorts records alphabetically, it gives different values
to uppercase and lowercase letters. However, CPAD averts this
problem by automatically converting lowercase input to uppercase.
It is extremely important, however, that the user place all
leading numbers and/or greek letters at the end of the entry,
separated by a comma (e.g., Aminobiphenyl,-4 rather than 4-
Aminobiphenyl). Otherwise, the entry will not be correctly
alphabetized in the sorted database upon the conclusion of the
add session. Any error will be evident in the main menu listing.
After the new chemical name has been entered, the associated
CAS number may also be entered in the format XXXXX-XX-X. No
spaces are allowed....use zeros rather than blanks (e.g., 00092-
67-1 rather than 92-67-1). A new record can be entered without
including a CAS number, but this procedure is to be discouraged
because it exempts the entry from the Duplicate Entry Protection
Feature (Figure 22). When a CAS number is entered on the ADD NEW
RECORD SCREEN, the program searches the database for that CAS
number. If it is found, the program notifies the user
accordingly and disallows the entry (Figure 22). Without such
protection, the database could in time become cluttered with
duplicate records for chemicals under one or more of their
synonyms. If the entry is confirmed as a new CAS number, then
the user is asked whether or not the data on the screen should be
saved (Figure 23). A "NO" answer clears the ADD NEW RECORD
SCREEN for another entry, while a "YES" answer saves the entries
on screen and prompts the user for another entry (Figure 24).
Entering "N" at the prompt when all entries have been made
will cause the modified database (i.e., the old records plus the
newly appended ones) to be re-sorted alphabetically by chemical
name to the backup database, LASTUPDT.DBF. Because this
procedure takes a little time, it is performed only once per
session, i.e., after all new records have been added. The un-
sorted, modified database, SPADDUCT.DBF, is then deleted. The
newly sorted database, LASTUPDT.DBF, is copied to the original
filename, SPADDUCT.DBF, and the latter's index files, CAS.NDX and
CHEM.NDX, are updated. LASTUPDT.DBF is retained as a backup.
Heed the warning (Figure 25) to backup SPADDUCT.DBF regularly.
16
-------
Figure 19 The References screen
(F8 1 EDIT SCREEN < F9 ) CONTINUE (FlOl QUIT
PROTEIN ADDUCT REFERENCES FOR AMINOPIPHENYL, 4-
1.) FOURTH ANNUAL REPORT ON CARCINOGENS (1985), NTP, PB 85-134633
2.) HAZARDOUS SUBSTANCES DATA BANK: 4-BIPHENYLAMINE (1989), NAT.LIB.MED.
3.) TANNENBAUM ET AL.(1986), PP.63-75 IN MECHANISMS OF TOBACCO CARCINOG.
4.) BRYANT ET AL. (1987), CANCER RES., 47: 602-608
5.) GREEN ET AL. (1984), CANCER RES., 44: 4254-4259
6.) RINGE ET AL. 1988), CHEM.RES.TOXICOL. 1:22-24
7.) SKIPPER ET AL. (1985), CANCER RES., 45: 5122-5127
AFTER VIEWING DATA, PRESS A FUNCTION KEY TO PROCEED.
Figure 20 The Add/Delete Menu
F9 RETURN TO MAIN MENU FlO = EXIT TO DOS
ADD/DELETE MENU
Add new chemical record to database
OR
Delete old chemical record from database
CHOOSE OPTION BY FIRST LETTER
17
-------
Figure 21 The Add Hew Record screen
ENTER DATA NOW OR PRESS RETURN TO EXIT LINE.
ADD NEW RECORD TO PROTEIN ADDUCT DATABASE
CHEMICAL NAME:
CAS NUMBER:
IMPORTANT I The FIRST CHARACTER in chemical entry MUST BE an
ENGLISH letter, otherwise the new record will not be properly
alphabetized in either the database or the menu listings.
Place all leading numbers and greek letters at the end of
entry preceded by a comma. For example: type Aminobiphenyl,4-
and Toluene,o-, NOT 4-Aminobiphenyl, aminobiphenyl,-4,
o-Toluene or toluene,-o.
Figure 22 The Duplicate Entry Protection Feature
ENTER DATA NOW OR PRESS RETURN TO EXIT LINE.
ADD NEW RECORD TO PROTEIN ADDUCT DATABASE
CHEMICAL NAME: BIPHENYLAMINE, PARA-
CAS NUMBER:
(NO SPACES ALLOWED. USE ZERO'S.)
WARNING 1 If you omit to enter a CAS number, this program
will be unable to protect you against future attempts to
inadvertently add duplicates of this entry. This is because
the Duplicate Entry Protection Feature keys on CAS number
rather than on chemical name.
ADD NEW RECORD TO PROTEIN ADDUCT DATABASE
CHEMICAL NAME: BIPHENYLAMINE, PARA-
CAS NUMBER: 00091-67-1
DATABASE ALREADY CONTAINS AMINOBIPHENYL, 4-
YOUR ENTRY HAS BEEN ABORTED. PLEASE PRESS ANY KEY TO TRY AGAIN.
18
-------
Figure 23 The Save New Data Prompt
ADD NEW RECORD TO PROTEIN ADDUCT DATABASE
CHEMICAL NAME:
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
CAS NUMBER: 99999-99-9
SHALL WE SAVE THIS INFORMATION? (Y or N)
Figure 24 The More/Done Prompt
ADD NEW RECORD TO PROTEIN ADDUCT DATABASE
CHEMICAL NAME:
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
CAS NUMBER: 99999-99-9
ENTER ANOTHER NEW CHEMICAL? (Y or N)
19
-------
Figure 25 The Re-Sort Database Prompt
ADD NEW RECORD TO PROTEIN ADDUCT DATABASE
CHEMICAL NAME:
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
CAS NUMBER:
*** WARNINGI!
99999-99-9
CAUTIONII ***
DO NOT INTERRUPT THIS program while new records are being
alphabetized (a comparatively lengthy process). To do so
would risk the corruption or even the deletion of the
database, SPADDUCT.DBF. Always keep an updated backup copy
of SPADDUCT.DBF on 'floppy', just in case.
PLEASE WAIT WHILE ADDITIONS ARE ALPHABETIZED.
Figure 26 The Delete Record Screen
PGUP/PGDN = SCROLL F9 = RETURN TO MAIN MENU
F10
EXIT TO DOS
(THERE ARE A TOTAL OF 23 RECORDS TO VIEW.)
SELECT CHEMICAL RECORD TO BE DELETED
1 ACRYLAMIDE
2 ACRYLONITRILE
3 AMINOBIPHENYL, 4-
4 BENZENE
5 BENZIDINE
6 BENZO[A]PYRENE
7 BENZYL CHLORIDE
Press 1st letter in chemical name to 'jump' through listing
or TYPE NUMBER of CHOICE (Press ENTER if <3 characters).
~
20
-------
THE DELETE RECORD SCREEN
The DELETE RECORD SCREEN is used to delete one or more
records from the database. It is accessed from the MAINMENU
screen by pressing F8 for the ADD/DELETE MENU, then pressing "D"
for the DELETE RECORD SCREEN (Figure 26) . The latter works in
exactly the same way that the MAINMENU screen does, except that
it is used to select a chemical for deletion rather than for data
display. First, the chemical is located, by entering the first
letter in the chemical"s name and/or using the PGUP and PGDN keys
(Figure 27). When a legal number is entered, the selection is
identified at the bottom of the screen and the user is prompted
to confirm his intention to delete that selection (Figure 28).
A positive response (i.e., "Y") to the Selection Confirmation
Prompt elicits the Deletion Confirmation Prompt "Are you sure?
Deletion is forever, you know.11. If the response is "Y", then
CPAD proceeds to delete the selected record while notifying the
user of both the action being taken, and the final result (Figure
29) . If the response is "N", then CPAD asks the user if he/she
wishes to delete another selection and, depending on the
response, returns the user to either the beginning of the DELETE
RECORD SCREEN or the ADD/DELETE MENU. A negative response (i.e.,
"N") to the Selection Confirmation Prompt elicits the prompt
"Delete Another Selection? (Y or N)". A second negative response
returns the user to the ADD/DELETE MENU; a positive response
returns the user to the beginning of the DELETE RECORD SCREEN.
Since the relative order of the remaining records is
unaffected by the deletion of one or more chemicals, it is not
necessary to re-sort the database. However, it is necessary to
re-index the database, i.e., to update the index files CHEM.NDX
and CAS.NDX. Because it takes much less time to index a database
than it does to sort a database, the record deletion routine of
CPAD runs much faster than does its record addition routine.
THE FIELD EDIT SCREENS
While data deletion performed at -the DELETE RECORD SCREEN is
an all-or-nothing affair, only the Chemical Name and CAS Number
for a new record can be entered at the ADD RECORD SCREEN. The
remaining contents of a chemical record may be added/edited
piecemeal at the appropriate FIELD EDIT SCREEN. The latter are
accessed by pressing F8 (EDIT) at the corresponding data display
screen. Apart from having grey backgrounds and highlighted input
fields, any given FIELD EDIT SCREEN has the same "look and feel"
as the corresponding DATA DISPLAY SCREEN. Most of the edit
screens present either one or two fields and are driven by one of
two programs, EDIT1FLD.PRG or EDIT2FLD.PRG. For reasons
discussed below, three of the field edit screens, i.e., The CAS
NUMBER EDIT SCREEN, the SYNONYMS EDIT SCREEN and the REFERENCES
EDIT SCREEN, are driven by their own separate programs.
21
-------
Figure 27 The Locate Record Prompt
PGUP/PGDN = SCROLL F9 = RETURN TO MAIN MENU F10 ° EXIT TO DOS
(THERE ARE A TOTAL OF 23 RECORDS TO VIEW.)
SELECT CHEMICAL RECORD TO BE DELETED
23 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
(END OF FILE)
Press 1st letter in chemical name to 'jump' through listing ¦ .
or TYPE NUMBER of CHOICE (Press ENTER if <3 characters) ' '
Figure 28 The Selection Confirmation Prompt
PGUP/PGDN = SCROLL F9 = RETURN TO MAIN MENU F10 = EXIT TO DOS
(THERE ARE A TOTAL OF 23 RECORDS TO VIEW.)
SELECT CHEMICAL RECORD TO BE DELETED
23 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
(END OF FILE)
DELETE RECORD FOR XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX?
(Y or N)
22
-------
Single-Field Screens
Eleven of the fifteen data display screens display the
contents of a single field for the selected record. Of those,
all but two (CASNUMBER and SYNONYMS) use the same procedure
(EDIT1FLD.PRG) to format the screen. (The exceptions,
MANUFACTURE, EXPOSURE, METABOLISM, CASNUMBER and SYNONYMS, are
considered below under separate headings.)
The options mode of each edit screen is entered by pressing
F8 (EDIT) at the desired data display screen (e.g., THE MAJOR
ADDUCTS SCREEN). Upon entering the options mode of the edit
screen (Figure 30), the data box is cleared and the user is given
three options: (1) return to the data display screen by pressing
F9, (2) view a help screen containing edit instructions by
pressing F2, or (3) proceed to edit data by pressing F8 again.
The EDIT-HELP SCREEN is reproduced in Figure 31 and those
instructions need not be repeated in full here. However, it is
worth repeating that all the single-field edit screens governed
by EDIT1FLD.PRG provide for self-formatting, unidirectional,
multi-line input.
Upon entering the edit mode of the edit screen (Figure 32),
the current data re-appears in the data box or window as
highlighted input lines (NOTE: the highlighting does not show up
in the figures), and the cursor is flashing at the beginning of
the first line. Although it is the same data that appeared on
the data display screen, it is probably not formatted the same.
Recall (from the INSTALLATION AND STARTUP section) that those
single-field data display screens that are governed by
EDIT1FLD.PRG have their data automatically formatted by
corresponding report form (.FRM) files. Edit each of the input
lines as if they were all part of one long line (i.e., do NOT
introduce extra spaces to avoid splitting a word between two
lines). Also, remember that you cannot back up to correct errors
made on a previous line. Instead, you will have to exit each
line sequentially, return to the data- display screen and start
the editing process all over again. Therefore, spend time to
save time by editing each line slowly and carefully. When all
lines have been exited, save or abort the changes and return to
the data display screen by giving the appropriate response at the
prompt (Figure 33). When finished editing data, exit any
remaining highlighted lines and save or abort changes by giving
the appropriate response (Y or N) at the prompt.
Double-Field Screens
The MANUFACTURE, EXPOSURE and METABOLISM data display
screens each display two fields in the same box or window. The
associated edit screens, of which Figure 33 is an example, are
23
-------
Figure 29 The Deletion confirmation Prompt
PGUP/PGDN = SCROLL F9 = RETURN TO MAIN MENU F10 = EXIT TO DOS
(THERE ARE A TOTAL OF 23 RECORDS TO VIEW.)
SELECT CHEMICAL RECORD TO BE DELETED
23 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
(END OF FILE)
THE RECORD FOR XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
HAS BEEN DELETED FROM THE DATABASE.
Figure 30 The Major Adducts Edit Screen-Options Mode
-------
Figure 31 The Edit-Help screen
EDIT - HELP SCREEN
WHEN ENTERING DATA, MAKE NO EFFORT TO FORMAT INPUT BEYOND ASSURING THAT
THERE IS A SPACE BETWEEN EVERY WORD AND SENTENCE. ESPECIALLY, DO NOT TRY TO
"WRAP AROUND" DATA AS IT IS ENTERED BY ADDING SUPERFLUOUS SPACES OR OMITTING
OTHERS. THE INPUT WILL BE AUTOMATICALLY FORMATTED BY THE APPROPRIATE DATA
DISPLAY SCREEN. IF, FOR EXAMPLE, A WORD ON THE EDIT SCREEN BEGINS ON THE LAST
PART OF ONE LINE AND ENDS ON THE FIRST PART OF THE NEXT LINE, IT WILL "WRAP
AROUND" PROPERLY ON THE DATA DISPLAY SCREEN. IF, HOWEVER, A WORD ENDS ON THE
LAST SPACE OF AN EDIT LINE, THE NEXT LINE MUST BEGIN WITH A SPACE RATHER THAN
WITH THE NEXT WORD. OTHERWISE, ON THE SELF-FORMATTING DATA DISPLAY SCREEN,
THE TWO WORDS WILL APPEAR AS A SINGLE WORD.
WHEN ONE LINE IS FILLED, THE CURSOR WILL AUTOMATICALLY JUMP TO THE NEXT
LINE. HOWEVER, IF YOU WISH TO SKIP A LINE WITHOUT CHANGES, OR YOU FINISH YOUR
ENTRY BEFORE THE LINE HAS BEEN FILLED, THEN YOU MUST PRESS OR THE
DOWN ARROW IN ORDER TO PROCEED TO THE NEXT LINE, FIELD, OR PROMPT. ONCE
BEGUN, THE EDIT PROCESS CANNOT BE INTERRUPTED. TO EXIT THE EDIT MODE, YOU
MUST PRESS AT EACH AND EVERY ONE OF THE REMAINING UNEDITED LINES.
JUST FOLLOW DIRECTIONS ON THE SCREEN FOR CAS NUMBER, SYNONYMS, AND REFERENCES.
EACH OF THESE SCREENS HAS ITS OWN SPECIAL EDITING PROGRAM.
(END OF HELP SCREEN)
PRESS ANY KEY TO RETURN TO EDIT SCREEN...
Figure 32 The Major Adducts Edit Screen-Edit Mode
EDIT SCREEN AT CURSOR. OR PRESS TO EXIT LINE.
ADDUCTS FORMED BY AMINOBIPHENYL, 4-
(DNA): N-(deoxyguanosin-8-yl)-ABP [2]. (Protein):
Sulfonamide adduct at the beta-93 cysteine residue of
hemoglobin [5,6], and 3-Tryptophan-Nl-yl)-4-acetyl-ABP
adduct at the Trp-214 residue of Serum albumin [7].
MAKE DESIRED CHANGES, THEN PRESS RETURN.
-------
governed by one procedure file (EDIT2FLD.PRG). They work the
same way that single-field edit screens do, except that the
flashing cursor jumps immediately from the bottom of the first
field to the top of the second. Be careful that data from the
first field does not overflow into the second field.
The CAS Number and Svnonvms Screens
The single-field edit screens CAS NUMBER and SYNONYMS are
each governed by their own separate procedure files (CASEDIT.PRG
and SYNEDIT.PRG), but they work the same way that the other edit
screens do. The CASNUMBER EDIT SCREEN (Figure 34) contains a
single input line and will accept only numbers as input (use
zeros in lieu of leading blanks).
The SYNONYMS EDIT SCREEN (Figure 35) displays six input
lines, one for each of up to six different synonyms for the
selected chemical name. In the database, all the synonyms for a
chemical are contained in a single field and separated by
semicolons. As a result, it is important to avoid the accidental
entry of semicolons when editing data in the synonyms field.
Portions of a single input line separated by semicolons will be
formatted on the data display screen as separate synonyms.
The References Screen
The REFERENCES EDIT SCREEN (Figure 36) displays seven input
lines. However, these input lines, unlike those of the SYNONYMS
screen, represent seven separate fields, one for each of a
maximum of seven citations. The separate procedure file
(REFSEDIT.PRG) that governs this screen differs from the others
in that it allows the user to randomly edit and re-edit lines
within a single edit session. This means that one can back up to
correct input errors in lines already exited without having to
exit the edit mode and start all over, again.
The references are limited to seven citations per chemical
for two reasons. First, all the CPAD data are contained in a
single database file (SPADDUCTS.DBF) for convenience. Each
chemical record already consumes the maximum storage space
allowed within the structural limitations of DBASE™, i.e.,
without splitting the database up into multiple files. Second,
CPAD was not designed to provide the detail that is more properly
sought in the scientific literature. Rather, it is intended to
concisely indicate the status of fundamental research on protein
adduct-forming chemicals as relates to their potential for
exposure monitoring. Also, the reference fields, which will be
continually updated along with the rest of CPAD's data fields,
should always include recent review articles or research papers
that can provide the basis of a larger literature search.
26
-------
Figure 33 The Exposure Data Edit Screen-Save Prompt
EDIT SCREEN AT CURSOR. OR PRESS TO EXIT LIME.
EXPOSURE DATA FOR AMINOBIPHENYL, 4-
SOURCES OF EXPOSURE
cigarette smoke and other com-
bustion products. Certain azo
dyes contain 4-abp as a con-
taminant and may release more
on metabolism.[2]
LEVELS OF EXPOSURE
Nanogram amounts in cigarette
smoke. Trace amounts in cer-
tain azo dyes such as FD6C
Yellow #5 and #6. 4-ABP and
4-Nitrobiphenyl (which yields
4-abp upon enzymatic nitro-
reduction) may occur in a
number of combustion products.
[2]
SAVE CURRENT CHANGES, NOW? (Y or N)
Figure 34 The CAS Number Edit Screen
ENTER NUMBERS ONLY. SPACKS MOT AT.T.QWED. USE ZEROS INSTEAD.
CAS NUMBERS FOR AMINOBIPHENYL, 4-
00092-67-1
MAKE DESIRED CHANGES, THEN PRESS RETURN.
27
-------
Figure 35 The Synonyms Edit Screen
EDIT SCREEN AT FLASHING CURSOR. OR HIT RETURN TO EXIT LINE.
SYNONYMS FOR AMINOBIPHENYL, 4-
4-AMINOBIPHNYL
p-BIPHENYLAMINE
[1,l'-BIPHENYL]-4-AMINE
p-AMINOBIPHENYL
p-AMINODIPHENYL
IMPORTANT I DO NOT - repeat, DO NOT - USE ANY SEMICOLONS.
That character is used internally to separate the individual
synonyms which, in the database, are combined in a single
field.
MAKE DESIRED CHANGES, THEN PRESS RETURN
Figure 36 The References Edit Screen
EDIT TEXT AT FLASHING CURSOR. OR PRESS TO EXIT LINE.
PROTEIN ADDUCT REFERENCES FOR AMINOBIPHENYL, 4-
1.) FOURTH ANNUAL REPORT ON CARCINOGENS (1985), NTP, PB 85-134633
2.) HAZARDOUS SUBSTANCES DATA BANK: 4-BIPHENYLAMINE (1989), NAT.LIB.MED.
3.) TANNENBAUM ET AL.(1986), PP.63-75 IN MECHANISMS OF TOBACCO CARCINOG.
4.) BRYANT ET AL.(1987), CANCER RES., 47: 602-608
5.) GREEN ET AL.(1984), CANCER RES., 44: 4*254-4259-
6.) RINGE ET AL.(1988), CHEM.RES.TOXICOL. 1: 22-24
7.) SKIPPER ET AL.(1985), CANCER RES., 45: 5122-5127
28
-------
REFERENCES
Carribis, Joseph-David (1987). DBASE™ III PLUS: The Complete
Reference. Osbourne McGraw Hill, Berkeley, California.
Liskin, Miriam (1988). Advanced DBASE™ III PLUS: Programming
and Techniques. Osbourne/McGraw Hill, Berkeley, California.
Schnell, Frank C. (1989). Protein Adduct-Forming Chemicals for
Exposure Monitoring: Chemicals Selected for Further Study. EPA
600/4-89/035.
29
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APPENDIX A
THE DATABASE STRUCTURE OF CPAD
Structure for database: C:SPADDUCT.DBF
Number of data records: 22*
Date of last update : 08/21/90
Field Field Name
1
CASNUMBER
2
CHEMICAL
3
SYNONYMS
4
MFGVOLUME
5
MANUFACTUR
6
USES
7
EXPOSOURCE
8
EXPOSURE
9
HEALTHFX
10
DETOX
11
ACTIVATION
12
HOSTFACTOR
13
ELECTROPHI
14
ADDUCTS
15
RATECNSTNT
16
BACKGROUND
17
DOSERESPON
18
METHOD
19
REF1
20
REF2
21
REF3
22
REF4
23
REF5
24
REF6
25
REF7
26
BLANK
TVDe
Width
Character
10
Character
46
Character
235
Character
68
Character
254
Character
254
Character
136
Character
254
Character
254
Character
254
Character
254
Character
254
Character
204
Character
254
Character
68
Character
204
Character
254
Character
254
Character
68
Character
68
Character
68
Character
68
Character
68
Character
68
Character
68
Character
1
Total bytes per record = - 3989
Inquiries regarding the availability of updates of
SPADDUCTS.DBF should be directed to Charles H. Nauman
at the following address: United States Environmental
Protection Agency, Environmental Monitoring Systems
Laboratory, Exposure Assessment Research Division, P.O.
Box 93478, Las Vegas, NV, 89193-3478.
A-l
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APPENDIX B
CHEMICALS IN CPAD DATABASE AS OF MARCH 1991
The 22 chemicals listed below represent those chemicals
of interest to the EPA that were identified as having
potential for exposure monitoring using protein adduct
measurements (EPA 600/4-89/035, Oct., 1989). Future updates
of CPAD (i.e., of the primary database file SPADDUCTS.DBF*)
will contain more data on more chemicals, reflecting the
rapid growth of research in molecular dosimetry.
Record#
chemical
1
ACRYLAMIDE
2
ACRYLONITRILE
3
AMINOBIPHENYL, 4-
4
BENZENE
5
BENZIDINE
6
BENZO[a]PYRENE
7
BENZYL CHLORIDE
8
CHLOROFORM
9
DIMETHYLBENZANTHRACENE, 7,12-
10
EPICHLORHYDRIN
11
ETHYLENE DICHLORIDE
12
ETHYLENE OXIDE
13
FORMALDEHYDE
14
METHYLENE BIS(2-CHLOROANILINE)
4,4'- , (MOCA)
15
NITROPYRENE, 1-
16
NITROSONORNICOTINE
17
PENTACHLOROPHENOL
18
PROPYLENE OXIDE
19
STYRENE
20
TOLUENE DIISOCYANATE, 2,4-
21
TOLUIDINE, o-
22
VINYL CHLORIDE
Inquiries regarding the availability of updates of
SPADDUCTS.DBF should be directed to Charles H. Nauman at the
following address: United States Environmental Protection
Agency, Environmental Monitoring Systems Laboratory,
Exposure Assessment Research Division, P.O. Box 93478, Las
Vegas, NV, 89193-3478.
B-l
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APPENDIX C
CPAD FILES: THE DBASE™ III PLUS VERSION
If DBASE™ III PLUS is installed on your computer, only the
files located under the CPAD.DB3 directory of the CPAD diskette
(listed below) need be transferred to a separate directory (e.g.,
C:\CPAD) on your hard drive. If DBASE™ III PLUS is not
installed on your computer, then all three DBRUN files from the
RUNTIME.DB3 directory must also be copied to C:\CPAD. On-screen
installation instructions are provided in the README files.
Filename Bvtes
README DB3 1255
README DB4 1485
README BAT 63
CPAD.DB3 :
START
BAT
778
TITLSCRN
EXE
7774
WAITMSG
TXT
401
PAD*DUCTS
PRG*
36256
BACKGRND
FRM
1990
ADCTFRMD
FRM
1990
D-R
FRM
1990
RCTVMTBL
FRM
1990
RATECNST
FRM
1990
MFG
FRM
1990
METHODS
FRM
1990
EXPOSURE
FRM
1990
METAB
FRM
1990
SYNONYMS
FRM
1990
USES
FRM
1990
HEALTHFX
FRM
1990
HOSTFCTR
FRM
1990
SPADDUCT
DBF
89088
LASTUPDT
DBF
92613
SPADDNEW
DBF
4855
CHEM
NDX
2560
CASNUM
NDX
1024
EOS
EXE
7286
SRCCODE DB3 *
OBJCODE DB3 *
USERSMAN.UAL
RUNTIME.DB3
Description:
Installation information.
Installation information.
Displays README Files.
Startup Batch File.
Opening graphics screen.
Loading Message
Main Program.
Data display form.
II II II
II II II
II II II
II II ft
II II II
II II II
II II II
II II II
II If II
II If II
II II II
II II II
The Primary Database.
Backup Database.
Temporary- Append Database.
Alphabetizes Chemicals.
Cas Number Index.
End of Session Screen.
Contains Source Code.
Contains 32 object files.
Contains Users'Manual.
Contains 3 DBRUN Files:
DBRUN.MSG, DBRUN.OVL,
AND DBRUN.EXE.
*PADDUCTS.PRG was developed from the files in the SRCCODE.DB3
and OBJCODE.DB3 directories. These files, which are listed on
the next page, are not required to run CPAD. They are included
only for users who may be interested in program development.
C-l
-------
APPENDIX C (continued)
Thirty two original DBASE™ III PLUS Program files were
written (left-hand column below). These files were compiled
using the DBASE™ utility DBC.COM. The compressed files (right-
hand column below) were then linked together using the DBASE™
utility DBL.COM, to form the single object file, PADDUCTS.PRG.
Directory of Directory of
A:\SRCC0DE.DB3 A:\0BJFILE.DB3
Filename
Bvtes
Filename
Bytes
MAINMENU
SRC
4456
MAINMENU
PRG
2048
ADDELMNU
SRC
910
ADDELMNU
PRG
602
SPADD
SRC
4728
SPADD
PRG
3149
SPADDEL
SRC
4346
SPADDEL
PRG
1956
DELPAK
SRC
1211
DELPAK
PRG
714
CHMORPAD
SRC
1005
CHMORPAD
PRG
633
CFLDMENU
SRC
1940
CFLDMENU
PRG
1337
pfldmenu
SRC
1943
PFLDMENU
PRG
1359
CASNUMBR
SRC
1153
CASNUMBR
PRG
685
CASEDIT
SRC
2364
CASEDIT
PRG
1446
MFG
SRC
1710
MFG
PRG
1106
EXPOSURE
SRC
1694
EXPOSURE
PRG
1094
METAB
SRC
1728
METAB
PRG
1095
SYNONYMS
SRC
1347
SYNONYMS
PRG
827
SYNEDIT
SRC
3367
SYNEDIT
PRG
2096
USES
SRC
1559
USES
PRG
934
HEALTHFX
SRC
1531
HEALTHFX
PRG
952
HOSTFCTR
SRC
1531
HOSTFCTR
PRG
954
VIEWALLC
SRC
552
VIEWALLC
PRG
226
RCTVMTBL
SRC
1544
RCTVMTBL
PRG
957
RATECNST
SRC
1561
RATECNST
PRG
960
DOSERSPN
SRC
1548
DOSERSPN
PRG
958
ADCTFRMD
SRC
1554
ADCTFRMD
PRG
938
BACKGRND
SRC
1594.
BACKGRND
PRG
977
METHODS
SRC
1560
METHODS
PRG
965
PADREFS
SRC
1324
PADREFS
PRG
816
REFSEDIT
SRC
2931
REFSEDIT
PRG
1866
EDIT1FLD
SRC
3838
EDIT1FLD
PRG
1806
EDIT2FLD
SRC
4330
EDIT2FLD
PRG
1985
VIEWALLP
SRC
548
VIEWALLP
PRG
224
VIEWALL
SRC
612
VIEWALL
PRG
294
HELPMSG
SRC
1634
HELPMSG
PRG
1514
The remaining directories (CPAD.411, SRCCODE.411 and
OBJCODE.411) on the CPAD diskette contain files that relate to a
version of CPAD that can only be used on computers that have
DBASE™ IV, version 1.1, installed on the hard drive. These
files are listed in Appendix D.
C-2
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APPENDIX D
CPAD FILES: THE DBASE™ IV VERSION
If you have DBASE™ IV version 1.1 on your hard disk, then
only the contents of the CPAD.411 directory of the CPAD diskette
need be copied to a separate directory (e.g., C:\CPAD) on your
hard drive. A stand-alone DBASE™ IV (1.1) version of CPAD is
not provided on the CPAD diskette because it would require three
times as much disk space as the DBRUN III PLUS version and still
would not run as well. Listed below are the contents of the
directories containing DBASE™ IV ver.1.1 CPAD files.
Npte that the primary database file SPADDUCTS.DBF is
identical in both CPAD versions. Thus, for current users of CPAD
(regardless of version), future updates of CPAD need consist of
only one file. Such updates, when available, may be obtained by
contacting Charles H. Nauman at the following address: United
States Environmental Protection Agency, Environmental Monitoring
Systems Laboratory, Exposure Assessment Research Division, P.O.
BOX 93478, Las Vegas, NV, 89193-3478.
Filename Bvtes
CPAD.411 :
START
BAT
62
WAITMSG
TXT
398
IBMPRO 1
PR2
808
PRNTFRM
PRF
698
TITLSCRN
EXE
7792
MAINMENU
DBO*
118636
SPADDUCT
DBF
88624
SPADDNEW
DBF
4854
LASTUPDT
DBF
88624
CHEM
NDX
2560
CASNUM
NDX
1024
EOS
EXE
7286
SRCCODE.411 :*
OBJCODE.411 :*
Description:
Startup Batch File.
Loading Message
Printer Driver
Print format file
Opening Graphics Screen.
Main Program
The Primary Database.
Temporary Append Database.
Backup Database.
Alphabetizes Chemicals.
Cas Number Index.
End of Session Screen.
Contains Source code
Contains unlinked Object
Code Files.
'MAINMENU.DBO was developed from the files in the SRCCODE.411
and OBJCODE.411 directories. These files, which are listed on
the next page, are not required to run CPAD, but are included for
those users who may be interested in program development.
D-l
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APPENDIX D (Continued)
Directory of Directory of
A:\SRCC0DE.411 A:\0BJC0DE.411
Filename
Bvtes
Filename
Bvtes
MAINMENU
PRG
4347
MAINMENU
DBO
3976
SPADD
PRG
4708
CHMORPAD
DBO
1296
SPADDEL
PRG
4346
CFLDMENU
DBO
2616
DELPAK
PRG
1211
SPADDEL
DBO
3996
METAB
PRG
1807
MFG
DBO
2448
CASEDIT
PRG
2433
HEALTHFX
DBO
2140
RATECNST
PRG
1640
EXPOSURE
DBO
2428
HELPMSG
PRG
1634
USES
DBO
2124
EXPOSURE
PRG
1773
EDIT1FLD
DBO
3836
BACKGRND
PRG
1636
RCTVMTBL
DBO
2152
EDIT1FLD
PRG
3845
HOSTFCTR
DBO
2104
VIEWALLC
PRG
552
HELPMSG
DBO
1884
PADREFS
PRG
1385
METAB
DBO
2440
ADDELMNU
PRG
910
EDIT2FLD
DBO
4236
SYNONYMS
PRG
1408
RATECNST
DBO
2156
SYNEDIT
PRG
3395
SYNONYMS
DBO
1992
CHMORPAD
PRG
1005
SYNEDIT
DBO
4076
CFLDMENU
PRG
1940
CASNUMBR
DBO
1564
PFLDMENU
PRG
1943
CASEDIT
DBO
2880
CASNUMBR
PRG
1172
VIEWALLC
DBO
820
HOSTFCTR
PRG
1585
ADDELMNU
DBO
1104
ADCTFRMD
PRG
1598
SPADD
DBO
4916
METHODS
PRG
1639
DELPAK
DBO
1416
MFG
PRG
1786
PFLDMENU
DBO
2624
EDIT2FLD
PRG
4331
ADCTFRMD
DBO
2140
VIEWALLP
PRG
548
BACKGRND
DBO
2160
VIEWALL
PRG
612
DOSERSPN
DBO
2164
REFSEDIT
PRG
2905
METHODS
DBO
2172
HEALTHFX
PRG
1610
PADREFS
DBO
1988
USES
PRG
1591
REFSEDIT
DBO
3532
RCTVMTBL
PRG
1623
VIEWALLP
DBO
812
DOSERSPN
PRG
1627
VIEWALL
DBO
1044
RCTVMTBL
FRM
1084
EXPOSURE
FRO
3840
HEALTHFX
FRM
1084
MFG
FRO
3844
MFG
FRM
1460
METAB
FRO
3808
METAB
FRM
1299
HEALTHFX
FRO
3684
EXPOSURE
FRM
1450
USES
FRO
3684
USES
FRM
1080
HOSTFCTR
FRO
3684
HOSTFCTR
FRM
1084
RCTVMTBL
FRO
3684
RATECNST
FRM
1084
RATECNST
FRO
3684
ADCTFRMD
FRM
1084
ADCTFRMD
FRO
3684
BACKGRND
FRM
1084
BACKGRND
FRO
3684
DOSERSPN
FRM
1084
DOSERSPN
FRO
3684
METHODS
FRM
1083
METHODS
FRO
3684
D-2
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Preissue Copy
PROJECT SUMMARY
USER'S GUIDE
COMPUTERIZED PROTEIN ADDUCTS DATABASE (CPAD)
Frank C. Schnell and Charles H. Nauman
ABSTRACT
This user's manual contains directions for the installation
and use of the computerized Protein Adducts Database (CPAD).
Most of this documentation is also available on-screen in the
form of CPAD's "Readme" files and program prompts. CPAD, a user-
friendly, menu-driven, stand-alone DBASE™ application, was
created to provide an efficient means of updating and
disseminating information on protein adducts relating to their
utility as dosimeters of exposure to environmental contaminants,
especially genotoxic and/or carcinogenic compounds. The
structure of the database as well as its initial contents were
derived primarily from the document, "Protein Adduct-Forming
Chemicals for Exposure Monitoring: Chemicals for Further Study"
(EPA/600/4-89/035).
Software for executing CPAD accompanies the User's Guide on
a single high density 3.5" diskette. The diskette contains (1)
two versions of CPAD that run with DBASE™ III PLUS and DBASE™
IV, version 1.1, respectively, (2) the DBRUN™ files needed to
run CPAD as a stand-alone DBASE™ III PLUS application, (3) a.
copy of the User's Manual (a WORDPERFECT™ 5.0 document file)
which may be viewed on screen or printed out, and (4) the source
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code and unlinked object code files used to develop CPAD's main
program. The latter files are not required to run CPAD and are
included only for the information of users who may be interested
in the program's design. See the back of this Project Summary
for ordering information.
INFORMATION
The U.S. Environmental Protection Agency (EPA) has developed
an initiative designed to develop, refine and apply appropriate
biomarkers for use in conjunction with environmental monitoring
data to provide better estimates of exposure and risk to
individuals and populations. Among the biomarkers under study
are macromolecular adducts formed in vivo by reactive
environmental chemicals or their metabolites.
A report entitled "Protein Adduct-Forming Chemicals For
Exposure Monitoring: Literature Summary and Recommendations"
(EPA/600/4-90/007) summarized the literature regarding adducts
formed by xenobiotics with proteins, particularly hemoglobin and
serum albumin, and examined the feasibility of their use as
dosimeters of exposure. Twenty-two chemicals of interest to the
EPA were recommended for further study and ranked according to
their potential utility in exposure monitoring by protein adduct-
based methods. These prioritized chemicals were then examined in
greater detail in a report entitled "Protein Adduct-Forming
Chemicals For Exposure Monitoring: Chemicals Selected for
Further Study" (EPA/600/4-89/035).
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It was anticipated that, due to rapid developments in the
field of molecular dosimetry, the information in the last-
mentioned protein adducts report, as well as the prioritized
chemicals list, itself, would require frequent amendments and
updates in the future. To facilitate that process, the
Computerized Protein Adducts Database (CPAD) was developed. The
structure of the database as well as its initial contents were
derived primarily from the last-mentioned project report
(EPA/600/4-89/035). The database includes entries on the
following topics: manufacture and use, sources and levels of
exposure, known health effects, metabolism (detoxification and
*
activation), host factors, reactive metabolites, adduct
characterization, rates of adduct formation (i.e., second order
rate constants), background adduct levels, dose-response
relationships, and methods of adduct detection.
PROCEDURE
CPAD is intended to run on an IBM-compatible PC with hard
disk under DOS. It can be run from a 3.5" drive, but this is not
recommended, as program execution is slowed down considerably.
The DBASE™ III PLUS version
This version of CPAD may be used with or without DBASE™ III
PLUS. If your computer has DBASE™ III PLUS installed, only the
files in the CPAD.DB3 Directory of the 3.5" CPAD diskette need be
copied to a separate subdirectory on your hard drive (e.g.,
c:\CPAD). These files will require approximately 270 K of
-------
memory. If your computer does not have DBASE™ III PLUS
installed, then the three DBRUN files provided must also be
copied into the CPAD directory on your hard disk. The resulting
stand-alone version of CPAD requires a total of 605 K.
The DBASE™ IV fi.D version
For the benefit of those who have DBASE™ IV, version l.l,
installed on their computers, a compatible version of CPAD has
been included on the CPAD diskette. To install this version of
CPAD, simply copy all the files from the CPAD.411 directory of
the CPAD diskette to a separate directory on your hard drive
%
(e.g.,c:\CPAD). You will need only about 325 KB of disk space
for the DBASE™ IV version. A stand-alone (Runtime) DBASE™ IV,
1.1 version of CPAD is not included, because it would require a
million bytes more than does the stand-alone DBASE™ III PLUS
version.
OPERATION
Getting Started
To run either version of CPAD, simply enter "START" from
within the subdirectory that contains the CPAD files (and the
three DBRUN files, in the stand-alone version). Alternatively,
TM
the compatible version of CPAD may be run from within DBASE III
PLUS or DBASE™ IV by entering "DO PADDUCTS" or "DO MAINMENU",
TM
respectively, at the dot prompt, provided that (1) DBASE is
loaded from within your CPAD directory, thereby making it the
-------
default directory, and (2) the DBASE™ directory is in your PATH
statement.
SEARCHING THE DATABASE
The main menu of CPAD is a scrolling, alphabetical list of
chemicals for which records exist in CPAD. When a chemical is
selected, the main menu closes and the field-selection menu
opens. The user may choose one of three options: (1) view only
those fields containing information on the selected chemical, (2)
view only those fields containing information on the protein
adducts formed by the chemical, or (3) browse through all the
*
data fields on the selected chemical. Chemical Data Fields
include CAS Number, Synonyms, Volume and Method of Manufacture,
Major Uses, Sources and Levels of Exposure, Health Effects,
Metabolism, and Host Factors. Protein Constant Adduct Data
Fields include Reactive Metabolites, Adducts Formed, (second
order) Rate Constant (of formation), Background Levels (of
adducts), Dose-Response Data, Methods of Detection, and
References. After selecting 1 or 2 above, the user may select to
view individual data screens or browse through all data screens
(i.e., Chemical or Protein Adduct) in sequence.
Modifying the Database
Existing data on a selected chemical may be edited/updated
at the appropriate data screen by entering Edit Mode. The Delete
Menu works the same way the Main Menu does, except that the
entire record for the selected chemical is deleted if the user's
-------
intent to do so is confirmed at the prompt. The Add Menu allows
the user to add new records (i.e., chemicals and CAS numbers,
only). A Duplicate Entry Protection Feature keys on CAS number
rather than chemical name. Any new chemical names added at the
Add Menu will subsequently appear in the alphabetical listing at
the Main Menu. All other data for new records is keyed in at the
individual data display screens in input mode, after selecting
the new chemical at the Main Menu.
SOFTWARE AVAILABILITY
The Computerized Protein Adducts Database (CPAD) can be
obtained by sending a single, formatted, high-density (1.44 MB),
3.5" diskette to the following address:
Dr. Charles H. Nauman
U.S. E.P.A., EMSL, MC-EAD
P.O. Box 93478
Las Vegas, NV 89193-3478
The CPAD Software, the accompanying User's Manual, and the
aforementioned protein adducts project reports EPA 600/4-90/007
and EPA/600/4-89/035 were written by Dr. Frank C. Schnell. He
may be contacted at the following address:
Lockheed Engineering and Sciences Co.
1050 E. Flamingo Rd.
Las Vegas, NV 89119
-------
INFORMATION BOX (for use by CERI)
The information in this document has been funded wholly or
in part by the United States Environmental Protection Agency
under Contract No. 68-CO-0049 to Lockheed Engineering and
Sciences Company. It has been subjected to the Agency's peer and
administrative review, and it has been approved for publication.
Mention of trade names or commercial products does not
constitute endorsement or recommendation for use.
The complete report, Order No. ; Cost , (subject
to change) will be available only from:
National Technical Information Service
5285 Port Royal Road
Springfield, VA 22161
The EPA Project Officer, Dr. Charles H. Nauman, can be
contacted at:
Environmental Monitoring Systems Laboratory
U.S. Environmental Protection Agency
Las Vegas, NV 89193-3478
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