Appendices1-5.pdf

Appendix 1: Historical and Estimated Workload

Historical and Estimated Workload

Studies at NCTR are funded by different sources and are designed for various purposes. For example, studies to be used as the basis for regulatory decisions by the FDA are required to be performed following GLP guidelines (21 CFR, Part 58; http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfCFR/CFRSearch.cfm?CFRPart=58&sho wFR=1), and some studies shall also follow OECD guidelines (http://www.oecd.org/env/ehs/testing/oecdguidelinesforthetestingofchemicals.htm).

The National Toxicology Program (NTP) funds several research projects at NCTR each year through an interagency agreement (IAG) between the National Institute of Environmental Health Sciences (NIEHS) and NCTR. NTP Specifications, describing requirements for NTP studies, may be found at: http://ntp.niehs.nih.gov/ntp/Test_Info/FinalNTP_ToxCarSpecsJan2011.pdf.

These studies are designed to provide sufficient data to form the basis for regulatory decisions;

therefore, most NTP studies shall follow GLP guidelines. Standard NTP studies (http://ntp.niehs.nih.gov/?objectid=72015DAF-BDB7-CEBA-F9A7F9CAA57DD7F5) include 14-day toxicity studies (range-finding studies), 13-week toxicity studies (subchronic studies), and 2-year bioassays (carcinogenicity studies). All three study types are performed at NCTR, often with additions to any aspect of the study, including but not limited to, the standard number of test groups and the standard tissue collection list. Additional studies are also performed as required based on the data needed for regulatory decisions. In the past, these studies have included mechanistic studies involving clinical chemistry and urinalysis, pharmacokinetic studies, teratology and reproductive studies, developmental studies, neurotoxicology studies, neurobehavioral studies, multi-generational studies, phototoxicology studies, perinatal toxicology studies, nanotoxicology studies, and methods development studies.

The pathology workload will be dependent upon the level of funding available to NCTR researchers for research protocols. Pathology services were required for 38, 48, 75, 64, and 56 studies in 2010, 2011, 2012, 2013, and 2014, respectively. At any given time, pathology services are being performed for 10-15 different studies. The estimates provided below are based on historical workload levels.

Table 1 shows the pathology workload at NCTR by year from 2005 through 2014. The Necropsy/Histology category represents traditional pathology from necropsy of animals through reading slides and archiving study materials. The Special Procedures category includes a wide variety of immunohistochemistry (IHC) tests, laser capture microdissection (LCMD), vaginal cytology analyses (both stained specimens and fresh, unstained smears), mammary whole mounts, and vaginal smears for sperm evaluation (VSSE). The Clinical Pathology category includes the number of animals for which some type of analysis was done and the different types of analyses. The Data Services category contains the number of Micropath data entries (or cases entered into the database system from pathologists’ notes), the total number of times databases were updated to verify data, the number of database files created, the total number of draft and final reports completed, and the number of Quality Assessments (QAS) and Pathology Working Groups (PWG) that were completed.

http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfCFR/CFRSearch.cfm?CFRPart=58&showFR=1 http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfCFR/CFRSearch.cfm?CFRPart=58&showFR=1 http://www.oecd.org/env/ehs/testing/oecdguidelinesforthetestingofchemicals.htm http://ntp.niehs.nih.gov/ntp/Test_Info/FinalNTP_ToxCarSpecsJan2011.pdf http://ntp.niehs.nih.gov/?objectid=72015DAF-BDB7-CEBA-F9A7F9CAA57DD7F5

Table 1. Historical Pathology Workload at NCTR from 2005 through 2014.

2005 2006 2007 2008 2009 2010 2011 2012 2013 2014

Necropsy/Histology Animals Necropsied 2707 1261 4427 1100 2324 5102 2183 3749 3274 4110 Laboratory Process

Complete 4075 1599 1746 2908 2021 1467 4788 2556 876 2591

Cases Assigned 4153 1729 1753 2538 1585 2063 2709 2381 1148 2360 Cases Archived Block

& Slide 4705 1199 1819 4047 1556 2139 2770 2244 2268 279

Wet Tissue Archived 2760 1074 3396 1805 2307 2308 1921 2219 2093 2968 Cassettes Trimmed 47071 12732 48968 26099 37723 10934 17861 16766 9766 41521 Cassettes Processed 52725 13129 48700 26430 39368 11737 23200 21106 10064 40957 Blocks Embedded 45352 13090 48417 26453 39371 11735 22794 21544 9501 38356 Blocks Sectioned 43585 19171 36609 34934 41084 18049 28730 22303 4828 26697 Slides Stained 44727 21431 37673 39306 35052 9826 28358 22262 5380 28377

Special Procedures Immunohistochemistry 2628 817 707 417 668 1347 929 5034 819 1687 Laser Capture

Microdissection 266 108 217 129 34

Vaginal Cytology 1900 262 380 5379 1748 3133 9279 Mammary Whole Mounts 289 34 474 Vaginal Smears for Sperm

Evaluation (VSSE) 1754 1930

Clinical Pathology Animals 2514 1521 2714 2027 2032 4485 2820 5552 2420 2749 Hematology (CBC's) 648 549 785 815 1361 1100 2332 2534 1020 1279

ELISA 6017 7635 4397 6781 2316 510 6511

RIA 3045 1120 1489 8931 7066 8090 5871 3311 440

Urinalysis 434 1774 2443 4677 137 393 Chemistries 4871 5014 14033 5837 10272 18216 27036 39051 15864 10345 Sperm Counts 80 49 336 182 968 1045 431 1025 Reticulocytes 120 114 354 127 130 190 392 293

2005 2006 2007 2008 2009 2010 2011 2012 2013 2014

Samples collected & frozen 1220 1080 447 2149 344 895 2467 2106 Platelet Isolation 408

Packed Cell Volume 293 ACT Testing 180

Data Services Micropath Data Entry 3951 2250 1399 3285 1398 1791 2229 1933 1369 961 Database Update 108 242 100 52 40 238 120 212 Database Files Created 142 Draft/Final Pathology

Reports 10 19 7 14 8 17 30 43 21 46

QAS/PWG 1 1 2 5 3 1 1

Figures 1 and 2 show the numbers of animals and cassettes, respectively, processed quarterly through pathology at NCTR from November 2004 through October 2014. The data are separated into two graphs due to the scale of the numbers – animal (or case) numbers are approximately ten times lower than the numbers of cassettes processed.

Figures 3 and 4 show the numbers of Special Procedures performed monthly in pathology at NCTR from November 2004 through October 2014. The data are separated into two graphs due to the scale of the numbers – LCMD and mammary whole mount processing were performed on a much smaller scale than IHC, vaginal cytology, and VSSE, especially in recent years. A list of IHC performed during this time period is shown in Table 2.

In recent years, vaginal cytology using fresh, unstained smears has become more commonly used to determine the stage of estrus for necropsy (Figure 3). VSSE has become commonly used to determine the mating date of rodents at NCTR (Figure 3). These two methods will likely continue to be used routinely, although the spike in vaginal cytology analyses in mid-2013 (Figure 3) will likely be an anomaly due to the unusually large scale of a single study requiring the technique.

Figures 5 and 6 show the numbers of clinical pathology samples processed quarterly by pathology at NCTR from November 2004 through October 2014. The tests are divided into two graphs due to the large number of types of tests and to the differences in the scales of the two graphs – enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), chemistry, and urinalysis analyses were generally performed on a much larger scale than other analyses.

Figures 7 and 8 show the numbers of studies for which Data Management services were provided from November 2004 through October 2014 for pathology at NCTR. The data are shown on separate graphs due to the large scale of the numbers of animals for which data was entered from pathologists’ notes (Micropath Data Entry; Figure 7) compared to the other data management tasks.

In Figure 8, “Database Created” refers to creating database files for individual studies. This will only be required as-needed when unusual circumstances occur and no file has already been created by another group. “Database Updates” include periodically running reports to ensure that data are captured properly.

Figure 8 shows the number of studies for which Draft or Final Pathology Reports were completed. The draft reports must go through NCTR’s QAU audit prior to being finalized. The Pathology Reports are not considered Final until they have been signed by the study director, so multiple rounds of edits may be required prior to finalizing the reports.

Figure 8 also shows the number of QAS/PWGs that were performed from 2005 to 2014. Areas outside Data Management will also likely be involved in the preparation for and completion of these functions as described under NTP Projects below.

Figure 9 shows the hours used monthly for all pathology contract work at NCTR from November 2004 through October 2014.

NTP Projects. Workload for NTP projects will depend upon funding levels. Approximately 2010 through 2015, NTP funding was and will be relatively high due to unusually large 90-day (~2010-2011) and 2-year (~2012-2015) studies. After approximately 2015, workload from NTP studies is expected to be near the levels of the years prior to 2010.

All chronic (2-year) and some subchronic (90-day) NTP studies require a QAS and a PWG. For the QAS, the number of blocks, wet tissues, and slides examined will be dependent upon study parameters and will vary from study to study. The reviewing pathologist(s) usually randomly chooses wet tissues, blocks, slides, and data from 10% of the animals in each test group, slides for 100% of the neoplasms found, and slides for any target organs in which an unusual amount of findings were noted in the Pathology Report. Based on historical QAS data, the number of blocks with accompanying paperwork ranges between approximately 1,600 and 3,500 and the number of slides with accompanying paperwork ranges between approximately 11,000 and 15,000. The wet tissues from 10% of study animals are set up by treatment group for review, ranging between approximately 75 and 125 animals, and the rest of the wet tissues are inventoried during the review.

Based on historical data, the number of slides reviewed during a PWG is between approximately 100 and 250.

CTP Projects. Researchers at the Center for Tobacco Products (CTP) collaborate with researchers at NCTR to evaluate the toxicity of compounds found in tobacco products. These collaborations have recently begun to include inhalation toxicology studies. Most of these studies are still in the planning stage, so the estimated pathology workload for these studies will likely increase over time.

The first inhalation toxicology studies at NCTR began during fiscal year 2014. The studies planned so far include an acute (14-day) study with a total of 234 rats, a subchronic (90-day) study with a total of 276 rats, and a pharmacokinetic analysis with a total of 341 rats. The acute and subchronic studies will follow GLP and OECD Guidelines. The number of inhalation studies is expected to increase with time. NCTR currently has one inhalation toxicologist and three staff fellows to perform all inhalation toxicology studies.

Some CTP projects do not involve inhalation. To date, only one non-inhalation study has required any pathology work. This study requires methods development, histology, IHC, and immunofluorescence techniques.

NCTR Projects. The workload level for NCTR projects will be dependent upon funding levels, but should remain approximately the same as in previous years.

Overall. The workload is highly dependent upon the availability of funding to the researchers at NCTR. For the first year of the next contract (~2015), the overall workload is expected to be relatively high due to an unusually large chronic NTP study. For the remaining years of the next contract (~2016-2020), the overall pathology workload is expected to be similar to that of approximately 2007 through 2009. Some techniques will likely be used more than they have been in the past, as discussed above, particularly vaginal cytology (fresh smears) and vaginal smears for sperm evaluation (VSSE).

Figure 1. Historical number of animals processed through pathology services contracts at NCTR. “Cases Assigned” refers to the number of cases (each case represents one animal) assigned to a pathologist for slide reading. “Cases Archived Block & Slide” refers to the number of cases (animals) archived in the block and slide archive. “Wet Tissue Archived” refers to the number of wet tissues (animals) archived in the wet tissue archive.

Figure 2. Historical numbers of cassettes processed through pathology services contracts at NCTR. Cassette/block/slide numbers are not directly related to number of tissues, since each may contain multiple tissues.

Figure 3. Historical numbers of immunohistochemistry, vaginal cytology, and vaginal smears for sperm evaluation (VSSE) analyses performed through pathology services contracts at NCTR. Vaginal cytology numbers include both stained specimens and fresh, unstained smears.

Figure 4. Historical numbers of laser capture microdissections (LCMD) and processing of mammary whole mounts through pathology services contracts at

NCTR.

Figure 5. Historical numbers of animals from which samples for clinical pathology were taken, hematology (CBC’s) analyses, reticulocyte counts, sperm counts, and samples collected and frozen through pathology services contracts at NCTR.

Table 2. Immunohistochemistry performed from November 2004 through October 2014 through the pathology contract at NCTR.

11 beta-HSD Cl-kit IHC Isolectin Para Influenza 17 betaHSD CMD Keratin PAS 3 Beta HSC CMV Ki-67 PAX-5 3-Cys-A COX-1 LDHA PCNA Adenovirus COX-2 LH PCNT Alcian blue CTGF Mac-2 PEMT Alpha-SMA ER-alpha Maleimide Peroxidase Polyscystin Androgen receptor ER-beta MDA Pyruvate Kinase Anti-Acetil-Histone H3 F4/80 Measles Virus Quinoproteins Anti-Caspase 3 Feulgen Stain - Liver Melanin A RelB Anti-Histone-macroH2A1 FHT Methylcytide S100 Anti-Trimethyl-Histone H3 FLT Methylene Blue SA beta-gal Anti-Trimethyl-Histone H4 Free sulfhydryl groups w/ maleimide perroxidase

MUC5AC SOCSI

APAP FSH MV Sox 9 AVPA Glutathione Myleoperoxidase sPLA2 AVPV Glycolmetacrylate Nitrotyrosine TCEP/Maleimide Peroxidase Basal body of cilia GMA NOS2 TdT C/EBP alpha IHC GST-P NSE Toludine Blue Capase 3 H2A.X Nuclear Fast Red Trimethyl histone Catalase HDAC9 Occludin Trimethyl-histone H3 CC10 Herpes Simplex Virus OV-6 TRL1 CD2 Herpes Virus p40 TRP-1 CD21 HRAS P450-scce TSH CD3 IHC Canine Distemper Virus p53 Tunel CD45R IHC Development p63 Z0-1 CD79z Inhibin alpha p73 ZAP-70 CK-10 Involucrin Pan-Ras

CK-7 IRAK-2 PAP

Figure 6. Historical numbers of enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), chemistry, and urinalysis analyses performed through pathology services contracts at NCTR.

Figure 7. Historical number of cases (animals) entered into the Micropath database from pathologists’ notes at NCTR.

Figure 8. Historical numbers of studies for which pathology data management tasks were performed at NCTR.

Figure 9. Historical total monthly pathology hours used at NCTR.

Appendix 2: User Guides for Electronic Systems

1. NCTR Experiment Activity Tracking (NEAT; 2 pages)

2. Path Track (22 pages)

3. Gross Pathology System (GPS; 82 pages)

4. Micropath (87 pages)

Prepared by R.O.W. Sciences, Inc.

Information Technology Staff

National Center for Toxicological Research Jefferson, AR 72079

NCTR

Experiment

Activity Tracking System

A Quick Reference

Guide

August 1999 #002-NEAT-1.0ref

NCTR

OVERVIEW

The NCTR Experiment Activity Tracking (NEAT) system is an online system which enables users enter their time worked and time spent toward assigned projects.

HOW TO...

Run the system - Click on the NEAT icon on your desktop. If the NEAT icon does not appear on your desktop, please contact the Help Desk at x7636.

Exit the system - To exit after entering your time, click the Project Time button to display the project window. Click the Close button on this window to return to the NEAT Main Menu. Click the Exit button on the Main Menu to exit the system.

Save changes - To save any changes you have made during the entry session, click the Save button on the project window.

THE LIST ICON

The List icon is present on a number of text fields in this system. Depending on the field name, clicking the List icon will display an appropriate list of information for you to enter into the field, such as project or pay period begin date.

Experiment Activity Tracking

USING THE NEAT SYSTEM

When you click on the NEAT icon on your desktop, the NEAT Main Menu displays options allowing you to Enter Employee Time and Print Employee Time Sheets.

Enter Employee Time

Click on the Enter Employee Time button on the NEAT Main Menu to display the Employee Time window. Your name and current pay period are displayed (make sure the appropriate pay period begin date and week number are selected.) <TAB> to the Work/Absent field, then click the down arrow to display a listing of valid time categories. Choose the appropriate category, then <TAB> to the day of the week and enter the number of hours. <TAB> to the next line to select another time category, and continue as needed until you have accounted for all of your time for that week.

Click on the Project Time button to display the Project Time window. A listing of the project numbers you charged time to during the last pay period is displayed. Enter the appropriate amount of time for each day for each project.

Select a milestone and task if necessary.

<TAB> to a blank line and enter another project number, either manually or by clicking the List icon. When you have finished entering your time, click the CALC TOTALS button to verify the time you have charged.

System

Click the Save button on the Project Time window, then click the Return button to re-display the Employee Time window. Repeat the process for the second week of the pay period. When the second week project time has been entered, click the Save button, then click the Print Time button to generate a copy of your timesheet. The timesheet will print to your default printer. Click the Close button to complete the session and return to the Main Menu. Give the timesheet to your timekeeper for entry into the EASE system.

Print Employee Time Sheets

Click the Print Employee Time Sheets button on the NEAT Main Menu to display a window that allows you to print your timesheet for a range of pay periods. Click OK to print your timesheet to your default printer.

Pathology Tracking System User Guide

ITS Doct #001-PTS-1.0

ITS

Pathology Tracking System

ITS Doct #001-PTS-1.0

This is the original version of the Pathology Tracking System User Guide, Doct #001-PTS-1.0.

Companion Publications: None

R.O.W. Sciences Information Technology Staff National Center for Toxicological Research

HFT-910

i

INFORMATION TECHNOLOGY STAFF

NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH

Pathology Tracking System User Guide

Table of Contents

SECTION PAGE NO.

1.0 INTRODUCTION .................................................... 1.1

1.1 SYSTEM DESCRIPTION ......................................... 1.1

1.2 PRINT CONVENTIONS .......................................... 1.1

1.3 FUNCTION KEYS .............................................. 1.2

2.0 SYSTEM OPERATION ................................................ 2.1

2.1 LOGGING ON THE SYSTEM ...................................... 2.1

2.2 SYSTEM MENU ................................................ 2.2

2.3 MAIN MENU .................................................. 2.3

2.3.1 Enter Counts ........................................ 2.4

2.3.2 Report and Inquiry Requests ......................... 2.7

2.3.3 Purge Experiments ................................... 2.10

2.3.4 Modify/Delete Count Data ............................ 2.11

2.3.5 Area Table Maintenance .............................. 2.13

2.4 REVIEW/PRINT REPORTS ....................................... 2.15

APPENDIX - Document Revision History ii

List of Figures

FIGURE PAGE NO.

Figure 2-1 System Menu .............................................. 2.2

Figure 2-2 Main Menu ................................................ 2.3

Figure 2-3 Enter Count Data Screen - Screen One ..................... 2.4

Figure 2-4 Enter Count Data Screen - Screen Two ..................... 2.5

Figure 2-5 Report/Inquiry Selection Menu ............................ 2.7

Figure 2-6 Purge Experiment Screen .................................. 2.10

Figure 2-7 Tracking File Correction Screen .......................... 2.11

Figure 2-8 Area Table Maintenance Screen ............................ 2.13

Figure 2-9 List of Report Filenames ................................. 2.15

Pathology Tracking System September 1990 User Guide #001-PTS-1.0

1.1

1.0 INTRODUCTION

This document provides both general and specific information related to the Pathology Tracking System. It is composed of two major sections. Section one describes the system and gives instructions for using this document. Section two explains how to enter data into the Pathology Tracking System.

1.1 SYSTEM DESCRIPTION

The Pathology Tracking System has three primary functions. The first function locates a case within the Pathology laboratory. The system displays the last area in which the case was located, allowing personnel to track a case's progress through the lab. The second function summarizes the status of all CIDs from a particular experiment. This allows personnel to estimate the amount of time it will take CIDs to go through all areas of the lab. The third function allows lab personnel to produce daily, monthly, and yearly workload reports, which summarize the number of slides, blocks, or CIDs processed in each area and gives totals by experiment and technician.

1.2 PRINT CONVENTIONS

This document uses different print styles to help you distinguish between

(1) data that you enter, (2) keys that you press, and (3) field names that appear on the screen. The following table summarizes the conventions used.

CONVENTION MEANING

ALL CAPS BOLDFACED, UNDERLINED Refers to an entry that you must type, or a field that you can change. For example:

Enter 1; The default response is N

<Boldfaced in angle brackets> Identifies a function key or function key sequence that you must press. For

Press <Enter>; Enter <GOLD><M>

Bold Faced Refers to a menu selection or field name on the screen. These may be in upper or lower case letters depending on how they appear on the screen. For

Select the 2 ENTER COUNTS option

Pathology Tracking System September 1990 User Guide #001-PTS-1.0

1.2

1.3 FUNCTION KEYS

The function keys you will use to enter data are described in the table below.

Note: Some function keys have different uses on different screens. These screen-specific functions are also listed in the table below.

FUNCTION KEY MEANING

<Enter> Brings up the selection you chose from the Main

Menu or allows you to continue to the next screen within a selection.

<GOLD><C> On the Enter Count Data Screen, <GOLD><C> allows you to complete a case. On the Tracking File Correction Screen and the Pathology Area Table <GOLD><C> modifies records.

<GOLD><D> Allows you to delete a record on the Pathology

Area Table.

<GOLD><M> Returns you to the Main Menu.

<GOLD><N> On the Tracking File Correction Screen, <GOLD><N> brings up the next record. On the Pathology Area Table, <GOLD><N> allows you to add records.

<GOLD><Q> Exits you from the screen you are working on and takes you back to the System Menu. Use this sequence at any time but be aware that your data will not be saved.

<GOLD><R> On the Enter Count Data Screen, <GOLD><R> allows you to restart a case. On the Pathology Area Table, <GOLD><R> allows you to retrieve a record.

<GOLD><X> Allows you to delete a record on the Tracking

File Correction Screen.

<Return> Use <Return> at the System Menu only. Once you have accessed the Main Menu, use <Enter>.

<Tab> Moves the cursor forward between fields.

Pathology Tracking System February 1994 User Guide 001-PTS-1.0

2.1

2.0 SYSTEM OPERATION

This section describes how to enter data into the system and run reports.

2.1 LOGGING ON THE SYSTEM

To log on to the Pathology Tracking System, type TPTH at the Project prompt and press <Return>. If you have done this correctly, the System Menu will appear.

2.2

2.2 SYSTEM MENU

When you type TPTH at the Project prompt and press <Return>, the System Menu appears. Figure 2-1 shows the System Menu.

Figure 2-1. System Menu

The table below describes each of the options on the System Menu.

FIELD DESCRIPTION

CHANGE PROJECT Allows you to exit the Pathology Tracking

System.

COLLECT DATA/CREATE REPORTS Allows you to choose one of the main functions of the system, such as data-entry functions, modify and delete functions, and report request functions.

REVIEW/PRINT REPORTS Lets you view or print reports that have been created. See Section 2.4 for a detailed description of Review/Print Reports.

PATHOLOGY TRACKING SYSTEM

CHANGE PROJECT ==> 1

COLLECT DATA/CREATE REPORTS ==> 2

REVIEW/PRINT REPORTS ==> 3

PLEASE ENTER SELECTION: _

2.3

2.3 MAIN MENU

When you choose option 2 COLLECT DATA/CREATE REPORTS from the System Menu and press <Return>, the Main Menu will appear. This menu lists the main functions of the Pathology Tracking System. Figure 2-2 shows the Main Menu.

Figure 2-2. Main Menu

The following table summarizes the options on the Main Menu.

FIELD DESCRIPTION

ENTER COUNTS Allows you to enter data for CIDs, including date received, area, technician, and count.

REPORT AND INQUIRY REQUESTS Allows you to generate reports.

PURGE EXPERIMENT DATA Allows you to delete all records associated with a selected experiment from the tracking file.

MODIFY/DELETE COUNT DATA Allows you to change or delete data.

AREA TABLE MAINTENANCE Allows you to add, delete, or modify

Pathology Area IDs and names.

A detailed description of each of these options is provided in the following sections.

P A T H O L O G Y T R A C K I N G S Y S T E M

PTM1M001

EXIT ==> 1

ENTER COUNTS ==> 2

REPORT AND INQUIRY REQUESTS ==> 3

PURGE EXPERIMENT DATA ==> 4

MODIFY/DELETE COUNT DATA ==> 5

AREA TABLE MAINTENANCE ==> 6

ENTER SELECTION ==> .

2.4

2.3.1 Enter Counts

To enter count data, select option 2 ENTER COUNTS from the Main Menu and press <Enter>; the first Enter Count Data Screen will appear. This screen (shown below in Figure 2-3) prompts you for the Carcass ID. Note: Only CIDs which have been received through the Pathology Receiving System are valid.

Figure 2-3. Enter Count Data Screen - Screen One

PTM2U001

ENTER COUNT DATA

09/05/90 08:36:52

ENTER CARCASS ID ==> ……………………

GOLD M MAIN MENU GOLD Q QUIT

2.5

When you have entered a valid CID, press <Enter> to display the second Enter Count Data Screen. Figure 2-4 shows this screen.

Figure 2-4. Enter Count Data Screen - Screen Two

The table below describes each of the fields on the second Enter Count Data Screen.

FIELD DESCRIPTION

DATE The date defaults to the current date; however, this date can be changed by the technician.

AREA Enter the code for the area in this field.

TECHNICIAN Enter the technician ID in this field.

COUNT Enter the count in this field.

PTM2U002

ENTER COUNT DATA

EXP/TEST 51901 CARCASS ID 5190100004

DATE ==> 900905

AREA ==> …..

TECHNICIAN ==> …..

COUNT ==> …..

GOLD M MAIN MENU GOLD Q QUIT GOLD R RESTART CASE GOLD C COMPLETE CASE

2.6

Enter the area, technician, and count data for the CID. Press <Enter> to view the corresponding text.

If you enter information that is not valid, the system will give you an error message. Press <Enter> to acknowledge and you will be allowed to re-enter data. Remember that the count units correspond to the area. If you change an area number, the count units will change accordingly.

Press <GOLD><C> to save your data when you are finished. If you have done this correctly, the system will display the message DATA ADDED TO DATA BASE - ENTER TO CONTINUE. Press <Enter> and the first Enter Count Data screen will appear. Continue entering data for more CIDs or press <GOLD><M> to return to the Main Menu. If you make a mistake entering data on the second Enter Count Data screen, press <GOLD><R> and you will return to the first screen without saving any data. From there, re-enter the CID or press <GOLD><M> to return to the Main Menu.

2.7

2.3.2 Report and Inquiry Requests

To generate reports and/or online queries, select option 3 REPORT AND INQUIRY REQUESTS from the Main Menu and press <Enter>, the Report/Inquiry Selection Menu will appear. Figure 2-5 shows your options on this menu.

Figure 2-5. Report/Inquiry Selection Menu

PTM2M001

REPORT/INQUIRY SELECTION MENU

CASE INQUIRY ==> 1 AREA WORKLOAD REPORT ==> 5

EXPERIMENT INQUIRY ==> 2 EXPERIMENT WORKLOAD REPORT ==> 6

AREA WORKLOAD INQUIRY ==> 3 AREA CID REPORT ==> 7

EXPERIMENT STATUS INQUIRY ==> 4

ENTER SELECTION ==>

GOLD Q QUIT GOLD M MAIN MENU

2.8

The table below describes each of the selections on the Report/Inquiry Selection Menu.

FIELD DESCRIPTION

CASE INQUIRY Displays the status of an individual case.

Enter the CID, and you will get a list of the areas the case has been through (sorted by date and area).

EXPERIMENT INQUIRY Displays the area, count, and units for an experiment. Enter the experiment and test number and you will get the number of items from that experiment which have been processed in each area of the lab.

AREA WORKLOAD INQUIRY Displays the total number of items processed in that area, broken down by experiment and technician. To select the areas, place an X by all the areas you want on the inquiry.

Note: Use <Tab> (not the arrow keys) to move between fields.

EXPERIMENT STATUS INQUIRY Displays the number of cases each area has processed. Enter the experiment and test number and you will get the number of CIDs from that experiment which have been processed in each area of the lab.

AREA WORKLOAD REPORT Generates most of the daily and monthly reports. Enter a date range and an area and you will get a list showing the total number of items processed in that area, broken down by experiment and technician. To select the areas, place an X by all the areas you want on the report. Note: Use <Tab> (not the arrow keys) to move between fields.

EXPERIMENT WORKLOAD REPORT Enter a date range to get a summary of the workload reports for all areas. Totals are given by experiment.

AREA CID REPORT Counts CIDs per area. Enter an experiment, test, and area for a date range, and you will get a list of CIDs processed by that area. To select the areas, place an X by all the areas you want on the report. Note:

Use <Tab> (not the arrow keys) to move between fields.

2.9

Choose the number of the inquiry or report you desire and press <Enter>. A second screen will appear which allows you to enter more detailed information.

(Each second screen is indigenous to a specific report.) If you selected one of the reports, you will have to enter either a date range, experiment/test, or a CID and press <Enter>.

Inquiries will be displayed on the screen; reports will go to the online report menu. To view reports, choose REVIEW/PRINT REPORTS from the System Menu (see Section 2.4).

When inquiries are displayed on the screen, the cursor is positioned at the MORE prompt. Press <Enter> once when the cursor is at the MORE prompt. Don't press <Enter> again until the system message changes. If you do, your inquiry will flash on the screen and the cursor will be back at the MORE prompt.

Press <Enter> when you are finished viewing the report and the system will prompt you with a yes or no question (also specific to the report you choose).

Type N and press <Enter> and you will return to the Report/Inquiry Selection Menu. From there, make another selection or press <GOLD><M> to return to the Main Menu.

2.10

2.3.3 Purge Experiments

To delete all records associated with a completed experiment from the tracking file, choose option 3 PURGE EXPERIMENT DATA from the Main Menu and press <Enter>. When you do this, the Purge Experiment Screen appears (shown in Figure 2-6).

Figure 2-6. Purge Experiment Screen

Enter the experiment and test number at the prompt and press <Enter>. The system will ask if you really want to delete this data. Press Y and the data for that experiment will be deleted. NOTE: If you want a yearly report containing this data, you must wait until after the end of the year to purge the experiment.

PURGE EXPERIMENT DATA

PLEASE ENTER THE EXPERIMENT/TEST NUMBER YOU WISH TO PURGE

2.11

2.3.4 Modify/Delete Count Data

To change or delete count data, choose option 4 MODIFY/DELETE COUNT DATA from the Main Menu and press <Enter>. The Tracking File Correction Screen shown in Figure 2-7 will appear.

Figure 2-7. Tracking File Correction Screen

The table below describes each of the fields on the Tracking File Correction

FIELD DESCRIPTION

CARCASS ID Enter the CID for the record you want to modify or delete.

DATE Enter the date of the record you want to modify or delete.

AREA Enter the area code for the record you want to modify or delete.

PTM2U006

TRACKING FILE CORRECTION

09/05/90 08:37:30

CARCASS ID ==> ………..

DATE ==> ……

AREA ==> …..

GOLD M MAIN MENU GOLD Q QUIT ENTER CONTINUE

2.12

Enter the key data for the record you want to modify or delete and press <Enter>. Data for the selected record will be displayed.

To modify data, type in your corrections and press <GOLD><C> to save them. If you have done this correctly, the system will display the message THIS RECORD

HAS BEEN MODIFIED ON THE FILE - ENTER TO CONTINUE.

To delete data, press <GOLD><X>. The system will ask if you really want to delete this data. Press Y, and the system will give the message THIS DATA HAS BEEN DELETED FROM THE FILE - ENTER TO CONTINUE. When you press <Enter> after the system message, you will return to the Tracking File Correction Screen.

From there, you can modify more data or press <GOLD><M> to return to the Main Menu.

2.13

2.3.5 Area Table Maintenance

To add, delete, or change a Pathology Area, choose option 6 AREA TABLE MAINTENANCE from the Main Menu and press <Enter>. Figure 2-8 shows the screen which appears.

Figure 2-8. Area Table Maintenance Screen

The table below describes each of the fields on the Area Table Maintenance

FIELD DESCRIPTION

PATHOLOGY AREA CODE A number that uniquely identifies the area.

PATHOLOGY AREA SHORT TEXT The abbreviated text that identifies the area.

PATHOLOGY AREA LONG TEXT The complete text that identifies the area.

EFFECTIVE START DATE The date the current status was set for the area.

PATHOLOGY AREA UNITS The unit of measure for the area.

ACTIVE INACTIVE FLAG Tells the current status of the area. Enter A or

I only.

PTNTABLE T A B L E M A I N T E N A N C E S Y S T E M 09/05/90

P A T H O L O G Y A R E A T A B L E

Path Area Code =========> Path Area Shor Text ====> Path Area Long Text ====> Effective Start Date ===> Path Area Units ========> Active Inactive Flag ===>

Gold M Main Menu Gold N Add Gold R Retrieve Record Gold Q Quit

2.14

To add a new Pathology Area, type in the data for the area and press <GOLD><N>. To modify an existing area, first retrieve the record by entering the Pathology Area Code and pressing <GOLD><R>. Then change or delete the record by using the appropriate function key. Press <GOLD><M> to return to the Main Menu.

2.15

2.4 REVIEW/PRINT REPORTS

When you select option 3 REVIEW/PRINT REPORTS from the System Menu, a list of report filenames will be displayed. Each filename is made up of several groups of characters which give information about the report. Figure 2-9 shows an example of a list of filenames and identifies each part of the filename.

Figure 2-9. List of Report Filenames

The table below describes the flags in Figure 2-9.

FLAG DESCRIPTION

1 The report number

2 Indicates that the report is a Pathology Tracking

Report.

3 The report type, where 001 = Experiment Workload Report 002 = Area Workload Report 003 = Area CID Report

4 The date (in YYMMDD format) when the report was created.

5 The time (in HHMMSS format) when you logged onto the

Pathology Tracking System.

6 The version number of the report.

2 5 3 6

1- TPTH_001_900906_143636.LIS;1

2- TPTH_002_900906_091221.LIS;1

3- TPTH_003_900906_143636.LIS;1

2.16

Select the number that corresponds to the report you want to view. When you are finished viewing the report, press <Control><Z> or <F10> to exit. The system will ask if you want a hardcopy of the report.

When you press Y, the system will prompt you for a printer destination. You may enter a printer or press <Return>. If you press <Return>, the report will print on the computer-room printer and reports will be placed in your distribution bin.

Gross Pathology System

ITS Doct #001-GRPH-3.0

ITS

ITS Doct #001-GRPH-3.0

This is an updated edition of the Gross Pathology System User Guide.

Companion Publications: None

ZTech, an ICF International Corporation

National Center for Toxicological Research

MC-910

INFORMATION TECHNOLOGY STAFF

NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH

S ection Page No.

1.0 INTRODUCTION ............................................................................................................................... 1.1

1.1 SYSTEM OVERVIEW ............................................................................................................... 1.1

1.2 BEFORE GETTING STARTED ................................................................................................. 1.1

1.2.1 Document Print Conventions ......................................................................................... 1.1

1.2.2 System Buttons and Icons ............................................................................................. 1.2

1.3 ACCESSING THE SYSTEM ..................................................................................................... 1.2

1.4 EXITING THE SYSTEM............................................................................................................. 1.3

2.0 PROTOCOL DEFINITION ................................................................................................................. 2.1

2.1 PROTOCOL TISSUE LIST ....................................................................................................... 2.2

2.1.1 Modify/Delete Required Organs and Tissues ................................................................ 2.3

2.1.2 Copying Organs and Tissues ........................................................................................ 2.5

2.1.3 Add a New Organ and Tissue Set ................................................................................. 2.7

2.2 TISSUE LIST DRIVER .............................................................................................................. 2.9

2.2.1 Copying Drivers............................................................................................................ 2.10

2.2.2 Adding Drivers ............................................................................................................. 2.12

2.2.3 Modifying Drivers.......................................................................................................... 2.13

2.2.4 Deleting Drivers............................................................................................................ 2.14

2.3 COPY ALL PROTOCOL INFORMATION ............................................................................... 2.14

2.4 GPS MENU ACCESS ............................................................................................................. 2.14

2.4.1 Add A User to the Gross Pathology Menu ................................................................... 2.16

2.4.2 Delete A User from the Gross Pathology Menu........................................................... 2.17

2.4.3 Modify User Authorization Status on the Gross Pathology Menu................................ 2.17

2.5 TGL NOTES TABLE ................................................................................................................ 2.18 i Uncontrolled when printed

3.0 DATA COLLECTION ......................................................................................................................... 3.1

3.1 NECROPSY LAB ...................................................................................................................... 3.2

3.1.1 Receiving ....................................................................................................................... 3.3

3.1.2 Necropsy ....................................................................................................................... 3.6

3.1.3 Organ Weights ............................................................................................................ 3.13

3.1.4 Check MG Correct ....................................................................................................... 3.16

4.0 DATA CORRECTION ....................................................................................................................... 4.1

4.1 RECEIVING .............................................................................................................................. 4.2

4.2 OBS AND TGLS ........................................................................................................................ 4.4

4.2.1 Modifying Pathology Condition Observations ............................................................... 4.7

4.2.2 Modifying Organ Observations ...................................................................................... 4.8

4.2.2.1 Modify an Observation..................................................................................... 4.8

4.2.2.2 Remove an Organ .......................................................................................... 4.9

4.2.2.3 Add an Organ ............................................................................................... 4.10

4.2.3 Modifying Inlife Clinical Observations ......................................................................... 4.10

4.2.4 Modifying TGL Observations ....................................................................................... 4.11

4.2.4.1 Modify an Existing TGL ................................................................................. 4.11

4.2.4.2 Add a New TGL ............................................................................................ 4.13

4.2.4.3 Remove a TGL ............................................................................................. 4.14

4.3 ORGAN WEIGHTS .................................................................................................................. 4.15

4.3.1 Add Organ ................................................................................................................... 4.17

4.3.2 Deleting Organ Weights ............................................................................................... 4.18

4.3.3 Modifying Organ Weights ............................................................................................ 4.18

4.4 REC/NEC COMMENTS .......................................................................................................... 4.19

4.4.1 Add Comment .............................................................................................................. 4.20

4.4.2 Modify Comment .......................................................................................................... 4.21

4.4.3 Delete Comment ......................................................................................................... 4.21

5.0 PATHOLOGIST MENU ..................................................................................................................... 5.1

5.1 NECROPSY REVIEW ............................................................................................................... 5.2

5.1.1 Reviewing and Approving CIDs ..................................................................................... 5.2

5.1.2 Modify CID...................................................................................................................... 5.3 ii

5.2 ANIMAL REVIEW ...................................................................................................................... 5.4

5.3 MODIFY CID ......................................................................................................................... 5.4

6.0 REPORTS ........................................................................................................................................ 6.1

6.1 INDIVIDUAL ANIMAL NECROPSY REPORT (IANR) ............................................................... 6.2

6.2 PROTOCOL DEFINITION ........................................................................................................ 6.3

6.3 IANR LISTING ........................................................................................................................... 6.4

7.0 CORRECT/DELETE CID ................................................................................................................... 7.1

7.1 CORRECT CID .......................................................................................................................... 7.2

7.2 DELETE CID .............................................................................................................................. 7.3

Appendix - Document Revision History iii

Gross Pathology System November 2011 User Guide #001-GRPH-3.0

1.0 INTRODUCTION

This manual was written as a guide for using the Gross Pathology System. Section 1.0 provides an overview of this manual and of the system as a whole. The remaining sections describe the various types of transactions and database records maintained through use of the system.

1.1 SYSTEM OVERVIEW

The Gross Pathology Data Collection System is used to automate the processes of Pathology Receiving and Necropsy Lab. These data records are stored on the Oracle Database and will be available for adhoc query and reporting through the numerous tools available for that purpose.

1.2 BEFORE GETTING STARTED

Before using the Gross Pathology System, you should be familiar with the print conventions used in this document; as well as the available screen icons and buttons.

1.2.1 Document Print Conventions

Different print styles are used in this document to help you distinguish between instructional text and field names and messages that appear on the screens. The following table summarizes the conventions used.

CONVENTION MEANING

ALL CAPS, BOLDFACED, UNDERLINED Refers to an entry that you must type.

For example:

Enter C; Enter 3

<Boldfaced in angle brackets> Identifies a function key or function key sequence that you must press. For example:

Press <Enter>; Press <Ctrl><F2>

Bold Faced Distinguishes a prompt, system message, or field name from the surrounding text. These may be in upper or lower case letters depending on how they appear on the screen. For example:

. . . in the Function field of the Enter Function: and/or Cage: prompt.

1.1

1.2.2 System Buttons and Icons

The following buttons and icons appear on various system screens within the system. The following table describes these tools and their uses.

BUTTON/ICON USE

List Icon The List icon is present on a number of screens in this system. Depending on what information the icon is associated with, such as an animal ID, clicking the List icon displays an appropriate list of options from which to choose. Narrow your search and reduce the number of choices for selection by typing the first few letters or numbers of your entry into the Find field

1.3 ACCESSING THE SYSTEM

To access the Gross Pathology System, do the following:

1. Select the GPS icon available in the Network Applications Folder (NAF) to display the Gross Pathology Data System Main Menu (Figure 1-1).

Figure 1-1. Gross Pathology System Main Menu

1.2

1.3 Uncontrolled when printed

2. Select the desired Gross Pathology function to open that function's data maintenance options (these functions are discussed in Sections 2.0 - 7.0).

1.4 EXITING THE SYSTEM

When you have completed data collection for the current session and wish to exit the Gross Pathology System, select the Exit option on the Gross Pathology System Main Menu (Figure 1-1).

2.0 PROTOCOL DEFINITION

All data collection experiments must have a defined protocol. The Protocol Definition function drives the organ and tissue lists that appear in different areas of the Gross Pathology System. This function allows you to modify and/or add organs or tissues to a protocol, copy organs and tissues from one experiment set or experiment to another, and create new organ and tissue sets.

To access the Protocol Definition functions, do the following:

1. Select the Protocol Definition option on the Gross Pathology System Main Menu (Figure 1-1) to display the Protocol Definition Menu Screen (Figure 2-1)

Figure 2-1. Protocol Definition Menu Screen

The following table describes the fields and buttons on this screen.

FIELD/BUTTON DESCRIPTION

Protocol Tissue List Displays the Protocol Tissue List Screen (Figure 2-2)

Tissue Driver List Displays the Protocol Set List Screen (Figure 2-7)

Copy All Protocol Info Displays the Copy Organs and Tissues – Create Drivers

Screen (Figure 2-8)

GPS Menu Access Displays the window for granting access to the

Pathologist Menu, Protocol Definition and Delete Animal

2.1

TGL Notes Table Displays the TGL Notes Table, which contains “canned” or preset notes that are used during necropsy. (Figure 2-13)

Exit Displays the Gross Pathology System Main Menu

Screen (Figure 1-1)

2. Select the desired Protocol Definition function by clicking the appropriate button on the Protocol Definition Menu Screen. The options on this screen are discussed in Sections 2.1 – 2.5).

2.1 PROTOCOL TISSUE LIST

The Protocol Tissue List function displays a listing of protocol-defined sets of tissues to be collected at necropsy.

To access the Protocol Tissue List function, do the following:

1. Click the Protocol Tissue List button on the Protocol Definition Menu Screen (Figure 2-1) to display the Protocol Tissue List Screen (Figure 2-2).

Figure 2-2. Protocol Tissue List Screen

2.2

Experiment Nbr Number designation for the experiment

Set Nbr Number designation for the set

Set Description Long text description of the set number

Process All Tgls Field designating whether or not all Trace gross lesions must be accounted for at trimming: Y=Yes, N=No

Select Displays the Protocol Required Organs…