Statement of Work_13 June 2012_Final.pdf

Attachment 1

Hosted Commercial In-Life Data Collection and Management System for

NTP

Background

The National Institute of Environmental Health Sciences (NIEHS) is one of 27 Institutes and Centers of the National Institutes of Health (NIH), Department of Health and Human Services (DHHS). The mission of the NIEHS is to reduce the burden of human illness and disability by understanding how the environment influences the development and progression of human disease. The Division of the National Toxicology Program (NTP) is an interagency program whose mission is to evaluate agents of public health concern by developing and applying tools of modern toxicology and molecular biology. The NTP maintains an objective, science-based approach in dealing with critical issues in toxicology and is committed to using the best science available to prioritize, design, conduct, and interpret its studies. To that end, the NTP is continually evolving to remain at the cutting edge of scientific research and to develop and apply new technologies.

In carrying out its mission, the NTP studies the effects of environmental agents in laboratory studies, which are performed predominantly at contract laboratories and then reviewed by the NTP. The NTP requires a hosted data management system to collect data from multiple laboratories and host the data in a secure central database which the NTP scientists can access in order to review and analyze the data. The system shall use the internet to transmit the collected data securely back to the hosted database.

Purpose

The purpose of this procurement is to obtain a system that allows:

a. Access to a hosted commercial in-life data collection and management system for use by personnel of the NTP and contract laboratories carrying out NTP-directed research for one base year and nine option years.

b. User access across multiple locations.

c. Performance of statistical tests, upload capability, and ability to meet usability requirements.

d. Housing of multiple NTP study types.

I. Scope and Tasks

A. System Functionality

1. The system shall:

a. Collect data from (1) in-life studies (body weights from balances calibrated using the system, feed and water consumption using calibrated balances, clinical observations using the NTP glossary given in Appendix 1; (2) necropsy room (organ weights from calibrated balances, gross observations and tissue/site linkage using the NTP glossary given in Appendix 1; (3) fetal pathology observations using the NTP glossary given in Appendix 1; (4) reproductive studies (pairing, mating, littering, pup and litter observations); (5) histopathology observations using the NTP modified histopathology glossary given in Appendix 1; (6) calculate daily gavage volumes for individual adult animals based on the most recent individual body weight.

b. House studies using NTP MOG (Modified One Generation) and RACB (Reproductive Assessment by Continuous Breeding) reproductive toxicology protocol templates. Such RACB studies cover 1 to 2 years in the laboratory, three generations (F0 breeder generation plus F1 and F2 generations), and approximately 3000 animals per study. Templates for these two protocols are given in Appendix 2.

c. Maintain system response time for data collection to within 30 seconds throughout the study period, and system response time for modifications to the study work schedule to within 5 minutes throughout the study period, barring network or system failure and agreed-upon maintenance windows. The contractor is not responsible for network integrity and response at NTP or at labs using the system.

d. Produce reports and tables of data, both summary and individual animal data, as well as supporting real-time data collection and data review during the data collection phases of the study.

e. Produce endpoint reports containing data for all litters for each mating pair, and litter averages for each litter plus the parents’ endpoint (for example sperm count or estrous cyclicity, age and weight at attainment of developmental markers).

f. Load custom glossaries for histology, gross observations, in-life observations, fetal pathology and organ sites and associated morphologies at both the system and individual study levels.

g. Create system-wide custom endpoints for data collection, and custom calculated endpoints based on the data collected.

h. Accept retrospective data in the form of Excel spreadsheets and incorporate the data into the system.

i. Directly accept data from a networked Hamilton Thorne CASA instrument.

j. Perform the following (but not limited to) statistical tests: Cochran-Armitage trend test, Chi-square test, Fisher’s exact test, Dunn’s test, ANOVA, Kaplan-Meier analysis, stepped graph display of animal death over time.

k. Contain a process whereby the rights of each user can be restricted to particular rights for a particular study.

l. Support real-time access by multiple laboratories in such a way that the data from one laboratory is not viewable or otherwise accessible by users from another laboratory, while all sets of data are available to NTP scientists.

m. Contain a secure reporting area where users are restricted to run reports on only the data they are authorized to see. The reports shall be saved to a secure area prior to download and printing, in such a fashion that reports generated by a laboratory are visible only to members of that laboratory.

n. Function in compliance with GLP (Good Laboratory Practice Regulations, defined by Federal

Register 43 FR 59985-60020 and any updates, and guidance from the US Food and Drug Association (FDA) for Good Laboratory Practice (GLP) as outlined in 21 CFR Part 11 and 58 and from the US Environmental Protection Agency (EPA) 40 CFR parts 160 and 792. Support audit trails and security controls on data input and change. Have electronic signature processes in compliance with 21 CFR Part 11.

o. Be in compliance with Section 508 of the Rehabilitation Act (29 U.S.C. 794d), as amended by the

Workforce Investment Act of 1998 (P.L. 105-220), August 7, 1998. The Contractor shall certify this capability annually.

p. The Contractor shall provide the system in a secure environment that conforms to the moderate security level described in the Federal Information Security Management Act of 2002 (FISMA), NIST Special Publication 800-53Rev3 and NIST800-63, level 1. The contractor shall certify this capability annually.

q. The Contractor shall perform Operational Qualification and Installation Qualification of the hosted system at the start of the contract award period and provide to the NTP a report describing this process and the results of the testing to demonstrate correct operation and installation.

r. Possess the capability for end users to easily create customized queries and reports based on NIEHS study data.

2. Additional Requirements at Contract Award

a. The Contractor shall train personnel at the NTP and contractor sites in the use of the System to be completed within four months of contract award. This training shall cover system security, the import of NTP glossaries, creation of endpoints, preparation of study schedules using the system, and data entry for in-life, pathology, and fetal pathology.

b. In Year 1, the Contractor shall provide 80 hours of consultation to members of NTP staff

/contractors on the use of the system to design and prepare tables. This training shall be in increments and may be done in person or via the web at the discretion of the Contractor.

c. All features listed in Section 1A and not in operation in the system at the time of contract award shall be fully functional and completed within 4 months of contract award. Any changes in the system to accomplish this shall be supported by Operational Qualification and Installation Qualification documentation prepared by the Contractor for the system installed for the NTP and supporting all requirements listed in Section 1A.

3. Validation of the System

Before the NTP can use the system for data collection, the system must be validated by the NTP and by contract labs using the system for use in a GLP environment. Following the award of the contract, the Contractor shall support the NTP process of GLP validation. This work shall consist of preparing a study template for each of the two reproductive study designs used by the NTP and detailed in Appendix 2, and then entering data into the system for each study design, as detailed in Appendix 3. This process shall be described in a Performance Qualification document to be prepared by the Contractor. Installation Qualification, Operational Qualification, and Performance Qualification shall be completed by the end of Year 1.

Once the validation is complete and the system is ready for use to collect data, the Contractor shall provide 40 hours of training in the data collection and data review/reporting processes supported by the system within 30 days of data collection capability being deployed.

If the system is altered by the Contractor, there shall be a process in place to comply with GLP validation requirements. The altered system shall be installed on a separate server within the production hosted environment for a period of time sufficient to permit the NTP to complete the GLP validation of the new system prior to the Contractor moving the new system to the production NTP database instance.

If changes are made in the system the Contractor shall provide documentation in compliance with the NTP change-control process and/or new Operational Qualification and Performance Qualification documentation at least 30 days prior to the installation of the updated system on a server for NTP GLP validation.

B. Maintenance

Beginning in Option 1 (Year 2), annual maintenance shall include 80 total hours of annual refresher training in the use of the system for current users at the NTP and NTP laboratories with material directed specifically at NTP studies, NTP templates and NTP report management. This material shall change as additional NTP study types are added to the system capabilities. This training shall be in increments and should be done in-person.

The NTP shall have the option to schedule training in 32 hour increments during the course of the contract, not to exceed two (2) 32 hour increments per year. This training shall be in addition to the training described for annual refresher training, new sites, and training when the system is altered.

The training shall be provided as needed at the discretion of the NTP. This training shall be done via the web.

The Contractor shall coordinate planned outages with the COTR. A planned outage may be needed to upgrade software or perform routine maintenance.

C. Support

Prior to installing a system with any system alterations, the Contractor shall provide a list of changes and/or new features being incorporated 30 days prior to installation. If the Contractor plans changes of sufficient scope to require Operational and Installation Qualification, this documentation shall be provided to the COTR. Training to address any substantive changes to the system shall be provided to all users of the system at the time the aforementioned changes are made.

The Contractor shall supply a help-desk staffed from 7AM to 11PM EST, seven days a week.

System users shall be able to contact the help desk through e-mail and telephone. The Contractor shall have a process in place to escalate help desk issues to ensure resolution in a timely manner.

The Contractor shall supply a copy of the help-desk logs to the COTR within 5 business days following the last calendar day of each month.

The Contractor shall supply a copy of the access logs to the COTR within 5 business days following the last calendar day of each month.

The Contractor shall provide a monthly export of the data and tables from the database and deliver this to the NTP within 5 business days following the last calendar day of each month.

The Contractor shall make regular backups of the data in the hosted system.

The Contractor shall test the data back up system every week by making a test of a file selected at random each week to ensure that backed up data are recoverable.

The hosted system shall reside on two or more load-balanced physical servers of sufficient capacity to support the usage by NTP and contract lab personnel.

Within the first four (4) months following contract award the Contractor and the COTR at the NTP shall develop a procedure for handling security incidents to be used under this contract.

II. User and Location Licenses

At the start of the contract, the Contractor shall supply licenses for 100 users at the NTP and at one additional contract laboratory site. User licenses shall be increased in blocks of 25 licenses, for a not to exceed amount of 350 licenses throughout the life of the contract. A user refers to a named individual with an account on the system. Such individuals reside either at the NTP or at a laboratory charged with carrying out studies for the NTP.

The Contractor shall provide additional licenses for new users in blocks of 25 to include:

1. Start-up training and support for users at additional contract laboratories.

2. Assistance with the connection of laboratory instruments at the new sites.

This training and support shall involve travel to the various locations when NTP contract laboratories are situated. At this time, all such laboratories are within the United States.

If third party software needs to be obtained to meet the requirements outlined in Section I.A.1.r., the Contractor shall provide five user licenses to a business intelligence (BI) software product that is compatible with the system in order to facilitate queries and generate reports based on NIEHS study data.

Further, the Contractor shall provide 80 hours of training in the use of this product to members of the NTP. This training may be in person or remote at the discretion of the Contractor and shall take place within 6 months of contract award.

The NTP plans to add additional sites as needed, for a not to exceed amount of 12 locations throughout the life of the contract.

User licenses and location licenses shall be provided throughout the life cycle of this contract, for one (1) base year and nine (9) option years, for a total not to exceed period of performance of ten (10) years.

III. Additional Features

A. System Usability Features

1. The system shall support setting work schedule tasks by study day as well as by subject start date, mated date, birth date and study week.

2. The system shall change the status of a female from mated to non-pregnant in situations such as the animal was incorrectly classed as mated.

3. The system shall permit the user to assign pups from a treatment group to up to ten different cohorts when the pups are transferred to the study.

4. Each report produced from the system under this procurement shall have a section 508-compliant format or version.

5. The system shall convert a dead pup to an adult when the user requests this.

6. The system shall output tables in Microsoft Excel format.

7. The system shall compute dose ingested in a feed or water delivery study for dams with litters using both of the following:

a. Considering only the dam during all the time pre-wean

b. Considering only the dam for days PND0-9 and the dam plus pups for the following pre-weaning days.

8. Upload retrospective data using a time by animals, an endpoint by animals, or a time by endpoint matrix entry screen (see Appendix 4, NTP-EstrousData.xlsx).

9. Collect data from ovarian follicles, including 7 sections through the tissue and counts for four types of cells, 20 – 40 counts per slide. The matrix entry screen in item (8) above can also be used for this process.

10. Collect and report the calendar dates of first and last pre-mating dosing in a generation within a

11. Collect and report the calendar dates of first and last weaning per litter in a generation within a

These capabilities shall be operational in the system by the end of Year 1.

B. Historical Control Database

The Contractor shall use the data within the system to create the NTP control database, which shall then be housed within the system. This control database shall contain data on the incidence of histological, fetal pathology and other findings in control animals from all NTP studies completed using the system, with dates of study start and termination, strain of animal, diet, route of administration and lab performing the study indicated in the database and available for filtering by the user. The Contractor shall collect this data from within the database. The contractor shall report this data for all NTP studies housed within the system. The user will view this historical control database in the system during the evaluation of findings from a particular study (using historical control data gathered within 5 years of that particular study). The system shall provide the user the choice of including or excluding the control values from the evaluated study in the historical control incidence value.

The historical control database shall be available to use as an analysis group in statistical tests.

The historical contract database shall be available in the system within the first year following data collection in the system.

IV. Statistical and Analysis Methods

A. Analysis for Reproductive and Developmental Toxicology

The system shall contain the following twelve (12) methods:

1. Guide users in using the NTP statistical decision tree: Jonckheere’s test (Jonckheere, 1954) shall be used to assess the significance of the dose-related trends and to determine whether a trend-sensitive test (Williams’ or Shirley’s test) is more appropriate for pairwise comparisons than a test that does not assume a monotonic dose-related trend (Dunnett’s or Dunn’s test). Jonckheere’s test is considered to be significant at a level of α = 0.01. Data with approximately normal distributions shall be analyzed with the parametric multiple comparison procedures of Dunnett (1955) and Williams (1971, 1972). Dunnett’s test shall be used if there is no significant trend, Williams’ test if there is a significant trend, both at α = 0.05. Data with skewed distributions shall be analyzed using the nonparametric multiple comparison methods of Shirley (1977, as modified by Williams, 1986 and Dunn, 1964). Dunn’s test shall be used if there is no significant trend, Shirley’s test if there is a significant trend, both at α = 0.05. Prior to statistical analysis, extreme values shall be identified by the outlier test of Dixon (1950) and examined by NTP personnel. Implausible values shall be eliminated from the analysis.

2. Apply multivariate analysis of variance (Morrison, 1976) to data to test for simultaneous equality of measurements across doses.

3. Compare the proportions of regular cycling females in each dosed group to the control group using the Fisher exact test (Gart et al., 1979). Because vaginal cytology data are proportions (the proportion of the observation period that an animal was in a given estrous stage), an arcsine transformation shall be used to bring the data into closer conformance with a normality assumption prior to analysis.

4. Construct tests for extended periods of estrus and diestrus based on a Markov chain model proposed by Girard and Sager (1987). For each dose group, a transition probability matrix shall be estimated for transitions among the proestrus, estrus, metestrus, and diestrus stages, with provision for extended stays within estrus and diestrus. Equality of transition matrices among dose groups and between the control group and each dosed group shall be tested using chi-square statistics.

5. Perform mixed effects logistic regression (pup is the unit of analysis, dose and survival time are predictors, litter is a random effect) with tests for trend with dose and pairwise comparisons with the control group.

6. Include different mean calculations for summarizing litter data: (a) mean of means for (e.g.) pup weights; (b) mean of all in group ignoring litter (e.g. total dead pups for a group); (c) repeated measure (for an endpoint from litters a, b, c in RACB protocol) – mixed effects ANOVA across generations; (d) developmental marker attainment, BW at birth – nested ANOVA by litter size (2 factors – dam and litters nested within dam); (e) covariate calculation of e.g. day of attainment of developmental markers using wean weight and/or litter size. The system shall calculate these statistics for each endpoint listed in the RACB and MOG protocols.

7. Use survival analysis including log-rank test or Cox’s proportional hazards model (Cox, 1972) for calculation of time to attainment of developmental markers (testes descent, vaginal opening, preputial separation) with multiple covariates, e.g. litter, animal weight at attainment of the developmental marker and animal weight at weaning.

8. The statistics module shall permit the control group in a statistical calculation to be specified by the user within the statistics report work flow.

9. Use the NTP estrous cyclicity algorithm (Appendix 4, NTP EstrousCyclicityAlgorithm.xlsx) to calculate the cycle parameters of the estrous cycle, starting from any of the four stages of the cycle, at the request of the system user.

10. Have the ability to include and exclude p-values from tables at the request of the user.

11. Permit the user to select any pair of groups within a study for pairwise statistical comparison. The pairwise comparisons shall be done using the methods described in point 6 above

12. Spearman’s Rank Order Correlation for ordinal variables, Mann-Whitney U non-parametric for tests with an upper limit cutoff, repeated measure ANOVA, test for homogeneity of variance, and the ability to transform data (to log or square root) if needed.

These twelve (12) methods shall be incorporated into the system by the end of Year 1.

B. Immunotoxicology Statistics

1. Immunotoxicology Workflow Number 1.

The system shall guide users in using the NTP statistical decision tree for immunotoxicology studies.

The data obtained using this study design shall be first tested for homogeneity of variances using the Bartlett's Chi Square Test, Bartlett, 1937. Homogeneous data shall be evaluated by a parametric one-way analysis of variance, Kruskall and Wallis, 1952. When significant differences occur, treatment groups shall be compared to vehicle control using Dunnett's t Test, Dunnett, 1955. Non-homogeneous data shall be evaluated using a non-parametric analysis of variance, Wilson, 1956. When significant differences occur, treatment groups shall be compared to vehicle control using the Wilcoxon Rank Test, Gross and Clark, 1975. Jonckheere's Test shall be used to test for dose-related trends across the vehicle and the treatment groups, Hollander and Wolfe, 1975. Student’s t Test shall be used to compare the positive control for the assay with the vehicle control, Sokal and Rohlf, 1981.

2. Immunotoxicology Workflow Number 2.

Additional tests shall include outlier analysis using Distribution box blots and Dixon’s test;

Spearman’s Rho trend test; Bartlett’s test and Levene’s test for homogeneity of variances. If data are homogeneous, then the ANOVA and Dunnett’s test are used. For nonhomogeneous data the Wilcoxon Rank test and Paired Wilcoxon Rank test are used. The Student’s t test is used for positive control data. The Jonckheere's Test shall be used to test for dose dependency among the vehicle and treatment groups.

The Immunotoxicology Workflows shall be incorporated into the system within the first six (6) months following contract award.

C. Carcinogenicity Study Statistics

1. Survival Analysis.

Statistical analyses for possible dose-related effects on survival: Cox’s (1972) method for testing two groups for equality and Tarone’s (1975) life table test to identify dose-related trends. All reported p values for the survival analyses should be two sided.

2. Calculation of Lesion Incidence.

The system shall calculate the incidence of lesions using the following method: The incidences of lesions are given as the numbers of animals affected at each site examined microscopically. When macroscopic examination is required to detect neoplasms in certain tissues before microscopic evaluation, the denominators shall consist of the number of animals that had a gross abnormality.

When neoplasms had multiple potential sites of occurrence the denominators shall consist of the number of animals on which a necropsy was performed.

3. Analysis of Neoplasm and Non-neoplastic Lesion Incidences.

The system shall use the Poly-k test (Bailer and Portier, 1988; Portier and Bailer, 1989; Piegorsch and Bailer, 1997) to assess neoplasm and non-neoplastic lesion prevalence. This test is a survival-adjusted quintal-response procedure that modifies the Cochran-Arbitrage linear trend test to take survival differences into account. More specifically, this method modifies the denominator in the quintal estimate of lesion incidence to approximate more closely the total number of animal years at risk. For analysis of a given site, each animal is assigned a risk weight. This value is one if the animal had a lesion at that site or if it survived until terminal sacrifice; if the animal died prior to terminal sacrifice and did not have a lesion at that site, its risk weight is the fraction of the entire study time that it survived, raised to the kth power.

This method yields a lesion prevalence rate that depends only upon the choice of a shape parameter for a Waybill hazard function describing cumulative lesion incidence over time (Bailer and Portier, 1988). The system shall permit the value of k to be specified, with a default value of k=3. The system shall adjust the variance of the Poly-3 statistic as recommended by Bailer and Williams (1993) to accommodate statistical variation introduced by the use of risk weights, which reflect differential mortality.

The system shall report pairwise comparisons of each dosed group with controls and a test for an overall dose-related trend. The system shall use continuity-corrected Poly-3 tests for the analysis of lesion incidence, and report one-sided p values. The system shall report the significance of lower incidences or decreasing trends in lesions as 1–p with the letter N added (e.g., p=0.99 is presented as p=0.01N).

These statistical methods shall be incorporated into the system by the end of Option 2 (Year 3).

V. Tables and Reports

A. Reproductive and Developmental Toxicology Reports

1. Test p-values shown on summary statistical reports.

Show the numeric p-value for a trend test or t-test in addition to including superscripts indicating significance in the table or report, at the discretion of the system user.

2. Cross-generation report.

This report shall contain two columns per group per endpoint. The first shall be the value for that endpoint for a given sire or dam, the second shall be the summary value for the pups (male, female or both, as the endpoint suggests) from that dam or sire. The summary values shall be calculated using the methods described in Section IV, Paragraph A, Number 6.

3. Multi-litter report.

This shall contain on one report the results of three or more litters in a generation plus a summary value for all the litters in a group combined. The format shall be litter letter in each row, dose groups across the top, with breaks for different endpoints if included on the same table. The summary values shall be calculated using the methods described in Section IV, Paragraph A, Number 6.

These reports shall be incorporated into the system by the end of Option 1 (Year 2).

B. Reproductive and Developmental Tables and Study Designs

1. Comparison of multiple groups in a study.

The system shall expand the capability for pairwise comparison of any pair of groups to statistical analysis of e.g. trend or ANOVA, or other statistical test for any set of 4 to 12 groups. This shall not be limited by generation or litter number.

2. Cross generational comparison

The system shall display a table containing summary data for a lineage of three or more generations for a given endpoint. In other words, the system shall display a report with endpoints given in rows and the columns consisting of (1) F0 values for that endpoint for each individual animal selected; (2) F1 summary values for each direct offspring of that individual; (3) F2 summary values for each second-generation offspring of that individual. The summary values shall be calculated using the methods described in Section IV, Paragraph A, Number 6.

The Reproductive and Developmental Tables and Study Designs shall be incorporated into the system by the end of Option 2 (Year 3).

VI. Additional Study Types

A. Immunotoxicology

1. Immunomodulation assays shall include (assay details are given in Appendix 5):

a. Endpoints including counts and percentages of T Cell, T Cell Subsets, B Cell, NK Cell, bone marrow cell, monocyte enumeration and bone marrow and splenic differentials.

b. Spleen IgM / IgM Antibody Response to a T-dependent Antigen, e.g. sRBC or KLH. Cell counts are performed on the original sample and the number of cells/spleen, Antigen Forming Cells (AFC) AFC/spleen and AFC/106 spleen cells determined. The data are expressed as specific activity (AFC/106 spleen cells) and total spleen activity (AFC per spleen).

c. Serum IgM Antibody Titers to a T-dependent Antigen, e.g. sRBC or KLH as measured by

Enzyme Linked Immunosorbent Assay (ELISA)

d. Mixed Leukocyte Response to DBA/2 Mouse Spleen Cells. Cells are cultured in the presence of

1 mCi 3H-thymidine and counted in a LKB liquid scintillation counter. Data are expressed as cpm/culture.

e. Macrophage Activation Factor Assay. Cells are incubated with B16F10 melanoma target cells at a ratio of 10:1, pulsed with 3H-thymidine, and harvested. The total 3H-thymidine counts (CPM) for each well are used to calculate the percent suppression of B16F10 proliferation.

f. Natural Killer Cell Activity: Spleen cell suspension are adjusted to obtain effector-to-target ratios of 200:1, 100:1, 50:1, 25:1, 12.5:1, and 6.25:1. The target cells, YAC-1 cells, are maintained in a stock culture and labeled with 200 mCi of 51Cr. Target cells are counted and 51Cr release compared to 100% release. The mean (± SE) percent cytotoxicity at each effector concentration is then determined for each exposure group.

2. The system shall upload data from Hypersensitivity studies containing the following endpoints within a single study (endpoint details are given in Appendix 5):

a. Primary Irritancy & Cumulative Percutaneous Toxicity Study: Animals are treated on 4 consecutive days by administration of test article or control to ear. Ear thickness at site of application is measured on Day 1 prior to treatment and 24 hours following the last treatment.

b. The percent ear swelling is calculated as the: [(mean thickness of the post treated ear / mean thickness of the pre-treated ear) X 100]-100. The percent ear swelling for the test article is compared to the percent swelling for the vehicle using a one-way analysis of variance followed by the Dunnett's t Test to determine the minimal irritating concentration, and the maximal non-irritating concentration.

c. Mouse Ear Swelling Test: This test occurs over 10 days, with treatment applied on days 1, 2, 3

(sensitization) and 8 (challenge). Ear measurements are taken on days 1, 9 and 10. The percent ear swelling is calculated as follows: [(mean thickness of both ears (24 or 48 hours post treatment) / mean thickness of both ears measured before challenge) X 100]-100.

d. Local Lymph Node Assay: Each animal is treated with one of up to eight dilutions (e.g. 100%, 50%, 25%, 10%, 5%, 2.5%, 1%, 0.5%) on Days 1, 2, and 3 of the assay. On Day 6 they receive an intravenous injection of 3H- thymidine. Data are presented as DPM (disintegrations per minute), calculated as: ([counts per minute minus the background count ]/ the efficiency of the Beta counter).

e. Immunofluorescent Staining of Lymph Node Subpopulations. Mice are treated with either test article or control on 4 consecutive days. On the fifth day mice are euthanized and the auricular lymph nodes removed, pooled and pressed into a single cell suspension. Cells are labeled in 96-well culture plates with 0.10 ml of the appropriate anti-mouse monoclonal antibodies, propidium iodide and then enumerated by flow cytometry.

The Immunotoxicology study design shall be incorporated into the system within six (6) months following contract award.

B. Neurotoxicology

The system shall upload data from neurobehavioral tests provided in a Microsoft Excel format and/or by directly uploading data from an instrument used to gather the data.

The Contractor shall provide an Option for acquiring data directly each instrument.

Neurobehavioral tests shall include:

1. Locomotor activity method of Howard et al., 1987. This data shall be transmitted to the system by the user in the form of summary data (beam breaks per minute). Other options include photocell or video pathway tracking. Data will include: (1) total ambulatory activity or distance travelled across the full 60 minute session; (2) the sequence of 5-minute epochs of total ambulatory activity counts or distance travelled over 60 minutes (3) total rearing activity across the full 60 minutes (4) the sequence of 5-minute epochs of total rearing activity counts over 60 minutes (5) time spent within each of 2 or 4 fields in the chamber.

2. Strength assessments of forelimb and hind limb grip strength measured by the resistance generated using a strain-gauge system. Individual response shall be recorded for 3 consecutive trials. Raw data shall include all trials in sequence of delivery. If more than one strain gauge is used an identifier shall be included on the data sheet.

3. Fear conditioning – data shall include latency of freezing behavior across test sessions.

4. Startle reactivity and pre-pulse startle inhibition. Reactivity to a novel stimulus (amplitude), habituation, and gating of the response (pre-pulse startle inhibition) using the method of Feifel and Reza, 1999. Raw data shall include each individual response (Vmax) for each session in sequence.

This will represent approximately 8 to 10 different endpoints collected over the test session. If more than one investigator then the identifier shall be included on the data sheet.

5. Shuttle box conditioned avoidance (method of Cooper et al, 1974 and Rigdon et al., 1996) Data to include (1) total number of crosses during acclimation period (2) total number of avoidances (3) total number of escapes (4) temporal pattern of avoidances and escapes across the test session (5) avoidance latency – average and temporal pattern over the test session (6) escape latency – average and temporal pattern over the test session (7) escape loss – total and pattern over the test session (8) observation of freezing behavior.

6. Morris Water Maze (method of Morris, 1981 with parametric development by Lindner, 1997) method options – observer or video tracking. Data to include: 1) latency to reach escape platform (repeated measures design over multiple training sessions) 2) average swim speed 3) Probe test – time spent in each of the quadrants of the water maze 4) video pathway tracking for swimming pattern in probe test 3) Retest – latency to reach new platform location and initial latency to reach previous platform location.

7. Operant Conditioning Paradigms – data will include acquisition of the bar press behavior for food reinforcement under a continuous reinforcement schedule – (number of reinforcements; number of bar presses). Training of subsequent more difficult schedule will generate data such as number of correct bar presses, number of incorrect bar presses, number of reinforcements, latency to first bar press.

The Neurotoxicology studies shall be incorporated into the system by the end of Year 1.

C. Carcinogenicity Study Design

The system shall be able to collect and report data from an NTP Toxicology and Carcinogenicity study with design specified here: http://ntp.niehs.nih.gov/ntp/Test_Info/FinalNTP_ToxCarSpecsJan2011.pdf, in sections IX (study protocols), VII (pathology), VI (Clinical pathology), XI (report formats), Appendix 5 (Individual Animal Necropsy Reports) and Appendix 6 (Procedures for Sperm Count and Vaginal Cytology Evaluation).

In brief, this requirement is that the system be able to capture data from acute toxicity studies of 2- or 13-week duration, and from carcinogenicity studies of 2-year duration. The system shall be compatible with both feed/water delivery, gavage and inhalation delivery routes. The details of such studies, including endpoints and report structures, are given in the NTP specifications listed above.

The NTP has specific requirements given in the design specifications above for report design and study design which the contractor shall accommodate within the system.

The system shall include the NTP neoplastic glossary, which shall be available to the Contractor during the second year of the contract. An example of the NTP glossary can be found in the NTP path code tables, http://jones.niehs.nih.gov:8080/pct/

The Carcinogenicity study design shall be incorporated into the system by the end of Option 2 (Year 3).

D. Cross-Fostering Study Design

The system shall support data collection and analysis using a cross-fostering study design. In this design all the pups in a litter are moved to the cage of a foster dam, and the pups from the foster dam are moved to the cage of a third dam and so on until no pup in the foster group is housed with its birth mother. This process: (1) moves pups only within a dose group, and if possible (2) only within one study day (preferably PND1). The system shall provide a method to randomly select litters to be moved in this manner.

In a second application of fostering, the system shall support the use of fostering to maintain litter pressure in other studies. The system shall permit one or more pups to be moved to the cage of a foster dam in order to balance the number of pups per litter. The foster pups shall be moved only within a dose group. The system shall record the IDs of the foster pups in such a way that they are not selected for use on the study post weaning.

The Cross-Fostering Study Design shall be incorporated into the system by the end of Option 2 (Year 3).

VII. Options Which May Be Exercised After Completion of Option 1 (Year 2).

1. The system shall support NTP RACB (Reproductive Assessment by Continuous Breeding) reproductive toxicology protocol templates covering four generations (F0 breeder generation plus F1, F2 and F3 generations), and 8000 individually-housed animals per study.

2. Presentation of data from adult male and female animals without an obligatory page beak in any table.

3. The system shall calculate gavage doses for pre-weaning pups based on most recent bodyweight.

4. A report format with only those descriptive statistics the NTP chooses to display (mean, SEM and N) on one row.

These Options may be exercised after the completion of Option 1 (Year 2). At this time, the NTP cannot determine which options shall be exercised or in what year these options may be exercised.

VIII. Reporting Requirements

Quarterly, the Contractor shall deliver a report summarizing the status of the system and progress made in the prior quarter. This report shall be delivered as an electronic Microsoft Word document to the COTR via e-mail.

Annually, the Contractor shall prepare a security report as directed by the COTR.

Annually, the Contractor shall provide a report documenting compliance with Section 508 of the Rehabilitation Act (29 U.S.C. 794d), as amended by the Workforce Investment Act of 1998 (P.L. 105- 220), August 7, 1998. These reports shall be delivered as an electronic Microsoft Word document to the COTR via e-mail.

The Contractor shall provide the system in a secure environment that conforms to the moderate security level described in the Federal Information Security Management Act of 2002 (FISMA), NIST Special Publication 800-53Rev3 and NIST800-63, level 1. The contractor shall certify this capability annually.

Prior to implementing any changes to the system to address capabilities described above the contractor shall deliver a short report which describes the approach which will be taken. Each report will be due six

(6) months prior to final delivery of the system with requested changes. Each report shall be delivered as an electronic Microsoft Word document to the COTR via e-mail.

IX. Deliverables

DELIVERABLE: DUE DATE: SUBMITTED TO: METHOD OF

SUBMISSION:

Access to system for 1 base year + 9 option year (Section II)

At award N/A N/A

System Functionality (Section I.A.1)

Within 4 months of contract award

N/A N/A

Training at NTP and Contractor Sites (Section I.A.2.a.)

At Award N/A N/A

80 hours of consultation on table design and preparation (Section I.A.2.b.)

By end of Year 1 N/A N/A

Validation of System (Section I.A.3.)

By end of Year 1 N/A N/A

40 hours of training in data collection/data review (Section I.A.3.)

Within 30 days of the availability of data collection capability

N/A N/A

80 hours of refresher training in system use (Section I.B.)

Annually, beginning in Option 1 (Year 2)

N/A N/A

Contractor to provide list of any changes to system/new features prior to installation (Section I.C.)

30 days prior to installation of new system / system with new features

COTR Via E-mail

Copy of help-desk logs (Section I.C.)

Within 5 business days following the last calendar day of each month

COTR Via E-mail

Copy of access logs (Section I.C.)

Within 5 business days following the last calendar day of each month

COTR Via E-mail

Monthly export of data and tables from database (Section I.C.)

Within 5 business days following the last calendar day of each month

COTR Via E-mail

Development of procedure for handling security incidents (Section I.C.)

Within 4 months of contract award

COTR Via E-mail

DELIVERABLE: DUE DATE: SUBMITTED TO: METHOD OF

80 hours of training on the use of third-party business intelligence software, if necessary (Section II)

Within 6 months of contract award.

N/A N/A

System Usability Features (Section III.A.)

By the end of Year 1 N/A N/A

Historical Control Database availability (Section III.B.)

Within 1st year following data collection

N/A N/A

Analysis for Reproductive & Development Toxicology (Section IV.A.)

By the end of Year 1 N/A N/A

Immunotoxicology Statistics (Section IV.B.)

Within 6 months after contract award

N/A N/A

Carcinogenicity Study Statistics (Section IV.C.)

By the end of Option 2 (Year 3)

N/A N/A

Reproductive & Developmental Toxicology Reports (Section V.A.)

By the end of Option 1 (Year 2)

N/A N/A

Reproductive & Developmental Toxicology Tables and Study Designs (Section V.B.)

By the end of Option 2 (Year 3)

N/A N/A

Immunotoxicology Study Design (Section VI.A.)

6 months after contract award

N/A N/A

Neurotoxicology Studies (Section VI.B.)

By the end of Year 1 N/A N/A

Carcinogenicity Study Design (Section VI.C.)

By the end of Option 2 (Year 3)

N/A N/A

Cross Fostering Study Design (Section VI.D.)

By the end of Option 2 (Year 3)

N/A N/A

Progress Report (Section

VIII)

Quarterly COTR, Contract Specialist

Via E-mail

Security Report (Section

VIII)

Annual COTR, Contract Specialist

Via E-mail

Section 508 Annual Report (Section VIII)

Annual COTR, Contract Specialist

Via E-mail

Certification of compliance with FISMA (Section VIII)

Annual COTR, Contract Specialist

Via E-mail

Report Outlining System Capabilities to be Implemented (Section

VIII)

6 months prior to final delivery of system capability

COTR Via E-mail

OPTIONS: DUE DATE: SUBMITTED TO: METHOD OF

32 hour increments of training (Section I.B.)

Throughout contract life cycle

N/A N/A

Blocks of 25 users (Section II)

NTE 250 additional users throughout contract life cycle (350 users total)

N/A N/A

Additional Lab Sites (Section II)

NTE 10 additional sites throughout the contract life cycle (12 sites total)

N/A N/A

Additional Lab Sites (Section II)

Unknown quantity in subsequent years beyond Option Year 2.

N/A N/A

Acquire study data directly from instrument in Neurotoxicology Studies (Section VI.B.)

Throughout contract life cycle

N/A N/A

Support NTP RACB reproductive toxicology protocol templates covering four generations and 8000 individually housed animals per study (Section VII.1.)

After Option 1 (Year 2) N/A N/A

Presentation of data from adult male and female animals on single page in a table (Section VII.2.)

After Option 1 (Year 2) N/A N/A

Calculate gavage doses for pre-weaning pups based on most recent body weight (Section

VII.3.)

After Option 1 (Year 2) N/A N/A

Report format with only the descriptive statistics the NTP chooses to display (Section VII.4.)

After Option 1 (Year 2) N/A N/A

Appendices:

Appendix 1 – NTP glossaries NTP-InLifeGlossary.xlsx NTP-HistoGlossary.xlsx NTP-fetalPathGlossary.xlsx NTP-GrossPathTissueSiteGlossary.xlsx NTP-GrossPathMorphologyModifier.xlsx

Appendix 2 – MOG and RACB templates MOG_current_508.doc RACB_508.doc

Appendix 3 – Performance Qualification process

Appendix 4 – Upload Screen NTP-EstrousData.xlsx NTP-EstrousCyclingAlgorithm.xlsx

Appendix 5 – Immunomodulation Assays

Appendix 6 – Sensitization Study Designs

Appendix 7 - References