PI: Heinemann, Allen Walter Title: Defining Trajectories of Linguistic, Cognitive-Communicative and Quality of 

Life Outcomes in Aphasia 

Received: 07/05/2018 FOA: PA18-287 

Clinical Trial:Optional 

Council: 01/2019 

Competition ID: FORMS-E FOA Title: Improving Outcomes for Disorders of Human Communication (R01 

Clinical Trial Optional) 

1 R01 DC017174-01A1 Dual: Accession Number: 4194643 

IPF: 6898901 Organization: REHABILITATION INSTITUTE OF CHICAGO D/B/A SHIRLEY RYAN 

ABILITYLAB 

Former Number: Department: 

IRG/SRG: LCOM AIDS: N Expedited: N 

Subtotal Direct Costs 

(excludes consortium F&A) 

Year 1: 

Year 2: 

Year 3: 

Year 4: 

Year 5: 

Animals: N 

Humans: Y 

Clinical Trial: N 

Current HS Code: 30 

HESC: N 

New Investigator: N 

Early Stage Investigator: N 

Senior/Key Personnel: Organization: Role Category: 

Allen Heinemann Ph.D Rehabilitation Institute of Chgo dba 

Shirley Ryan AbilityLab 

PD/PI 

Leora Cherney Ph.D Rehabilitation Institute of Chgo dba 

Shirley Ryan AbilityLab 

MPI 

Andrea Domenighetti Rehabilitation Institute of Chgo dba 

Shirley Ryan AbilityLab 

Co-Investigator 

Marwan Baliki Rehabilitation Institute of Chgo dba 

Shirley Ryan AbilityLab 

Co-Investigator 

Elliot Roth Rehabilitation Institute of Chgo dba 

Shirley Ryan AbilityLab 

Co-Investigator 

Linda Foster Rehabilitation Institute of Chgo dba 

Shirley Ryan AbilityLab 

Co-Investigator 

Allan Kozlowski Ph.D Mary Free Bed Rehabilitation Hospital Co-Investigator 
0MB Number 4040.0001 

ExpirationDate 10/31/2019 

APPLICATION FOR FEDERAL ASSISTANCE 3. DATE RECEIVED BY STATE State Application Identifier 

SF 424 (R&R) 

1. TYPE OF SUBMISSION* 4 .a. Federal Identifier 

DC017174 

0 P b. Agency Routing Number re application • Application 0 Changed/Corrected 

Application 

2. DATE SUBMITTED Application Identifier c. Previous Grants.gov Tracking Number 

5. APPLICANT INFORMATION Organizational DUNS*: 

Legal Name·: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Department: 

Division: 

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Prefix: Mrs. First Name·: Evelyn Middle Name: Scott Last Name·: Dilisio Suffix: 

Position/Title: Executive Director, Research Administration 

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7. TYPE OF APPLICANT* M: Nonprofit with 501C3 IRS Status (Other than Institution of Higher 

Education) 

Other (Specify): 

Small Business Organization Type 0 Women Owned O Socially and Economically Disadvantaged 

8. TYPE OF APPLICATION* If Revision, mark appropriate box(es). 

ONew • Resubmission OA. Increase Award OB. Decrease Award OC. Increase Duration

0 Renewal OContinuation O Rev O D. Decrease Duration O E. Other {specify) : ision 

Is this application being submitted to other agencies?* OYes eNo What other Agencies? 

9. NAME OF FEDERAL AGENCY* 10. CATALOG OF FEDERAL DOMESTIC ASSISTANCE NUMBER 

National Institutes of Health TITLE: 

11. DESCRIPTIVE TITLE OF APPLICANT'S PROJECT* 

Defining Trajectories of Linguistic, Cognitive-Communicative and Quality of Life Outcomes in Aphasia 

12. PROPOSED PROJECT 13. CONGRESSIONAL DISTRICTS OF APPLICANT 

Start Date· 

04/01/2019 

Ending Date· 

03/31/2024 

1111 

Funding Opportun ty Number: PA 18-287 . Received Date: Tracking Number: GRANT12670047 

2018-07 05T15 37 27.000 04:00 Page 1 
SF 424 (R&R) APPLICATION FOR FEDERAL ASSISTANCE Page 2 

14. PROJECT DIRECTOR/PRINCIPAL INVESTIGATOR CONTACT INFORMATION 

Prefix: Dr. First Name·: Allen Middle Name: Last Name•: Heinemann Suffix: Ph.D 

Position/Title: Director 

Organization Name•: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Department: 

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16.IS APPLICATION SUBJECT TO REVIEW BY STATE 

EXECUTIVE ORDER 12372 PROCESS?* 

15. ESTIMATED PROJECT FUNDING 

a.YES Q THIS PREAPPLICATION/APPLICATION WAS MADE 

a. Total Federal Funds Requested· AVAILABLE TO THE STATE EXECUTIVE ORDER 1.237.2 

b. Total Non-Federal Funds· PROCESS FOR REVIEW ON: 

c. Total Federal & Non-Federal Funds· DATE: 

d. Estimated Program Income· b.NO e PROGRAM IS NOT COVERED BY E.O. 1 237 2; OR 

Q PROGRAM HAS NOT BEEN SELECTED BY STATE FOR 

REVIEW 

17. By signing this application, I certify (1) to the statements contained in the list of certifications* and (2) that the statements herein 

are true, complete and accurate to the best of my knowledge. I also provide the required assurances * and agree to comply with 

any resulting terms if I accept an award. I am aware that any false, fictitious, or fraudulent statements or claims may subject me to 

criminal, civil, or administrative penalties. (U.S. Code, Title 18, Section 1001) 

e I agree• 

•The list of certifications and assurances, or an Internet site where you may obtain this list, is contained in the announcement or agency specific instructions. 

18. SFLLL or OTHER EXPLANATORY DOCUMENTATION File Name: 

19. AUTHORIZED REPRESENTATIVE 

Prefix: Mrs. First Name·: 1111 Middle Name: - Last Name·: 1111 Suffix: 

Position/Title•: Executive Director, Research Administration 

Organization Name•: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Department: 

Division: 

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Signature of Authorized Representative* Date Signed* 

07/05/2018 

20. PRE-APPLICATION File Name: 

21. COVER LETTER ATTACHMENT File Name: 

Tracking Number: GRANT12670047 Funding Opportun ty Number: PA 18-287.. Received Date: 

2018-07 05T15 37 27.000 04:00 Page2 
Contact PD/PI: Heinemann, Allen Table of Contents 

424 R&R and PHS-398 Specific 

Table Of Contents 

SF 424 R&R Cover Page............................................................................................................1 

Table of Contents...................................................................................................................3 

Performance Sites.....................................................................................................................4 

Research & Related Other Project Information......................................................................6 

Project Summary/Abstract(Description)..............................................................................7 

Project Narrative....................................................................................................................8 

Facilities & Other Resources................................................................................................9 

Equipment.............................................................................................................................12 

Research & Related Senior/Key Person................................................................................15 

Research & Related Budget Year - 1......................................................................................50 

Research & Related Budget Year - 2......................................................................................53 

Research & Related Budget Year - 3......................................................................................56 

Research & Related Budget Year - 4......................................................................................59 

Research & Related Budget Year - 5......................................................................................62 

Budget Justification................................................................................................................65 

Research & Related Cumulative Budget...............................................................................70 

Research & Related Budget - Consortium Budget (Subaward 1).......................................71 

Research & Related Budget - Consortium Budget (Subaward 2).......................................88 

Research & Related Budget - Consortium Budget (Subaward 3).....................................105 

Total Direct Costs Less Consortium F&A...........................................................................122 

PHS398 Cover Page Supplement.........................................................................................123 

PHS 398 Research Plan.........................................................................................................125 

Introduction to Application...............................................................................................126 

Specific Aims......................................................................................................................127 

Research Strategy..............................................................................................................128 

PHS Human Subjects and Clinical Trials Information....................................................140 

Study 1: Defining Trajectories of Linguistic, Cognitive-Communicative and Quality of 

Outcomes in Aphasia.....................................................................................................142 

Inclusion Enrollment Reports....................................................................................148 

Multiple PD/PI Leadership Plan........................................................................................160 

Bibliography & References Cited.....................................................................................161 

Consortium/Contractual Arrangements...........................................................................170 

Letters of Support..............................................................................................................176 

Resource Sharing Plan(s).................................................................................................179 

 Page 3
0MB Number: 4040-0010 

ExpirationDate: 10/31/2019 

Project/Performance Site Location(s) 

Project/Performance Site Primary Location O I am submitting an application as an individual, and not on behalf of 

a company, state, local or tr bal government, academia, or other type of 

organization. 

Rehabilitation Institute of Chgo dba Shirley Ryan Organization Name: Abilitylab 

Duns Number: 

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Project/Performance Site Location 1 O I am submitting an application as an individual, and not on behalf of 

a company, state, local or tr bal government, academia, or other type of 

organization. 

Organization Name: 

DUNS Number: 

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Project/Performance Site Congressional District-: 

Mary Free Bed Rehabilitation Hospital 

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Funding Opportunity Number: PA 18 287. Received Date: Tracking Number: GRANT12670047 

2018-07 05T15:37:27.000 04:00 
Northwestern University 

Contact PD/Pl: Heinemann, Allen 

Project/Performance Site Location 2 O I am submitting an application as an individual, and not on behalf of 

a company, state, local or tr bal government, academia, or other type of 

organization. 

Organization Name: 

DUNS Number: 

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Page 5 

Funding Opportunity Number: PA 18 287. Received Date: Tracking Number: GRANT12670047 

2018-07 05T15:37:27.000 04:00 
Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287. Received Date: 

OMB Number: 4040-0001

Expiration Date: 10/31/2019

RESEARCH & RELATED Other Project Information

Are Human Subjects Involved?* ● Yes ❍ No 

1.a. If YES to Human Subjects 

Is the Project Exempt from Federal regulations? ❍ Yes ● No 

If YES, check appropriate exemption number: 1 2 3 4 5 6 7 8 

If NO, is the IRB review Pending? ● Yes ❍ No 

IRB Approval Date: 

Human Subject Assurance Number 00001553

Are Vertebrate Animals Used?* ❍ Yes ● No 

2.a. If YES to Vertebrate Animals 

Is the IACUC review Pending? ❍ Yes ❍ No 

IACUC Approval Date: 

Animal Welfare Assurance Number 

Is proprietary/privileged information included in the application?* ❍ Yes ● No 

4.a. Does this project have an actual or potential impact - positive or negative - on the environment?* ❍ Yes ● No 

4.b. If yes, please explain: 

4.c. If this project has an actual or potential impact on the environment, has an exemption been authorized or an 

environmental assessment (EA) or environmental impact statement (EIS) been performed? 

❍ Yes ❍ No 

4.d. If yes, please explain: 

Is the research performance site designated, or eligible to be designated, as a historic place?* ❍ Yes ● No 

5.a. If yes, please explain: 

Does this project involve activities outside the United States or partnership with international 

collaborators?* 

❍ Yes ● No 

6.a. If yes, identify countries: 

6.b. Optional Explanation: 

Filename 

Project Summary/Abstract* 1242-Heinemann_Abstract.pdf

Project Narrative* 1243-Heinemann_ProjNarrative.pdf

Bibliography & References Cited 1244-Heinemann_Refs.pdf

10.Facilities & Other Resources 1245-Heinemann_Facilities.pdf

11.Equipment 1246-Heinemann_Equipment.pdf

 

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Stroke imposes significant burdens on the health and quality of life of survivors and their caregivers, and presents 

a major public health issue in terms of healthcare costs and lost productivity. Aphasia adds to the cost of strokerelated care. Many stroke survivors with aphasia receive therapy in inpatient rehabilitation facilities. However, 

aphasia recovery is variable and there is limited evidence on the benefits of inpatient rehabilitation on outcomes. 

The objective of this study is to describethe trajectories of linguistic, cognitive-communicative, and health-related 

quality of life (QoL) outcomes following stroke in persons with aphasia during inpatient and outpatient rehabilitation to 18 months following stroke. A sampleof 300 consecutively-admitted stroke patients with aphasia recruited 

at three Midwestern rehabilitation hospitals will complete measures of linguistic and cognitive-communicative 

performance, and the Quality of Life in Neurological Disorders (Neuro-QoL) Measurement System instruments 

during rehabilitation and at 6-,12-, and 18- months post-stroke. We will model outcomes as individual and group 

trajectories, allowing us to develop individual predictions which could inform clinical planning and decision-making for new patients. The Specific Aims are to: 

Aim 1: Establish a prospective cohort of stroke patients with aphasia, and define their typical trajectory of linguistic, cognitive-communicative, and health-related QoL recovery at admission to and discharge from the IRF, 

and at 6, 12, and 18 months post onset. 

Aim 2: Identify factors that are associated with linguistic, cognitive-communicative, and health-related QoL outcomes from among the following: patient factors including demographic and clinical characteristics related to 

stroke and aphasia; treatment variables including inpatient and outpatient aphasia therapy characteristics and 

informal aphasia services; and biomarkers, including genetic and neuroimaging biomarkers. 

Aim 3: Evaluate the stability of the models of linguistic, cognitive-communicative, and health-related QoL outcomes recovery that are developed from Aims 1 and 2. 

This study is innovative in its use of (1) standardized assessments that measure not only linguistic outcomes but 

also communication and QoL outcomes; (2) patient-centered, self-report instruments such as Neuro-QoL to detect clinically important change through 18 months post-stroke; (3) individual growth curve analysis to describe 

recovery trajectories and examine associations between demographic, lesion, aphasia, genetic, and speech and 

language therapy characteristics; (4) biomarkers that have been implicated in promoting neuroplasticity; (5) resting state functional magnetic resonance imaging to evaluate the association between network pathology and 

recovery from aphasia; (6) information on type, amount, and duration of aphasia treatment provided in clinical 

settings; and (7) information on informal aphasia services following discharge from formal therapy. 

Project Summary/Abstract Page 7
 

 

 

Project Narrative 

This study describes trajectories of linguistic, cognitive-communicative, and health-related QoL outcomes during 

inpatient and outpatient rehabilitation to 18 months in a sample of 300 adults with aphasia using demographic, 

lesion, aphasia, genetic polymorphisms, and speech and language therapy characteristics as predictors. 

Project Narrative Page 8
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Facilities 

The Shirley Ryan AbilityLab (formerly the Rehabilitation Institute of Chicago) 

The Shirley Ryan AbilityLab (SRALab) is an internationally recognized specialty hospital and healthcare network dedicated to the care and rehabilitation of individuals with physical disabilities. Recognized by U.S. News 

and World Report as the number one rehabilitation provider for 27 consecutive years, SRALab has been a 

leading center for over 60 years. SRALab shares facilities and teaching staff with the NU-McGaw Medical Center and affiliated hospitals. The Department of PM&R of NU’s Feinberg School of Medicine, is housed at

SRALab, which has 42-attending PM&R physicians, and 151 consulting physician specialists. The Joint Commission accredits AbilityLab. 

Clinical Services: The SRALab opened in March 2017 two blocks south of the old RIC flagship hospital. It is 

expanded significantly from the old RIC, with 27 floors, 1.2 million square feet, with 242 all private, inpatient 

beds. Last year, the organization served approximately 58,000 patients from 43 states and 64 countries. The 

SRALab infuses biomedical science and research into the clinical environment. Traditional therapy gyms are 

replaced with Ability Labs. Within each Lab clinicians, researchers, and patients collaborate in open space and 

real time. The Labs are organized by functional outcome rather than by diagnosis and include: Think & Speak 

(Speech & Cognition); Arms & Hand (Fine Motor); Legs & Walking (Gait and Locomotion); Strength & Endurance 

(Total Body); and Pediatrics. The clinical staff includes Physical Therapy, Occupational Therapy, Speech Language Pathology, Neuropsychology, Therapeutic Recreation, Rehabilitation Nursing, Case Management, a Behavioral Specialist, Family Counselors and Vocational Rehabilitation Counselors. Admission decisions are based 

on need for medical and rehabilitation services, and not on ability to pay. This policy ensures accessibility for all 

people who need these services. 

Specialized services available at AbilityLab that are not available at many rehabilitation hospitals include the 

Technology Center, the ExpertEvalTM Second Opinion Program, Brain Injury Circle of Caring Program, the 

AMiCous Program (Disorder of Consciousness program), TBI Global Patient Services Program, eight Day Rehabilitation Programs, Vision Clinic, Spasticity Clinic, Mild TBI Clinic, Vocational Rehabilitation Services, The 

Wirtz Sports Program and Galvin Center for Health and Fitness, and the LIFE (Learning, Innovation, Family, 

Empowerment) Center and website (https://www.sralab.org/lifecenter). 

SRALab provides comprehensive rehabilitative care to a wide range of persons with disabilities in in- and outpatient settings. More than 40% of admissions come from minority backgrounds. Medicare covers about 40% of 

inpatient admissions, while 35% are funded by managed care insurers and 25% by Medicaid. This population 

provides clinicians with opportunities to evaluate the feasibility and utility of standardized assessments. 

Stroke Rehabilitation Program: Stroke constitutes the largest diagnosis of patients admitted for inpatient rehabilitation care at RIC. In fiscal year 2016, SRALab admitted 522 inpatients with a primary diagnosis of stroke. 

Inpatients receive comprehensive and intensive rehabilitation services from an interdisciplinary rehabilitation 

team. The program is unique in focusing on high intensity of training. 

Communication Disorders: Currently, within the SRALab’s main building, Communication Disorders services are 

provided to an estimated 900 patients with neurogenic communication disorders per year. In addition, there are 

eight community based Day-Rehabilitation Programs which are strategically located to serve a large geographic 

region of the greater Chicago area. Two Day-Rehabilitation programs are located in the City; the others are

located in suburban areas. For example, one is approximately 20 miles north of the city in Northbrook, while 

another is located approximately 20 miles south west of the city in Willowbrook. Having multiple locations allows 

access to a larger number of potential subjects for research activities. 

As of June 2018, there were 101 licensed speech-language pathologist across the continnum of care. This 

includes 25 inpatient SLPs, 26 DayRehab SLPs, 10 outpatient SLPs, 21 flex staff, 3 Tech Center SLPs, 5 

research SLPs, and 11 SLPs in leadership positions. In a recent survey, 68 of 73 (93%) clinical SLPs indicated 

that they work routinely with patients with aphasia. Of these 68 SLPs, 33% reported having more than 10 years 

experience and 25% reported 5-10 years of experience. 

Co-PI Cherney has an Aphasia Research Lab in the Think and Speak Lab located on the 25th floor of SRALab. 

The Lab has 1300 square feet of space, including six private offices for treating patients and/or research subjects 

as well as 12 carrels in open space for research staff, graduate students and post-doctoral fellows. The Aphasia 

Research Lab has 10 desktop PC’s that are dedicated to research activities in general and 12 laptop computers

that are dedicated to specific research projects. A separate computer lab with four terminals is dedicated to 

research participants. 

Facilities & Other Resources Page 9
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Center for Rehabilitation Outcomes Research (CROR). Co-PI Heinemann is PI of projects funded by the Department of Defense, PCORI, NIDILRR, and the Craig H. Neilsen Foundation. He directs the Center for Rehabilitation Outcome Research (CROR), a rehabilitation-focused health services research program. Staff members include four doctoral-level scientists, a project manager, two project coordinators, a data analyst, and six 

research assistants. Under Dr. Heinemann’s leadership, CROR has gained recognition for outcome studies 

and measurement of various disability domains. CROR manages the Rehabilitation Measures Database, an 

on-line compendium of measures, clinician observed instruments, and patient-reported outcome tools. Dr. 

Heinemann is Co-PI of AbilityLab’s SCI Model Systems project. He has been involved in numerous other collaborative projects such as development of the PROMIS, Neuro-QoL, SCI-QoL, and TBI-QoL. 

Imaging Facilities. Resting State fMRI scans will be acquired at the SRALab. The imaging floor at the SRALab 

houses a Siemens Prisma 3T whole-body MRI scanner. This is equipped with Siemens 64- and 20-channel 

head-neck coils as well as a Tx/Rx CP head coil. The scanner performs basic and clinical research including 

EPI, higher-order shimming, CINE, MR angiography, and spectroscopy. The Prisma hardware has 128 independent whole-body channels with a two-channel transmit system, a 60 cm bore, and an industry-leading XR 

gradient coil capable of imaging at 80mT/m with slew rates in excess of 200 T/m/s, per axis, at a duty cycle of 

100% simultaneously on all axes. The scanner relies on the SRALAB imaging/radiology floor infrastructure, 

which is staffed with two MRI technologists, research nurses, research managers and an administrative assistant. The MRI suite contains MRI-compatible audio, visual, and somatosensory stimulation equipment as well as 

eye-tracking and behavioral response devices. 

Biologics Lab. The Biologics Lab comprises approximately 5,000 square feet of dedicated and fully equipped 

laboratory space on the 26th floor of SRALab; staff will perform the genetic experiments proposed in this application. The space is set up to allow execution of many tissue, cellular, and molecular techniques including: 

metabolic measurements, histology, immunohistochemistry, immunocytochemistry, cell and tissue handling and 

cryopreservation, proteins and DNA extraction and analysis, microbiology, phase contrast, confocal and fluorescence imaging, muscle fibers and muscle bundles biomechanics, FACS sorting and cell culture. Dr. 

Domenighetti’s group has dedicated office space on the same floor. Offices are fully equipped with computers 

for writing and data analysis (e.g., MATLAB, SPIKE2, SPSS, SIGMAPLOT, SAS, Adobe software and Microsoft 

Office), as well as printers, a scanner, fax machine and access to Northwestern University library and internet 

networks. 

Research infrastructure: SRALab has a full complement of staff available with experience in research administration, including a Director of Grants Administration who functions as the administrative official for the institution, business support managers, a grants financial analyst, and administrative support staff. Research Administration facilitates and tracks submission of human subject research in conjunction with Northwestern University’s Institutional Review Board, and several faculty members in the Department of Physical Medicine and Rehabilitation serve on the review panels. Research Administration works with the Institute’s Finance and Accounting offices and with the General Counsel’s office in establishing and tracking research accounts, establishing

contractual agreements, invoicing, financial agency reporting, and development of Research Policies and Procedures. The Searle Rehabilitation Research Center of the SRALab has extensive experience in managing large, 

grant-supported research programs. Our extramural research portfolio exceeds $20 million with over 300 active 

projects. The Center employs over 180 individuals. 

Alexian Brothers Rehabilitation Hospital 

The Alexian Brothers Rehabilitation Hospital (ABRH) offers comprehensive inpatient services, day rehabilitation, 

outpatient services, specialty programs and on-site physician services. ABRH is a partnership between AMITA 

Health and the Shirley Ryan AbilityLab, offering convenient access to the same expert care that has earned 

SRALab the ranking of “Best Rehabilitation Hospital in America” by U.S. News & World Report every year since 

1991. 

Clinical Services: ABRH has 72 inpatient rehabilitation beds, as well as an intensive, interdisciplinary Day Rehabilitation program that treats patients with stroke and other neurological disorders. During FY 2016, ABRH 

admitted 340 patients with a primary diagnosis of stroke. Inpatient treatment includes services from board-certified physiatrists, as well as physical, occupational, and speech therapy. ABRH also has several specialized 

programs, including Women’s Health Rehabilitation, and Vestibular/Balance Rehabilitation with state-of-the-art 

balance testing equipment. The NeuroCom Smart Equitest aids therapists in their evaluation and treatment of 

individuals with neurological impairments that result in balance deficits. The KineAssist robotic device is also 

used for the treatment of individuals with neurological impairments that result in balance and gait deficits. There 

Facilities & Other Resources Page 10
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

are 16 speech-language pathologists who provide services in inpatient, outpatient and day rehabilitation programs. ABRH also offers a community Conversation Support Group that provides people with aphasia and 

apraxia of speech the opportunity to practice their conversational skills with others who experience similar difficulties. The group meets weekly with approximately 20 people coming throughout the year and an average of 8 

people attending each week. The group has a wide age range of attendees from their 20s to 80s. The group 

serves a wide range of impairment levels from mild to moderate-severe. 

Research Infrastructure: AMITA Health is committed to advancing medicine by developing new ways to treat 

disease through research studies and clinical trials. AMITA Health is engaged in over 120 clinical trials, offered 

through the Behavioral Health Hospital, the Neurosciences Institute, the Heart and Vascular Institute, and the 

Cancer Institute. AMITA Health provides administrative support of research activities throughout the health system through its Office of Clinical Research, which has formed an Institutional Review Board to oversee ethical 

aspects of research. 

Mary Free Bed Rehabilitation Hospital 

Mary Free Bed (MFB) Rehabilitation Hospital is the main campus for a regional network and continuum of postacute care services that extends across the lower peninsula of the state of Michigan. It is accredited by the Joint 

Commission. 

Clinical Services: MFB operates a 119-bed inpatient rehabilitation facility which admits more than 300 persons 

for stroke rehabilitation annually. The MFB campus also hosts a 48-bed subacute rehabilitation unit, and adult 

and pediatric outpatient programs. 

There are 61 credentialed speech-language pathologists (SLPs) employed across the MFB Network, who have 

been licensed with the American Speech-Language-Hearing Association for an average of 8.5 years. Of these, 

37 are employed at the main campus: 18 Inpatient, 9 Outpatient, 2 Cover/Float, and 8 Weekend. Of the inpatient 

SLPs, 88% (16/18) SLPs report treating patients with aphasia, with a median 96.5% rating of comfort in treating 

patients with aphasia. Of the 16 inpatient SLPs who treat aphasia, 50% report more than 10 years of experience, 

and 37.5% report experience ranging from 5 -10 years. 

Research Infrastructure: The MFB Research and Innovation Center is led by Director of Research John F. Butzer, MD. The Department was organized in 2014, and has since secured nearly a million dollars in external 

funding through donations, federal, and private foundation research grants. Allan J. Kozlowski, PhD joined the 

department in 2016 and serves as the Director of Outcomes Research. Additional staff include a Clinical Research Project Manager, a Research PT, and Research Assistants, who are funded in part by extramural grants 

and Department funds. A healthcare research consultant has been retained to aid in program development and 

growth. Research and Innovation receives technical and analytical support from MFB Departments of Information 

Technology and Decision Support. Mary Free Bed has a robust enterprise data warehouse to house electronic 

health record data. The Research and Innovation office suite includes eight private and semi-private offices, 

work space for post-doctoral fellows, students, and interns, and a conference room. Computer workstations are 

available for all department members, with software support from Mary Free Bed and from Michigan State University. All Department personnel are equipped with a laptop and docking station with complete Microsoft Office 

software, access to the MFB enterprise data warehouse, and other packages required for individuals. Dr. Kozlowski’s laptop is equipped with SAS, R, and HLM-7 software required for the basic and advanced statistics 

described in this proposal. Research and Innovation personnel have access to a complete online medical library 

through Michigan State University. 

The MFB Information Technology and Decision Support Departments work cooperatively to manage respectively 

the information infrastructure, data storage, and security; and data management and processing. Defined data 

from the MFB e medical record platforms (Cerner, Athena), scheduling, and financial systems are exported to 

the enterprise data warehouse daily. MFB Network providers will also contribute as data sharing agreements are 

established. The plan is to have data from all post-acute care encounters for MFB Network patients captured in 

the enterprise data warehouse and linked by a common universal patient ID number. The Information Technology Department also hosts the MFB REDCap platform, which is used for all Research Department studies, and 

some administrative and clinical applications that cannot be built into the EMR or other systems. The Decision 

Support Department manages data processing issues, and has implemented the Tableau© reporting platform 

as the interface between the EDW and the personnel who need information. 

Facilities & Other Resources Page 11
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The ShirleyRyan AbilityLab (formerly the Rehabilitation Institute of Chicago) 

Imaging Equipment. The imaging floor at the SRALab houses a Siemens Prisma 3T whole-body MRI scanner. 

The imaging suite is equipped with Siemens 64- and 20-channel head-neck coils as well as a Tx/Rx CP head 

coil. The scanner performs basic and clinical research including EPI, higher-order shimming, CINE, MR angiography, and spectroscopy. The Prisma hardware has 128 independent whole-body channels with a two-channel transmit system, a 60 cm bore, and an industry-leading XR gradient coil capable of imaging at 80mT/m with 

slew rates in excess of 200 T/m/s, per axis, at a duty cycle of 100% simultaneously on all axes. The MRI suite 

contains MRI-compatible audio, visual, and somatosensory stimulation equipment as well as eye-tracking and 

behavioral response devices. 

Biologics Lab. The Biologics Lab is equipped with chemicalfume hood, and biological safety cabinets and equipment to perform research on tissue or cell culture experiments. Offices are fully equipped with computers for 

writing and data analysis (e.g., MATLAB, SPIKE2, SPSS, SIGMAPLOT, SAS, Adobe software and Microsoft 

Office), as well as printers, a scanner, fax machine and access to Northwestern University’s Galter Health Sciences library and internet networks. Specific equipment includes: 

Biochemistry, molecular biology and general equipment: 

 Temperature regulated water bath 

 Shaker incubator (New Brunswick Scientific Excella E24) 

 96‐well microplate reader (Synergy HTX) 

 PCR Thermal cyclers (Bio-Rad T100) 

 Real-Time PCR (Bio-Rad CFX96) 

 UPLC System (Shimadzu Prominence HPLC with RF-20 and UV Detectors) 

 Gel imaging equipment (Syngene PXi) 

 UVP UV/While Transilluminator (analytikjena) 

 pH Meter (Mettler Toledo) 

 Refrigerated and regular centrifuges (2x Eppendorf 5810R, 2x Eppendorf 5424R, Eppendorf 5427R, 2x 

Eppendorf 5414D, 3x Eppendorf 5702R) 

 SDS‐PAGE and agarose gel electrophoresis equipment (Bio‐Rad and Life Technologies) 

 Tissue homogenizer (Bullet Blender 24) 

 Digital Microbalance (Shimadzu) 

 Top loader Balance (Sartorius) 

 ‐80 0

C ultra low freezers (4x New Brunswick U725) 

 Standard refrigerators/freezers (7 units, ThermoScientific) 

 General bench and table-top laboratory equipment (Pipettes, micro-centrifuges, plate heaters, water 

baths, stirrers, vortexers, drybath, thermomixer, etc.) 

 Flasks Scrubber Dishwasher (Steris Reliance 400XLS) 

 Autoclaving system (2x Steris AMSCO 250LS) 

 Water Purification System (Elga) 

Histology, immunohistochemistry and microscopy: 

 Leica RM 2155 automatic microtome 

 2x Leica CM3050S cryostats with a disposable blade holder and knife holder 

 Leica DM6000 B phase contrast microscope package 

 Epifluorescence Leica DMi8 inverted microscope with life-cell imagining capability 

 Confocal Leica DMi8 inverted microscope 

Cell culture: 

 5x Tissue culture hoods (ThermoScientific 1300 Series A2) 

 6x CO2/O2 incubators (Panasonic) 

 Liquid nitrogen containers for cell storage (Thermo Scientific Locator 4 Plus) 

 Leica DMi1 microscopes for cell visualizations 

 Refrigerated centrifuge (Eppendorf 5810R) 

 Standard refrigerator/freezer (Thermo Scientific) 

Equipment Page 12
 

 

 

 

 EVE automatic cell counter 

 xCELLigence RTCA DP Instrument (ACEA) 

 FACS cell sorter FaxMelody (BD) 

 Maestro Pro excitable cells analyzer (Axion BioSystems) 

Equipment Page 13
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Additional equipment: 

 Muscle lever system, Model 305B 305B 

 Balance, Mettler PC440 

 Muscle lever system, Model 360B 360B 

 Microscope, MZ FLIII fluorescent dissecting MZFLIII 

 Centrifuge, Eppendorf desktop 5415D 

 Force transducer, Aurora Scientific 405A 

 Centrifuge, Tabletop Spectrafuge 16M 

 Balance, Mettler AE50 AE50 

 Muscle lever system, Model 300B 300B 

 Centrifuge, mini C-1200 

 Power supply, electrophoresis PowerPac 200 

 UV transilluminator LM-20E 

 Microscope, Leica MZ12.5 dissecting MZ12 

 Stimulator, Pulsar 6bp 6bp 

 Microscope, MZ16 Stereomicroscope MZ16 

 Transmitted light base, microscope n/a 

 2x Fiber optic light source, Schott KL1500 

 Centrifuge, Eppendorf desktop 5415D 

 Centrifuge, mini 

 2x Vortexers 

 Muscle lever system, Model 300C-LR 300C-LR 

 Aurora High-Speed length controller 318B 

 Microscope, Nikon microphot-SA 

 Sony camera control unit DXC-760MD 

 Patch-clamp setup 

 2x muscle fiber and muscle bundle biomechanics setups. 

Equipment Page 14
OMB Number: 4040-0001 

Expiration Date: 10/31/2019 

RESEARCH & RELATED Senior/Key Person Profile (Expanded)

PROFILE - Project Director/Principal Investigator

Prefix: Dr. First Name*: Allen Middle Name  Last Name*: Heinemann

Position/Title*: Director

Organization Name*: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab

Department:

Division:

Street1*:

Street2:

City*:

County:

State*:

Province:

Country*: USA: UNITED STATES

Zip / Postal Code*:

Suffix: Ph.D

Phone Number*:  Fax Number: 

E-Mail*: 

Credential, e.g., agency login: 

Project Role*:  PD/PI Other Project Role Category: 

Degree Type:  Ph.D Degree Year:  1982

Attach Biographical Sketch*: File Name: 1235-Heinemann_Bio.pdf

Attach Current & Pending Support: File Name:

Tracking Number: GRANT12670047 Page 15

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
Contact PD/PI: Heinemann, Allen

PROFILE - Senior/Key Person

Prefix: Dr. First Name*: Leora Middle Name R. Last Name*: Cherney

Position/Title*: Scientific Chair, Think & Speak Lab, SRALAB

Organization Name*: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab

Department:

Division:

Street1*:

Street2:

City*:

County:

State*:

Province:

Country*: USA: UNITED STATES

Zip / Postal Code*:

Suffix: Ph.D

Phone Number*:  Fax Number: 

E-Mail*: 

Credential, e.g., agency login

Project Role*:  PD/PI Other Project Role Category: 

Degree Type:  Ph.D Degree Year:  1990

Attach Biographical Sketch*: File Name: 1236-Cherney.pdf

Attach Current & Pending Support: File Name:

PROFILE - Senior/Key Person

Prefix: Dr. First Name*: Andrea Middle Name  Last Name*: Domenighetti

Position/Title*: Research Scientist

Organization Name*: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab

Department:

Division:

Street1*:

Street2:

City*:

County:

State*:

Province:

Country*: USA: UNITED STATES

Zip / Postal Code*:

Suffix: 

Phone Number*:  Fax Number: 

E-Mail*: 

Credential, e.g., agency login: 

Project Role*:  Co-Investigator Other Project Role Category: 

Degree Type:  Ph.D Degree Year: 

Attach Biographical Sketch*: File Name: 1237-Domenighetti_Bio.pdf

Attach Current & Pending Support: File Name:

Tracking Number: GRANT12670047 Page 16

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
Contact PD/PI: Heinemann, Allen

PROFILE - Senior/Key Person

Prefix: Dr. First Name*: Marwan Middle Name N. Last Name*: Baliki

Position/Title*: Research Scientist

Organization Name*: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab

Department:

Division:

Street1*:

Street2:

City*:

County:

State*:

Province:

Country*: USA: UNITED STATES

Zip / Postal Code*:

Suffix: 

Phone Number*:  Fax Number: 

E-Mail*: 

Credential, e.g., agency login: 

Project Role*:  Co-Investigator Other Project Role Category: 

Degree Type:  Ph.D Degree Year:  2009

Attach Biographical Sketch*: File Name: 1238-Baliki_Bio.pdf

Attach Current & Pending Support: File Name:

PROFILE - Senior/Key Person

Prefix: Dr. First Name*: Elliot Middle Name J. Last Name*: Roth

Position/Title*: Co-Medical Director

Organization Name*: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab

Department: Brian Innovation Center

Division:

Street1*:

Street2:

City*:

County:

State*:

Province:

Country*: USA: UNITED STATES

Zip / Postal Code*:

Suffix: 

Phone Number*:  Fax Number: 

E-Mail*: 

Credential, e.g., agency login: 

Project Role*:  Co-Investigator Other Project Role Category: 

Degree Type:  M.D. Degree Year:  1982

Attach Biographical Sketch*: File Name: 1239-Roth_Bio.pdf

Attach Current & Pending Support: File Name:

Tracking Number: GRANT12670047 Page 17

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
Contact PD/Pl: Heinemann, Allen 

PROFILE - Senior/Key Person 

Prefix: First Name*: Linda Middle Name W. Last Name*: Foster Suffix: 

Position/Title*: Research Coordinator 

Organization Name*: Rehabilitation Institute of Chgo dba Shirley Ryan Abilitylab 

Department: 

Division: 

Street1*: 

Street2: 

City*: 

County: 

State*: 

Province: 

Country*: USA: UNITED STATES 

Phone 

Zip/ Postal 

Number*: 

Code*: -

Fax Number: 

E-Mail*: 

Credential, e.g., agency login: 

Project Role*: Co-Investigator Other Project Role Category: 

Degree Type: M.S Degree Year: 1987 

Attach Biographical Sketch*: File Name: 1240-Foster_Bio .pdf 

Attach Current & Pending Support: File Name: 

PROFILE - Senior/Key Person 

Prefix: Dr. First Name*: Allan Middle Name J. Last Name*: Kozlowski Suffix: Ph.D 

Position/Title*: Assistant Professor 

Organization Name*: 

Department: 

Division: 

Street1*: 

Street2: 

City*: 

Mary Free Bed Rehabilitation Hospital 

Province: 

County: 

Country*: 

State*: -

USA: UNITED STATES 

Phone 

Zip/ Postal 

Number*: 

Code*: -

Fax Number: 

E-Mail*: 

Credential, e.g., agency login: 

Project Role*: Co-Investigator Other Project Role Category: 

Degree Type: Ph.D Degree Year: 2010 

Attach Biographical Sketch*: File Name: 1241-Kozlows ki_Bio.pdf 

Attach Current & Pending Support: File Name: 

Page 18 

Track Funding Opportunity Number: PA 18 287 . Received Date: ing Number: GRANT12670047 

2018 07 05T15:37:27.000 04:00 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

BIOGRAPHICAL SKETCH 

Provide the following information for the Senior/key personnel and other significant contributors. 

Follow this format for each person. DO NOT EXCEED FIVE PAGES. 

NAME: Allen W. Heinemann, Ph.D. 

eRA COMMONS USER NAME: 

POSITION TITLE: Professor, Physical Medicine and Rehabilitation, Feinberg School of Medicine, Northwestern University 

Director, Center for Rehabilitation Outcomes Research, Shirley Ryan AbilityLab (formerly the Rehabilitation Institute of Chicago) 

EDUCATION/TRAINING 

INSTITUTION AND LOCATION DEGREE Completion Date FIELD OF STUDY 

Washington State University, Pullman, WA 

University of Kansas, Lawrence, KS 

University of Kansas, Lawrence, KS 

BS 

MA 

PhD 

05/1977 

05/1980 

08/1982 

Psychology 

Psychology 

Psychology 

A. Personal Statement 

As Director of the Center for Rehabilitation Outcomes Research at the Shirley Ryan AbilityLab (formerly the 

Rehabilitation Institute of Chicago), I have the requisite expertise and experience to serve as co-PI of this application. Since 1985, I have led the AbilityLab’s Center for Rehabilitation Outcomes Research, a health services research program with a focus on outcomes measurement. Our work included the original Rasch analysis of the Functional Independence Measure that demonstrated it is comprised of reliable subscores of motor 

and cognitive function. Other outcomes measurement-related funded projects led to the development of the 

Quality of Life in Neurological Disorders (NeuroQoL) measurement system, the TBI Quality of Life Measurement System, the Orthotics Prosthetics User Survey, the Patient-Reported Outcome Measurement System 

(PROMIS), the Spinal Cord Injury Functional Index (SCI-FI), and the Substance Abuse for Vocational Rehabilitation Screener (SAVRS), among others. I collaborated with Dr. Cherney on aphasia-related projects that generated three publications. I serve as co-PI of the Midwest Regional SCI Model System and served as co-I of 

the Midwest Regional TBI Model System from 2008-12; I consult with the currently-funded TBI Model Systems’ 

Global Outcome Measures Module. I provide leadership for Northwestern University’s integrated post-doctoral 

fellowship program in Health Services and Outcomes Research. Our most recent RRTC led to the development of the Rehabilitation Measures Database, an on-line compendium of systematic reviews of outcome instruments that are suitable for research and clinical applications. My research interests focus on health services research, psychosocial aspects of rehabilitation including substance abuse, and measurement issues in 

rehabilitation. The peer-reviewed publications to which I contributed were the result of funding from NIH, NIDILRR, (RRTCs on rehabilitation outcome measurement, DRRP on health services research, ARRT), the Patient-Centered Outcomes Research Institute, Centers for Disease Control, the Social Security Administration, 

the Substance Abuse and Mental Health Services Administration, among others. I have been elected a fellow 

of the American Congress of Rehabilitation Medicine and the American Psychological Association (Division 

22). As co-Editor-in-Chief for the Archives of Physical Medicine and Rehabilitation, I have a unique opportunity 

to evaluate and provide leadership on this multisite study of aphasia recovery. 

Per Scopus, my 337 publications have generated 8,347 citations and an h-index of 47 (June 22, 2018). 

B. Positions and Honors 

Positions and Employment 

1982-1985 Assistant Professor, Psychology, Illinois Institute of Technology, Chicago IL 

1985-1987 Assistant Professor, PM&R, Northwestern University Feinberg School of Medicine, Chicago IL 

1985-1988 Assistant Director, Center for Rehabilitation Outcomes Research, RIC, Chicago, IL 

1988-1996 Associate Professor, PM&R, Northwestern University Feinberg School of Medicine, Chicago IL 

1988-present Director, Center for Rehabilitation Outcomes Research, RIC, Chicago, IL 

1996-present Professor, PM&R, Northwestern University Feinberg School of Medicine, Chicago IL 

1996-present Senior Faculty Fellow, Center for Healthcare Studies, Northwestern University Feinberg School 

of Medicine, Chicago IL 

1996-present Associate Director of Research, Rehabilitation Institute of Chicago, Chicago, IL 

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Other Experience and Professional Memberships 

1999-2004 Behavioral Medicine: Interventions and Outcomes study section member, NIH, Center for Scientific Review, Department of Health and Human Services 

2003- 2007 Member, Function, Integration and Rehabilitation Sciences Subcommittee, National Institute of 

Child Health and Human Development Initial Review Group, NICHD 

2004-2005 Member, Model Systems Review Panel, National Institute on Disability and Rehabilitation Research 

2004-2005 President, Division 22 (Rehabilitation Psychology), American Psychological Association 

2004-2005 President, American Congress on Rehabilitation Medicine 

2005 Member, Committee to Study the Listing of Impairments and Agency Access to Medical Expertise in the Social Security Disability Determination Process, National Academy of Medicine 

2005 Member, Medicare Payment Advisory Commission (MedPAC) Panel on Post-Acute Care 

2005 Chair, Planning Meeting Board on Military and Veterans Health, Medical Follow-Up Agency, National Academy of Medicine 

2005-2013 Secretary/Treasurer, Foundation for Rehabilitation Psychology (Board service continues) 

2006-2013 Member, Board of Scientific Counselors, National Center for Injury Prevention and Control, CDC 

2009-present Member, Standing Committee of Medical Experts to Assist Social Security on Disability Issues, 

National Academy of Medicine 

2013-present Co-Editor-in-Chief, Archives of Physical Medicine and Rehabilitation 

Honors 

1998 Harold Yuker Award for Research Excellence (outstanding article in Rehabilitation Psychology) 

with D Hawkins for “Substance abuse and medical complications following spinal cord injury,” 

43, 219-231 

1998 Fellow, American Psychological Association, Division of Rehabilitation Psychology 

2000 Roger Barker Distinguished Career Award, Division 22 (Rehabilitation Psychology), APA, “in 

recognition of outstanding lifetime contributions to the science of rehabilitation psychology” 

2003 Essie Morgan Excellence Award, American Association of Spinal Cord Injury Psychologists and 

Social Workers 

2004 Harold Yuker Award for Research Excellence (outstanding article appearing in Rehabilitation 

Psychology) with NA Doninger for “Predicting community integration following TBI with health 

and cognitive status measures,” 48, 156-166 

2005 Fellow, American Congress of Rehabilitation Medicine 

2009 Anthony M. Solomon Lecturer in Clinical Neuropsychology, Rusk Institute of Rehabilitation Medicine, New York, NY 

2013 John S. Coulter Lecturer, American Congress of Rehabilitation Medicine 

2017 Dembo-Wright Award Lecturer, Rehabilitation Psychology Conference 

C. Contribution to Science 

1. Evaluating the effectiveness and efficiency of rehabilitation services is a major focus of my research. This 

topic reflects the major financing changes affecting the medical rehabilitation industry over the past several 

decades. Fee-for-service payment has been replaced by a prospective payment system in most post-acute 

care settings. Providers who can organize services to achieve maximum benefit at minimum cost should 

thrive, while others that fail to assess the needs and rehabilitation potential of the people they serve will not. 

I sought opportunities with the Uniform Data System for Medical Rehabilitation, the largest data management service for rehabilitation hospitals, to describe and predict the functional improvement of children and 

adults, which resulted in a series of publications. 

a) Heinemann A. Measuring effectiveness of psychological services during medical rehabilitation. 

Rehabilitation Psychology. 1997;42(2):148. 

b) Chen CC, Heinemann AW, Granger CV, Linn RT. Functional gains and therapy intensity during 

subacute rehabilitation: a study of 20 facilities. Arch Phys Med Rehabil. 2002;83(11):1514-1523. 

PMID: 12422318. 

c) Heinemann AW, Roth EJ, Rychlik K, Pe K, King C, Clumpner J. The impact of stroke practice 

guidelines on knowledge and practice patterns of acute care health professionals. J Eval Clin Pract. 

2003;9(2):203-212. PMID: 12787184. 

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d) Chen CC, Heinemann AW, Bode RK, Granger CV, Mallinson T. Impact of pediatric rehabilitation 

services on children's functional outcomes. The American journal of occupational therapy : official 

publication of the American Occupational Therapy Association. 2004;58(1):44-53. PMID: 14763635 

2. Early in my academic career, I came to appreciate that instruments developed using item response theory 

methods offer substantial benefits over classical test theory methods. I sought and received funding from 

the CDC and NIDILRR to develop Rasch model-based, interval-level function measures that have greater 

precision and sensitivity than ordinal-level instruments. I helped rehabilitation researchers appreciate that 

they can diagnose misfitting items and test takers, evaluate rating scale properties and item set dimensionality, and create easy-to-administer key forms that allow scoring in the clinic without a computer. My collaboration with Ben Wright and Michael Linacre at the University of Chicago and Carl Granger at SUNY Buffalo 

led to a series of publications that demonstrated the Functional Independence Measure can form measures 

of motor and cognitive function. Subsequently, I have worked with many colleagues in the U.S. and overseas to evaluate established and develop new instruments. 

a) Heinemann AW, Linacre JM, Wright BD, Hamilton BB, Granger C. Relationships between 

impairment and physical disability as measured by the functional independence measure. Arch Phys 

Med Rehabil. 1993;74(6):566-573. PMID: 8503745. 

b) Granger CV, Hamilton BB, Linacre JM, Heinemann AW, Wright BD. Performance profiles of the 

functional independence measure. Am J Phys Med Rehabil. 1993;72(2):84-89. PMID: 8476548. 

c) Linacre JM, Heinemann AW, Wright BD, Granger CV, Hamilton BB. The structure and stability of the 

Functional Independence Measure. Arch Phys Med Rehabil. 1994;75(2):127-132. PMID: 8311667. 

d) Heinemann AW, Harvey RL, McGuire JR, Ingberman D, Lovell L, Semik P, Roth EJ. Measurement 

properties of the NIH Stroke Scale during acute rehabilitation. Stroke. 1997;28(6):1174-1180. PMID: 

9183346. 

3. Participation in activities of choice is a long-term goal of rehabilitation service providers and valued by persons living with disabilities. Employment, volunteering, leisure and recreation, and activities with family and 

friends are common goals. How to characterize participation outcomes in more sophisticated ways than 

counting the frequency of engagement or time spent in activities has challenged rehabilitation researchers. 

Myriad measures have been developed for populations with intellectual, psychiatric, sensory, and physical 

disabilities, but few have used contemporary measurement approaches. Thus, we lack a lingua franca to 

describe the participation benefits of rehabilitation. I worked with Spinal Cord and Traumatic Brain Injury 

Model Systems collaborators and others to organize an international conference that defined optimal approaches to measuring participation outcomes. 

a) Whiteneck GG, Dijkers MP, Heinemann AW, Bogner JA, Bushnik T, Cicerone KD, Corrigan JD, Hart 

T, Malec JF, Millis SR. Development of the Participation Assessment with Recombined Tools-Objective for Use After Traumatic Brain Injury. Archives of Physical Medicine and Rehabilitation. 

2011;92(4):542-551. PMID: 21367393 

b) Wong AW, Heinemann AW, Wilson CS, Neumann H, Fann JR, Tate DG, Forchheimer M, Richards 

JS, Bombardier CH. Predictors of participation enfranchisement after spinal cord injury: the mediating 

role of depression and moderating role of demographic and injury characteristics. Arch Phys Med Rehabil. 2014;95(6):1106-1113. PMID: 24561060 

4. The lived experience of disablement in community settings, particularly quality of life, is a recurring theme of 

my work. It is important to look beyond the brief period of inpatient or outpatient rehabilitation services to a 

life in the community. Two RRTCs explored the precursors and consequences of impairment and functional 

limitations on the quality of life of adults with physical disabilities. My collaborators and I developed a measure of participation, the Community Participation Indicators, during the first RRTC and a set of environmental factor measures using item response theory methods during the second RRTC. This work built on my 

early involvement in the PROMIS network, which led to development of quality of life measures for persons 

with neurologic disorders (NeuroQoL) and then for traumatic brain injury and spinal cord injury. 

a) Heinemann AW, Magasi S, Hammel J, Carlozzi NE, Garcia SF, Hahn EA, Lai JS, Tulsky D, Gray 

DB, Hollingsworth H, Jerousek S. Environmental Factors Item Development for Persons with Stroke, 

Traumatic Brain Injury and Spinal Cord Injury. Arch Phys Med Rehabil, 96(4) 589-595 DOI: 

http://dx.doi.org/10.1016/j.apmr.2013.11.024. PMCID: PMC4593403. 

b) Heinemann AW, Magasi S, Bode RK, Hammel J, Witeneck GG, Bogner J, Corrigan JD. Measuring 

enfranchisement: importance of and control over participation by people with disabilities. Arch Phys 

Med Rehabil. 2013;94(11):2157-2165. PMID: 23769764. 

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c) Tulsky DS, Kisala PA, Lai JS, Carlozzi N, Hammel J, Heinemann AW. Developing an Item Bank to 

Measure Economic Quality of Life for Individuals with Disabilities. Arch Phys Med Rehabil. 

2014.PMID: 24736400 

d) Garcia SF, Hahn EA, Magasi S, Lai JS, Semik P, Hammel J, Heinemann AW. Development of SelfReport Measures of Social Attitudes that Act as Environmental Barriers and Facilitators for People 

with Disabilities. Arch Phys Med Rehabil, 96(4) 596-603 DOI: 

http://dx.doi.org/10.1016/j.apmr.2014.06.019. PMCID: PMC4297740. 

5. Research capacity building has been an important focus of my professional activities since I competed successfully for a rehabilitation-focused, health services research-training grant in 1998. Since then, I have renewed the 5-year Advanced Rehabilitation Research Training award from NIDILRR on three occasions, in 

synchrony with renewal of a T32 award from AHRQ led by Jane Holl, Director, Center for Healthcare Studies and Director, Center for Education in Health Sciences in Northwestern’s Institute for Public Health and 

Medicine. Because of this success, I was invited by NIDILRR staff to serve as keynote speaker at two national capacity-building conferences. I have served as a keynote speaker on research training topics at the 

Rehabilitation Medicine Summit sponsored by the Foundation for PM&R in 2005 and a National Center for 

the Dissemination of Disability Research sponsored Task Force on Systematic Review and Guidelines. 

a) Bode R, Heinemann AW, Chen D. Measuring the impairment consequences of spinal cord injury. 

American Journal of Physical Medicine & Rehabilitation. 1999;78(6):582-594. PMID:10574175. 

b) Deutsch A, Granger C, Fiedler R, DeJong G, KaneRL, Ottenbacher KJ, Heinemann AW, Naughton 

JP, Trevisan M. Outcomes and reimbursement of inpatient rehabilitation facilities and subacute 

rehabilitation programs for medicare beneficiaries with hip fracture. Medical Care. 2005;43(9):892-

901. PMID: 16116354. 

c) Mallinson TR, Manheim LM, Almagor O, Demark HM, Heinemann AW. Trends in the supply of 

inpatient rehabilitation facilities services: 1996 to 2004. Arch Phys Med Rehabil. 2008;89(11):2066-

2079. PMID: 18996234 

d) Kozlowski AJ, Heinemann AW. Using individual growth curve models to predict recovery and activities of daily living after spinal cord injury: an SCIRehab project study. Arch Phys Med Rehabil. 

2013;94(4 Suppl):S154-164 e151-154. PMID: 23527771 

Complete List of Published Work 

https://www.ncbi.nlm.nih.gov/sites/myncbi/allen.heinemann.1/bibliography/47569747/public/?sort=date&direction=descending 

D. Research Support 

Active Projects 

DOD W81XWH-17-1-0157 (Heinemann) 9/1/17-8/31/19 

Evaluating the Utilization and Efficiency of Wearable Exoskeletons for SCI Rehabilitation 

Goal of this application is to acquire information that will guide patient evaluation strategies, training strategies, 

and clinical decision plans to enable the safe and effective use of robotic exoskeletons to enhance mobility in 

Veterans and civilians with SCI. 

NIDILRR 90SI5022-01-00 (Chen/Heinemann) 9/30/16-9/29/21 

The Midwest Regional Spinal Cord Injury Model System 

The goal of this project is to investigate the effect of acute intermittent hypoxia alone and in combination with 

high-intensity task-specific training on upper extremity function in individual with chronic incomplete cervical 

SCI. 

DOD/CDMRP W81XWH-16-1-0788 (Heinemann) 9/30/16-9/29/19 

Enhancing quality of orthotic services with process and outcome information 

Goal of this project is to help the Defense Health Program improve understanding of the benefits of orthotic 

devices, treatments, and rehabilitation strategies. 

Craig H. Neilsen Foundation (Heinemann) 5/1/16 – 4/30/19 

Implementing SCI-QOL into Clinical Practice to Enhance Patient Engagement 

This application adapts and evaluates implementation strategies designed to promote routine use of PROs in 

SCI rehabilitation. 

Biosketches Page 22
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

NIDILRR 90DP0025-01-00 (Boninger) 10/01/12-9/29/18 

Collaboration on Mobility Training (COMIT) Role: Co-Investigator 

Goal of the project is to evaluate effectiveness of training in wheeled mobility at multiple sites 

Craig H. Neilsen Foundation (Kisala) 4/30/16-4/30/19 

Clinical Adaption of the SCI-QOL Psychosocial Measures Role: Site PI 

Goal of this project is to improve psychosocial outcomes such as emotional well-being and quality of life in individuals with SCI. 

NIDILRR H133P130013 (Heinemann) 10/1/13-9/30/18 

Advanced Rehabilitation Research Training in Health Services Research 

Goal of this project/Specific Aims: The goal of this project is to provide an integrated, interdisciplinary, collaborative training program for early career scholars focusing on rehabilitation-related health services research. 

Recently Completed Projects 

NIDILRR 90SI5009-02-00 (Chen/Heinemann) 10/01/11 – 09/29/17 

Midwest Regional Spinal Cord Injury Care System 

The goals of MRSCICS are to advance the outcomes of our previous Model Systems research, continue to 

study the effectiveness of innovative treatment strategies; and evaluate the benefits of a well-designed, comprehensive, coordinated, interdisciplinary continuum of care that lead to improved outcomes for persons with 

SCI. 

AHRQ 5K12HS023011-01 (Cella) 9/1/14-7/31/17 

Northwestern University Patient-Centered Intervention and Engagement Training Role: Mentor 

Goal of this project is to provide a clear path to independence beginning with an innovative idea, that is, to 

identify the global problem of adherence to the attributes that are associated with adherence, apply preference 

weights tot the relative importance of these attributes using choice modeling, and build patient-centered physical activity recommendations based on an individual’s preferred attributes. 

CD-12-11-4201 Supplement (Heinemann) 9/01/13 – 07/31/17 

Patient Centered Outcomes Research Institute (PCORI) 

The goal of this project is evaluate the feasibility of developing quality measures from patient-reported outcome 

measures. 

Dept. of Veteran Affairs VA69D-15-C-0107 (Heinemann) 12/01/2014-11/30/2015 

Functional Needs Assessment in Persons with SCI 

Goal: Consult on measurement and outcome issues in career development award 

NIH R24HD065702 (Ottenbacher) 7/01/2010-5/31/2015 

Univ. of Texas Medical Branch (UTMB) 

Center for Rehabilitation Research Using Large Datasets Role: Co-I 

Goal: Provide mentoring services to scientists seeking to improve knowledge of how to use large datasets 

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OMB No. 0925-0001/0002 (Rev. 08/12 Approved Through 8/31/2015) 

BIOGRAPHICAL SKETCH 

Provide the following information for the Senior/key personnel and other significant contr butors. 

Follow this format for each person. DO NOT EXCEED FIVE PAGES. 

NAME: Leora R. Cherney 

eRA COMMONS USER NAME (credential, e.g., agency login): 

POSITION TITLE: Professor, Physical Medicine and Rehabilitation & Communication Sciences and Disorders; 

Scientific Chair, Think & Speak Lab, Shirley Ryan AbilityLab 

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, 

include postdoctoral training and residency training if applicable. Add/delete rows as necessary.) 

INSTITUTION AND LOCATION 

DEGREE 

(if 

applicable) 

Completion 

Date 

MM/YYYY 

FIELD OF STUDY 

University of Cape Town, Cape Town, South Africa 

Northwestern University, Evanston, IL 

Northwestern University, Evanston, IL 

B.A. 

M. A. 

Ph.D. 

1978 

1980 

1990 

Logopaedics 

Speech-Language Pathol 

Speech-Language Pathol 

A. Personal Statement 

I am well-prepared to serve as Co-PI on this R01 submission. My professional research career of 35+ years 

has focused on communication problems associated with stroke, with expertise in the area of aphasia. I 

founded the Aphasia Center at the Rehabilitation Institute of Chicago in 2001, and the past 15+ years have 

been devoted specifically to developing innovative treatments for aphasia and evaluating their efficacy. I have 

a continuous record as PI on federal, private, and industry-sponsored research grants, including an NIH R01 

and five NIDILRR field-initiated studies. The various topics of my research include: studies assessing the 

delivery of treatment using novel software with a digital therapist given face-to-face and over the internet; a 

clinical trial evaluating the addition of a pharmacologic agent, L-dopa, to behavioral language therapy; and 

studies examining how acquisition can be optimized and forgetting minimized by manipulating various 

treatment parameters that affect how people with aphasia learn. I led a study examining the effects of epidural 

cortical stimulation combined with speech-language therapy for aphasia and have held an R21 evaluating online tDCS combined with speech therapy in a small group of subjects with aphasia. I have a demonstrated 

record of successful, productive and cutting-edge research in the area of aphasia treatment that includes both 

single-subject research studies and randomized clinical trials, and that measures outcomes relative to both 

impairment and participation levels. I have worked collaboratively with Drs. Heinemann, Kocherginsky, and 

Baliki, and have published in the area of aphasia with each of these colleagues. I have the research expertise, 

administrative skills, and clinical knowledge of rehabilitation, aphasia and outcomes to ensure the successful 

completion of this multi-site longitudinal study. 

Cherney, L. R., Babbitt, E. M., Semik, P., & Heinemann, A. W. (2011). Psychometric Properties of the 

Communication Confidence Rating Scale for Aphasia (CCRSA): Phase 1. Topics in Stroke Rehabilitation, 

18, 352-360. doi: 10.1310/tsr1804-352 

Cherney, L. R., Kaye, R. C., & van Vuuren, S. (2014). Acquisition and maintenance of scripts in aphasia: a 

comparison of two cuing conditions. Am J Speech Lang Pathol, 23(2), S343-360. 10.1044/2014 AJSLP-13-

0097 

Babbitt, E. M., Worrall, L. E., & Cherney, L. R. (2016). Intensive Comprehensive Aphasia Programs (ICAP): 

Who benefits? Topics in Language Disorders. 36, 168-184. 10.1097/TLD.0000000000000089 

Lee, J. B., Kocherginsky, M., & Cherney, L. R. (2018) Attention in Individuals with Aphasia: Performance on 

the Conners’ Continuous Performance Test-2nd Edition. Neuropsychological Rehabilitation. Published 

online: 18 Apr 2018. doi.org/10.1080/09602011.2018.1460852 

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B. Positions and Honors 

1981-1986 Staff Speech Language Pathologist, Department of Communicative Disorders, 

Rehabilitation Institute of Chicago, Chicago, Illinois. 

1986- 1996 Clinical Researcher, Communicative Disorders, Rehabilitation Institute of Chicago 

1987-1988 Consultant/Clinical Instructor, Physical Medicine and Rehabilitation, Chicago Neurosurgical 

Center, Chicago, IL 

1988-89, 2000-02 Instructor, Department of Communicative Disorders, Northern Illinois University, DeKalb, IL 

1990-1996 Assistant Professor, Physical Medicine and Rehabilitation, Northwestern University Medical 

School, Chicago, IL 

1992, 1994-1998 Adjunct, Communication Sciences and Disorders, Northwestern University, Evanston, IL 

1996-2002 Clinical Educator, Center for Clinical Excellence, Rehabilitation Institute of Chicago, 

Chicago, IL 

1996-2009 Associate Professor, Physical Medicine and Rehabilitation, Northwestern University Medical 

School, Chicago, IL 

1999-2010 Associate Professor, Communication Sciences & Disorders, Northwestern University, 

Evanston, Illinois. 

2002-2017 Research Scientist/Senior Research Scientist, Rehabilitation Institute of Chicago, Chicago, 

IL 

2009-present Professor, Physical Medicine and Rehabilitation, Northwestern University Medical School, 

Chicago, IL 

2011-present Professor, Communication Sciences and Disorders, Northwestern University, Evanston, IL 

2017-present Scientific Chair & Coleman Foundation Chair, Think & Speak, Shirley Ryan AbilityLab, 

Chicago, IL 

Board Certified – Academy of Neurologic Communication Disorders and Sciences 

Fellow, American Speech-Language-Hearing Association; Fellow and Honors, Illinois Speech-Language 

Hearing Association. 

Editorial Board, Aphasiology, Archives of Physical Medicine & Rehabilitation, Topics in Stroke Rehabilitation. 

Veterans Administration grant review panel: Sensory Systems and Communication, August, 2011, March 

2012, August 2012, February 2013. 

National Institutes of Health Grant Review Panels: December 2013, March 2014, January & September 2015. 

2017 ACRM / National Stroke Association Excellence in Post-Acute Stroke Award. Recognizes outstanding 

clinical, intellectual, and service contributions in the area of stroke. 

C. Contributions to Science 

1. The literature on upper limb recovery after focal cortical injury in both animal models and human stroke 

survivors suggests that high intensity rehabilitation is necessary to induce neuroplasticity. The extent to 

which these findings translate to the treatment of aphasia is not clear. In 2008 and 2010, my colleagues 

and I completed systematic reviews of the literature and concluded that intensive treatment was favored 

over less intensive treatment, but differences in the chronicity of the aphasia (acute versus chronic) and the 

targeted level of the outcome measure (impairment versus activity/participation) influenced findings. In my 

own research, we have demonstrated neurophysiological changes on fMRI following treatment and have 

found a positive correlation between treatment intensity and outcomes, a topic that many researchers 

continue to investigate with regards to the treatment of aphasia. 

a. Cherney, L. R. & Small, S. L. (2006). Task-dependent changes in brain activation following 

therapy for nonfluent aphasia: Discussion of two individual cases. Journal of the International 

Neuropsychological Society, 12, 828-842. doi.org/10.1017/S1355617706061017 

b. Cherney, L. R., Patterson, J., Raymer, A., Frymark, T., & Schooling, T. (2008). Evidence-Based 

Systematic Review: Effects of Intensity of Treatment and Constraint-Induced Language Therapy for 

Individuals with Stroke-Induced Aphasia. Journal of Speech, Language, and Hearing Research, 51, 

1282-1299. doi: 10.1044/1092-4388(2008/07-0206) 

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2. 

3. 

c. Lee, J. B., Kaye, R. C., Cherney, L. R. (2009). Conversational script performance in adults with 

non-fluent aphasia: Treatment intensity and aphasia severity. Aphasiology, 23(7), 885-897.

10.1080/02687030802669534 

d. Cherney, L. R. (2012). Aphasia treatment: Intensity, dose parameters, and script training. 

International Journal of Speech-Language Pathology, 14, 424-31.

doi.org/10.3109/17549507.2012.686629 

Researchers are investigating ways to enhance treatment outcomes in aphasia rehabilitation. Cortical 

stimulation may be an adjuvant to speech and language treatment to facilitate neuroplasticity. There 

are several methods of delivering cortical brain stimulation to modulate cortical excitability. I conducted 

the only controlled study evaluating targeted epidural cortical delivered concurrently with intensive 

speech–language therapy for treatment of chronic non-fluent aphasia. Six weeks of epidural cortical 

stimulation to the ipsilesional premotor cortex in combination with speech and language treatment was 

feasible, safe, and promoted increased improvements as compared to the control group that received 

speech and language treatment without cortical stimulation. This study has informed other studies that 

investigate less invasive methods of cortical stimulation. 

a. Cherney, L. R., Erickson, R. K., & Small, S. L. (2010). Epidural Cortical Stimulation as Adjunctive 

Treatment for Non-Fluent Aphasia: Preliminary Findings. Journal of Neurology, Neurosurgery, and 

Psychiatry, 81(9), 1014-1021. 10.1136/jnnp.2009.184036 

b. Cherney, L. R., Harvey, L. R., Babbitt, E. M., Hurwitz, R., Kaye, R. C., Lee, J. B., & Small, S. L. 

(2012). Epidural cortical stimulation and aphasia therapy. Aphasiology, 26(9), 1192-1217. 

10.1080/02687038.2011.603719 

c. Cherney, L. R. (2016). Epidural Cortical Stimulation as Adjunctive Treatment for Nonfluent 

Aphasia: Phase 1 Clinical Trial Follow-up Findings. Neurorehabil Neural Repair, 30(2), 131-42. 

doi.org/10.1177/1545968315622574 

d. Cherney, L. R., Babbitt, E. M., Hurwitz, R., Rogers, L. M., Wang, X., Harvey, R. L., Parrish, T., & 

Stinear, J. (2013). Transcranial Direct Current Stimulation (tDCS) and Aphasia: The Case of Mr. 

C. Topics in Stroke Rehabilitation, 20(1).5-21. doi.org/10.1310/tsr2001-5 

Since it appears that better outcomes result from more intensive treatment, I have been investigating 

how we can leverage technology to provide more intensive and cost-effective treatment. I have led an 

initiative to develop and computerize several treatment approaches and we are investigating their 

efficacy. Results to date have been positive. Participants are able to practice intensively with improved 

outcomes. The scientific impact has been two-fold – our studies have stimulated interest in computerbased treatment in general, and more specifically, there has been increased attention to the particular 

treatments that have been developed, with further investigation of these treatments by others. 

a. Cherney, L. R., Halper, A. S., Holland, A. L. & Cole, R. (2008). Computerized Script Training for 

Aphasia: Preliminary Results. American Journal of Speech-Language Pathology, 17, 19-34. 

10.1044/1058-0360(2008/003) 

b. Mannheim, L., Halper, A. S. & Cherney, L. R. (2009). Patient-Reported Changes in 

Communication after Computer-Based Script Training for Aphasia. Archives of Physical Medicine 

and Rehabilitation, 90(4), 623-627. 10.1016/j.apmr.2008.10.022 

c. Cherney, L. R. (2010). Oral Reading for Language in Aphasia (ORLA): Evaluating the Efficacy of 

Computer-Delivered Therapy in Chronic Nonfluent Aphasia. Topics in Stroke Rehabilitation, 17(6), 

423-431. 10.1310/tsr1706-423 

d. Kaye, R. C. & Cherney, L. R. (2016). Script templates: A practical approach to script training in 

aphasia. Topics in Language Disorders, 2016; 36:136-153. doi: 10.1097/TLD.0000000000000086 

More recently, there has been an emphasis on patient-reported outcomes. I led the development of a 

patient-reported outcome scale that addresses not just communication in persons with aphasia, but 

4. 

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communication confidence. This construct, associated with self-efficacy, had not previously been 

discussed in the aphasia literature. The assessment tool, the Communication Confidence Rating Scale 

for Aphasia (CCRSA), was developed and validated using Rasch Analysis methods. It is currently 

being used by researchers in the United States, Canada, England, and Australia. 

a. Babbitt, E.M. & Cherney, L. R. (2010). Communication Confidence in Persons with Aphasia. 

Topics in Stroke Rehabilitation, 17(3), 197-206. 10.1310/tsr1703-214 

b. Cherney, L. R., Babbitt, E. M., Semik, P., & Heinemann, A. W. (2011). Psychometric Properties 

of the Communication Confidence Rating Scale for Aphasia (CCRSA): Phase 1. Topics in 

Stroke Rehabilitation, 18, 352-360. doi: 10.1310/tsr1804-352 

c. Babbitt, E.M., Heinemann, A. W., Semik, P., & Cherney, L. R. (2011). Psychometric Properties 

of the Communication Confidence Rating Scale for Aphasia (CCRSA): Phase 2. Aphasiology, 

25, 727-735. doi.org/10.1080/02687038.2010.537347 

5. The intensive comprehensive aphasia program (ICAP) is a service-delivery model that, based on the 

notion of neuroplasticity, provides intensive treatment to persons with aphasia. At the same time, it 

addresses all domains of the ICF including the impairment and the activity/participation domains. 

There has been relatively little research regarding the efficacy, effectiveness and cost-effectiveness of 

the ICAP, although more and more clinical programs, nationally and internationally, are offering such 

services. Since 2011, I have spear-headed an initiative that introduced its acronym, defined its 

characteristics, and identified research gaps and recommendations for future investigations. This has 

resulted in several ongoing studies within the scientific community, including an RCT on which I am 

currently the PI. 

a. Rose, M. L., Cherney, L. R., & Worrall, L. E. (2013). Intensive Comprehensive Aphasia Programs: 

An international survey of practice. Topics in Stroke Rehabilitation, 20, 379-387. 10.1310/tsr2005-

379 

b. Babbitt, E. M., Worrall, L. E., & Cherney, L. R. (2013). Clinician perspectives of an Intensive 

Comprehensive Aphasia Program. Topics in Stroke Rehabilitation, 20, 398-408. 10.1310/tsr2005-398 

c. Hula, W. D., Cherney, L. R., & Worrall, L. E. (2013). Setting a research agenda to inform Intensive 

Comprehensive Aphasia Programs. Topics in Stroke Rehabilitation, 20, 409-420. 10.1310/tsr2005-

409 

d. Babbitt, E. M., Worrall, L., & Cherney, L. R. (2015). Structure, processes, and retrospective 

outcomes from an intensive comprehensive aphasia program. American Journal of Speech 

Language Pathology, 24(4), S854-63. 10.1044/2015 AJSLP-14-0164 

My bibliography: 

http://www.ncbi.nlm.nih.gov/sites/myncbi/leora.cherney.1/bibliography/43924728/public/?sort=date&direction=ascending and 

http://scholar.google.com/citations?user=-UgIYgkAAAAJ&hl=en 

D. Research Support 

ACTIVE 

The Carl & Marilynn Thoma Foundation (Cherney) 3/01/2018 – 2/28/2023 

Brain Network Properties and Intensive Aphasia Therapy 

This project uses resting state fMRI in persons with aphasia before and after they receive intensive aphasia 

treatment to examine specific brain network properties and determine their role in predicting responsiveness to 

treatment. 

Role: Principal Investigator 

90IFRE0007-01-00 (Cherney) 10/01/2017 – 9/30/2020 

NIDILRR Field Initiated Program 

Improving electronic written communication in persons with aphasia: A clinical trial 

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This project evaluates the extent to which a novel treatment (T-WRITE) improves hand-written language 

versus text messaging in persons with aphasia, and assesses whether there are subsequent positive 

effects on the participant’s social connectedness and ultimately health-related quality of life (HRQOL). 

Role: Principal Investigator 

H133B140012 (Roth) 10/01/2014 – 9/30/2019 

NIDILRR Rehabilitation Engineering Research Center 

Project 3: The Intensive Comprehensive Aphasia Program (ICAP): A Randomized Clinical Trial 

This study is a randomized clinical trial that compares the efficacy and cost-effectiveness of an ICAP that 

provides 60 hours of intensive treatment over three weeks (i.e. 4 hours a day, 5 days a week for 3 weeks) to 

rehabilitation that provides the same amount and type of comprehensive treatment but is distributed over 15 

weeks (i.e. 2 hours, twice a week for 15 weeks). 

Role: Principal Investigator on Project 3 

H133E130019 (Rymer) 10/01/2013 – 9/30/2018 

NIDILRR Rehabilitation Engineering Research Center 

Project 2: Time Distribution of Computer-Based Script Training in Aphasia 

This project conducts a series of intervention studies to examine the rate and extent to which persons with 

aphasia learn and subsequently forget, following one or more treatment sessions. Mathematical modeling will 

develop algorithms to predict best outcomes based on treatment schedules. Then we explore how clinicians 

utilize these algorithms together with patient performance data from each session to make clinical decisions 

about the timing of subsequent sessions. 

Role: Principal Investigator on Project 2 

H133P120013 (Cherney) 10/01/2012 - 9/30/2018 

NIDILRR Advanced Rehabilitation Research Training Program (ARRT) 

Interventions for Neurologic Communication Disorders 

This training grant provides two years of intensive training to post doctoral fellows who are committed to a 

career in rehabilitation research. It provides training in the development of skills necessary to conduct high 

quality independent interdisciplinary funded research in the rehabilitation of clinical populations with 

communication disorders that accompany neurological conditions including stroke, traumatic brain injury, and 

Parkinson’s disease.

Role: Principal Investigator/Project Director 

COMPLETED (in last 2 years) 

1R01DC011754 (Cherney) 07/08/2011 – 12/30/2017 

NIH/NIDCD 

Aphasia Rehabilitation: Modulating Cues, Feedback & Practice 

We are conducting a series of intervention studies to examine how different treatment variables (cues, 

feedback, task complexity) and practice conditions (blocked/random, massed/distributed) affect short-term 

acquisition and long-term maintenance and generalization of a skill in the rehabilitation of chronic aphasia. 

Role: Principal Investigator 

H133G120123 (Cherney) 10/01/2012 – 9/30/2016 

NIDILRR Field Initiated Program 

Enhancing Written Communication in Persons with Aphasia: A Clinical Trial 

This randomized controlled trial for persons with chronic aphasia evaluates the efficacy of an intensive 

computer-based treatment program that targets sentence-level oral and written language skills. 

Role: Principal Investigator 

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BIOGRAPHICAL SKETCH 

Provide the following information for the Senior/key personnel and other significant contributors. 

Follow this format for each person. DO NOT EXCEED FIVE PAGES. 

NAME: Domenighetti, Andrea Alberto 

eRA COMMONS USER NAME (credential, e.g., agency login): 

POSITION TITLE: Research Scientist and Assistant Professor 

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, 

include postdoctoral training and residency training if applicable. Add/delete rows as necessary.) 

INSTITUTION AND LOCATION 

DEGREE 

(if 

applicable) 

Completion 

Date 

MM/YYYY 

FIELD OF STUDY 

University of Geneva - Switzerland 

University of Geneva - Switzerland 

University of Melbourne - Australia 

University of California, San Diego - USA 

BSc 

DipSc 

PhD 

Post-doc

10/1997 

03/1998 

12/2006 

12/2010 

Biology 

Vascular biology 

Muscle cell biology & 

physiology 

Muscle cell biology & 

physiology 

A. Personal Statement 

As a principal investigator (PI) at the Shirley Ryan AbilityLab (SRAlab), I aim to identify new mechanisms relating 

to muscle tissue and muscle stem cell dysfunction, as well as genetic and epigenetic modifications affecting 

muscle and nerve plasticity in patients with spinal cord and brain injury (cerebral palsy and stroke). Before joining 

the SRAlab in 2015, I spent 15+ years training and working in leading academic Institutes around the world, 

including the University of California in San Diego (UCSD), the University of Lausanne (Switzerland) and the 

University of Melbourne (Australia). During these years, my scientific work and interests focused on molecular 

and cellular mechanisms associated with cardiac muscle diseases and skeletal muscle dysfunction, creating or 

using animal models, isolated cells, electrophysiology, video imaging, functional genomic and molecular biology. 

Since 2014, my research interests have shifted towards more translational research, relevant to brain and spinal 

cord injury, as well as neuromuscular disorders. My current group of research is fully integrated into the Biologics 

Lab at the SRAlab and in the PM&R Department at Northwestern University. I strongly believe that the 

combination of my long-standing experience working with molecular, genomic, biochemical assays, as well as 

patient biopsies would make my group highly suitable to support the genetic analyses proposed for this project. 

We have already optimized the SNP assays proposed in this application and my lab is currently using these 

same assays in separate clinical studies investigating therapy outcomes in patients with spinal cord injury and 

stroke. The following three publications reflect some of the depth and breadth that I have accumulated over the 

years as an experimental biologist and physiologist, but also as a research scientist highly concerned with clinical 

outcomes and therapeutic approaches for patients. 

i. Domenighetti AA, Chu PH, Wu T, Sheikh F, Gokhin DS, Guo LT, Cui Z, Peter AK, Christodoulou DC, 

Parfenov MG, Gorham JM, Li DY, Banerjee I, Lai X, Witzmann FA, Seidman CE, Seidman JG, Gomes AV, 

Shelton GD, Lieber RL, Chen J. Loss of FHL1 induces an age-dependent skeletal muscle myopathy 

associated with myofibrillar and intermyofibrillar disorganization in mice. Hum Mol Genet. 2014;23(1):209-

25. PMID: 23975679; PMCID: 3916749. 

ii. Feingold B, Mahle WT, Auerbach S, Clemens P, Domenighetti AA, Jefferies JL, Judge DP, Lal AK, 

Markham LW, Parks WJ, Tsuda T, Wang PJ, Yoo SJ; American Heart Association Pediatric Heart Failure 

Committee of the Council on Cardiovascular Disease in the Young; Council on Clinical Cardiology; Council 

on Cardiovascular Radiology and Intervention; Council on Functional Genomics and Translational Biology; 

and Stroke Council. Management of Cardiac Involvement Associated With Neuromuscular Diseases: A 

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Scientific Statement From the American Heart Association. Circulation. 2017 Aug 24 [Epub ahead of print] 

PMID: 28838934. 

iii. Domenighetti AA, Mathewson MA, Pichika R, Sibley LA, Zhao L, Chambers HG, Lieber RL. Loss of 

myogenic potential and fusion capacity of muscle stem cells isolated from contractured muscle in children 

with cerebral palsy. Am J Physiol Cell Physiol. 2018. doi: 10.1152/ajpcell.00351.2017. PubMed PMID: 

29694232. 

B. Positions and Honors 

Positions and Employment 

1998-1999: Research Assistant – Division of Hypertension, Lausanne University Hospital, Switzerland. 

1999-2004: PhD fellow - Department of Physiology, The University of Melbourne, Australia. 

2004-2006: Research Associate and PhD fellow, Department of Pharmacology & Toxicology, University of 

Lausanne, Switzerland. 

2007-2010: Postdoctoral fellow - Department of Medicine, Cardiology, University of California, San Diego. 

2011-2013: Assistant Project - Department of Medicine, Cardiology, University of California, San Diego. 

2014-2015: Assistant Project - Department of Orthopaedic Surgery, University of California, San Diego. 

2015-pres: Research Scientist– Rehabilitation Institute of Chicago/Shirley Ryan AbilityLab. 

2015-pres: Research Assistant Professor – Department of Physical Medicine & Rehabilitation, 

Northwestern University. 

Other Experience and Professional Memberships 

1995-1997: President elected of the Biology Student Association – University of Geneva. 

1995-1998: Member elected of the Geneva University Council. Student representative. 

1997-1998: Member elected of the Council of the Faculty of Sciences at Geneva University. 

2000-2005: Member of the Australian Physiological & Pharmacological Society (APPS). 

2001-2002: Member elected of the board of the APPS. Postgraduate representative. 

2002-2005: Member of the Australasian Section of the International Society of Heart Research (ISHR). 

2003-2010: Member of the Swiss Cardiovascular Research and Training Network. 

2010-2015: Member of the American Section of the ISHR. 

2007-pres.: Professional member of the American Heart Association (AHA). 

2009-pres.: Member of the American Society for Cell Biology (ASCB). 

2015-pres.: Member of the Orthopaedic Research Society (ORS). 

2016-pres.: Member of the Society for Muscle Biology. 

Honors: 

1998-1999: Research Fellowship from the Roche Research Foundation. 

2000-2004: International Postgraduate Research Scholarship (IPRS) and Melbourne International Research 

Scholarship (MIRS) from the University of Melbourne. 

2000-2001: Young Researcher/Doctoral Fellowship from the Swiss National Science Foundation. 

2001: Young Investigator Travel Award from the IUPS (International Union of Physiological Sciences). 

2002: W.G. Nayler Prize (Award for the best scientific presentation at the ISHR - Australia). 

2004: Novartis Prize for the best scientific presentation at the 10th Cardiovascular Biology and Clinical 

Implications Meeting, Thun - Switzerland. 

2007: Pfizer Excellence Award in Cardiovascular Research – Switzerland. 

2007-2009: Advanced Postdoctoral Fellowship from the Swiss National Science Foundation. 

2011: Elected Fellow of the American Heart Association (FAHA). 

2013: Life Technologies Prize for best poster presentation, 1st Alternative Muscle Club Conference, San 

Diego, CA 

2015: Award for best poster presentation, 3rd Alternative Muscle Club Conference, Tucson, AZ. 

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C. Contribution to Science 

1. I started my scientific career at the University of Geneva in Switzerland where I obtained a Diploma degree 

in Biology examining vasodilatory intercellular calcium waves, propagating through gap junctions in coronary 

endothelial cell cultures in vitro. After my degree, I moved to the Division of Hypertension at the University of 

Lausanne (Switzerland). As a Research Assistant, I collaborated on investigations looking at the role of 

neuroendocrine activation in the development of myocardial dysfunction, using tissue-isolated mouse 

neonatal cardiomyocytes in vitro. 

i. Domenighetti AA, Beny JL, Chabaud F, Frieden M. An intercellular regenerative calcium wave in porcine 

coronary artery endothelial cells in primary culture. J Physiol. 1998;513 (Pt 1):103-16. PMID: 9782162; 

PMCID: PMC2231269. 

ii. Pellieux C, Sauthier T, Domenighetti A, Marsh DJ, Palmiter RD, Brunner HR, Pedrazzini T. 

Neuropeptide Y (NPY) potentiates phenylephrine-induced mitogen-activated protein kinase activation in 

primary cardiomyocytes via NPY Y5 receptors. Proc Natl Acad Sci U S A. 2000;97(4):1595-600. PMID: 

10660688; PMCID: PMC26480. 

2. After obtaining scholarships and fellowships from both industry (Roche) and academic entities (the University 

of Melbourne and the Swiss National Science Foundation), I was able to join the Department of Physiology 

at the University of Melbourne in Australia, from which I obtained my PhD degree. During my PhD training, I 

developed and used various techniques of video imaging, single cell contractility, electrophysiology and 

cDNA microarrays to investigate genome-wide gene expression profiles and mechanisms of excitationcontraction coupling regulating cardiac myocytes function during agonist- and metabolism-induced heart 

failure in mice. After my PhD training, I worked as a Research Associate in the Department of Pharmacology 

& Toxicology at the University of Lausanne. During this time, I successfully exchanged and implemented my 

skills in cell biology and functional genomics, using microarrays to study new candidate genes responsible 

for the development of angiotensin-induced heart failure and developing EKG measurements on mouse 

models of cardiac hypertrophy and heart failure. 

i. Domenighetti AA, Wang Q, Egger M, Richards SM, Pedrazzini T, Delbridge LM. Angiotensin II-mediated 

phenotypic cardiomyocyte remodeling leads to age-dependent cardiac dysfunction and failure. 

Hypertension. 2005;46(2):426-32. PMID: 15998712. 

ii. Gavillet B, Rougier JS, Domenighetti AA, Behar R, Boixel C, Ruchat P, Lehr HA, Pedrazzini T, Abriel 

H. Cardiac sodium channel Nav1.5 is regulated by a multiprotein complex composed of syntrophins and 

dystrophin. Circ Res. 2006;99(4):407-14. PMID: 16857961. 

iii. Croquelois A, Domenighetti AA*, Nemir M, Lepore M, Rosenblatt-Velin N, Radtke F, Pedrazzini T. 

Control of the adaptive response of the heart to stress via the Notch1 receptor pathway. J Exp Med. 

2008;205(13):3173-85. PMID: 19064701; PMCID: PMC2605223 (* co-first authorship). 

iv. Wang Q, Domenighetti AA*, Schafer SC, Weber J, Simon A, Maillard MP, Pedrazzini T, Chen J, Lehr 

HA, Burnier M. Impact of salt on cardiac differential gene expression and coronary lesion in normotensive 

mineralocorticoid-treated mice. Am J Physiol Regul Integr Comp Physiol. 2012;302(9):R1025-33. PMID: 

22403797 (* co-first authorship). 

3. After receiving an advanced post-doctoral fellowship from the Swiss National Science Foundation, I joined 

the University of California, San Diego (UCSD). I focused my research on cardiac complications and skeletal 

muscle dysfunction associated with absence of the LIM-only domain protein FHL1 in FHL1-null mice. After 

successfully writing and obtaining a NIH-R21 grant for the laboratory (to produce new FHL1-mutant mouse 

models mimicking disease-causing point mutations in patients), I was promoted to assistant Project Scientist 

at the UCSD. During my tenure in Cardiology, I also developed and created genetically-modified mouse 

models to study the effects of clinically-relevant FHL1 mutations on cardiac function and development of 

muscle impairment. 

i. Sheikh F, Raskin A, Chu PH, Lange S, Domenighetti AA, Zheng M, Liang X, Zhang T, Yajima T, Gu Y, 

Dalton ND, Mahata SK, Dorn GW, 2nd, Brown JH, Peterson KL, Omens JH, McCulloch AD, Chen J. An 

FHL1-containing complex within the cardiomyocyte sarcomere mediates hypertrophic biomechanical 

stress responses in mice. J Clin Invest. 2008;118(12):3870-80. PMID: 19033658; PMCID: PMC2575833. 

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ii. Bertrand AT, Bonnemann CG, Bonne G, FHL1 myopathy consortium. 199th ENMC international 

workshop: FHL1 related myopathies, June 7-9, 2013, Naarden, The Netherlands. Neuromuscul Disord. 

2014;24(5):453-62. PMID: 24613424. 

iii. Christodoulou DC, Wakimoto H, Onoue K, Eminaga S, Gorham JM, DePalma SR, Herman DS, 

Teekakirikul P, Conner DA, McKean DM, Domenighetti AA, Aboukhalil A, Chang S, Srivastava G, 

McDonough B, De Jager PL, Chen J, Bulyk ML, Muehlschlegel JD, Seidman CE, Seidman JG. 5'RNASeq identifies Fhl1 as a genetic modifier in cardiomyopathy. J Clin Invest. 2014;124(3):1364-70. PMID: 

24509080; PMCID: PMC3934171. 

iv. Domenighetti AA, Chu PH, Wu T, Sheikh F, Gokhin DS, Guo LT, Cui Z, Peter AK, Christodoulou DC, 

Parfenov MG, Gorham JM, Li DY, Banerjee I, Lai X, Witzmann FA, Seidman CE, Seidman JG, Gomes 

AV, Shelton GD, Lieber RL, Chen J. Loss of FHL1 induces an age-dependent skeletal muscle myopathy 

associated with myofibrillar and intermyofibrillar disorganization in mice. Hum Mol Genet. 2014;23(1):209-

25. PMID: 23975679; PMCID: PMC3916749. 

4. Since 2014, my research interests have shifted towards preclinical and translational research relevant to 

striated (cardiac and skeletal) muscles function and regeneration in patients with brain injury, spinal cord 

injury and neuromuscular disorders. In particular, my laboratory has recently published a manuscript entitled 

“Loss of myogenic potential and fusion capacity of satellite cells isolated from contractured muscle in children 

with cerebral palsy” (Am J Physiol). Our study show that muscle contractures in children with cerebral palsy 

are associated with premature loss of muscle stem cells myogenic potential in vitro. Application of specific 

class of cytidine analogs may revert this phenotype. 

i. Blondelle J, Shapiro P, Domenighetti AA, Lange S. Cullin E3 Ligase Activity Is Required for Myoblast 

Differentiation. J Mol Biol. 2017; 429(7):1045-1066. PMID: 28238764; PMCID: PMC5395100. 

ii. Feingold B, Mahle WT, Auerbach S, Clemens P, Domenighetti AA, Jefferies JL, Judge DP, Lal AK, 

Markham LW, Parks WJ, Tsuda T, Wang PJ, Yoo SJ; American Heart Association Pediatric Heart Failure 

Committee of the Council on Cardiovascular Disease in the Young; Council on Clinical Cardiology; 

Council on Cardiovascular Radiology and Intervention; Council on Functional Genomics and 

Translational Biology; and Stroke Council. Management of Cardiac Involvement Associated With 

Neuromuscular Diseases: A Scientific Statement From the American Heart Association. Circulation. 2017 

Aug 24 [Epub ahead of print] PMID: 28838934. 

iii. Domenighetti, AA, Lieber RL. U.S. Provisional Patent App. No. 62/572,609, Methods for Treating 

Contractured Muscle and Related Cultured Cells. 

iv. Domenighetti AA, Mathewson MA, Pichika R, Sibley LA, Zhao L, Chambers HG, Lieber RL. Loss of 

myogenic potential and fusion capacity of muscle stem cells isolated from contractured muscle in children 

with cerebral palsy. Am J Physiol Cell Physiol. 2018. doi: 10.1152/ajpcell.00351.2017. PubMed PMID: 

29694232 

Complete List of Published Work: 

http://www.ncbi.nlm.nih.gov/sites/myncbi/1ZivfqtckH7/bibliograpahy/40574815/public/?sort=date&direction=asc 

ending 

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D. Research Support 

Ongoing Research Support: 

2015-present: startup and lab development fund from the Shirley Ryan AbilityLab. 

Completed Research Support: 

R24 HD050837 Domenighetti 07/01/2014-06/30/2015 

Title: Discovering new epigenetic pathways that regulate skeletal muscle homeostasis 

Goal: Startup fund to create a Pax7-specific satellite cell and Tamoxifen-inducible knockout mouse line for 

EHBP1L1 (Pax7-CreER+/- EHBP1L1LoxP/LoxP) and to define the biological role of EHBP1L1 in isolated satellite 

cells in vitro and adult skeletal muscle in vivo. 

R21 AR061024 Chen (PI) 07/01/2011-06/30/2013 

Title: The role of FHL1 in Emery-Dreifuss and Reducing Body myopathies. 

Goal: The goal of this proposal is to understand the role that FHL1 plays in skeletal muscle growth and 

homeostasis and to understand why different mutations in FHL1 result in different myopathies. Creation of two 

mutant mouse models recapitulating human FHL1 mutations is proposed. 

Role: Assistant Project Scientist 

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OMB No. 0925-0001 and 0925-0002 (Rev. 10/15 Approved Through 10/31/2018) 

BIOGRAPHICAL SKETCH 

Provide the following information for the Senior/key personnel and other significant contributors. 

Follow this format for each person. DO NOT EXCEED FIVE PAGES. 

NAME: Marwan Nabil Baliki 

eRA COMMONS USER NAME (credential, e.g., agency login): 

POSITION TITLE: Research Scientist, Rehabilitation Institute of Chicago 

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral 

training and residency training if applicable. Add/delete rows as necessary.) 

INSTITUTION AND LOCATION 

DEGREE 

(if applicable) 

Completion 

Date 

MM/YYYY 

FIELD OF STUDY 

American University of Beirut, Lebanon 

American University of Beirut, Lebanon 

Northwestern University, Chicago 

Northwestern University, Chicago 

B.S. 

M.S 

Ph.D. 

Post-doctoral 

fellow 

1998 

2001 

2009 

2013 

Biology 

Neuroscience 

Neuroscience 

Neuroscience 

A. Personal Statement 

My research seeks to define the brain neural mechanisms underlying the processing of normal and pathological 

sensory and cognitive processes in humans. My research encompasses both novel methodological and 

theoretical constructs that enable us to formulate physiological and behavioral models that allows us to 

investigate the impact of medical interventions in clinical setting such as identifying brain based biomarkers for 

onset of symptoms following injury or brain reorganization in response to specific treatments. The majority of my 

past research focused on the study of chronic pain. Only by providing key neural information about pain, can we 

explicate the brain process and behavioral changes associated with chronic pain. Pain has been classically 

studied from the viewpoint of peripheral afferent inputs, spinal cord coding, and brainstem descending 

modulation. My recent studies utilized state of the art neuroimaging techniques and modelling such as using 

graph theory to analyze resting state changes in clinical conditions compared to controls. I am looking forward 

to utilizing my extensive expertise in brain imaging analysis to investigate functional and anatomical 

reorganization in patients suffering from aphasia. This will allow us to unravel the brain physiological and 

anatomical properties associated with aphasia, and thus for the first time identify biomarkers that can be used 

as targets for efficacious therapy and aid in the rehabilitation efforts of people with aphasia. I have been working 

closely with Dr. Cherney (the co-principle investigator of this proposal) for the past year on several projects that 

focus on identifying brain networks underlying language expression and comprehension in patients with aphasia. 

We have already studied more than 40 patients and have a manuscript entitled “Brain network topology 

influences response to intensive comprehensive aphasia treatment” accepted for publication. The Shirley Ryan 

Abilitylab provides all necessary tools for the success of this collaboration and project. 

B. Position and Honors 

Positions and Employment 

2000 - 2001 Teaching assistant, Depart of Morphology, American University of Beirut 

2001 - 2003 Research Assistant, Department of Physiology, Northwestern University 

2012 - 2015 Research Associate, Department of Physiology, Northwestern University 

2015 - Research scientist, Shirley Ryan AbilityLab (formerly Rehab. Inst. Of Chicago) 

2015 - Assistant Professor, Physical Medicine and Rehabilitation, Northwestern university 

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Other Experiences and Professional Memberships 

2001 - Member, Society for Neuroscience 

2003 - Member, Human Brain Mapping Member, 

2003 - International Association for the Study of Pain 

2005 - Member, American Pain Society 

2016 - Associate Editor of Pain 

C. Contributions to Science 

1-Characterization of the brain’s network properties 

The utility of neuroimaging of health and disease requires an understanding of how the brain dynamically 

processes complex information flow on local (region to region) and global (module to module) scales. Using 

graph theory to estimate how information is dynamically shared between and across brain regions, we 

revealed for the first time that brain activity can be understood as a synchronous network with small world 

properties. With 964 citations since 2005, this paper has made a seminal contribution across multiple 

disciplines based on its application of graph theory to brain dynamic properties. 

a. Eguíluz VM, Chialvo DR, Cecchi GA, Baliki MN, Apkarian AV. Scale-free brain functional networks. 

Phys Rev Lett. 2005 Jan 14;94(1):018102. PubMed PMID: 15698136. 

b. Cecchi GA, Rao AR, Centeno MV, Baliki MN, Apkarian AV, Chialvo DR. Identifying directed links in 

large scale functional networks: application to brain fMRI. BMC Cell Biol. 2007 Jul 10;8 Suppl 1:S5. 

PubMed PMID: 17634095; PubMed Central PMCID: PMC1924510. 

c. Baliki MN, Mansour AR, Baria AT, Apkarian AV. Functional reorganization of the default mode network 

across chronic pain conditions. PLoS One. 2014;9(9):e106133. PubMed PMID: 25180885; PubMed 

Central PMCID: PMC4152156. 

d. Mansour A, Baria AT, Tetreault P, Vachon-Presseau E, Chang PC, Huang L, Apkarian AV, Baliki MN. 

Global disruption of degree rank order: a hallmark of chronic pain.. Sci Rep. 2016 Oct 11;6:34853. 

PMID: 27725689 

2 - Understanding the impact of chronic pain on brain anatomical and functional properties 

Advances in imaging technology have enabled non-invasive probing of human brain properties in clinical chronic 

pain conditions, and our understanding of the brain mechanisms underlying the development and processing of 

chronic pain is undergoing rapid changes. My work greatly contributed to our current understanding of the brain 

functional and anatomical reorganization with chronic pain, including the 1) distinguishing brain activity for 

different clinical pain conditions from each other and acute pain, 2) identifying the impact of brain on default brain 

functions and resting state dynamics and 3) localizing the association of chronic pain with abnormal structural 

changes. The impact of my work has resulted in an h index of 35 and at least 6000 citations. I will use my 

extensive expertise in brain imaging analysis to examine brain functional and anatomical reorganization in 

patients with aphasia. 

a. Chronic pain and the emotional brain: specific brain activity associated with spontaneous fluctuations of 

intensity of chronic back pain. Baliki MN, Chialvo DR, Geha PY, Levy RM, Harden RN, Parrish TB, 

Apkarian AV. J Neurosci. 2006 Nov 22;26(47):12165-73. PMID: 1712204; PMCID: PMC4177069 

b. Beyond feeling: chronic pain hurts the brain, disrupting the default-mode network dynamics. Baliki MN, 

Geha PY, Apkarian AV, Chialvo DR. J Neurosci. 2008 Feb 6;28(6):1398-403. PMID: 18256259 

c. The cortical rhythms of chronic back pain. Baliki MN, Baria AT, Apkarian AV. J Neurosci. 2011 Sep 

28;31(39):13981-90. PMID: 21957259; PMCID: PMC3214084 

d. Functional reorganization of the default mode network across chronic pain conditions. Baliki MN, 

Mansour AR, Baria AT, Apkarian AV. PLoS One. 2014 Sep 2;9(9):e106133. doi: 

10.1371/journal.pone.0106133. eCollection 2014 . [PubMed - in process], PMID:25180885; PMCID: 

PMC4152156. 

Biosketches Page 35
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

e. Brain morphological signatures for chronic pain. Baliki MN, Schnitzer TJ, Bauer WR, Apkarian AV. PLoS 

One. 2011;6(10):e26010. PMID: 22022493; PMCID: PMC3192794 

3 - Identifying a neurobiological model for vulnerability to chronic pain 

There are many examples in the clinical literature demonstrating that only a proportion of patients with a particular 

disease or injury go on to develop chronic pain. I lead the first neuroimaging longitudinal study that enabled us 

to identify early brain biomarkers that predicted the development of chronic pain with 80% accuracy following an 

acute back injury. We showed that the functional and anatomical properties within the cortico-limbic system, 

especially functional and anatomical connectivity between the reward circuitry and frontal brain regions plays an 

integral part in the transition of acute to chronic pain. These results – and for the first time – alluded that the brain 

plays an integral part in the development of chronic pain, and provided a neurobiological model that might 

contribute to the advancement of evidence-based interventions that will greatly enhance strategies for pain 

management 

a. Nociception, Pain, Negative Moods, and Behavior Selection. Baliki MN, Apkarian AV.Neuron. 2015 Aug 

5;87(3):474-91. doi: 10.1016/j.neuron.2015.06.005. Review. PMID: 26247858; PMCID: PMC4529956 

b. Corticostriatal functional connectivity predicts transition to chronic back pain. Baliki MN, Petre B, Torbey 

S, Herrmann KM, Huang L, Schnitzer TJ, Fields HL, Apkarian AV. Nat Neurosci. 2012 Jul 1;15(8):1117-

9 PMID: 22751038; PMCID: PMC3411898 

c. Resting-state functional reorganization of the rat limbic system following neuropathic injury. Baliki MN, 

Chang PC, Baria AT, Centeno MV, Apkarian AV. Sci Rep. 2014 Sep 2;4:6186. PMID:25178478; PMCID: 

PMC4151103 

Complete List of Published Work 

http://www.ncbi.nlm.nih.gov/pubmed/?term=baliki+M 

D. Research Support 

Active research 

Sedgwick Pain Study (Baliki) 1/1/2018 – 12/31/2019 

Sedgwick Claims Management Services 

Identifying behavioral and brain biomarkers underlying successful pain management and functional 

rehabilitation in injured workers. Role: Principle Investigator 

P50 (Apkarian) 

National Institute of Health 

Center for Chronic Pain and Drug Abuse 

Role: Co-Investigator 

7/1/2018 – 6/30/2023 

The Carl & Marilynn Thoma Foundation (Cherney) 

Brain Network Properties and Intensive Aphasia Therapy 

3/01/2018 – 2/28/2023 

This project uses resting state fMRI in persons with aphasia before and after they receive intensive aphasia 

treatment to examine specific brain network properties and determine their role in predicting responsiveness to 

treatment. 

Role: Co-Investigator 

Completed research 

Fidelity (Baliki) Sep 01, 2009 – Aug 31, 2010 

Functional and anatomical changes in different types of chronic pain 

Role: Principle Investigator 

Biosketches Page 36
 

 

Nielsen Foundation (Baliki) Sep 01,2016 – Aug 31, 2017 

Brain functional and anatomical reorganization in the management of chronic pain 

Role: Principle Investigator 

Biosketches Page 37
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

BIOGRAPHICAL SKETCH 

Provide the following information for the Senior/key personnel and other significant contributors. 

Follow thisformat for each person. DO NOT EXCEED FIVE PAGES. 

NAME: Elliot J. Roth, MD 

eRA COMMONS USER NAME (credential, e.g., agency login): 

POSITION TITLE: Professor and Chairman, Physical Medicine and Rehabilitation 

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, 

include postdoctoral training and residency training if applicable. Add/delete rows as necessary.) 

INSTITUTION AND LOCATION 

DEGREE 

(if 

applicable) 

Completion 

Date 

MM/YYYY 

FIELD OF STUDY 

Washington University, St. Louis, MO 

Northwestern Univ. Medical School, Chicago, IL 

Cook County Hospital, Chicago, IL 

Northwestern University Feinberg School of 

Medicine, Chicago, IL 

Rehabilitation Institute of Chicago, Chicago, IL 

AB 

MD 

Intern 

Resident 

Fellow 

1978 

1982 

1983 

1985 

1986 

Chem./Human Serv. Ed 

Medicine 

Internal Medicine 

Physical Medicine & 

Rehabilitation 

Stroke Rehabilitation 

A. Personal Statement 

Elliot Roth, MD brings more than 25 years of experience in rehabilitation patient care,research, teaching, and 

program leadership for patients with stroke, traumatic brain injury and other neurological conditions. His 

research and academic interests are in the areas of novel methods to enhance recovery, improve functional 

outcomes, and prevent associated medical conditions for people with disabling conditions. He currently is 

Project Director of a Rehabilitation Research and Training Center on health and function for people with 

physical disabilities and he recently completed a Rehabilitation Research and Training Center grant on stroke 

rehabilitation, which he led for 20 years. He is also PI on several other research projects focused primarily on 

neurorehabilitation. Dr. Roth is the Chairman of the Department of Physical Medicine & Rehabilitation at 

Northwestern University’s Feinberg School of Medicine. In addition to his research and administrative 

responsibilities, he has an active medical practice, specializing in the care and treatment of patients with a 

variety of physically disabling conditions, focusing predominantly on the rehabilitation management of patients 

with stroke. In this study, Dr. Roth will assist with determining subject eligibility as needed across all sites, 

reviewing clinical MRI scans, and providing input on other medically-related information including medications 

and the presence of co-morbidities. 

B. Positions and Honors 

Positions and Employment: 

1986-1991 Assistant Professor, Physical Medicine and Rehabilitation (PM&R), Northwestern University 

Feinberg School of Medicine (NUFSM), Chicago, IL 

1986- Attending Physician, Rehabilitation Institute of Chicago (RIC), Chicago, IL 

1986- Attending Physician, Northwestern Memorial Hospital (NMH), Chicago, IL 

1987-1990 Associate Director, Midwest Regional Spinal Cord Care System, NUFSM/RIC/NMH 

1990-1994 Founder & Director, Center for Stroke Rehabilitation, RIC, Chicago, IL 

1991-1994 Associate Professor, PM&R, NUFSM 

1993-2014 Project Director, Rehabilitation Research and Training Center on Stroke Rehabilitation, U.S. 

Department of Education, National Institute on Disability and Rehabilitation Research 

1994- Chairman, Rehabilitation Medicine, Northwestern Memorial Hospital, Chicago, IL 

1994-2007 Senior Vice President and Medical Director, Rehabilitation Institute of Chicago, Chicago, IL 

1994- Chairman, Rehabilitation Medicine, Northwestern Memorial Hospital, Chicago, IL 

1994- The Paul B. Magnuson Professor and Chairman, PM&R, NUFSM 

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2008- Project Director, Midwest Regional Traumatic Brain Injury Model System, RIC 

2010-2012 Interim Medical Director, Brain Injury Medicine and Rehabilitation Program, RIC 

2012-2017 Medical Director, Patient Recovery Unit, RIC 

2017- Co-Medical Director, Brain Innovation Center, Shirley Ryan Abilitylab 

2014- Project Director, Rehabilitation Research and Training Center on Health and Function for People 

with Physical Disabilities, U.S. Department of Education, National Institute on Disability and 

Rehabilitation Research 

Other Experience and Professional Activities 

1992- Co-Editor in Chief, Topics in Stroke Rehabilitation 

1993 - Editorial Board, Archives of Physical Medicine and Rehabilitation 

1993 -2009 Editorial Board, American Journal of Physical Medicine and Rehabilitation 

1994 -2006 Editorial Board, Journal of Neurological Rehabilitation 

1995 U.S. Patent No. 5397337 - Method and Apparatus for Artificially Stimulating Cough Reflexwith 

Robert J. Jaeger, Ph.D. 

2002-2003 Member, Technical Expert Panel to Develop Inpatient Rehabilitation Quality Measures 

2010--2012 Chairman, Research Committee, American Academy of Physical Medicine and Rehabilitation 

2012-- Chairman, Evidence-BasedPractice Committee, American Academy of Physical Medicine and 

Rehabilitation 

Honors 

1992,96,00,06,08 Voted one of the Outstanding Physicians in Chicago by Chicago Magazine 

1999-2000; 03; Named one of the Best Physicians in Chicago by Castle-Connolley Publishers 

06-07;10-18 

2004 John W. Goldschmidt, MD Award for Excellence in Rehabilitation, National Rehabilitation 

Hospital, Washington, DC 

2007 Elected to Alpha Omega Alpha Medical Honorary Society, NUFSM 

2015 Distinguished Clinician Award, American Academy of Physical Medicine and Rehabilitation 

C. Contributions to Science 

1. Early in my academic career, my research focused on understanding the cognitive dysfunction that 

often accompanied a traumatic spinal cord injury. My colleagues and I were the first to describe the occurrence 

and the impact that these deficits on can have on rehabilitation outcomes. Cognitive functioning is associated 

with medical stability, the patient's ability to assimilate the necessary skills for survival and adaptation after 

spinal cord injury, and readmission patterns after discharge for initial inpatient rehabilitation. 

a. Morris J, Roth E, Davidoff G. Mild closed head injury and cognitive deficits in spinal-cord-injured 

patients: incidence and impact. JHead Trauma Rehabil. 1986;1(2):31-42. 

b. Davidoff G, Roth E, Morris J, Bleiberg J, Meyer PR. Assessment of closed head injury in trauma-related 

spinal cord injury. Paraplegia. 24:97-104; 1986. 

c. Roth E, Davidoff G, Thomas P, Doljanac R, Dijkers M, Berent S, et al. A controlled study of 

neuropsychological deficits in acute spinal cord injury patients. Paraplegia. 27:480-489;1989. 

d. Davidoff GN, Roth EJ, Richards JS. Cognitive deficits in spinal cord injury: epidemiology and outcome. 

Arch Phys Med Rehabil. 1992;73:275-284. 

2. Another area of interest early in my academic and clinical career was in the course functional recovery 

after a neurological injury such as a spinal cord injury or stroke. Our research team examined howimpairment 

related to functional outcomes and howthis affected the course of rehabilitation. We also investigated how 

these factors influenced long-term community outcomes. 

a. Yarkony GM, Roth EJ, Heinemann AW, Lovell L, Wu Y. Functional skills after spinal cord injury 

rehabilitation: three-yearlongitudinal follow-up.Archives of Physical Medicine and Rehabilitation. 

1988;69:111-114. 

b. Roth EJ, Lovell LL. Seven Year Trends in Stroke Rehabilitation: Patient Characteristics, Medical 

Complications, and Functional Outcomes.Topics in Stroke Rehabilitation. 2003;9(4):1-9. 

Biosketches Page 39
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

c. Roth EJ. Lovell L. Community skill performance and its association with the ability to perform everyday 

tasks by stroke survivors one year following rehabilitation discharge. Topics in Stroke Rehabilitation. 

2007;14(1):48-56. PMID: 17311790 

d. Cramer SC, Wolf SL, Adams HP Jr, Chen D, Dromerick AW, Dunning K, Ellerbe C, Grande A, Janis S, 

Lansberg MG, Lazar RM, Palesch YY, Richards L, Roth E, Savitz SI, Wechsler LR, Wintermark M, 

Broderick JP. Stroke Recovery and Rehabilitation Research: Issues, Opportunities, and the National 

Institutes of Health StrokeNet. Stroke. 2017;48(3):813-819. PMID: 28826022 

3. My clinical practice helped to inform several aspects of my research. One important area was on how 

medical complications and pre-existing comorbid conditions influenced the outcomes of patients during and 

after rehabilitation. I became especially interested in cardiopulmonary complications as these had tremendous 

impact on mortality and morbidity. Identifying clinical factors that are associated with increased risk of 

experiencing medical complications is valuable to facilitate the implementation of appropriate prevention and 

management interventions. These studies represent the impact of medical complications on outcomes. 

a. Roth EJ. Lovell L. Harvey RL. Bode RK. Delay in transfer to inpatient stroke rehabilitation: the role of 

acute hospital medical complications and stroke characteristics. Topics in Stroke Rehabilitation. 

2007;14(1):57-64. PMID: 17311791 

b. Marciniak C, Korutz AW, Lin E, Roth E, Welty L, Lovell L. Examination of selected clinical factors and 

medication use as risk factors for pneumonia during stroke rehabilitation: a case-control study. 

American Journal of Physical Medicine and Rehabilitation. 2009;88(1):30-38. PMID: 19096289 

c. Roth E, Stenson K, Powley S, Oken J, Primack S, Nussbaum S, Berkowitz M. Expiratory muscle 

training in spinal cord Injury: A randomized controlled trial. Arch Phys Med Rehabil. 91:857-861, 2010. 

PMID: 20510974 

d. Pellicane AJ, Millis SR, Do KD, Temme KE, Sayyad A, Oswald MC, Roth EJ. The effect of protein and 

calorie intake on prealbumin, complications, length of stay, and function in the acute rehabilitation 

inpatient with stroke. NeuroRehabilitation. 33(3):367-76 2013. PMID: 23949068 

4. Another area of research interest that has been heavily influenced by my clinical practice is in mobility 

and gait. Recovery of walking is a primary goal for patients after a stroke or spinal cord injury. For those 

patients for whom walking is not feasible, there is a compelling need to develop methods for improved mobility. 

I have been involved in investigating parameters such as amount and intensity of practice that appear to be 

contributors to improved function in patients post-stroke. I also have been involved in investigating and 

developing methods for mobility in patients who use wheelchairs. 

a. Kim J, Park H, Bruce J, Rowles D, Holbrook J, Nardone B, West D, Laumann A, Roth E, Ghovanloo M. 

Assessment of the Tongue-DriveSystem using a Computer, a Smartphone, and a Powered-Wheelchair 

by People With Tetraplegia. IEEE Trans Neural Syst Rehabil Eng. 2016 26(1):68-78. PMID: 25730827 

b. Hornby TG, Holleran CL, Leddy AL, Hennessy P, Leech KA, Connolly M, Moore JL, Straube D, Lovell 

L, Roth E. Feasibility of Focused Stepping Practice During Inpatient Rehabilitation Poststroke and 

Potential Contributions to Mobility Outcomes. Neurorehabil Neural Repair. 2015 Nov;29(10):923-32 

PMID: 25721233 

c. Hornby TG, Holleran CL, Hennessy PW, Leddy AL, Connolly M, Camardo J, Woodward J, Mahtani 

G, Lovell L, Roth EJ. Variable Intensive Early Walking Poststroke (VIEWS): A Randomized 

Controlled Trial. Neurorehabil Neural Repair 2016 Jun;30(5):440-50 PMID: 26338433 

d. Hornby TG, Moore JL, Lovell L, Roth EJ. Influence of skill and exercise training parameters on 

locomotor recovery during stroke rehabilitation. Curr Opin Neurol. 2016;29(6):677-683. PMID: 

27748688 

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D. Research Support 

Active Research Support 

90RT5027 (Roth) 10/1/14 – 09/30/19 

NIDILRR, Administration for Community Living 

Rehabilitation Research and Training Center on Developing Optimal Strategies in Exercise and 

Survival Skills to Increase Health and Function 

The Center’s projects will explore the role of motor priming and intensity of training to improve walking ability, 

determine the optimal dosing of intensive aphasia treatments, and develop a peer health navigator program 

that will improve the ability of people with disabilities to access community resources and the social 

environment. We will measure the economic and social value of each project. 

Role: Principal Investigator and Center Director 

5R01HD082216-02 (Wu) 8/6/15-7/30/20 

NIH/NICHD 

Date of Project Period: 

Constraint induced movement therapy for walking in individuals post stroke 

This project will test whether the efficacy of locomotor training will be improved through the application of 

constraint induced movement therapy to lower limb of individuals post-stroke during treadmill training. 

Role: Co-Investigator 

R01 (Roth/Kamper) 4/1/14-3/31/19 

NIH 

Altering Activation Patterns in the Distal Upper Extremity after Stroke 

The goal of the proposed study is to explore the therapeutic benefit of a multimodality treatment combining the 

administration of a pharmacological agent for reducing unwanted neuromuscular hyperexcitability with a 

training paradigm focused on expanding exploration of the muscle activation workspace. 

Role: Principal Investigator 

16SDG30980033 (Suresh) 7/1/16-6/30/19 

American Heart Association 

Tracking the evolution of spasticity in acute stroke 

The objective of this study is to track the time course of spasticity development in acute stroke survivors with 

experimental and clinical measures that would provide us with information regarding the neural source of reflex 

excitability. 

Role: Investigator 

4U10NS086608-04 (Prabhakaran) 9/30/13-7/31/18 

NINDS 

The Chicago Stroke Trials Consortium 

Stroke Trials Network – Regional Coordinating Stroke Centers 

Goal is to create a regional coordinating stroke centerthat will facilitate the execution of larger stroke clinical 

trials. 

Role: Co-Investigator 

U10NS077271-06 (Simuni) 9/1/11-6/30/25 

NIH/NINDS 

Clinical Research Sites for the Network of Excellence in Neuroscience Clinical Trials (NEXT Sites) 

Participation in this network will enable us to contribute expertise and research subjects to neurological 

clinical trials and provide training for junior investigators to enable them to develop independent research 

careers. 

Role: Co-Investigator 

Biosketches Page 41
 

 

 

 

 

 

 

 

 

 

 

Spastic Paralysis Research Foundation of the 10/1/97-9/30/18 

Kiwanis of Illinois and Eastern Iowa (Roth) 

Nutrition and Wellness in Persons with Stroke and Brain Injury 

This is a series of studies on the role of nutrition in influencing outcomes after stroke or brain injury. 

Role: Principal Investigator 

Completed Research Support 

H133B080031 (Roth) 10/01/08 – 09/30/14 

NIDRR, Department of Education 

Rehabilitation Research and Training Center on Enhancing the Functional and Employment Outcomes 

of Individuals Who Experience a Stroke 

Purpose of this project is to develop and evaluate technology and programs designed to assist stroke survivors 

in community participation and vocation. 

Role: Principal Investigator and Director 

Biosketches Page 42
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

BIOGRAPHICAL SKETCH 

Provide the following information for the Senior/key personnel and other significant contributors. 

Follow this format for each person. DO NOT EXCEED FIVE PAGES. 

NAME: Linda Weil Foster 

eRA COMMONS USER NAME (credential, e.g., agency login): 

POSITION TITLE: Research Coordinator 

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, 

include postdoctoral training and residency training if applicable. Add/delete rows as necessary.) 

INSTITUTION AND LOCATION 

DEGREE 

(if applicable) 

Start Date 

MM/YYYY 

Completion 

Date 

MM/YYYY 

FIELD OF STUDY 

Tulane University, New Orleans, LA 

Duke University, Durham, NC 

BS 

MS 

06/1985 

05/1987 

Psychology 

Physical Therapy 

A. Personal Statement 

Because of my experience in clinical care and research, as well as my management experience, I am well 

suited to participate in this research project. Throughout my professional career, I have worked extensively 

with stroke patients, many with aphasia. From 2008-2010, I conducted a research study with stroke survivors 

utilizing a robotic device called the KineAssist. I currently treat outpatients, primarily stroke survivors, utilizing 

the KineAssist for physical therapy treatment. From 2014-2016, I was involved in a study funded by the 

Patient-Centered Outcomes Research Institute (PCORI) and titled “Developing Quality Metrics from PatientReported Outcomes”. For this study, I had the opportunity to work closely with Dr. Heinemann. The study was 

conducted at both the Shirley Ryan AbilityLab (formerly Rehabilitation Institute of Chicago) and the Alexian 

Brothers Rehabilitation Hospital and involved enrolling and evaluating patients with a neurological diagnosis. 

My role in the current study will be similar to that of the PCORI study. With the research speech and language 

pathologist, I will supervise the research assistant assigned to the Alexian Brothers Rehabilitation Hospital, to 

ensure that recruitment goals are met and quality data obtained. 

B. Positions and Honors 

Positions and Employment 

1987-1992 Physical Therapist, Medical College of Virginia Hospitals, Richmond Virginia 

1992-1998 Senior Physical Therapist, Rehabilitation Institute of Chicago, Chicago IL 

1998-2004 Allied Health Manager, Rehabilitation Institute of Chicago, Chicago IL 

2004-2008 Clinical Manager, Day Rehabilitation, Rehabilitation Institute of Chicago at Alexian Brothers, Elk 

Grove Village, IL 

2008-Present Research Coordinator, Shirley Ryan AbilityLab/Rehabilitation Institute of Chicago at Alexian 

Brothers Rehabilitation Hospital, Elk Grove Village, IL 

Other Experience and Professional Memberships 

1985-Present Member, American Physical Therapy Association 

1992-Present Member, Illinois Physical Therapy Association 

Biosketches Page 43
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

C. Contribution to Science 

1. Heinemann, A.W., Deutsch, A., Cella, D., Cook, K.F., Foster, L., Miskovic, A., Davis, K., & Goldsmith, 

A. Feasibility of Collecting Patient-Reported Outcomes for Inpatient Rehabilitation Quality Reporting. 

Health Services Research Journal. 15 JUN 2017, DOI: 10.1111/1475-6773.12729 

2. Schalet, B., Kallen, M., Heinemann, A.W., Deutsch, A., Cook, K. F., Foster, L., Cella, D. Using 

PROMIS Pain Interference Items to Improve Quality Measurement in Inpatient Rehabilitation Facilities. 

JAMDA. (2018) 

For the PCORI project I was the site co-investigator and liaison for the Alexian Brothers Rehabilitation Hospital. 

My responsibilities included assisting in subject recruitment, research coordination, and dissemination of 

research results. 

Summary of PCORI results: 

• Collection of patient-reported outcome measures (PROMS) during and after an IRF (Inpatient 

Rehabilitation Facility) stay from persons with neurological disorders is feasible 

• A substantial proportion of patients require assistance 

• The majority of patients could use a tablet computer and were willing to complete the survey one-month 

after discharge 

• Multiple reminders and telephone interviews were required for follow up surveys; results would be 

biased without research follow-up efforts 

Conclusions: 

• Collection of patient-reported data while still in hospital results in a higher response rate 

• Most follow-up response differences are more favorable 

D. Research Support 

Ongoing Research Support 

None 

Completed Research Support 

CD12-11-4201 (PCORI) Heinemann (PI) 09/01/2013-08/31/2016 

Developing Quality Metrics from Patient-Reported Outcomes for Medical Rehabilitation 

Goals of the project were: 

1. to identify issues that are important to the quality of care for rehabilitation patients that are amenable to 

the collection of patient-reported outcomes (PROMS) 

2. evaluate the feasibility of collecting PROMS 

3. specify items required for quality measure development and design data collection modules that can 

be used in quality improvement efforts and to demonstrate accountability of health care delivery 

Biosketches Page 44
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

OMB No. 0925-0001 and 0925-0002 (Rev. 10/15 Approved Through 10/31/2018) 

BIOGRAPHICAL SKETCH 

Provide the following information for the Senior/key personnel and other significant contributors. 

Follow this format for each person. DO NOT EXCEED FIVE PAGES. 

NAME: Allan J. Kozlowski, PhD 

eRA COMMONS USER NAME (credential, e.g., agency login): 

POSITION TITLE: Assistant Professor, Department of Epidemiology and Biostatistics, Michigan State 

University College of Human Medicine; and Director of Outcomes Research at Mary Free 

Bed Rehabilitation Hospital 

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, 

include postdoctoral training and residency training if applicable. Add/delete rows as necessary.) 

INSTITUTION AND LOCATION 

DEGREE 

(if 

applicable) 

Completion 

Date 

MM/YYYY 

FIELD OF STUDY 

University of British Columbia, Vancouver CAN 

University of British Columbia, Vancouver CAN 

Rehabilitation Institute of Chicago, Chicago USA 

B.Sc. (PT) 

PhD 

06/1991 

11/2010 

09/2012 

Physical Therapy 

Rehabilitation Sciences 

Postdoctoral Fellowship 

A. Personal Statement 

I have the expertise, knowledge, skill, and access to resources necessary to successfully carry out my roles as 

described in the proposed research project. In regard to my role as Site PI at Mary Free Bed Rehabilitation 

Hospital, I have lead or co-authored seven manuscripts and co-instructed courses on topics of longitudinal 

modeling. As PI or co-Investigator on several Department-, State-, and private foundation-funded grants, I am 

familiar with the regulatory and procedural requirements of implementing human subjects’ research. In regard 

to my role as data analyst, I have the knowledge, skill, and experience required to perform the required data 

analyses, including longitudinal methods that model outcomes as trajectories. I am familiar with measurement 

issues related to the primary and secondary outcome measures, and covariates including biomarkers. I have 

established relationships with the senior researchers on this proposal. Over the past eight years collaborated 

and published with Allen W. Heinemann, PhD, and have a collegial relationship established over the past 

seven years with Leora Cherney, PhD, CCC-SLP. 

1. Kozlowski AJ, Heinemann AW. Using individual growth curve models to predict recovery and activities of 

daily living after spinal cord injury: an SCIRehab project study. Arch Phys Med Rehabil. 2013 Apr;94(4 

Suppl):S154-64.e1-4. PubMed PMID: 23527771. 

2. Kozlowski AJ, Singh R, Victorson D, Miskovic A, Lai JS, Harvey RL, Cella D, Heinemann AW. Agreement 

Between Responses From Community-Dwelling Persons With Stroke and Their Proxies on the NIH 

Neurological Quality of Life (Neuro-QoL) Short Forms. Arch Phys Med Rehabil. 2015 Nov;96(11):1986-

92.e14. Epub 2015 Jul 21. PubMed PMID: 26209471; PubMed Central PMCID: PMC4628567. 

3. Kozlowski AJ, Cella D, Nitsch KP, Heinemann AW. Evaluating Individual Change With the Quality of Life 

in Neurological Disorders (Neuro-QoL) Short Forms. Arch Phys Med Rehabil. 2016 Apr;97(4):650-4.e8. 

Epub 2015 Dec 29. PubMed PMID: 26740062; PubMed Central PMCID: PMC4994512. 

4. Kozlowski AJ, Frank H, Miriam LL, Sandra M, Susan G, et al. Effect of exoskeleton-assisted locomotor 

training on recovery rate of motor functioning for inpatients with stroke compared to historical controls. 

Phys Ther. Forthcoming; Under review. 

Biosketches Page 45
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

B. Positions and Honors 

Positions and Employment 

1991-1997 Physical Therapist, Workers’ Compensation Board of British Columbia, Richmond, Canada

1997-2003 Rehabilitation Manager, Workers’ Compensation Board of British Columbia, Richmond, Canada

2004-2010 Pre-doctoral Candidate, Rehabilitation Research Training Programs, Faculty of Medicine, 

University of British Columbia, Vancouver, Canada 

2005-2010 Clinical Instructor (Contract): “RSPT514 Clinical Practice I”, Department of Physical Therapy,

University of British Columbia, Vancouver BC, Canada 

2010 Physical Therapist (contract), CBI Rehabilitation, Burnaby BC, Canada 

2010-2013 Fellow, Center for Rehabilitation Outcomes Research, Rehabilitation Institute of Chicago, and 

the Center for Healthcare Studies, Feinberg Medical School, Northwestern University, Chicago 

IL 

2011-2013 Instructor (Contract): “RHSC505 Measurement for Assessment, Planning, and Evaluation”,

Online Master of Rehabilitation Science Program, University of British Columbia, Vancouver BC, 

Canada 

2012 Course Developer (Contract): “RHSC505 Measurement for Assessment, Planning, and

Evaluation”, Online Master of Rehabilitation Science Program, University of British Columbia,

Vancouver, Canada 

2012 Adjunct Faculty (Contract Instructor): “OT410 Research Methods”, Department of Occupational 

Therapy, University of Illinois at Chicago, Chicago IL 

2013-2016 Assistant Professor, Department of Rehabilitation Medicine, Icahn School of Medicine at Mount 

Sinai, New York, NY 

2016-Present Assistant Professor, Department of Epidemiology and Biostatistics, Michigan State University, 

Grand Rapids, MI; and Director of Outcomes Research, Mary Free Bed Rehabilitation Hospital, 

Grand Rapids, MI 

Committee Service 

1992-1994 Board Member, Association of Physiotherapists and Massage Practitioners of British Columbia 

1994-1997 Board Member, College of Physical Therapists of British Columbia 

1994-1995 Chair, Code of Ethics Development Committee, College of Physical Therapists of British 

Columbia 

1994-1997 Chair, Patient Relations Committee, College of Physical Therapists of British Columbia 

1996-1997 Investigator, Inquiry Committee, College of Physical Therapists of British Columbia 

2004-2007 Department Representative, Graduate Student Society, University of British Columbia 

2006-2007 Chair, Oversight Committee, Graduate Student Society, University of British Columbia 

2006-2007 Member, Back Strain Task Force, Physiotherapy Association of British Columbia 

2007-2008 Graduate Student Representative, Department Head Search Committee, Department of 

Physical Therapy, University of British Columbia (UBC) 

2010 Member, “Physician’s Briefings: Work Related Disorders” Development Committee,

Physiotherapy Association of British Columbia 

2012-2014 Member, American Congress of Rehabilitation Medicine, (ACRM) Measurement Networking 

Group 

2013-Present Member, ACRM, Spinal Cord Injury Interdisciplinary Special Interest Group, Member 

2014-Present Secretary, ACRM, Spinal Cord Injury Measurement Networking Group 

Professional Memberships 

1987-2010 Physiotherapy Association of British Columbia (PABC) 

1987-Present Canadian Physiotherapy Association (CPA), Membership Number 15211 

1991-Present College of Physical Therapists of British Columbia (CPTBC), Reg. 02686 (Inactive as of January 

2011) 

2004-Present American Physical Therapy Association (APTA), Membership Number 166155 

Other Professional Activities 

2010-Present Manuscript Reviewer, Archives of Physical Medicine and Rehabilitation 

2014 Grant reviewer, Rick Hansen Institute 

Biosketches Page 46
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

2014-Present Manuscript Reviewer, PM&R journal 

2014-2015 Special Issue Guest Editor, Topics in Spinal Cord Injury Rehabilitation 

2015 Grant reviewer, National Multiple Sclerosis Society 

2015-Present Manuscript Reviewer, Journal of the Peripheral Nervous System 

C. Contribution to Science 

1. Longitudinal Modeling. My most significant contribution has been in demonstrating and promoting the use 

of longitudinal analytic methods, including trend analysis and individual growth curve modeling, to rehabilitation 

science and practice. Unlike many clinical and research outcomes, most rehabilitation results are not well 

represented as a dichotomy or simple change in status, but rather evolve in a predictable pattern over a period 

of time, which may span multiple interventions. Trend analyses facilitate modeling of best-fit trajectories while 

IGC analyses explain individual variance around the trajectory parameters. Trend analyses permit the 

comparison of recovery rates as an outcome, and thus are suited to examining treatment effects provided 

during recovery in randomized controlled trials. IGC methods can construct individual trajectories, which have 

the prognostic potential, and thus could improve treatment planning and clinical decision-making. In addition to 

previously cited works, also see 

a. Pretz CR, Kozlowski AJ, Chen Y, Charlifue S, Heinemann AW. Trajectories of Life Satisfaction following 

Spinal Cord Injury. Archives of Physical Medicine and Rehabilitation. Forthcoming; In press. 

b. Hart T, Kozlowski AJ, Whyte J, Poulsen I, Kristensen K, Nordenbo A, Heinemann AW. Functional 

recovery after severe traumatic brain injury: an individual growth curve approach. Arch Phys Med Rehabil. 

2014 Nov;95(11):2103-10. Epub 2014 Jul 7. PubMed PMID: 25010537. 

c. Kozlowski AJ, Hyland F, Ludwig ML, Marrone S, Golden S, Yensr N et al. Prototype individual growth 

model for inpatient recovery of motor function in persons recovering from stroke. Phys Ther 2017;Under 

Review. 

2. Measurement and psychometrics. Another significant contribution lies in works to evaluate measurement 

accuracy and precision of new and existing rehabilitation outcome measurement instruments, and to facilitate 

clinical application of such instruments. Instrument validation is an ongoing, context-specific endeavor, which 

facilitates research applications. However, clinical application of an instrument requires the ability to interpret 

change for individual patients, which is not always possibly from published research results. Although recently 

published, the article listed in my personal statement in interpreting individual change on the Neuro-QoL short 

forms has generated positive feedback. In addition to previously cited works, also see 

a. Pretz CR, Kean J, Heinemann AW, Kozlowski AJ, Bode RK, Gebhardt E. A Multidimensional Rasch 

Analysis of the Functional Independence Measure Based on the National Institute on Disability, 

Independent Living, and Rehabilitation Research Traumatic Brain Injury Model Systems National 

Database. J Neurotrauma. 2016 Jul 15;33(14):1358-62. Epub 2016 Jan 28. PubMed PMID: 26559881. 

b. Pretz CR, Kozlowski AJ, Charlifue S, Chen Y, Heinemann AW. Using Rasch motor FIM individual growth 

curves to inform clinical decisions for persons with paraplegia. Spinal Cord. 2014 Sep;52(9):671-6. Epub 

2014 Jun 17. PubMed PMID: 24937699. 

c. Bode RK, Heinemann AW, Kozlowski AJ, Pretz CR. Self-scoring templates for motor and cognitive 

subscales of the FIM instrument for persons with spinal cord injury. Arch Phys Med Rehabil. 2014 

Apr;95(4):676-679.e5. Epub 2013 Dec 3. PubMed PMID: 24309071. 

3. Exoskeleton Feasibility and Safety. I have also provided a significant contribution to the emerging 

literature on powered exoskeleton applications. In addition to the articles cited below, I have two manuscripts in 

preparation from a pilot project to test the feasibility and safety of a powered exoskeleton by persons with 

multiple sclerosis. To our knowledge, this study was the first to test an exoskeleton with persons with MS. 

Biosketches Page 47
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

a. Kozlowski AJ, Bryce TN, Dijkers MP. Time and effort required by persons with spinal cord injury to learn 

to use a powered exoskeleton for assisted walking. Top Spinal Cord Injury Rehabil. Top Spinal Cord Inj 

Rehabil. 2015 April 24; In 21(2):110-21. 

b. Bryce TN, Dijkers MP, Kozlowski AJ. Framework for Assessment of the Usability of Lower-Extremity 

Robotic Exoskeletal Orthoses. Am J Phys Med Rehabil. 2015 Nov;94(11):1000-14. PubMed PMID: 

26098923. 

c. Kozlowski AJ, Fabian M, Lad D, Delgado A. Feasibility and safety of a powered exoskeleton for assisted 

walking for persons with multiple sclerosis: a single-group preliminary study. Arch Phys Med Rehabil. 2017; 

under review. 

d. Delgado A, Lad D, Fabian M, Kozlowski AJ. A Cross-Sectional Study on the Metabolic and Physiological 

Responses to Exoskeleton-2 Assisted Walking for Persons with Multiple Sclerosis. Arch Phys Med Rehabil. 

2017; under review. 

Complete List of Published Work in MyBibliography: 

http://www.ncbi.nlm.nih.gov/sites/myncbi/1FAZBdTNHbUkE/bibliography/47391004/public/?sort=date&directio 

n=ascending 

D. Research Support 

ON GOING RESEARCH SUPPORT 

None 

COMPLETED RESEARCH SUPPORT IN LAST 3 YEARS 

1. Title: Feasibility and utility of routine exoskeleton walking. 

Role: PI. Funding Agency: Department of Rehabilitation Medicine Development Fund (anonymous 

donations collected with assistance of Mount Sinai’s Development Office). 

Grant #: Not Applicable. 

Funding period: 09/01/2013 – 08/31/2015. 

Project Goal: Test the safety and feasibility of a powered lower extremity exoskeleton for persons with 

spinal cord injury. 

2. Title: Ekso Wearable Robotic Walking System for Persons with SCI. 

Role: PI. Funding Agency: Craig H. Neilsen Foundation – Quality of Life. 

Grant #: 250542. 

Funding period: 07/01/2013 – 06/30/2014. 

Project Goal: Fund purchase of a powered lower extremity exoskeleton for spinal cord injury research. 

3. Title: Mount Sinai Spinal Cord Injury Research Program Shared Equipment and Bridge Funding. 

Role: Co-Investigator (PI: Marcel Dijkers, PhD). 

Funding Agency: New York State Department of Health and the Spinal Cord Injury Research Board. 

Grant #: C029126. 

Funding period: 10/01/2013 – 02/28/2014. 

Project Goal: Fund purchase of equipment for spinal cord injury research. 

4. Title: Modeling Functional Outcome from Spinal Cord Injury and Traumatic Brain Injury Model Systems 

Databases with Individual Growth Methods. 

Role: Sub-Investigator (PI: Ken Ottenbacher, PhD). 

Funding Agency: NIH. 

Grant #: R24-HD065702. 

Funding period: 10/01/2013 – 02/28/2014. 

Project Goal: Fund effort and training for modeling of rehabilitation outcomes for persons with spinal cord 

injury or traumatic brain injury as trajectories. 

Biosketches Page 48
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

5. Title: Rehabilitation Robotics Research Program Research Assistant Funding. 

Role: PI. 

Funding Agency: Peter Jay Sharp Foundation. 

Grant #: Not Applicable. 

Funding period: 07/01/2014 – 06/30/2015. 

Project Goal: Fund effort for a Research Assistant. 

6. Title: Expanding capacity for multi-site SCI research. 

Role: PI. 

Funding Agency: New York State Department of Health and the Spinal Cord Injury Research Board. 

Grant #: C030090. 

Funding period: 10/01/2014 – 02/28/2015. 

Project Goal: Fund effort for research personnel and purchase of equipment for spinal cord injury 

research. 

7. Title: Spinal Cord Injury Research Institutional Support. 

Role: PI. 

Funding Agency: New York State Department of Health and the Spinal Cord Injury Research Board. 

Grant #: C030171 

Funding period: 12/01/2014 – 03/31/2015. 

Project Goal: Fund effort for research personnel and purchase of equipment for spinal cord injury 

research. 

8. Title: Feasibility of the ReWalkTM exoskeleton-assisted walking for persons with multiple sclerosis. 

Role: PI. 

Funding Agency: National Multiple Sclerosis Society. 

Grant #: PP3359. 

Funding period: 01/01/2015 – 12/31/2015. 

Project Goal: Test the safety and feasibility of a powered lower extremity exoskeleton for persons with 

multiple sclerosis. 

Biosketches Page 49
4 

OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  1

❍ Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project 

Enter name of Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2019 End Date*: 03-31-2020 Budget Period: 1 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allen Heinemann Ph.D PD/PI 3.00 

2 . Dr. Leora Cherney PhD PD/PI 3.00 

3 . Dr. Elliot Roth Co-Investigator 0.24 

4 . Dr. Marwan Baliki PhD Co-Investigator 1.20 

5 . Dr. Andrea Domenighetti PhD Co-Investigator 1.20 

6 . Dr. Linda Foster PhD Co-Investigator 1.20 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 SLP 6.00 

1 Project Manager 6.00 

1 Research Assistant 12.00 

1 Research Assistant 6.00 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 50

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 1 

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project ❍ Subaward/Consortium 

Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2019 End Date*: 03-31-2020 Budget Period: 1 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 51

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 1 

❍ Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project 

Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2019 End Date*: 03-31-2020 Budget Period: 1 

F. Other Direct Costs Funds Requested ($)* 

1. Materials and Supplies 

2. Publication Costs 

3. Consultant Services 

4. ADP/Computer Services 

5. Subawards/Consortium/Contractual Costs 

6. Equipment or Facility Rental/User Fees 

7. Alterations and Renovations 

8 . Subject Reimbursement 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MTDC 

Total Indirect Costs 

Cognizant Federal Agency HHS, Arif Karim 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1234-

Heinemann_BudgetJust_Final.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 52

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

-----

0MB Number: 4040-0001 

Contact PD/Pl: Heinemann, Allen Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period 2 

ORGANIZATIONAL DUNS*: 

Budget Type*: • Project O Subaward/Consortium 

Enter name of Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2020 End Date*: 03-31-2021 Budget Period: 2 

I.._.......... 

A. Senior/Key Person.

Prefix First Name* Middle. Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. ••••••••••••-•••• Allen -• .. ••••-•••••••••-•••••••••-•••••••••••••••••••••••••• Heinemann ••••••••••••••••••••••••••••••••••••••••--••• Ph.D •o•-•••••-• PD/Pl o••-•••••••-••••••••-•••••••-•••••• 2.40 ....... ...................................................J I.._.......... .. .............. -........ . 2. Dr. Leora Cherney PhD PD/PI ....... 2.40 ...................................................J I.._.......... .. .............. -........ . .. .............. -........ . .. ..... 1.20 ...................................................J I.._.......... .. .............. -........ . 1.20. .. ..... ...................................................J I.._.......... .. .............. -........ . .. ..... 1.20 ...................................................J I.. _.......... .. .............. -.......... .. Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

6. Dr. Linda Foster PhD Co-Investigator

4. Dr. Marwan Baliki PhD Co-Investigator

5. Dr. Andrea Domenighetti PhD Co-Investigator

3. Dr. Elliot Roth Co-Investigator 0.24.

B. Other Personnel.

Number of Project Role*. Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel*.

Post Doctoral Associates ................................................................................................................................................................................................................................................................................................................................................................................... Graduate Students 

....... " ..................... Undergraduate.

Students.......................................................................................................................................................... " ................... " ........................... " .......................................... " ................... " .................. ".. Secretarial/Clerical .......................................................................................................................................................................................................................................................................................................................................................................................... SLP 6.00 

Project.Manager. 6.00 ....... - ..................... . .................................................................................................................. . ............................................... -.............. .. Research Assistant 12.00 ............................................................................................................................................................................................................................................................. Research Assistant 6.00 

Research Associate 0.60 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A 8} (Funds Requested) 

Page 53 

Tracking Number: GRANT12670047 Funding Opportunity Number: PA 18 287 . Received Date: 2018 07 05T15:37:27 000-04:00

5 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 2 

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project ❍ Subaward/Consortium 

Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2020 End Date*: 03-31-2021 Budget Period: 2 

C. Equipment Description

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions)

2. Foreign Travel Costs

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance

2. Stipends

3. Travel

4. Subsistence

5. Other:

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

 Page 54

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 2 

❍ Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project 

Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2020 End Date*: 03-31-2021 Budget Period: 2 

F. Other Direct Costs Funds Requested ($)* 

1. Materials and Supplies 

2. Publication Costs 

3. Consultant Services 

4. ADP/Computer Services 

5. Subawards/Consortium/Contractual Costs 

6. Equipment or Facility Rental/User Fees 

7. Alterations and Renovations 

8 . Subject Reimbursement 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MTDC 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1234-

Heinemann_BudgetJust_Final.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 55

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  3

❍ Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project 

Enter name of Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2021 End Date*: 03-31-2022 Budget Period: 3 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allen Heinemann Ph.D PD/PI 2.40 

2 . Dr. Leora Cherney PhD PD/PI 2.40 

3 . Dr. Elliot Roth Co-Investigator 0.24 

4 . Dr. Marwan Baliki PhD Co-Investigator 1.20 

5 . Dr. Andrea Domenighetti PhD Co-Investigator 1.20 

6 . Dr. Linda Foster PhD Co-Investigator 1.20 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 144,685.00 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 SLP 6.00 

1 Project Manager 6.00 

1 Research Assistant 12.00 

1 Research Assistant 6.00 

1 Research Associate 0.60 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 56

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 

5 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 3 

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project ❍ Subaward/Consortium 

Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2021 End Date*: 03-31-2022 Budget Period: 3 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 57

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 3 

❍ Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project 

Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2021 End Date*: 03-31-2022 Budget Period: 3 

F. Other Direct Costs Funds Requested ($)* 

1. Materials and Supplies 

2. Publication Costs 

3. Consultant Services 

4. ADP/Computer Services 

5. Subawards/Consortium/Contractual Costs 

6. Equipment or Facility Rental/User Fees 

7. Alterations and Renovations 

8 . Subject Reimbursement 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MTDC 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1234-

Heinemann_BudgetJust_Final.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 58

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  4

❍ Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project 

Enter name of Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2022 End Date*: 03-31-2023 Budget Period: 4 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allen Heinemann Ph.D PD/PI 2.40 

2 . Dr. Leora Cherney PhD PD/PI 2.40 

3 . Dr. Elliot Roth Co-Investigator 0.24 

4 . Dr. Marwan Baliki PhD Co-Investigator 1.20 

5 . Dr. Andrea Domenighetti PhD Co-Investigator 1.20 

6 . Dr. Linda Foster PhD Co-Investigator 1.20 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 SLP 6.00 

1 Project Manager 6.00 

1 Research Assistant 12.00 

1 Research Assistant 6.00 

1 Research Associate 0.60 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 59

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 

5 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 4 

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project ❍ Subaward/Consortium 

Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2022 End Date*: 03-31-2023 Budget Period: 4 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 60

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 4 

❍ Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project 

Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2022 End Date*: 03-31-2023 Budget Period: 4 

F. Other Direct Costs Funds Requested ($)* 

1. Materials and Supplies 

2. Publication Costs 

3. Consultant Services 

4. ADP/Computer Services 

5. Subawards/Consortium/Contractual Costs 

6. Equipment or Facility Rental/User Fees 

7. Alterations and Renovations 

8 . Subject Reimbursement 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MTDC 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1234-

Heinemann_BudgetJust_Final.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 61

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

-----

I.._.......... 

0MB Number: 4040-0001 

Contact PD/Pl: Heinemann, Allen Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period 5 

ORGANIZATIONAL DUNS*: 

Budget Type*: • Project O Subaward/Consortium 

Enter name of Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2023 End Date*: 03-31-2024 Budget Period: 5 

A. Senior/Key Person.

Prefix First Name* Middle. Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allen Heinemann Ph.D PD/Pl 2.40 ••••••••••••-••••-• .. ••••-•••••••••-•••••••••-••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••--••• •-•••• •o•-•••••-•o••-•••••••-••••••••-•••••••-•••••• ....... ...................................................J I.._.......... .. .............. -........ . 2. Dr. Leora Cherney PhD PD/PI 2.40 ....... ...................................................J I.._.......... .. .............. -........ . 3. Dr. Elliot Roth Co-Investigator 0.24 .. .............. -........ . 4. Dr. Marwan Baliki PhD Co-Investigator 1.20 ....... ...................................................J I.._.......... .. .............. -........ . 5. Dr. Andrea Domenighetti PhD Co-Investigator .. ..... 1.20 ...................................................J I.._.......... .. .............. -........ . 1.20 6. Dr. Linda Foster PhD Co-Investigator .. ..... ...................................................J I.. _.......... .. .............. -.......... .. Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel.

Number of Project Role*. Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel*.

Post Doctoral Associates ................................................................................................................................................................................................................................................................................................................................................................................... Graduate Students 

....... " ..................... Undergraduate.

Students.......................................................................................................................................................... " ................... " ........................... " .......................................... " ................... " .................. ".. Secretarial/Clerical .......................................................................................................................................................................................................................................................................................................................................................................................... SLP 6.00 

Project.Manager. 6.00 ....... - ..................... . .......................................................... ......................................................................................................... - .............. ... Research Assistant 12.00 ............................................................................................................................................................................................................................................................. Research Assistant 6.00 

Research Associate 0.60 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A 8} (Funds Requested) 

Page 62 

Tracking Number: GRANT12670047 Funding Opportunity Number: PA 18 287 . Received Date: 2018 07 05T15:37:27 000-04:00

5 
Contact PD/Pl: Heinemann, Allen 

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 5 

ORGANIZATIONAL DUNS*: 

Budget Type*: • Project O Subaward/Consortium 

Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2023 End Date*: 03-31-2024 Budget Period: 5 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1.Domestic Travel Costs (Incl. Canada, Mexico, and U.S.Possessions) 

2. Foreign Travel Costs 

Total Travel Cost -

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5.. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Page 63 

Funding Opportunity Number: PA 18 287 . Received Date: 

2018-07-05T15 37:27.000 04:00 

Tracking Number: GRANT12670047 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 5 

❍ Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ● Project 

Organization: Rehabilitation Institute of Chgo dba Shirley Ryan AbilityLab 

Start Date*: 04-01-2023 End Date*: 03-31-2024 Budget Period: 5 

F. Other Direct Costs Funds Requested ($)* 

1. Materials and Supplies 

2. Publication Costs 

3. Consultant Services 

4. ADP/Computer Services 

5. Subawards/Consortium/Contractual Costs 

6. Equipment or Facility Rental/User Fees 

7. Alterations and Renovations 

8 . Subject Reimbursement 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MTDC 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1234-

Heinemann_BudgetJust_Final.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 64

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
Budget Justification 

Shirley Ryan Abilitylab (formerly the Rehabilitation Institute of Chicago) 

Personnel 

Table 1: RIC Personnel Allocation (Calendar M onths) 

Personnel Role 

Year 

1 

Year 

2 

Year 

3 

Year 

4 

Year 

5 

Allen Heinemann Co-Principal lnvestiaator 3.00 2.40 2.40 2.40 2.40 

Leora Cherney Co-Principal Investigator 3.00 2.40 2.40 2.40 2.40 

Elliot Roth Co-Investigator 0.24 0.24 0.24 0.24 0.24 

Linda Foster Co-lnvestiaator 1 .20 1 .20 1 .20 1 .20 1 .20 

Andrea Domenighetti Co-Investigator 1 .20 1 .20 1 .20 1 .20 1 .20 

Marwan Baliki Co-Investigator 1 .20 1 .20 1 .20 1 .20 1 .20 

TBD Proiect Manaaer 6.00 6.00 6.00 6.00 6.00 

Raieswari Pichika Research Associate 0.60 0.60 0.60 0.60 

TBD Research Assistant 12.00 1 2.00 12.00 12.00 12.00 

TBD Research Assistant 6.00 6.00 6.00 6.00 6.00 

Rosalind Hurwitz Speech Language Pathologist 6.00 6.00 6.00 6.00 6.00 

Allen Heinemann, PhD, PD/Pl, 3 CAL in Y1 when the grant is starting up and 2.4 CAL in Y2-Y5. As the 

Director of the Center for Rehabilitation Outcomes Research, Dr. Heinemann has over 25 years of experience 

in outcomes research and will provide scientific leadership to ensure fulfillment of the programmatic, fiscal , and 

reporting requirements of this project. In addition, he will oversee the project manager and data analyst. 

Leora R. Cherney, PhD, PD/P! , 3 CAL in Y1 when the grant is starting up and 2.4 calendar months Y2-Y5. Dr. 

Cherney is the Scientific Chair, Think & Speak at the SRALab and the Director of the Center for Aphasia 

Research and Treatment. She has over 30 years of experience in adult neurologic communication disorders, 

with an emphasis on treatment research in persons with aphasia. She will provide scientific and fiscal 

leadership in all aspects of the project, and specifically will oversee the speech-language pathologist and 

research assistants relative to data collection from participants with aphasia. 

Elliot Roth, MD, Co-Investigator, 0.24 CAL months in each of Y1-Y5. Dr. Roth is the Chair of the 

Department of Physical Medicine & Rehabilitation at Northwestern University's Feinberg School of Medicine 

and an attending at the SRALab. His primary role will be to provide expertise in stroke rehabilitation including 

assistance with determining subject eligibility and review of clinical MRI scans. 

Linda Foster, MS, Co-Investigator, will serve as site Pl at ABRH at 1 .20 CAL in Y1-Y5. As a Physical 

Therapist and researcher who has significant experience with the stroke population, she will work with the 

research speech-language pathologist to oversee the site research assistant in recruitment and data collection. 

Andrea Domenighetti, PhD, Co-Investigator, an Investigator in the Biologics Lab at SRALab will oversee the 

genomics aspect of the project. He will devote 1 .20 CAL months in Y1 -Y5. He will also work closely with 

Rajeswari Pichika PhD, who will conduct the actual assays in Y2 and Y4. Their expertise is in biochemical 

and molecular properties of muscle and they are investigating novel methods of cell culture assays in stroke. 

Dr. Domenighetti, will participate in publication and dissemination of study results including abstracts, 

presentations, and manuscripts that arise from this work. 

Rajeswari Pichika, PhD. , Research Associate in the Biologics Lab at the SRALab will conduct the assays in 

under the direction of Dr. Domenighetti. She will devote 0.60 CAL months in Y2-Y5. 

M arwan Baliki, PhD, Co-Investigator, will oversee the imaging aspects of the project, including the conduct 

and interpretation of the resting state and anatomical scans obtained from SRALab participants. He also will 

review clinical scans from participants at the ABRH and MFRH sites to determine lesion size and location. Dr. 

Page 65 

Attachment 

1 
Budget Justification 

2 

state of the art brain imaging technology. He will devote 1.20 CAL months in Y1-Y5. He 

 results including abstracts, presentations, and 

 Y1-Y5 to overseeing day-to-day project operations 

 meetings to facilitate project aims and requirements, ensure data 

(including saliva samples) and documentation consistency across sites, monitor project enrollment, 

 at the SRALab. Together with the research speech-language pathologist, he will 

 Research Speech-Language Pathologist has over ten years’ experience 

 Aphasia Research and Treatment at the SRALab where her primary responsibility has been 

 project, she will devote 6 CAL months effort in Y1-Y5 to 

 in supported communication techniques for 

 in the administration of the assessment battery, periodically 

 and rescore a portion of the assessments (at least 10%) to ensure 

months effort in Y1-Y5 to recruitment, screening potential 

 and executing data collection activities at the SRALab (formerly the 

Rehabilitation Institute of Chicago) under the direction of the research speech-language pathologist. She also 

 making monthly phone calls to participants to review their participation in any outpatient 

 other communication-focused activities. She will be responsible for 

 activities, under the direction of the project manager. 

effort in Y1-Y5 to recruitment, screening potential 

 and executing data collection activities at ABRH under the direction of 

She also will be responsible for making monthly phone calls to 

 participation in any outpatient therapy, aphasia conversation groups, or other 

She will be responsible for maintaining accurate organization and record of 

 manager. 

calculated at DHHS approved rate: %. % inflation rate is used for all salary 

the Co-Principal Investigators (and others as appropriate) to disseminate 

per meeting in Y1-Y4; 4 meetings in Y5; Total for 5 

fares, hotel, ground transportation, and per diem 

by automobile and reimbursed at the rate allowed by the IRS; economy airfare 

charges and the General Services Administration-allowed per diem rates are used. Travel expenses will be 

cover expenses associated with project start-up 

 the study protocol and standard operating procedures, paper to print fliers and test forms, 

 budgeted over Y2-Y5 to cover printing and test form 

(iPad Neuro-QoL Application, SPSS Base/Advanced/Regression Statistics 

Package, Mplus Base Program/Combination Add-On and Winsteps) 

 Page 66

 

 

 

 

Baliki has expertise in 

will participate in publication and dissemination of study 

manuscripts that arise from this work. 

TBD Project Manager, will devote 6 CAL months effort in 

across sites. He will organize project 

collection 

and schedule rs-fMRIs 

supervise the SRALab’s research assistants. 

Rosalind Hurwitz, MA CCC-SLP, 

in the Center for 

as a “blind” assessor in various clinical trials. In this 

train the site PIs, project manager and research assistants 

aphasia. She will also train the research assistants 

observe them to ensure consistency, 

reliability. 

TBD, Research Assistant, will devote 12 CAL 

participants, obtaining informed consent, 

will be responsible for 

therapy, aphasia conversation groups, or 

maintaining accurate organization and record of all study 

TBD, Research Assistant, will devote 6 calendar months 

participants, obtaining informed consent, 

the research speech-language pathologist. 

participants to review their 

communication-focused activities. 

all study activities, under the direction of the project 

Fringe benefits 

RIC’s fringe benefits are 

calculations. 

Travel 

Travel expenses are budgeted for 

study findings during Y1-Y5 (2 meetings per year at 

years = ). Expenses cover conference fees, airline 

expenses. Ground travel will be 

reimbursed in accordance with SRALab policy. 

Other Direct Costs 

Office supplies are budgeted at 

Office Supplies 

for Y1. Y1 will 

including binders for 

and other general office supplies. An additional $ is

needs. 

Computer Software 

). 

Attachment
Budget Justification 

3 

 1, the Connors Continuous Performance Test 3 software 

) will need to be purchased for ABRH and MFRH. The SRALab already has 

 licensing for the iPad Toolbox Application which will be 

 the computer adapted administration of the Neuro-QoL item banks. SPSS, Mplus, and Winsteps 

 We have budgeted SPSS licenses at each beginning in Y2 

and Winsteps require a one-time fee of and 

 and Winsteps licenses for Data Analyst in Y1 and Co-Investigator 

Each site will require a Western Aphasia Batteryreplenishment of forms in subsequent years. Other 

 will need to be photocopied and are included under office supplies. 

an iPad with accommodation accessories ) 

videocamera and tripod so that every assessment 

 needed. We estimate the cost of this equipment to be per site for a 

 We expect that 

 at the start of their participation in the project and prior to any dropper participant for an estimated participants. 

 a reduced rate of per minutes of scanning 

to peer-reviewed journals. Dissemination will continue 

 with an expected total budget of to cover open access fees. 

recruit 400 participants with a first admission due to stroke and aphasia and admitted to one of the 3 

 will over-recruit to account for 15% attrition at 6 months and another 

Each site will recruit 100 participants with complete 

after the inpatient rehabilitation discharge assessment. 

for the 12-month visit, and for the 18-month 

 will receive a total of which is budgeted at a total 

 those subjects who do not complete all assessments. The 

 energy, and transportation costs. 

DHHS approved rates: 

and thereafter- Provisional 

 Page 67

 

 

 

 

 

 

 

 

A total of is budgeted for software. In Year – 

each for a total of 

one for use there. We also budgeted per year for 

required for 

licenses will be required for data analysis. 

for the Data Analyst and Y3 for the PI. Mplus 

respectively. We will purchase Mplus 

Kozlowski in Y2. 

Lab Equipment ($ ) 

Data collection requires 

Revised to be purchased in Y1 with 

of equipment during Y1. 

behavioral assessments 

In Y1, each site will also require 

for the NeuroqoL administration. 

The research assistant at each site will be provided with a 

DNA Saliva Test Kits have been budgeted at

can be recorded for later review as 

total of in Y1. 

saliva collection will occur on all subjects 

out. These funds are distributed through Y1-Y3. 

Radiology services ) 

We estimate that the resting state fMRI costs will be 

Research radiology costs at the SRALab are offered at 

time. 

Publication Costs 

By the end of Y2, we expect to submit publications 

through the end of the project 

Subject Reimbursement ($ Y1-Y5) 

We will 

data collection facilities during Y1-Y3. We 

10% attrition at the 18-month data collection time points. 

data across all time points. Participants will receive 

The honorarium will increase to for the 6-month visit, 

follow-up. Therefore, those completing all assessments 

of . An additional is budgeted for 

honorarium covers subjects’ time, 

Indirect Costs 

F&A has been calculated based on the following 

• MTDC Beginning 09/01/18 – 08/31/20 

Attachment
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Budget Justification 

Mary Free Bed Rehabilitation Hospital 

Defining Trajectories of Linguistic, Cognitive-Communicative and Quality of Life 

Outcomes in Aphasia 

Personnel 

Allan J. Kozlowski PhD, Site Principal Investigator (2.4 CAL months for Years 1-5) 

Dr. Kozlowski is contracted from Michigan State University – College of Human Medicine, 

Department of Epidemiology and Biostatistics, to be the Director of Outcomes Research at 

Mary Free Bed Rehabilitation Hospital (MFBRH). As Site PI he will oversee the administration 

and operations of the Mary Free Bed site and coordinate the communication, interactions and 

data sharing with the research team at Shirley Ryan AbilityLab. Dr. Kozlowski will play a major 

role in statistical analysis and data interpretation. He will also participate in administrative 

meetings. (Dr. Kozlowski’s salary is contracted directly from Michigan State University) 

John F. Butzer MD, Site Senior Advisor (0.6 CAL months for Years 1-5) 

Dr. Butzer is the Director of Research at MFBRH. As a senior manager at MFBRH he will 

oversee the personnel and address institutional concerns arising from site administration and 

operations. Dr. Butzer will advise Dr. Kozlowski on institutional and staffing issues. He will also 

participate in administrative meetings. 

TBD, Research Assistant (6 CAL months for Years 1 & 5; 12 CAL months for Years 2-4) 

The research assistant will report directly to Ms. Virva, the Site Coordinator, to assist with the 

engagement and recruitment of individuals with stroke and their families. S/he will be 

responsible for timely data collection and be knowledgeable in test administration and 

supported communication strategies for persons with aphasia. 

Roberta Virva PT, MS, Site Coordinator (1.2 CAL months for Years 1-5) 

Ms. Virva’s responsibilities include managing the day to day activities of the project and to 

oversee and coordinate the activities of the other personnel. She has responsibility for 

developing systems to monitor progress, to identify problems, and to take appropriate 

corrective action. She will also participate in analyzing and interpreting results and will 

participate in the administrative meetings as needed. 

TBD, Speech-Language Pathologist (0.24 calendar months for Years 1-4) 

The speech-language pathologist (SLP) will report directly to Ms. Virva, the Site Coordinator, 

to assist with review and coding of SLP therapy activities during data collection. S/he will also 

advise the research team on questions of eligibility regarding aphasia, and advise the research 

assistant with regard to interaction with participants and aphasia test administration, as 

needed. 

Salaries are anticipated to increase annually 

Fringe Rate 

Fringe benefits are calculated at % 

Indirect Costs 

The indirect cost rate for subcontracts in this proposal is set at the de minimis rate of as 

MFBRH does not yet have a negotiated F&A rate. 

 Page 68 Attachment

4 
 

 

 

 

 

 

 

 

 

 

Budget Justification 

Michigan State University 

Dr. Kozlowski is an MSU faculty member with a fixed term employee with contract to MFRH. His effort will be 

paid through MSU. Subsequently, MSU will receive an Off-campus indirect cost rate 

Northwestern University 

Year 1: 5% 

Years 2-5: 15% 

responsible for the development and implementation of statistical and data management components 

of the project, including developing data collection tools and case report forms, setting up the REDCAP 

database, overseeing data quality throughout the study period, preparing quality assurance reports, 

and performing statistical analysis of the data. has extensive experience as a 

biostatistician working with observational studies, clinical trials and data management, and she is 

currently the Leader of the Statistics and Data Management Core leader for a multi-site NIDILRRfunded clinical trial of hypoxia in patients with spinal cord injury. 

Data Analyst (MS level) 

Year 1: 15% 

Years 2-5: 5%

collection tools and case report forms, set up the REDCap database, produce regular data monitoring 

reports, and assist with final statistical analyses. 

PhD, will lead this project’s Statistical and Data Management Core, which will be 

A Data Analyst (MS level) will be hired to work under guidance to develop data

 Page 69 Attachment

5 
RESEARCH & RELATED BUDGET - Cumulative Budget 

Totals ($)

Section A, Senior/Key Person

Section B, Other Personnel

Total Number Other Personnel

Total Salary, Wages and Fringe Benefits

(A+B)

Section C, Equipment

Section D, Travel

1. Domestic 

2. Foreign

Section E, Participant/Trainee Support

Costs

1. Tuition/Fees/Health Insurance

2. Stipends

3. Travel

4. Subsistence

5. Other

6. Number of Participants/Trainees

Section F, Other Direct Costs

1. Materials and Supplies

2. Publication Costs

3. Consultant Services

4. ADP/Computer Services

5. Subawards/Consortium/Contractual

Costs

6. Equipment or Facility Rental/User

Fees

7. Alterations and Renovations

8. Other 1

9. Other 2

10. Other 3

Section G, Direct Costs

(A thru F)

Section H, Indirect Costs

Section I, Total Direct and Indirect Costs

(G + H)

Section J, Fee

Section K, Total Costs and Fee (I + J)

Tracking Number: GRANT12670047 Page 70

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
1 

OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  1

ORGANIZATIONAL DUNS*

Budget Type*: ❍ Project ● Subaward/Consortium

Enter name of Organization: Northwestern University 

Start Date*: 04-01-2019 End Date*: 03-31-2020 Budget Period: 1 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . PhD PD/PI 0.60 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 Master's Level Statistician 1.80 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 71

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 1 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Northwestern University 

Start Date*: 04-01-2019 End Date*: 03-31-2020 Budget Period: 1 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 72

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 1 

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Organization: Northwestern University 

Start Date*: 04-01-2019 End Date*: 03-31-2020 Budget Period: 1 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MTDC 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1261-NU Justification.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 73

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
1 

OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  2

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium

Enter name of Organization: Northwestern University 

Start Date*: 04-01-2020 End Date*: 03-31-2021 Budget Period: 2 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . PhD PD/PI 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 Master's Level Statistician 0.60 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 74

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 2 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Northwestern University 

Start Date*: 04-01-2020 End Date*: 03-31-2021 Budget Period: 2 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 75

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 2 

● Subaward/Consortium 

Organization: Northwestern University 

ORGANIZATIONAL DUNS* 

Budget Type*: ❍ Project 

Start Date*: 04-01-2020 End Date*: 03-31-2021 Budget Period: 2 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MTDC 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1261-NU Justification.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 76

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
1 

OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  3

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Enter name of Organization: Northwestern University 

Start Date*: 04-01-2021 End Date*: 03-31-2022 Budget Period: 3 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . PhD PD/PI 0.60 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 Master's Level Statistician 0.60 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 77

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 3 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Northwestern University 

Start Date*: 04-01-2021 End Date*: 03-31-2022 Budget Period: 3 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 78

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 3 

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Organization: Northwestern University 

Start Date*: 04-01-2021 End Date*: 03-31-2022 Budget Period: 3 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MTDC 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1261-NU Justification.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 79

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
1 

OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  4

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Enter name of Organization: Northwestern University 

Start Date*: 04-01-2022 End Date*: 03-31-2023 Budget Period: 4 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. PhD PD/PI 0.60 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 Master's Level Statistician 0.60 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 80

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 4 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Northwestern University 

Start Date*: 04-01-2022 End Date*: 03-31-2023 Budget Period: 4 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 81

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 4 

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Organization: Northwestern University 

Start Date*: 04-01-2022 End Date*: 03-31-2023 Budget Period: 4 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MTDC 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1261-NU Justification.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 82

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
1 

OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  5

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Enter name of Organization: Northwestern University 

Start Date*: 04-01-2023 End Date*: 03-31-2024 Budget Period: 5 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. PhD PD/PI 1.80 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 Master's Level Statistician 0.60 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 83

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 5 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Northwestern University 

Start Date*: 04-01-2023 End Date*: 03-31-2024 Budget Period: 5 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 84

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 5 

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Organization: Northwestern University 

Start Date*: 04-01-2023 End Date*: 03-31-2024 Budget Period: 5 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MTDC 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1261-NU Justification.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 85

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
Page 86 

Attachment 
RESEARCH & RELATED BUDGET - Cumulative Budget 

Totals ($)

Section A, Senior/Key Person

Section B, Other Personnel

Total Number Other Personnel

Total Salary, Wages and Fringe Benefits

(A+B)

Section C, Equipment

Section D, Travel

1. Domestic 

2. Foreign

Section E, Participant/Trainee Support

Costs

1. Tuition/Fees/Health Insurance

2. Stipends

3. Travel

4. Subsistence

5. Other

6. Number of Participants/Trainees

Section F, Other Direct Costs

1. Materials and Supplies

2. Publication Costs

3. Consultant Services

4. ADP/Computer Services

5. Subawards/Consortium/Contractual

Costs

6. Equipment or Facility Rental/User

Fees

7. Alterations and Renovations

8. Other 1

9. Other 2

10. Other 3

Section G, Direct Costs

(A thru F)

Section H, Indirect Costs

Section I, Total Direct and Indirect Costs

(G + H)

Section J, Fee

Section K, Total Costs and Fee (I + J)

Tracking Number: GRANT12670047 Page 87

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  1

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium

Enter name of Organization: Michigan State University 

Start Date*: 04-01-2019 End Date*: 03-31-2020 Budget Period: 1 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allan Kozlowski PhD PD/PI 2.40 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 88

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 1 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Michigan State University 

Start Date*: 04-01-2019 End Date*: 03-31-2020 Budget Period: 1 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 89

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 1 

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Organization: Michigan State University 

Start Date*: 04-01-2019 End Date*: 03-31-2020 Budget Period: 1 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MODIFIED TOTAL DIRECT COST 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1262-MSU_Budget 

Justification.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 90

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  2

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium

Enter name of Organization: Michigan State University 

Start Date*: 04-01-2020 End Date*: 03-31-2021 Budget Period: 2 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allan Kozlowski PhD PD/PI 2.40 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 91

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 2 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Michigan State University 

Start Date*: 04-01-2020 End Date*: 03-31-2021 Budget Period: 2 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 92

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 2 

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Organization: Michigan State University 

Start Date*: 04-01-2020 End Date*: 03-31-2021 Budget Period: 2 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MODIFIED TOTAL DIRECT COST 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1262-MSU_Budget 

Justification.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 93

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  3

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium

Enter name of Organization: Michigan State University 

Start Date*: 04-01-2020 End Date*: 03-31-2022 Budget Period: 3 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allan Kozlowski PhD PD/PI 2.40 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 94

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 3 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Michigan State University 

Start Date*: 04-01-2020 End Date*: 03-31-2022 Budget Period: 3 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 95

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 3 

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Organization: Michigan State University 

Start Date*: 04-01-2020 End Date*: 03-31-2022 Budget Period: 3 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MODIFIED TOTAL DIRECT COST 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1262-MSU_Budget 

Justification.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 96

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  4

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium

Enter name of Organization: Michigan State University 

Start Date*: 04-01-2022 End Date*: 03-31-2023 Budget Period: 4 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allan Kozlowski PhD PD/PI 2.40 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 97

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 4 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Michigan State University 

Start Date*: 04-01-2022 End Date*: 03-31-2023 Budget Period: 4 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 98

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
Contact PD/Pl: Heinemann, Allen 

• Subaward/Consortium 

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 4 

ORGANIZATIONAL DUNS*: 

Budget Type*: O Project 

Organization: Michigan State University 

Start Date*: 04-01-2022 End Date*: 03-31-2023 Budget Period: 4 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MODIFIED TOTAL DIRECT COST -

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

Funds Requested ($1"1 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1262-MSU_Budget 

Justification.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Page 99 

Funding Opportunity Number: PA 18 287 . Received Daete: 

2018-07-05T15 37:27.000 04:00 

Tracking Number: GRANT12670047 
OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  5

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium

Enter name of Organization: Michigan State University 

Start Date*: 04-01-2023 End Date*: 03-31-2024 Budget Period: 5 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allan Kozlowski PhD PD/PI 2.40 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 100

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 5 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Michigan State University 

Start Date*: 04-01-2023 End Date*: 03-31-2024 Budget Period: 5 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 101

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 5 

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Organization: Michigan State University 

Start Date*: 04-01-2023 End Date*: 03-31-2024 Budget Period: 5 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . MODIFIED TOTAL DIRECT COST 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1262-MSU_Budget 

Justification.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 102

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

BUDGET JUSTIFICATION 

Subawardee: Michigan State University 

SENIOR/KEY PERSONNEL: 

Principal Investigator: Dr. Allan Kozlowski will serve as Co-Investigator to provide expertise on longitudinal 

methodology and statistical modeling on this project.Dr. Kozlowski has the knowledge and experience in study 

design and model building using hierarchical linear regression methods to capture individual differences in 

change over time. Funds are requested to support 20% of PI’s effort (around 2.4 Person-month) each year over 

the five years of the project period. An escalation rate of % per year for PI’s salary has been calculated for the 

period. 

FRINGE BENEFITS: 

MSU Faculty and Staff fringes should be calculated using the Specific Identification (SI) method. Under SI, 

fringe costs are based on average actual costs and individual participation in retirement. MSU charges fringe 

benefits as direct costs and charges sponsors for actual costs only. 

INDIRECT COSTS: 

MSU’s Facilities and Administrative (F&A) rates is % On-campus and % Off-campus for the period from 

July 1, 2016 to June 30, 2019. % Off-campus F&A rate is used for this project as Dr. Kozlowski is located in 

MFB facilities. Modified Total Direct Costs (MTDC) is the base to which the F&A rate is applied. MTDC 

consists of all direct salaries and wages, applicable fringe benefits, materials and supplies, services, travel and up 

to the first of each subaward. MTDC shall exclude equipment, capital expenditures, charges for patient 

care, rental costs, tuition remission, scholarships and fellowships, participant support costs and the portion of 

each subaward in excess of This agreement was negotiated through the Department of Health and 

Human Services, 

 Page 103 Attachment
RESEARCH & RELATED BUDGET - Cumulative Budget 

Totals ($)

Section A, Senior/Key Person

Section B, Other Personnel

Total Number Other Personnel

Total Salary, Wages and Fringe Benefits

(A+B)

Section C, Equipment

Section D, Travel

1. Domestic 

2. Foreign

Section E, Participant/Trainee Support

Costs

1. Tuition/Fees/Health Insurance

2. Stipends

3. Travel

4. Subsistence

5. Other

6. Number of Participants/Trainees

Section F, Other Direct Costs

1. Materials and Supplies

2. Publication Costs

3. Consultant Services

4. ADP/Computer Services

5. Subawards/Consortium/Contractual

Costs

6. Equipment or Facility Rental/User

Fees

7. Alterations and Renovations

8. Other 1

9. Other 2

10. Other 3

Section G, Direct Costs

(A thru F)

Section H, Indirect Costs

Section I, Total Direct and Indirect Costs

(G + H)

Section J, Fee

Section K, Total Costs and Fee (I + J)

Tracking Number: GRANT12670047 Page 104

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
3 

OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  1

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Enter name of Organization: Mary Free Bed Rehabilitation Hospital 

Start Date*: 04-01-2019 End Date*: 03-31-2020 Budget Period: 1 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allan Kozlowski PhD PD/PI 0.00 2.40 

2 . Dr. John F. Butzer MD Co-Investigator 0.00 0.60 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 Research Assistant 6.00 

1 Site Coordinator 1.20 

1 Speech-Language Pathologist 0.24 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 105

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 1 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Mary Free Bed Rehabilitation Hospital 

Start Date*: 04-01-2019 End Date*: 03-31-2020 Budget Period: 1 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 106

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 1 

● Subaward/Consortium 

Organization: Mary Free Bed Rehabilitation Hospital 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Start Date*: 04-01-2019 End Date*: 03-31-2020 Budget Period: 1 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . Modified Total Direct Costs 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1263-MFB_BudgetJust.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 107

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
3 

OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  2

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Enter name of Organization: Mary Free Bed Rehabilitation Hospital 

Start Date*: 04-01-2020 End Date*: 03-31-2021 Budget Period: 2 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allan Kozlowski PhD PD/PI 0.00 2.40 

2 . Dr. John F. Butzer MD Co-Investigator 0.00 0.60 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 Research Assistant 12.00 

1 Site Coordinator 1.20 

1 Speech-Language Pathologist 0.24 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 108

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 2 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Mary Free Bed Rehabilitation Hospital 

Start Date*: 04-01-2020 End Date*: 03-31-2021 Budget Period: 2 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 109

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 2 

● Subaward/Consortium 

Organization: Mary Free Bed Rehabilitation Hospital 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Start Date*: 04-01-2020 End Date*: 03-31-2021 Budget Period: 2 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . Modified Total Direct Costs 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1263-MFB_BudgetJust.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 110

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
3 

OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  3

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Enter name of Organization: Mary Free Bed Rehabilitation Hospital 

Start Date*: 04-01-2021 End Date*: 03-31-2022 Budget Period: 3 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allan Kozlowski PhD PD/PI 0.00 2.40 

2 . Dr. John F. Butzer MD Co-Investigator 0.00 0.60 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 Research Assistant 12.00 

1 Site Coordinator 1.20 

1 Speech-Language Pathologist 0.24 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 111

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 3 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Mary Free Bed Rehabilitation Hospital 

Start Date*: 04-01-2021 End Date*: 03-31-2022 Budget Period: 3 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 112

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 3 

● Subaward/Consortium 

Organization: Mary Free Bed Rehabilitation Hospital 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Start Date*: 04-01-2021 End Date*: 03-31-2022 Budget Period: 3 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . Modified Total Direct Costs 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1263-MFB_BudgetJust.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

Tracking Number: GRANT12670047 Page 113

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
3 

OMB Number: 4040-0001 

Contact PD/PI: Heinemann, Allen

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  4

● Subaward/Consortium 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Enter name of Organization: Mary Free Bed Rehabilitation Hospital 

Start Date*: 04-01-2022 End Date*: 03-31-2023 Budget Period: 4 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allan Kozlowski PhD PD/PI 0.00 2.40 

2 . Dr. John F. Butzer MD Co-Investigator 0.00 0.60 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 Research Assistant 6.00 

1 Site Coordinator 1.20 

1 Speech-Language Pathologist 0.24 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 114

Tracking Number: GRANT12670047 Funding Opportunity Number: PA-18-287 . Received Date: 2018-07-05T15:37:27.000-04:00 
 

Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 4 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Mary Free Bed Rehabilitation Hospital 

Start Date*: 04-01-2022 End Date*: 03-31-2023 Budget Period: 4 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

Tracking Number: GRANT12670047 Page 115

Funding Opportunity Number: PA-18-287 . Received Date: 

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Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 4 

● Subaward/Consortium 

Organization: Mary Free Bed Rehabilitation Hospital 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Start Date*: 04-01-2022 End Date*: 03-31-2023 Budget Period: 4 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . Modified Total Direct Costs 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1263-MFB_BudgetJust.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

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2 

Contact PD/PI: Heinemann, Allen

OMB Number: 4040-0001 

Expiration Date: 10/31/2019 

RESEARCH & RELATED BUDGET - SECTION A & B, Budget Period  5

ORGANIZATIONAL DUNS*

Budget Type*: ❍ Project ● Subaward/Consortium 

Enter name of Organization: Mary Free Bed Rehabilitation Hospital 

Start Date*: 04-01-2023 End Date*: 03-31-2024 Budget Period: 5 

A. Senior/Key Person 

Prefix First Name* Middle Last Name* Suffix Project Role* Base Calendar Academic Summer Requested Fringe Funds Requested ($)* 

Name Salary ($) Months Months Months Salary ($)* Benefits ($)* 

1 . Dr. Allan Kozlowski PhD PD/PI 2.40 

2 . Dr. John F. Butzer MD Co-Investigator 0.60 

Total Funds Requested for all Senior Key Persons in the attached file 

Additional Senior Key Persons: File Name: Total Senior/Key Person 

B. Other Personnel 

Number of Project Role* Calendar Months Academic Months Summer Months Requested Salary ($)* Fringe Benefits* Funds Requested ($)* 

Personnel* 

Post Doctoral Associates 

Graduate Students 

Undergraduate Students 

Secretarial/Clerical 

1 Research Assistant 6.00 

1 Site Coordinator 1.20 

Total Number Other Personnel Total Other Personnel 

Total Salary, Wages and Fringe Benefits (A+B) 

RESEARCH & RELATED Budget {A-B} (Funds Requested) 

 Page 117

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Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTION C, D, & E, Budget Period 5 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project ● Subaward/Consortium 

Organization: Mary Free Bed Rehabilitation Hospital 

Start Date*: 04-01-2023 End Date*: 03-31-2024 Budget Period: 5 

C. Equipment Description 

List items and dollar amount for each item exceeding $5,000 

Equipment Item Funds Requested ($)* 

Total funds requested for all equipment listed in the attached file 

Total Equipment 

Additional Equipment: File Name: 

D. Travel Funds Requested ($)* 

1. Domestic Travel Costs ( Incl. Canada, Mexico, and U.S. Possessions) 

2. Foreign Travel Costs 

Total Travel Cost 

E. Participant/Trainee Support Costs Funds Requested ($)* 

1. Tuition/Fees/Health Insurance 

2. Stipends 

3. Travel 

4. Subsistence 

5. Other: 

Number of Participants/Trainees Total Participant Trainee Support Costs 

RESEARCH & RELATED Budget {C-E} (Funds Requested) 

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Funding Opportunity Number: PA-18-287 . Received Date: 

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Contact PD/PI: Heinemann, Allen

RESEARCH & RELATED BUDGET - SECTIONS F-K, Budget Period 5 

● Subaward/Consortium 

Organization: Mary Free Bed Rehabilitation Hospital 

ORGANIZATIONAL DUNS*: 

Budget Type*: ❍ Project 

Start Date*: 04-01-2023 End Date*: 03-31-2024 Budget Period: 5 

F. Other Direct Costs Funds Requested ($)* 

Total Other Direct Costs 

G. Direct Costs Funds Requested ($)* 

Total Direct Costs (A thru F) 

H. Indirect Costs 

Indirect Cost Type Indirect Cost Rate (%) Indirect Cost Base ($) Funds Requested ($)* 

1 . Modified Total Direct Costs 

Total Indirect Costs 

Cognizant Federal Agency 

(Agency Name, POC Name, and POC Phone Number) 

I. Total Direct and Indirect Costs Funds Requested ($)* 

Total Direct and Indirect Institutional Costs (G + H) 

J. Fee Funds Requested ($)* 

K. Total Costs and Fee Funds Requested ($)* 

L. Budget Justification* File Name: 1263-MFB_BudgetJust.pdf 

(Only attach one file.) 

RESEARCH & RELATED Budget {F-K} (Funds Requested) 

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BUDGET JUSTIFICATION 

Mary Free Bed Rehabilitation Hospital 

PA17-139 

Defining Trajectories of Linguistic, Cognitive-Communicative and Quality of Life 

Outcomes in Aphasia 

Personnel 

Allan J. Kozlowski PhD, Site Principle Investigator (2.4 calendar months for Years 1-5) 

Dr. Kozlowski is contracted from Michigan State University – College of Human Medicine, 

Department of Epidemiology and Biostatistics, to be the Director of Outcomes Research at 

Mary Free Bed Rehabilitation Hospital (MFBRH). As Site PI he will oversee the administration 

and operations of the Mary Free Bed site and coordinate the communication, interactions and 

data sharing with the research team at Shirley Ryan AbilityLab. Dr. Kozlowski will play a major 

role in statistical analysis and data interpretation. He will also participate in administrative 

meetings. (Dr. Kozlowski’s salary is contracted directly from Michigan State University) 

John F. Butzer MD, Site Senior Advisor (0.6 calendar months for Years 1-5) 

Dr. Butzer is the Director of Research at MFBRH. As a senior manager at MFBRH he will 

oversee the personnel and address institutional concerns arising from site administration and 

operations. Dr. Butzer will advise Dr. Kozlowski on institutional and staffing issues. He will also 

participate in administrative meetings. 

TBD, Research Assistant (6 calendar months for Years 1 & 5; 12 calendar months for 

Years 2-4) 

The research assistant will report directly to Ms. Virva, the Site Coordinator, to assist with the 

engagement and recruitment of individuals with stroke and their families. S/he will be 

responsible for timely data collection and be knowledgeable in test administration and 

supported communication strategies for persons with aphasia. 

Roberta Virva PT, MS, Site Coordinator (1.2 Calendar months for Years 1-5) 

Ms. Virva’s responsibilities include managing the day to day activities of the project and to 

oversee and coordinate the activities of the other personnel. She has responsibility for 

developing systems to monitor progress, to identify problems, and to take appropriate 

corrective action. She will also participate in analyzing and interpreting results and will 

participate in the administrative meetings as needed. 

TBD, Speech-Language Pathologist (0.24 calendar months for Years 1-4) 

The speech-language pathologist (SLP) will report directly to Ms. Virva, the Site Coordinator, 

to assist with review and coding of SLP therapy activities during data collection. S/he will also 

advise the research team on questions of eligibility regarding aphasia, and advise the research 

assistant with regard to interaction with participants and aphasia test administration, as 

needed. 

Salaries are anticipated to increase annually 

Fringe Rate 

Fringe benefits are calculated at 

Indirect Costs 

The indirect cost rate for subcontracts in this proposal is set at the de minimis rate of as 

MFBRH does not yet have a negotiated F&A rate. 

 Page 120 Attachment
RESEARCH & RELATED BUDGET - Cumulative Budget 

Totals ($)

Section A, Senior/Key Person

Section B, Other Personnel

Total Number Other Personnel

Total Salary, Wages and Fringe Benefits

(A+B)

Section C, Equipment

Section D, Travel

1. Domestic 

2. Foreign

Section E, Participant/Trainee Support

Costs

1. Tuition/Fees/Health Insurance

2. Stipends

3. Travel

4. Subsistence

5. Other

6. Number of Participants/Trainees

Section F, Other Direct Costs

1. Materials and Supplies

2. Publication Costs

3. Consultant Services

4. ADP/Computer Services

5. Subawards/Consortium/Contractual

Costs

6. Equipment or Facility Rental/User

Fees

7. Alterations and Renovations

8. Other 1

9. Other 2

10. Other 3

Section G, Direct Costs

(A thru F)

Section H, Indirect Costs

Section I, Total Direct and Indirect Costs

(G + H)

Section J, Fee

Section K, Total Costs and Fee (I + J)

Tracking Number: GRANT12670047 Page 121

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
ie

Contact PD/Pl: Heinemann, Allen 

Total Direct Costs less Consortium F&A 

NIH policy (NOT OD 05-004) allows applicants to exc ude consortium/contractual F&A costs when determining if an application fa lls at or beneath any appl icable direct cost lim t. When a direct

cost limet is s ecified in an FOA the followin table can be used to determeine f our a lication faells within that limet. 

-

iee iee

Category Budget Period 1 Budget Period 2 Budget Period 3 Budget Period 4 Budget Period 5 TOTALS 

Total Direct Costs less Consortium F&A - - - -

Page 122 

Tracking Number: GRANT12670047 Funding Opportunity Number: PA 18 287. Received Date: 2018 07 05T 15:37:27 000-04:00 
   

PHS 398 Cover Page Supplement OMB Number: 0925-0001

Expiration Date: 03/31/2020

1. Vertebrate Animals Section

Are vertebrate animals euthanized? ❍ Yes ● No

If "Yes" to euthanasia

Is the method consistent with American Veterinary Medical Association (AVMA) guidelines?

❍ Yes ❍ No

If "No" to AVMA guidelines, describe method and provide scientific justification

2. *Program Income Section

*Is program income anticipated during the periods for which the grant support is requested?

❍ Yes ● No

If you checked "yes" above (indicating that program income is anticipated), then use the format below to reflect the amount and

source(s). Otherwise, leave this section blank.

*Budget Period *Anticipated Amount ($) *Source(s)

Tracking Number: GRANT12670047 Page 123

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
Contact PD/PI: Heinemann, Allen

PHS 398 Cover Page Supplement

3. Human Embryonic Stem Cells Section

*Does the proposed project involve human embryonic stem cells? ❍ Yes ● No

If the proposed project involves human embryonic stem cells, list below the registration number of the specific cell line(s) from the

following list: http://grants.nih.gov/stem_cells/registry/current.htm. Or, if a specific stem cell line cannot be referenced at this time,

check the box indicating that one from the registry will be used:

Specific stem cell line cannot be referenced at this time. One from the registry will be used.

Cell Line(s) (Example: 0004):

4. Inventions and Patents Section (Renewal applications)

*Inventions and Patents: ❍ Yes ❍ No

If the answer is "Yes" then please answer the following:

*Previously Reported: ❍ Yes ❍ No

5. Change of Investigator/Change of Institution Section

❏ Change of Project Director/Principal Investigator

Name of former Project Director/Principal Investigator

Prefix:

*First Name:

Middle Name:

*Last Name:

Suffix:

❏ Change of Grantee Institution

*Name of former institution:

Tracking Number: GRANT12670047 Page 124

Funding Opportunity Number: PA-18-287 . Received Date: 

2018-07-05T15:37:27.000-04:00 
 

 

PHS 398 Research Plan OMB Number: 0925-0001

Expiration Date: 03/31/2020

Introduction

1. Introduction to Application 1247-Heinemann_Intro.pdf (for Resubmission and Revision applications)

Research Plan Section

2. Specific Aims

3. Research Strategy*

4. Progress Report Publication List

1248-Heinemann_SpecAims.pdf

1249-Heinemann_ResStrat.pdf

Other Research Plan Section

5. Vertebrate Animals

6. Select Agent Research

7. Multiple PD/PI Leadership Plan

8. Consortium/Contractual Arrangements

9. Letters of Support

10. Resource Sharing Plan(s)

11. Authentication of Key Biological and/or

Chemical Resources

1250-HeinemannCherney_MultPI.pdf

1251-Heinemann_LOI.pdf

1252-Heinemann_LOS .pdf

1253-Heinemann_DataSharPlan.pdf

Appendix

12. Appendix

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Introduction to the Revised Submission 

The reviewers identified several concerns, including absence of a theoretical model and mechanistic hypotheses, generalizability of study findings, limited aphasia expertise, additional variables that could influence aphasia recovery, inclusion criteria, and fMRI procedures. This revised submission addresses these concerns. 

Absence of a Theoretical Model and Mechanistic Hypotheses: A reviewer noted that the application did not 

specify clearly the mechanisms by which predictors might interact to influence the course of aphasia recovery 

and observed that the development of a holistic path model for aphasia recovery would be of great significance. The reviewer noted that we specified factors that may be important for cognitive, linguistic, and QOL 

outcomes, but noted the absence of socioeconomic status, history of psychiatric disorder, major medical 

comorbidities, leukoaraiosis, and prescribed medications, particularly SSRIs. In this revision, we provide a 

model (Figure 2) that describes hypothesized relationships between model components (e.g., genomic testing 

with treatment dosage). We appreciate and adopted the suggestion to include additional factors that may contribute to cognitive, linguistic, and QOL outcomes, and included them in this revision. 

Relatedly, a reviewer noted the absence of hypotheses to guide analyses involving genetic tests and justification of specific genes. This revision clarifies that we selected SNPs based on published studies, including Brain 

Derived Neurotrophic Factor, Apolipoprotein E, Insulin Growth Factor 1, Catechol-O-methyltransferase, Fibroblast Growth Factor 2, and Vascular Endothelial Growth Factor A. We provide citations justifying the SNPs 

based on demonstrated modulation of neuroplasticity in stroke patients and effects on stroke recovery. 

Generalizability of Study Findings: A reviewer noted that all sites are in the Midwestern U.S. and was concerned that results may not generalize. While all study sites are within 200 miles of each other, we revised the 

facility descriptions to emphasize the diverse demographic and stroke characteristics. We will treat “facility” as 

a fixed effect and examine site as a factor. We report information about the representativeness of stroke patients served by the collaborating inpatient rehabilitation facilities (IRFs) in Human Subjects, and demonstrate 

that we will recruit a demographically-representative sample with a wide range of stroke severity. 

Clinical and Research Expertise in Stroke and Aphasia: A reviewer was concerned that team members do 

not have aphasia research experience. While not all team members have extensive aphasia experience, co-PI 

Cherney is an international expert on aphasia recovery and treatment; co-PI Heinemann is a coauthor on several of her publications.1,2 Other key personnel bring expertise in individual growth curve modeling with rehabilitation populations (Kozlowski3-8), advanced biostatistical design (Kocherginsky), and quality of life research 

(Heinemann9,10). We share authorship on several stroke-related manuscripts. Cherney and Baliki have worked 

together over the last 18 months and have conducted two aphasia studies using fMRI. One has been accepted 

for publication in Neuroreh bilit tion. 

11 We have revised the key personnel’s personal statements to highlight 

their aphasia and collaborative experience, as well as their unique contribution to this project. Research assistants with direct contact with participants will receive extensive training about aphasia, supported communication, and test administration for persons with aphasia from co-PI Cherney and research speech-language 

pathologist (SLP) Hurwitz, who has over 10 years of experience evaluating persons with aphasia. 

Additional Variables Affecting Retention and Aphasia Recovery: A reviewer noted factors that could influence aphasia recovery and attrition, including neurologic conditions, global health status, and medical conditions that could affect recovery such as congestive heart failure, advanced stage cancer, and end stage renal 

disease. In response, we will assess these factors and have added plans to evaluate nonrandom attrition and 

aphasia recovery. A reviewer suggested that we consider adding an MRI sequence to quantify leukoaraiosis. 

We appreciate this insight and now propose the required sequences and analytic tools. 

Inclusion Criteria: A reviewer was concerned that requiring participants to provide informed consent would 

exclude individuals with significant comprehension deficits and reduce generalizability of the results. We 

acknowledge that attrition may vary by extent of recovery, SES, health status, and other non-random factors. 

We will train staff members who are consenting patients to use supported communication strategies with picture-based materials. This protocol will allow us to consent a large proportion of patients with severe aphasia. 

Need for Careful Registration Procedures in fMRI: A reviewer was concerned regarding normalization of 

stroke brains to standard templates and lack of details regarding rs-fMRI analyses. We now describe registration procedures in greater detail, including linear and non-linear registration that decrease warping in brains 

with large strokes. In addition to utilizing the Human Connectome Project pipelines, we will use specific registration tools that are optimized for stroke. We clarify that only patients at SRALab will be scanned using the 3T 

Siemens Prisma. We will use different atlases and parcellation schema in our resting state and anatomical 

analyses. Brain networks will be constructed using either a whole brain voxel-wise approach or various validated parcellation schemas ranging from 90 - 500 ROIs. We will include white matter and subcortical regions. 

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Specific Aims 

Stroke is a major public health issue with life-long consequences for millions of survivors and their caregivers. 

Aphasia is a common consequence with a prevalence of approximately 2,000,000.12 Rehabilitation approaches 

for aphasia continue to evolve, though we know little about the dose, timing, and components of therapy that 

could ameliorate cognitive, linguistic, and communicative deficits. Needed is an adequately powered, prospective study of a cohort in which we can evaluate models of aphasia recovery considering person, stroke, and 

therapy characteristics. This longitudinal cohort study evaluates a multi-faceted model of linguistic, cognitivecommunicative, and health-related quality of life (QoL) recovery in persons with stroke-related aphasia up to 18 

months after onset, and evaluates the contribution of patient, stroke-related, and treatment factors that affect 

outcomes. Language recovery in post-stroke aphasia is variable and difficult to predict.13-18 A multitude of factors 

including demographic, clinical, and treatment variables affect short- and long-term outcomes. However, there 

is limited agreement on the extent to which these factors predict recovery. Results across studies may be contradictory because of methodological differences including the heterogeneity of samples, the selection of outcome measures with most studies using only linguistic measures, small samples, and retrospective designs. To 

understand aphasia recovery better, there is a critical need for a large, prospective, methodologically-sound 

study that takes into consideration these issues. 

Some factors such as therapy utilization can be modified to improve outcomes. Our earlier work19-21 described 

therapy utilization during stroke rehabilitation and evaluated the contribution of therapy characteristics and length 

of stay to functional gains. Therapy intensity accounted for about 1⁄4 of the variance in functional gains. This work 

was a valuable first step in describing therapy utilization and sets the stage for a focused study of speech and 

language therapy utilization for persons with aphasia, a description of functional gains during rehabilitation, and 

tracking of patients after discharge. Frequent assessments will allow us to describe the course or traject ry of 

recovery. Defining recovery trajectories will allow clinicians to know when patients are recovering on par with, 

exceeding, or lagging behind expected recovery, and to modify therapies to optimize function and QoL. 

In addition to therapy characteristics which may affect language recovery, patient factors including demographic 

and clinical characteristics such as the type and severity of the initial aphasia, the size and location of the lesion, 

and variability in brain networks may affect recovery.17,22 Variations in genetic polymorphisms such as brainderived neurotrophic factor (BDNF) affect neuroplasticity and may affect response to rehabilitation.23-25 We include these factors in a model of aphasia recovery which we will test empirically. Patients’ perspectives on their 

linguistic and communicative outcomes and QoL are also critical in monitoring and improving rehabilitation services; however, rehabilitation programs rarely collect patient-reported outcome measures (PROMs). 

We propose a model of aphasia recovery that identifies both patient factors and treatment variables as key 

predictors of aphasia recovery. Our overall goal is to evaluate a model using individual growth curve analysis as 

a method to understand better the linguistic, cognitive-communicative, and health-related QoL outcomes in 

adults with post-stroke aphasia. We will investigate the association of patient factors (i.e., demographic and 

clinical characteristics) and treatment variables on outcomes. We will also determine the effects of neurobiological patient factors such as brain and genetic biomarkers in this model of aphasia recovery. We will recruit a 

large cohort of patients with aphasia from three IRFs and follow them through inpatient and outpatient therapy 

to 18 months. The Specific Aims are to: 

Aim 1: Establish a prospective cohort of stroke patients with aphasia, and define their typical trajectory of linguistic, cognitive-communicative, and health-related QoL recovery at admission to and discharge from the IRF, 

and at 6, 12, and 18 months post onset. 

Aim 2: Identify factors within the proposed model that are associated with linguistic, cognitive-communicative, 

and health-related QoL outcomes from among: 

a) Patient factors, including demographic and clinical characteristics related to stroke and aphasia; 

b) Treatment variables, including inpatient and outpatient aphasia therapy characteristics and informal 

aphasia services; and 

c) Biomarkers, including genetic and neuroimaging biomarkers. 

Aim 3: Evaluate the stability of the models of linguistic, cognitive-communicative, and health-related QoL outcomes recovery that are developed in Aim 2. 

We expect that findings from this large, prospective longitudinal cohort study will provide a detailed understanding of the effects of speech and language therapy characteristics and other participant and aphasia-related factors on patients’ outcome trajectories, which will inform clinical practice and rehabilitation service delivery during 

and following inpatient rehabilitation. 

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Significance 

Stroke and Aphasia Epidemiology: Approximately 17 million people worldwide experience a first stroke annu 

ally26 of which 610,000 occur in the United States.27 Although stroke prevalence has remained relatively sta 

ble,28,29 stroke prevalence will likely rise due to the aging population and increasing rates of stroke risk factors, 

including diabetes mellitus, obesity, and physical inactivity.27 Advances in acute stroke treatment and inpatient 

management have improved stroke survival greatly30 with fewer than 130,000 deaths occurring per year,28,31 and 

a 38% decrease in strokerelated mortality from 2000 to 2010.28,29,32 However, stroke remains a leading cause 

of longterm disability.27 One of the most devastating consequences of stroke is aphasia, which occurs in about 

1/3 of patients.3335 Aphasia impairs, to varying degrees, understanding and expression of oral language, reading, 

and writing. Reduced language skills can have significant negative effects on participation in rehabilitation and 

subsequent functional outcomes, as well as on social, vocational, and recreational activities. People with aphasia 

report isolation, loneliness, loss of autonomy, restricted activities, role changes, stigmatization and depression.36 

41 Aphasia is not just an acute event, but has continuing effects.42,43 Aphasia affects family and friends, with a 

growing literature recognizing the negative effects on family and community life.4450 As more individuals survive 

acute stroke, the need for effective rehabilitation strategies to reduce aphasiarelated disability becomes urgent. 

Limitations of Current Treatment Services: Approaches to the management and rehabilitation of aphasia con 

tinue to evolve. The medical model focuses on treating impairment and restoring language function.51 Over the 

past two decades, therapists have embraced functional/social models of intervention that focus on the broad life 

context of the person.5254 Despite research on the importance of participation for persons with aphasia, health 

care policies and insurance coverage of treatment have not kept up with this paradigm shift. Insurers typically 

cover therapy that targets impairments, and evidence supporting an association between impairmentbased 

treatment and broader outcomes related to communication and QoL is lacking. 

The duration and intensity of rehabilitation therapy is severely limited.5558 The timing, amount, and duration of 

inpatient therapies and the facility where patients receive rehabilitation services depends greatly on insurance 

coverage. Commercial insurers usually adopt the Centers for Medicare and Medicaid Services (CMS) therapy 

requirements; however, there is great variability in the extent of coverage due to varying definitions of medical 

necessity. CMS requires IRFs to deliver 3 hours of therapy per day at least 5 days per week, although there is 

limited evidence to support this level of therapy intensity. Patients may receive 3 hours per day through a com 

bination of physical therapy (PT), occupational therapy (OT), and speechlanguage pathology (SLP) services. 

Persons with aphasia may receive limited treatment targeting their language and communication deficits during 

an IRF stay. The mean length of stay in an IRF for stroke rehabilitation is 14.6 days.59 For outpatient rehabilita 

tion, CMS imposes therapy caps that limit rehabilitation services based on expenditures. The 2018 therapy caps 

are for PT and SLP therapy services combined, and for OT services. In practice, most patients 

reach these therapy caps in less than two months. Thus, patients who receive both inpatient and outpatient 

rehabilitation exhaust their benefits within three months. Insurers limit rehabilitation despite the accumulating 

evidence on neural plasticity that indicates the importance of intensive therapy in rehabilitation6063 as well as 

studies demonstrating that even those with chronic aphasia may benefit from intensive treatment.6466 

Understanding the trajectories of functional recovery and QoL improvement – and how this is related to therapy 

exposure – will enable postacute care providers to develop an evidence base that enables clinicians to plan 

rehabilitation therapies that are tailored to individual needs, and maximize functional and QoL outcomes while 

minimizing the cost of stroke rehabilitation. 

Quality of Life after Stroke: Stroke survivors experience reduced QoL compared to agematched peers;67,68 they 

often face limitations in performing housework, shopping, preparing meals, and traveling beyond their commu 

nity. Functional limitations result in social isolation, depression, and a lack of purpose.67,68 Aphasia reduces QoL 

further.41,69 People with aphasia report worse QoL after stroke than people without aphasia, even when their 

physical abilities, wellbeing, and social support are comparable.41,70 Although disability is prevalent, most pa 

tients achieve functional gains during IRF stays. Patients who receive inpatient stroke rehabilitation achieve a 

mean gain of 29.7 points on total Functional Independence Measure (FIMTM) scores (108 point range); their 

mean gain on Motor FIMTM scores is 24.2 points (78 point range), and Cognitive FIMTM scores gain 5.5 points 

(30 point range).71 Reducing functional limitations, including communication through effective rehabilitation ther 

apies may result in improved overall QoL. 

The Trajectory of Aphasia Recovery: Language recovery in poststroke aphasia is variable and difficult to predict 

even in the first 90 days poststroke.1318 A multitude of interacting variables affect short and longterm outcomes. 

Figure 2 illustrates the interaction of these variables and their effects on outcomes. We distinguish three cate 

gories of outcomes: linguistic, cognitivecommunicative, and healthrelated QOL. We suggest that the major 

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contributors to achievement of these outcomes are patient characteristics and the aphasia treatment that they 

receive. We know little about patterns of recovery for linguistic, cognitivecommunicative, and QOL outcomes 

after stroke. Effective aphasia treatment requires that we understand factors associated with higher plateaus of 

recovery, faster recovery rates, and both higher plateaus and faster recovery rates. 

Patient characteristics include demographic 

characteristics such as age, sex, education, 

SES, and handedness, as well as clinical varia 

bles that are related to the stroke such as lesion 

size and location, stroke severity, type and se 

verity of aphasia, medical comorbidities, and 

medications. Genetic and brain biomarkers may 

influence the expression of patient characteris 

tics. While patient characteristics typically can 

not be modified to any great extent, aphasia 

treatment variables, including type, amount and intensity, can be modified in order to maximize outcomes. 

There is limited agreement on the extent to which specific variables predict recovery. For example, lesion size 

is an important predictor of recovery in most72,73 but not all studies,16,73 with larger lesions predicting poorer 

aphasia recovery. Yet a lesion occurring in a critical language area may be a more important predictor of lan 

guage recovery than lesion size alone.74,75 New methods suggest that the integrity of areas remote from the 

lesion and alterations in network connectivity affect language recovery.7679 Patient factors such as sex, age, 

handedness, and education have been the focus of investigation, often with inconclusive results.15,17,22 Similarly, 

the type and initial severity of aphasia affect recovery in some, but not all, studies.75,80,81 Results may appear 

contradictory because of methodological differences including the heterogeneity of samples, the selection of 

outcome measures, with most studies only selecting linguistic measures, such as the Western Aphasia Battery 

Revised (WABR),82 and the timing of endpoint assessments. Many studies recruited small sample sizes, and 

not all the studies are prospective. To understand aphasia recovery better, there is a critical need for large, 

prospective, methodologically sound studies that take into consideration multiple factors that affect outcomes. 

With regard to aphasia treatment, hundreds of studies, systematic reviews, metaanalyses and expert opinion 

conclude that aphasia treatment is beneficial.8386 Although there is little evidence indicating that one treatment 

is more effective than others,86 13 there is an accumulating body of evidence that suggests the amount, intensity, 

and duration of therapy affects recovery regardless of the type and severity of the aphasia.75,8689 Yet, we know 

little about the characteristics of aphasia therapy provided during inpatient rehabilitation, the gains made during 

this early treatment period, and longterm outcomes. Given the chronicity of the disorder, individuals typically 

seek continuing outpatient treatment in hospital and university clinics, as well as alternate services through apha 

sia centers,90,91 intensive comprehensive aphasia programs,92,93 and research studies. Any model of aphasia 

recovery must consider variables associated with treatment both during and after inpatient rehabilitation. 

Genetic Variations May Affect Outcomes: Genetic variations are genomewide modifications in DNA sequences 

among individuals of a population. Unlike genetic mutations, polymorphisms are relatively frequent DNA varia 

tions that are not diseasecausing but can affect physiological systems, especially when interacting with other 

genetic variants or environmental cues.94 Singlenucleotide polymorphisms (SNP) are a common type of poly 

morphism; they are a variation of the genetic code in a single base pair wherein one nucleotide replaces another, 

leading to changes in gene or protein sequence, expression, structure, and activity. SNPs can lead to biological 

variations in molecular and cellular processes that have functional and systemic consequences.94,95 

Stroke activates multiple biological pathways, neuroprotective or detrimental to the brain, resulting in neurophys 

iologic, hemodynamic, and biochemical changes that determine outcome. Increasingly, patient management 

includes an evaluation of diseaserelated genetic polymorphisms affecting neuroplasticity, which is the ability of 

neural networks to adapt their functional organization at the cellular and molecular levels in response to stroke 

and poststroke rehabilitation.23,96 Language recovery may be mediated by neuroplasticity.97 98 One contributor 

to language recovery could be genetic predisposition based on neuroplasticityassociated SNPs. 

Despite promising advances in identifying SNPs associated with poststroke motor and cognitive skill recov 

ery,24,99,100 identification of SNPs predictive of language recovery in stroke patients has been relatively unsuc 

cessful. A recent study investigating the influence of the BDNF Val66Met polymorphism on language recovery 

in poststroke aphasia found no significant differences between carriers and noncarriers in the level of language 

improvement, suggesting that the BDNF polymorphism alone did not influence aphasia recovery.101 Another 

study suggested a nearly statistically significant increase in prevalence of aphasia in stroke patients with the 

Research Strategy Page 129
genotype APOE-e4 compared with other APOE genotypes. 102 Many complex human diseases and traits cluster 

in famil ies and are influenced by interaction of multiple genetic and environmental factors.

103 Therefore, we will 

consider the interactions (epistasis) between multiple neurotrophic factors and their polymorphisms rather than 

individual SNPs. We will investigate the genetic association and interactions of SNPs in genes that are l inked to 

neuroplasticity at the cellular and molecular level in post-stroke recovery, 104 including growth factors mediating 

neurogenesis, ang iogenesis, synaptic remodeling, and neuroprotection (see Table 4 for specific polymorphisms 

and references). We will use multifactor dimensionality reduction statistical methods10 to identify significant genetic outcome predictor models. We hypothesize that language recovery after stroke is modulated by epistatic 

interactions between two or more SNPs. We will integrate this genetic analysis with other factors (neuroimaging, 

clinical and demographic characteristics) as part of a model that provides a detailed understanding of the effects 

of speech and language therapy and other aphasia-related factors on patients' outcome trajectories. 

Baseline Network Status May Be a Biomarker of Recovery: A resting state, functional magnetic resonance imaging (rs-fMRI) scan captures brains activity when a participant is not performing a specific task. A recent stroke 

recovery and rehabilitation consensus statement identified resting state functional connectivity as a promising 

candidate biomarker of recovery.

105 Several studies suggest that measures of inter- and intra-network connectivity predict outcomes and treatment response across multiple domains. Only a few studies have explored rsa76 78• fMRI in aphasia 1 06 with results indicating a relationship between aphasia severity and an acute disruption of 

connectivity within the language network.

107 However, small samples and different analytical approaches limit 

interpretation. We will use multi-modal brain imaging techniques such as diffusion tensor imaging and rs-fMRI in 

a subsample of 100 participants. The ease with which these brain images are acquired make it a practical method 

for persons with limited ability to perform tasks during an fMRI because of aphasia.76 More importantly, an increasing body of evidence from clinical studies show that baseline brain properties play a key role in the emergence and manifestation of behavioral symptoms in multiple neurological disorders.

108 rs-fMRI has been used to 

identify the neural networks underlying language processing and their modulation in response to therapy.

107 

While changes in interhemispheric connectivity appear to be consistently related to language deficits, functional 

correlates underlying aphasia and its recovery remains relatively unexplored due to small populations and the 

lack of structured longitudinal studies that examine short and long term outcomes.

107 Within this framework, the 

study proposed here will be seminal in identifying the brain mechanisms that influence aphasia recovery. 

Advances in Modeling Outcomes: Rehabilitation outcomes, unlike those in other areas of medicine, evolve over 

prolonged periods, and commonly result in permanent residual impairments, activity limitations, and participation 

restrictions. Consequently, outcomes of recovery after stroke are not suited to point-in-time difference measurements (e.g., admission to discharge), which complicates efforts to evaluate the effectiveness of therapies provided to augment recovery. Service-based outcome measurement procedures, such as those required for IRFs, 

measure at admission and discharge on a trajectory that continues to improve. Even when measurements are 

made at multiple times, group-level analyses preclude interpretation of individual differences in recovery patterns, 109.110 limiting their utility and translation to clinical practice. 

Figure 1 : Longitudinal Models. Outcomes modeled ongitudinally can be fit with different mathematical functions depending on howindvidual evel data

are dist ributed over time. (A) Lohse et al. modeled recovery of b alance and temed walk data from outpatients as linear tra ector es, defined by an intercept

and constantrate of change.111 (8) Hart et al. modeled motor and cognitive recovery after traumat ic brain ineury during inpatientrehabilitation as curvilinear

(cubic) trajectories, defined by an intercept and instantaneous rate of change.• (C) Pretz et al. modeled motor recovery after spinal cord inury from inpatient

rehabi litat on through communety life as non-linear (negateve exponential) tra ector es), defined by three parameters that descr be rapid change to a plat 5 Personal, condition, treatment, and/or social/environmental can explain individual level variance in the trajector es providing descr iptions of the path 

of recovery at the indvidual level, which could potenteally serve as pateient-specific prognoses ie

Longitudinal designs that employ mixed-effects methods allow us to describe individuals' change over 

time.

109,1 10,1 12·1 1 3 These methods include individual growth curve (IGC) models, also known as random slopes 

3·5•6·1 14 and intercepts models, which have been used to describe recovery for persons with spinal cord injury, 4•1 1 5 acquired brain injury, 1 17 and stroke.

7·1 18 Trend lines, or trajectories, are modeled simultaneously for each 

person, where the trajectory shape is determined by the best fit to the data (Figure 1 ). Instead of modeling and 

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comparing group differences as means at each time point, the group trend (fixed effects) is modeled as the 

average of the intercept and slope for the individual trend lines. Individual differences in the trajectory parameters 

(random effects) are also modeled; thus, we can test betweengroup differences and covariate associations with 

trajectory parameters. Differences on the intercept indicate individual variability at baseline, and differences on 

the slope indicate individual variability in rates of change. We can model various trajectories including linear 

(Figure 1A), curvilinear (1B), and nonlinear trajectories (1C), depending on which function best fits the data. 

These models retain individual differences and describe outcomes as trajectories for individuals defined by a set 

of covariate associations, such as demographic, impairment, and therapy characteristics: they can explain indi 

vidual variations on trajectory parameters. For example, we developed an IGC model using FIMTM motor scores 

for persons with paraplegia.5 The majority of functional recovery occurs during the first year postinjury, but Pretz5 

demonstrated that individuals also vary in the time from admission to when gains diminish.5 Knowledge of the 

expected level and timing of a plateau for a given individual allows therapists to sequence and time therapies to 

patients’ unique needs. IGC models also allow construction of individuallevel trajectories based on specific val 

ues of the covariates in the model112 enhancing personalized rehabilitation. Longitudinal models represent the 

most appropriate method to describe recovery and to examine betweengroup and individual differences related 

to rehabilitation therapies received during and following inpatient rehabilitation. 

Innovation 

Understanding recovery trajectories at the individual level is a crucial first step toward extending the promise of 

precision medicine to rehabilitation. Our objective is to describe and predict the trajectories of recovery over the 

first 18 months following stroke, using standardized assessments to evaluate linguistic, cognitivecommunica 

tive, and QoL changes. The aims of this proposal are innovative and timely. There are no prospective, longitu 

dinal, multisite studies that report trajectories of aphasia recovery to 18 months and their associations with 

patient, lesion, aphasia, genomic, and rehabilitation characteristics. This study is innovative in seven respects: 

(1) We will use standardized assessments that extend beyond linguistic assessments such as the WABR to 

include communication and QoL measures; QoL measures have seldom been included as outcome measures 

in aphasia studies.119 (2) We will use patientcentered, selfreport instruments including NeuroQoL which was 

developed with modern, mixed methods that included patient and clinician input. The NeuroQoL measurement 

system assesses concerns that are relevant to patients, but research with this instrument has typically excluded 

patients with aphasia; its use here allows us to compare our sample with population norms. (3) We will use novel 

IGC models to describe recovery trajectories and examine associations between demographic, lesion, aphasia, 

genetic, and speech and language therapy characteristics. IGC modeling allows us to build interactive tools to 

describe individual trajectories, which will provide clinicians with evidencebased prognoses. Trajectories gener 

ated by an interactive tool based on multiple characteristics represent a patientcentered approach, which will 

provide the bestavailable evidence for recovery potential of new patients. (4) To identify new genetic pathways 

involved in language recovery following stroke, we will assess the association between multiple SNPs and bi 

omarkers that may promote neuroplasticity and assess their association with recovery from aphasia up to 18 

months poststroke. (5) We will use a novel technology (rsfMRI) to explore the functional connectivity in resting 

state networks in 100 participants and evaluate the association of network pathology with recovery from aphasia 

at 18 months poststroke; doing so allows us to identify specific and objective biomarkers and explore the brain 

mechanisms underlying aphasia recovery. (6) We will collect information on the type, amount, and duration of 

aphasia treatment provided at three IRFs and assess the association of inpatient therapy with outcomes at 18 

months. Although there is a large research literature on the efficacy of aphasia treatment when provided in 

controlled, experimental environments, few investigations have focused on aphasia treatment in clinical settings. 

(7) We will collect data related to services and other activities that persons with aphasia participate in following 

discharge from formal therapy, allowing us to test an integrative model of aphasia recovery. 

Cumulatively, this study will provide comprehensive resources for clinicians in modeling aphasia recovery and 

support the development of patientcentered therapies. A better understanding of recovery can assist with prog 

nosis, allowing patients and caregivers to plan, helping clinicians choose appropriate therapies, providing bench 

marks against which to measure change, and allowing therapy adjustments if patients do not attain benchmarks. 

Responsiveness to PA-17-139: This application addresses a primary topic listed in the funding announcement, 

specifically identifying patient and provider variables that predict outcomes for adults with communication disorders, including QoL and psychosocial adjustment. Investigators have expertise in health services and outcomes 

research, adult neurological communication disorders with a specific focus on aphasia treatment research, 

growth modeling and statistics, genomics, and imaging. The project focuses on practicerelevant questions and 

follows individuals with aphasia in diverse, realworld settings. 

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Approach 

Overview 

We propose an observational cohort study at three IRFs with expertise in strokerelated aphasia. We will assess 

function weekly during the IRF stay with the IRF Patient Assessment Instrument; at admission and discharge 

with the NIH Stroke Scale; and at admission and/or discharge, 6, 12, and 18months poststroke with selected 

linguistic assessments and selfreport instruments as outlined in Table 3. We will extract information about 

speech and language therapy from in and outpatient records. Speech therapists at each site will document 

therapy sessions on a template that allows abstraction of therapy details. We will use IGC models for analysis 

of recovery trajectories. 

Study Population: We will enroll indi Table 2. Stroke Patient Admissions with Aphasia at Participating IRFs 

viduals admitted to each of three Joint and Likely Sample in Past 12 Months 

Commissionaccredited IRFs: The 

Shirley Ryan AbilityLab, Alexian Broth 

ers Rehabilitation Hospital in Elk Grove 

Village, IL, and Mary Free Bed Reha 

bilitation Hospital in Grand Rapids, MI, 

for a total of 300 patients followed to 18 

months. Inclusion criteria are a primary diagnosis of a first stroke with aphasia, age 21 years and older, and first 

admission for inpatient rehabilitation. Table 2 shows the number of stroke admissions with aphasia over the past 

fiscal year. Based on our experience with a PatientCentered Outcomes Research Institutefunded study requir 

ing patient selfreport capacity,10 as well as the percentage of patients who are likely to consent to participate, 

we expect to complete enrollment within 30 months. As described in the power analysis, a sample of 300 at 18 

months allows a robust longitudinal analysis and provides sufficient power to estimate the IGC models. We will 

overrecruit by 100 patients (400 consented patients), estimating 15% attrition by 6months and another 10% 

attrition by 18months. 

Inpatient ‘Rehabilitation Facility Admissions 

Eligible Likely to 

Consent 

Shirley Ryan AbilityLab (AbilityLab) 

Alexian Brothers Rehabilitation Hospital (ABRH) 

Mary Free Bed Rehabilitation 

Hospital (MFBRH) 

Totals 

Aims and Hypotheses 

Aim 1: Establish a prospective cohort of stroke patients with aphasia, and define their typical patterns (trajecto 

ries) of linguistic, cognitivecommunicative, and healthrelated QoL recovery. 

Hypothesis 1: Linguistic outcomes (WABR AQ) improve to 6months poststroke and then slow, whereas cog 

nitivecommunicative outcomes (CPIB) and QoL outcomes improve to 18months poststroke. 

Aim 2: Identify factors that are associated with linguistic, cognitivecommunicative, and healthrelated QoL out 

comes from among: 

a) Patient factors, including demographic and clinical characteristics related to stroke and aphasia; 

b) Treatment variables, including inpatient and outpatient aphasia therapy characteristics and informal 

aphasia services; and 

c) Biomarkers, including genetic and neuroimaging biomarkers. 

Hypothesis 2a: Patients with smaller lesions, fewer comorbidities, and less severe initial aphasia achieve greater 

gains in linguistic, cognitivecommunicative, and healthrelated QoL than patients with larger lesions, more 

comorbidities, and more severe aphasia. 

Hypotheses 2b: Patients who begin speech and language therapy earlier and receive therapy that is more inten 

sive and longer in duration achieve greater linguistic, cognitivecommunicative, and healthrelated QoL than 

patients who begin speech and language therapy later and receive less intensive therapy. And, 

Patients who receive longer duration outpatient and other formal and informal aphasia services achieve greater 

linguistic, cognitivecommunicative, and healthrelated QoL than patients who receive shorter periods of therapy. 

Hypothesis 2c: Biomarkers including the presence or absence of critical neuroplastic polymorphisms and the 

degree of resting state connectivity interact with patients’ demographic and clinical characteristics to influence 

linguistic, cognitivecommunicative, and healthrelated QoL outcomes. 

Aim 3: Evaluate the stability of the linguistic, cognitivecommunicative, and healthrelated QoL outcomes recov 

ery models from Aim 2. 

Hypothesis 3: Models selected in Aim 2 will be stable, that is, the variables in the final model appear in the 

majority of bootstrapped replications, and prediction error (i.e., the difference between an observed and predicted 

score at any time point) is no greater than the minimally clinical important difference for each outcome. 

Research Strategy Page 132
c... 

4.. 

Preliminary Studies 

Characterization of Therapy Components: We described patterns of therapy utilization during inpatient rehabilitation and evaluated the importance of rehabilitation service characteristics in terms of focus, intensity, and 

length of stay on functional gains.

19 21 Controlling for stroke severity, longer lengths of stay and more intensive 

function-focused OT predicted self-care gains, while longer stays predicted cognitive gains. In this earl ier work, 

persons with aphasia were not represented adequately, a common occurrence in stroke research. We also assessed patient status at IRF admission and daischarge only, leaving us unable to describe the trajectory of patient 

improvement and how a mix of therapies contributed to longer-term functional gains. To plan clinical interventions, clinicians need detailed information about the trajectory of change that patients are likely to experience 

during and following inpatient stroke rehabilitation and how rehabilitation therapies affect recovery trajectories. 

Individual Growth Modeling of Recovery Traiectory: We developed an IGC model using FIaMTM motor subscale 

data for persons with paraplegia in the SCI Model Systems National Database.5 Most recovery from SCI occurs 

during the first year post-injury, but we demonstrated that recovery of individuals with specific demographic, 

injury, and rehabilitation characteristics can slow at different times after rehabilitation admission .

5 We also constructed an individual-level trajectory model based on specific values for the covariates included in a model; 

5•1 12 clinicians can use this model to facilitate treatment planning.

Extraction and Analysis of Therapy Data from Billing Records: We extracted therapy charges for 71 stroke patients admitted in a recent month from AbilityLab bi lling records. Patients had a median length of stay of 12 days 

(SD=9.2). The median quarter-hour units of PT, OT, and SLP was and the median daily number 

of quarter-hour units was While the daily median PT and OT units were correlated strongly (0.61 ), 

the relationship between PT and SLP and OT and SLP was weaker Length of stay 

was negatively correlated with each discipline's therapy units such that 

patients with longer stays tended to receive fewer services per day. OT, PT, and SLP units were correlated 

negatively -with length of stay. However, bil ling records do not contain the information about therapy 

activities that IRF SLPs will log during their treatment sessions. 

Association of Anatomical and Functional Brain Properties 

with Outcomes: Fig ure 3 shows lesion data from 8 patients 

with left hemisphere strokes and aphasia who received 4 1 

weeks of intensive therapy. We collected structural and rsfMRI scans and behavioral assessments before and after 

treatment. We utilized a variety of brain imaging metrics to 

Figure 3. Topography of Stroke. Leson overay map in atlasspace. investigate the effects of baseline anatomical and functional 

Coor scae: number of subjects Witn lesons at eacn voxel brain properties on treatment outcome and del ineate the 

brain functional reorganization in response to treatment. In this preliminary study we were able to identify specific 

rs-fMRI connectivity that influences language and spatial attention improvements following treatment. 

Behavior Changes during Therapy: A battery of clinically-relevant and standard 

tests were used to assess language and 

attention abilities. Overall, patients 

achieved significant improvements across 

most language and attentional domains: 

Boston Naming Test (BNT), Aphasia Quotient (AQ), WAB-R Repetition (Rep), Raven's Progressive Matrixes (RAV) and 

Connor's Continuous Performance Test 

(CPT-2) showed significant changes following treatment (p < 0.05), while 

changes in WAB-R Reading and Writing 

scores suggested trends (p = 0.116 and p 

Figure 4. Correlation matrices and factor analyses of behavioural scores. (a) Heat map (left) snow 

ne correlat on across all benavoural scores at baseline (vs t 1). Tabe (rignt)snows principe component anaysis. Two man factors were iden f ed, factor 1 contaned an language domains. AQ, wnile factor 2 

contaned CPT. RAV loaded equally on botn factors. (b) Benavour scores after tnerapy (vis t 2) snows s milar associatons to baseline. (c) Scatter pot snows tne correlaton between benaviour cnanges n AO

(factor1 )and CPT (factor 2). Despite botn benavoural measures snowng sgnifcantimprovement, tnere i i were no correlaton between tnem. Higner scores ndicate better improvement.

= 0.073, respectively). Principal component analysis revealed that behavioral measures at baseline formed two 

factors that explained 85% of the variance. The first factor, labelled AQ, comprised all language related processes including the BNT, AQ, Rep, Reading and Writing. The second factor included only the CPT II score 

(Figure 4a). Similarto visit 1 scores, behavioral data following treatment loaded on the two factors and explained 

88% of the variance (Figure 4b ). These results suggest that a common central mechanism underlying languagerelated performance is probably independent from the mechanism involved in attention-related tasks. 

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Research Strategy 
Relationship between brain properties and behavioral changes. We investigated the extent to which anatomical 

and functional brain properties at baseline predict treatment gains using a correlational model. Lesion size was 

not related to AQ (r=O.23, NS) or CPT-2 gains (r = -0.1 1 , NS). We also investigated the relationship between 

lesion location and outcome using a voxel-wise logistic regression.

120 There was no correlation between lesion 

location and outcome. However, we observed that AQ changes were associated primarily with a cluster in the 

left temporal lobe, while CPT-2 changes were associated with lesions in the frontal cortex and superior parietal 

lobes. A larger sample will allow us to evaluate these associations in greater detail. 

We also used advanced graph theoretical analysis to characterize global and local brain properties during rsfMRl .121

·

122 First, we generated brain graphs using functional connectivity estimated between each pair of the 

264 functional brain regions. 123·

124 Then, we computed global and local functional properties of individual brain 

graphs using the brain connectivity toolbox (https://sites.google.com/site/bctnet/). Global network properties included clustering (information segregation), global efficiency (information integration), and modularity (the neardecomposability of the network into a community structure of sparsely interconnected modules).

121 Efficiency at 

baseline was associated with AQ (p<O.OS), but not CPT (p=O.23) improvements. Modularity did not correlate with 

AQ (p=O.13) or CPT (p=O.23) changes aftertreatment. Finally, interhemispheric connectivity was only associated 

with CPT improvements (p<O.OS). In addition to global properties, we examined whether functional connectivity 

between distinct brain networks (modules or communities) play a role in determining outcomes. Inter-modular 

connectivity for S% density brain networks were generated by computing the total number of connections between any two modules and normalizing it by the total number of possible connections (Figure Sa). Association 

between modular connectivity and behavioral changes was assessed using a simple correlation analysis. We 

observed that AQ improvement showed a significant dependence on connectivity between the default-mode 

network and auditory regions (Figure Sb). CPT improvement showed a significant positive correlation with connectivity strength of the salience network and visual areas (Figure Sc). 

These results show that improvement of aphasia symptoms following intensive therapy can be explained in part 

by baseline brain connectivity properties. Improvements 

across behavioral domains are dependent on global and 

125 system-specific connectivity.

Instrumentation 

Participants will complete assessments at specific time 

points from admission to the IRF to 18 months poststroke. Table 3 lists study instruments by construct and 

indicates when participants will complete them. 

We will ask patients to report Demographic Characteristics, then reconcile them with information in their medical records. 

Clinical Characteristics, including stroke type, location, 

and volume, will be extracted from medical records. We 

will score the Charlson Comorbidity Index according to 

published criteria.

126 At each assessment time, we will collect information on current medications. 

We selected 7 stroke-relevant Neuro-QoL item banks for 

CAT administration:

9

·

127

·

128 Fatigue, Sleep Disturbance, 

Depression, Cognitive Function, Communication, Satisfaction with Social Roles and Activities, and Ability to ParFigure 5. Treatment outcomes are driven by specific network connectivity 

(a) Moelulality based connectivity maps were constructed by add ng all ROI

connections between any g ven par of Modules and normalZing by tne max­ mum number of connections. (b) Scatter plots snow tne modular connectivity 

{dens ty = 5%} tnat was signifcantly (p<0 05, FDR corrected} related to treat­ ment. Improvement in AO scores was unquely correlate<! to connectivty between defau t-mode network and auditory network, wnile Improvement in CPT 

II was related to increase<! connectvty between SAN and visual network. In­ i i serts snow tne connectvty across an densties.

ticipate in Social Roles and Activities. We will include one PROMIS item bank, Global Health, which measures 

overall physical and mental health. 

The National Institutes of Health Stroke Scale (NIHSS) is a brief measure of neurological impairment.129 It 

allows comparison of patients across settings and demonstrates excellent inter-rater reliability for acute stroke 

130·131 patients. Baseline scores predict outcomes to 90 days.132 The NIHSS demonstrates adequate to excellent 

133 concurrent validity with diffusion weighted MRI lesion volumes and perfusion-weight hypoperfusion volumes.

All persons performing NI HSS will be trained and certified.134 

The Apraxia of Speech Rating Scale (ASRS).135 We will distinguish between participants with apraxia of 

speech plus aphasia and those with aphasia alone using speech errors with words of increasing length and 

relative vowel duration in three-syllable words with weak-strong stress pattern (e.g., banana, potato). 1 36 Then, 

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Research Strategy 
for those with apraxia of speech plus aphasia, we will use the ASRS, 135 a valid 1 6-item rating scale, to quantify 

the presence or absence, relative frequency, and severity of characteristics associated with apraxia. The ASRS 

is scored during and/or after l istening to the individual 's speech during conversational speech, picture description, word and sentence repetition, and alternating and sequential diadochokinetic speech tasks. 

Table 3. Study Instrumentation and Assessment Timing 

Instrument Time 

(min) Construct Mode When 

Demographic Characteristics 

Sociodemographic Information* s Various Interview At 

Clinical Characteristics 

Stroke characteristics* - Person characteristics Medical record review A 

CT/MRI review for lesion size and location - Brain structure Medical record review A 

Charlson Comorbidity lndex126 - Body structure and function Medical record review A 

Medication review - Various 

Medical record review 

& patient reported AD 6 12 18 

Neuro-Qol Fatigue, Sleep Disturbance, Depression* 10 Fatigue, s leep, mood, Patient-reported AD 6 12 18 

135 Apraxia of Speech Rating Scalee 10 Motor-speech planning Performance test AD 6 12 18 

NIH Stroke Scaele* (NIHSS) 10 

Sensory, mentale, movement-related & communication functions 

Interview A&D 

Inpatient Rehabilitation Facileity Patient Assessment 

Inventory (I RF-PAI) (formerly the FIM'M Instrument) - Movement-related, self care, 

mentael functions Medical record review A W612 18 

Biomorkers 

Resting state brain fMRI (Abielitylab subsample, 100) 30 Network connectivity Imaging A 

Genetic samples s DNA po lymorphisms Saeliva sample A 

Aphasia Treatment 

Inpatient SLP Therapy - Current Procedeural Termienology 

codes, therapy taxonomy 

Medical, financial recoerds; patient log 

E 6 12 18 

Outpatient community groups, Private pay therapy - CPT codes, therapy taxonomy 

Medical, financial recoerds; patient log Weekly after 

discharge 

Outcomes - Linguistic 

Western Aphasia Battery-Revised (WAB-R) 60 Aphasia severity and classification 

Performance test AD 6 12 18 

Outcomes - Cognitive-Communicative 

Communication Participation Item Bank (CPIB) 10 Participation in life situations, 

controel over participation Patient-reported AD 6 12 18 

Connor's Continuous Performance test-3 (CPT 3) lS Attention Performance test AD 6,12,18 

Communication Confidence Rating Scale for Aphasia 

(CCRSA) 10 Communication confidence Patient-reported AD 6 12 18 

Communication Effectiveness Index (CETI) 10 Comemunication in everyday environmeents 

Caregiver reported AD 6 12 18 

Neuro-Qol Cognitive Fu nction* s Cognition Patient-reported AD 6 12 18 

Outcomes - Health-Related QOL 

Stroke & Aphasia Quality of Life Scale-39 (SAQoL39) 10 Stroke & aphasia-reelated Qol Patient-reported AD 6 12 18 

Neuro-Qol Satisfaction with Social Roles & Activities, Ability to Participate in Social Roles & Activities* 

lS Community, social and civic life Patient-reported AD 6 12 18 

PROMIS Global Heaelth s Gleobal health Patient-reported AD 6 12 18 

Global Rating of Change (GRC) 2 Patients' global perception of 

improvement Patient-reported D 6 12 18 

• NINOS Common Data Elements, mcludmg SES, educat on, age, sex, race/ethnicity, handedness; stroke etiology, location, etc.

* A=admission, Dedischa rge, E=Every day, Weweekly, 6e6-months post-stroke, 1 2=12 months post stroke, 18=18 months post stroke 

The IRF Patient Assessment Instrument (IRF-PAI) is required by Medicare for payment. Similar to the 

FIMTM137, it uses a ?-point rating scale. Nurses and therapists complete it routinely at IRF admission and discharge. Study sites will collect scores weekly. Subscores reliably measure self-care, mobility, communication, 

and cognition.137 

The Western Aphasia Battery-Revised (WAB-R)82 measures linguistic (reading, writing, auditory comprehension, naming) and non-linguistic skills (drawing, calculation, block design). It demonstrates excellent reliability 

and validity.

138-

140 The Aphasia Quotient (AQ) provides a global measure of aphasia severity and serves as the 

primary linguistic outcome. The AQ characterizes 8 aphasia types and severity. The Language Quotient (LQ) 

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includes reading and writing skills. The Cognitive Quotient (CQ) measures aspects of cognitive behaviors includ 

ing calculation, praxis, drawing and visualspatial skills in addition to oral and written language. 

The Communicative Participation Item Bank (CPIB)141 (primary communicative outcome) is a 10item, generic 

selfreport short form measuring communicative participation. Developers used IRT methods with selfreport 

data from 701 individuals with neurologic disorders and head and neck cancer. Evidence supports its validity for 

use with persons with aphasia.142 

Connor’s Continuous Performance Test-3143 is a computerized assessment of attention, specifically inatten 

tiveness, impulsivity, sustained attention, and vigilance. It is used widely with children and adults with ADHD and 

other neurological disorders.144,145 It has been used to identify attention deficits in individuals with aphasia.146 

The Communication Confidence Rating Scale for Aphasia (CCRSA)1,2,147 is a 10item selfreport measure 

that assesses confidence in a variety of different situations and people. Rasch analysis demonstrated that it can 

distinguish three levels of confidence in tasks of varying difficulty and across severities of aphasia.1,2 

The Communicative Effectiveness Index (CETI)148 provides information about the functional significance of 

changes resulting from SLP treatment and consists of 16 items that assess social needs, life skills, basic needs, 

and health threats. Caregivers who have an opportunity to observe the individual with aphasia are respondents. 

It demonstrates evidence of reliability and reliability,148 and it is sensitive to change in communication behaviors. 

The Stroke and Aphasia Quality of Life Scale-39 (SAQoL39)149 (primary healthrelated QoL outcome) is an 

adaptation of the Stroke Specific Quality of Life Scale150 for persons with aphasia. It measures physical, psycho 

social, communication QoL, and energy. Published reports describe use with stroke patients without aphasia151 

and proxy respondents; there are small to moderate differences between patient and proxy responses.152 It has 

been translated widely.153158 

PROMIS Global Health provides a summary index of physical and mental health.54 It includes 10 items selected 

from PROMIS item banks; it correlates highly with the EQ5D, another widely used measure of QOL. These 

global health scales can be used to summarize physical and mental health. 

Global Rating of Change (GRC). Patients will complete a global rating of change at 6, 12, and 18 months post 

stroke to measure perceived improvement from baseline and from the previous time point. This method permits 

testing for change from baseline to 6, 12, and 18 months; 6 to 12 and 18 months, and from 12 to 18 months. We 

will use a GRC item with a stem of “How would you say your ability to communicate has changed since [prior 

time point]”, and 5 response levels of 1=worse, 0=no change, 1=a little better, 2=much better, 3=very much 

better. We will calculate sensitivity and specificity of each response option to estimate the point of least misclas 

sification, which will determine the threshold for minimal improvement.159 

Single-Nucleotide Polymorphism Genotyp- Table 4. SNP-Specific Assays 

ing. We will investigate SNPs previously char 

acterized in genes, including Brain Derived 

Neurotrophic Factor (BDNF), Apolipoprotein E 

(APOE), Insulin Growth Factor 1 (IGF1), Cate 

cholOmethyltransferase (COMT), Fibroblast 

Growth Factor 2 (FGF2), and Vascular Endo 

thelial Growth Factor A (VEGFA). These SNPs 

modulate neuroplasticity in stroke patients and 

affect poststroke recovery (references in Table 

4). We will use Oragene Discover OGR600 sa 

liva kits (DNA Genotek, Inc.) and extract DNA 

using the Gentra Puregene Buccal Cell Kit (Qi 

agen) to identify SNPs. We will test DNA quality 

and purity, including A260/A280 ratios and vis 

ualization on agarose gels. We will quantify DNA yield using an Eppendorf BioSpectrometer and store purified 

DNA in 80C freezers. 

Gene/ 

Protein 

SNP Codon 

Change 

Amino Acid 

Change 

Life Technologies 

Assay ID 

BDNF160,161 rs6265 ATG, GTG M66V C_11592758_10 

BDNF100 rs11030119 Intronic (A/G) C_31701027_10 

BDNF104 rs10835210 Intronic (A/C) C_1751795_10 

APOE162 rs429358 CGC, TGC R130C C_3084793_20 

APOE162 r7412 CGC, TGC R176C C_904973_10 

IGF1163 rs7136446 Intronic (C/T) C_2801095_10 

IGF1163 rs9989002 Intronic (A/G) C_29575558_10 

COMT163 rs4680 ATG, GTG M158V C_25746809_50 

FGF2104 rs308379 Intronic (A/T) C_802931_10 

VEGFA104 rs833069 Intronic (C/T) C_11400863_20 

We will use PCRbased TaqMan SNP Genotyping assays, also known as TaqMan Allelic Discrimination assays, 

to genotype SNPs.164 These products use the 5 ́endonuclease property of the DNA polymerase to amplify and 

detect specific SNP alleles in purified genomic DNA samples.165 Each assay allows genotyping for a specific 

SNP. It requires forward and reverse PCR primers and two allelespecific TaqMan DNA probes labeled with 

fluorescent reporter dyes (FAM or VIC reporter molecules) that recognize and hybridize to the biallelic SNP 

inside the DNA region amplified by realtime PCR (Figure 6). Each biallelic SNP will be genotyped with TaqMan 

Research Strategy Page 136
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Allelic Discrimination assays using the AssayOnDemand service of Life Technologies (Thermo Fisher). Assays 

are available commercially and optimized by Life Technologies at Thermo Fisher. We will perform reactions in a 

96well format in a total volume of 5 UL containing 5 ng of purified DNA, 1× TaqMan assay, and 1× genotyping 

master mix (Thermo Scientific). Realtime PCR cycling will consist of initial denaturation for 15 minutes at 95°C, 

40 cycles with denaturation of 15 seconds at 96°C, and annealing and extension for 60 seconds at 60°C. We 

will acquire signals using a C1000 Touch Thermal Cycler (BioRad); results of the assay will be determined by 

CFX Manager software provided with the thermal cycler (BioRad). We will confirm and test results for false 

positives using the independent statistical clustering method kmeans.166 We will analyze genegene interactions 

between SNPs that have been linked to neuroplasticity at the cellular and molecular level in poststroke recovery, 

including growth factors mediating neurogenesis, angiogenesis, synaptic remodeling and neuroprotection (see 

Table 4 for the specific polymorphisms). We will identify significant predictor models using multifactordimen 

sionality reduction methods,167 10 in which multidimensional genotypes are classified into high and lowrisk 

groups. An indicator for the highrisk group is defined in the first step. In the second step, the indicator variable 

for the highrisk group is considered a covariate, with other adjusted covariates in the regression model. Then, 

the significance of a genegene interaction is obtained by testing the indicator variable of the highrisk group. 

Neuroimaging Data Collection and Analysis. Table 5. Neuroimaging measurements 

AbilityLab patients will receive two rsfMRI scans 

to estimate reliability, a highresolution (1 mm) T1 

anatomical scan, a T2 FLAIR axial scan, and two 

shell DTI scanning method, which provides more 

precise estimates of Fractional Anisotropy (FA) 

and of probabilistic tractography. This protocol as 

sures structural imaging will be available for all pa 

tients and functional connectivity imaging for 100 

patients. We will complete brainimaging analysis 

on freeshare software including FIMRIB software 

library (FSL),168 SPM,169 FreeSurfer,170 Caret,171 

and ad hoc routines written in Matlab, C++, Pearl, 

and Awk. We will use brain imaging data to quantify a number of measurements (Table 5) that will be used in 

Aim 2c. All anatomical and functional brain imaging data preprocessing and quality control will be performed 

using validated pipelines adapted from the Human Connectome Project.172 Highresolution T1 images will be 

used to investigate global and local structural properties including global brain volume, voxelwise based gray 

matter density and shape of cortical and subcortical structures, as well as lesion size (mm3

) and location. Global 

structural properties will be measured using SIENAX that estimates total brain tissue volume from a single image, 

normalized for skull size. It first strips nonbrain tissue and uses the brain and skull images to estimate the scaling 

between the subject’s image and standard space. It then runs automated tissue segmentation to estimate the 

volume of brain tissue and multiplies this value by the estimated scaling factor to reduce headsize variability 

between subjects. Regional gray matter properties will be assessed using the automated voxel based morphom 

etry toolbox from FSL. This analysis includes brain extraction and segmentation, and nonlinear registration to a 

standard gray matter template using FNIRT. We will take extra care during the registration steps to ensure min 

imal warping due to the presence of lesions. Lesion masks drawn on the highresolution anatomical scans will 

be used as a mask to perform a Virtual Brain Transplant.173 The T2 FLAIR scan will be used to quantify leu 

koaraiosis volume in patients using the FLAIRhistoseg method, that has been shown to be accurate and repro 

ducible.174 Functional brain properties will be assessed using rsfMRI and graph theory analysis tools. Brain 

networks will be constructed and studied at multiple correlation thresholds and parcellation sizes. Nodes of the 

brain functional network will be defined using either a whole brain voxelwise approach or various validated 

parcellation schemas ranging from 90  500 ROIs.175 Since the value of the chosen threshold is important, we 

will test several threshold values, from a conservative threshold of 2% connection density (sparse networks) to 

a lenient threshold corresponding to 50% link density (dense networks). We will assess topological properties of 

the graphs using the open source brain connectivity toolbox (BCT, https://sites.google.com/a/brainconnectivity 

toolbox.net/bct). Properties include clustering (a measure of information segregation), global efficiency (a meas 

ure of information integration), and modularity (a global measure of the neardecomposability of the network into 

a community structure of sparsely interconnected modules).121,122 We will assess nodal properties of various 

regions of interest, in addition to global topological properties. 

Outcome measures Global Local 

Functional 

Functional connectivity in IFG and STG 

Network properties (Clustering, efficiency and modularity) 

√ 

√ 

√ 

√ 

Anatomical (gray matter) 

Lesion volume 

Lesion location 

Gray matter density 

Subcortical volume and shape 

Gray matter microstructural changes 

√ 

√ 

√ 

√ 

√ 

Anatomical (white matter) 

Fractional anisotropy (FA) 

Leukoaraiosis 

Network properties (Clustering, efficiency and modularity) √ 

√ 

√ 

√ 

Research Strategy Page 137
ent Assessment Instrument ported by ,-- IRFs to CMS on the Patia F-igu_6 __ A..... -re_ l le-lic-D-is-cr-im-in_a_tio_n_A_ss-ay-s-for_C_OM_T__rS4_68_0_p_o-l y-

-

We wi ll use DTI to examine white matter property changes, specifically 

FA, which is sensitive to a range of pathologies using FMRIB's Diffusion 

Toolbox. We will correct DTI images for eddy currents that can cause 

stretches and shears in the diffusion-weighted images and head motion 

artifacts. A diffusion tensor model will be fitted at each voxel to determine 

voxel-wise FA, reflecting the degree ofdiffusion anisotropy within a voxel. 

Individual FA data will be realigned nonlinearly into a high-resolution 

common space (standard 1 mm). We will create and thin a group mean 

FA image to create a skeleton representing the centers of all tracts common to the group. Then, we will project individual FA images on this skeleton and compare it across individuals and conditions. We wi ll perform 

probabi listic tractography using PROBTRACKX to generate a wholebrain tractography for each voxel or ROI. We will use pair-wise voxel 

connection strengths to construct whole brain or region-specific connectivity matrices. We will generate matrices from connection probabil ities of 

voxels or ROls and evaluate them using graph theory methods. 

Rehabilitation Therapy Services. We will use the information reto characterize therapies. IRFs report total minutes of individuala, morphism. FAM- and VIC abeled probes specf c for each all e

GTG and ATG respect

e, 

vey, are incuded in the PCR assay. A m s - group, and co-treatment therapy for SLP each week. We will 

train SLPsto use a log on their tablets during each therapy ses- match between probe and targeted DNA sequence reduces the efficency of probe hybridzaton, ONA ampl ification and fluorescence 

det on. A. An equ ent 

cates t ent A i

ncrease in both FAM and VIC s gnals 

s heterozygote for rs4680 (GTG/ATG, or 

. ec val

SIon to report the startand stop t·1mes of each treatment task anda ndi hat Pa 

n FAM signal vs. VIC signal ndicatesthat Patient 

e (GTG/GTG, or G/G). 

GIA). B. indicate the language modality (auditory comprehension, oral ncrease i

s homozygoteforthe FAM based allel

to 

B

expression, reading comprehension, written expression) that is 

the focus. SLP minutes and activities derived from therapist logs and notes will be used to summarize therapy 

for inpatient and outpatient settings. A survey of 56 SLPs across the 3 IRFs revealed that the SLPs were proficient at identifying the targeted treatment modalities. Extensive SLP training will be provided before and throughout the study to ensure accuracy. Ten percent of the treatment sessions will be video-recorded, so that the 

treatment logs can be checked for reliability. In addition, we will extract SLP therapists' progress notes and code 

details about therapy activities and patient participation. We will aggregate this information weekly throughout 

173 174 each patient's stay, guided by the rehabilitation therapy taxonomy work led by Whyte and colleagues. 1 03, •

After inpatient discharge, study participants or caregivers will complete a weekly checklist of outpatient therapies 

and other formal and informal rehabil itation services. A research assistant will call patients weekly d uring the first 

two months after discharge and then monthly to review and summarize the therapy and other service information. 

StatisticalAnalysis 

Sample Size Considerations. We base the sample size on the following considerations given the complex 

nature ofthe proposed longitudinal models that constitute the primary analyses. Although power analysis software is available for randomized mixed effects study designs, 

176 no software is available for single group, observational mixed effects designs such as the proposed individual growth curve models. Simulation could offer an 

alternative approach to power estimation, but would rely on multiple assumptions about model parameters and 

variabi lity. To our knowledge, preliminary data are not available to allow us to make such assumptions regarding 

8 1 1 1 1 13 177 long-term recovery of aphasia or Qol. Published models3-5• • • • use different outcomes and time points, 

and thus are insufficient for the model simulations required for this design. In general , samples larger than 500 

are recommended for IGC models; 109 however, descriptive models have been reported for samples as small as 

220.

4 Oberfeld and Franke178 showed that generalized linear mixed models with repeated measures (i.e., SAS© 

PROC MIXED) control Type I error rates well under most conditions when the outcome is normally distributeda

and the sample size is 30 or larger. Thus, we propose a sample of 300 at 18 months, which allows confidencea

in robust trend analyses and sufficient power to develop viable models within the limits of the funding .a

Based on our experience with stroke patients10 we anticipate a 15% loss to follow-up at 6 months and an additional 10% loss at 18 months; thus, we will recruit 400 patients to retain 300 by the 18-month follow-up. Based 

on our experience, we expect to enroll 400 patients in approximately 30 months (Table 2). IGC models can 

accommodate missing data under the missing at random assumption , allowing participants with missing evaluation points to be retained in models. Thus, participants who miss an assessment time point but remain in the 

study for subsequent points are not lost; patient dropout is more of a concern for the missing at random assumption than for power. We will include all available longitudinal assessments for IGC modeling of all outcome 

measures to define post-stroke recovery trajectories. 

Page 138 

ResearchStrategy 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Aim 1. Unconditional Model Determination: We will construct separate unconditional IGC models, with time as 

the only predictor, for each of the primary and secondary outcome measures (Table 3). Outcomes with ordinal 

scales may be transformed to interval measures, including the IRFPAI subscales, using Rasch analysis.179181 

For each outcome, we will determine whether recovery pattern over time is linear, curvilinear (quadratic or cubic 

polynomial), or nonlinear (negative exponential, Figure 1). These models will include random subject intercept 

and slope, and the withinsubject correlation between repeated measurements will be modeled using an appro 

priate variance structure (spatial correlation). Model fit will be assessed using residual plots and other diagnostic 

techniques, and the bestfitting model will be selected based on the Akaike and Bayesian information criteria. 

We will use PROC MIXED and PROC NLMIXED in SAS©. As a sensitivity analysis, we will also fit models 

treating time as a categorical variable to see whether the estimates are consistent with fitted models. These 

models will define the typical pattern of recovery in this patient population. 

Aim 2. Conditional Model Determination: For each outcome, the selected unconditional model from Aim 1 will 

be expanded to include additional covariates (fixed effects). Based on the conceptual model Figure 2, these 

multivariable models will include time (and its appropriate functional form), and one of the following sets of co 

variates as described in Table 3: demographic characteristics (Aim 2a), clinical characteristics (Aim 2a); therapy 

characteristics (Aim 2b); and imaging biomarkers (including lesion size and location based on the multimodal 

parcellation atlas of the human cortex,182 and absolute values of network connectivity from imaging studies) or 

genetic markers from assays (Aim 2c). Model selection strategy will follow a purposeful model selection approach 

described by Hosmer and Lemeshow;53 we will investigate clinicallyrelevant interactions and explore functional 

forms of continuous predictors. Model fit will be assessed using residual plot and other diagnostics methods. 

Next, we will combine the variables from the selected multivariable models in each of the 4 groups (demographic 

+ clinical, demographic + biomarkers, demographic + clinical + biomarkers, demographic + clinical + treatment, 

and demographic + clinical + biomarkers + treatment) to test the relationships in Figure 2, assess the additional 

effects of the variables in each conceptual group, and reduce to the most parsimonious model. We will use the 

final IGC models, after validation in Aim 3, to construct an interactive tool which clinicians can use to produce 

individual trajectories by specifying values for each patient, stroke, and therapy covariate. 

The fitted models allow us to test Aim 1 and 2 hypotheses. For Aim 1, we expect curvilinear trajectories as the 

bestfit models for all outcomes, but that linguistic outcomes improve to plateau around 6 months poststroke, 

whereas cognitivecommunicative and QoL outcomes improve to plateau at around 18 months. We expect lesion 

size and initial aphasia severity (Aim 2a) and neuroplastic polymorphisms associations (Aim 2c) will have nega 

tive associations, and that CPT units (Aim 2b) and resting state connectivity (Aim 2c) will be positive. 

Aim 3. Model Stability: Model validation requires an external sample, which is beyond the scope of this study. 

Thus, we will evaluate the stability of the final models selected in Aim 2 using bootstrap and crossvalidation. 

Stability refers both to the variables included in the model and its predictive ability.183 To evaluate variable se 

lection, we will use bootstrap to resample cases B=500 times. First, we will fit each of the models from Aim 2 to 

the resampled data sets, and examine the bootstrap distribution of the estimated parameters and estimate the 

proportion of models in which each predictor was selected. Variables with low selection probabilities will be 

reconsidered for inclusion. Next, we will backward select each sample starting with the full model and will esti 

mate the probability of selection for each variable. As in Altman and Andersen,183 we will consider updating the 

final model by including variables with high probability of selection. To examine predictive validity, we will exam 

ine each model using Monte Carlo crossvalidation with repeated random subsampling. We will split cases ran 

domly into training and validation sets R=500 times, and fit the final model with the same set of predictors as 

selected in the final models in Aim 2 using the training sample in each split. We will use these training set 

parameter estimates to obtain fitted values for each subject in the validation set at the time points shown in Table 

3. Because the outcome is a continuous variable in IGC models, we will use the median absolute deviation 

between the observed and predicted outcome at each time point as the measure of model performance. We will 

use the median absolute deviation distribution across the R splits to obtain confidence intervals. We will consider 

the model to have good predictive performance if the median absolute deviation is less than or equal to the MCID 

value estimated for the relevant time point for the instrument. The results of the bootstrap and crossvalidation 

analyses will allow us to confirm the stability of the models selected in Aim 2, and to refine them if necessary. 

Potential Problems, Alternative Strategies, and Benchmarks for Success. The project timeline provides 

benchmarks for project success. Potential problems involve slow participant accrual and high attrition. The re 

cruitment and retention plan addresses these issues. We will extend accrual or add an additional site to assure 

we have a sample of 300 at 18 months, if needed. We have allowed sufficient time in the work plan for these 

possibilities. We will rebudget resources to meet slow accrual or low retention, if needed. 

Research Strategy Page 139
PHS Human Subjects and Clinical Trials Information OMB Number: 0925-0001 and 0925-0002

Expiration Date: 03/31/2020

Are Human Subjects Involved 

Is the Project Exempt from Federal regulations? 

Exemption Number 

Other Requested Information 

● Yes 

❍ Yes 

❏ 1 ❏ 2 

❍ 

● 

❏ 3 

No 

No 

❏ 4 ❏ 5 ❏ 6 ❏ 7 ❏ 8 

Funding Opportunity Number: PA-18-287 Received Date: Tracking Number: GRANT12670047 2018-07-05T15:37:27.000-04:00 

 Page 140
Human Subject Studies 

Study# Study Title Clinical Trial? 

1 Defining Trajectories of Linguistic, Cognitive-Communicative and Quality of Life Outcomes in No 

Aphasia 

Funding Opportunity Number: PA-18-287 Received Date: Tracking Number: GRANT12670047 2018-07-05T15:37:27.000-04:00 

 Page 141
Section 1 - Basic Information (Study 1) OMB Number: 0925-0001 and 0925-0002

Expiration Date: 03/31/2020

1.1. Study Title * 

Defining Trajectories of Linguistic, Cognitive-Communicative and Quality of Life Outcomes in Aphasia 

1.2. Is this study exempt from Federal ❍ Yes ● No Regulations * 

1.3. Exemption Number ❏ 1 ❏ 2 ❏ 3 ❏ 4 ❏ 5 ❏ 6 ❏ 7 ❏ 8 

1.4. Clinical Trial Questionnaire * 

1.4.a. Does the study involve human participants? ● Yes ❍ No 

1.4.b. Are the participants prospectively assigned to an intervention? ❍ Yes ● No 

1.4.c. Is the study designed to evaluate the effect of the intervention on the ❍ Yes ● No participants? 

1.4.d. Is the effect that will be evaluated a health-related biomedical or ● Yes ❍ No behavioral outcome? 

1.5. Provide the ClinicalTrials.gov Identifier (e.g. 

NCT87654321) for this trial, if applicable 

Funding Opportunity Number: PA-18-287 Received Date: Tracking Number: GRANT12670047 2018-07-05T15:37:27.000-04:00 

 Page 142
Section 2 - Study Population Characteristics (Study 1) 

2.1. Conditions or Focus of Study

❍ This longitudinal cohort study evaluates linguistic, cognitive-communicative, and health-related quality of life (QoL) recovery

in persons with stroke-related aphasia up to 18 months after onset.

2.2. Eligibility Criteria

We will enroll individuals with a primary diagnosis of stroke and aphasia on first admission to each of three Joint Commissionaccredited IRFs: The Shirley Ryan AbilityLab, Alexian Brothers Rehabilitation Hospital (ABRH) in Elk Grove Village, Illinois,

 and Mary Free Bed Rehabilitation Hospital (MFBRH) in Grand Rapids, Michigan, for a total of 300. Inclusion criteria are

 a primary diagnosis of a first stroke with aphasia, age 21 years and older, first admission for inpatient rehabilitation, and

 sufficient cognitive capacity to provide informed consent and participate in testing.

2.3. Age Limits Min Age: 21 Years Max Age:

2.4. Inclusion of Women, Minorities, and Children 1254-HeinemannWomen.pdf

2.5. Recruitment and Retention Plan 1255-CherneyRetention.pdf

2.6. Recruitment Status Not yet recruiting

2.7. Study Timeline 1256-Heinemann Timeline.pdf

2.8. Enrollment of First Subject 10/01/2019 Anticipated

Funding Opportunity Number: PA-18-287 Received Date: Tracking Number: GRANT12670047 2018-07-05T15:37:27.000-04:00 

 Page 143
Inclusion of Women and Minorities 

The Shirley Ryan AbilityLab and the Alexian Brothers Rehabilitation Hospital are located in Cook County in the 

State of Illinois. The AbilityLab is located in the city of Chicago; Alexian is in Elk Grove Village in the northwest 

corner of the county. The AbilityLab attracts patients who are representative of the city of Chicago, whereas 

Alexian attracts patients more representative of the State of Illinois. The 2013 census estimates for the State of 

Illinois indicate a distribution by race of 77.7% White, 14.7% Black or African-American, 5.1 % Asian, and the 

remainder composed of small percentages of other groups; 16.5% of the population was Hispanic (see 

http://www.lb 7 .uscourts.gov/documents/14c95482.pdf). 

Cook County, which includes the city of Chicago, has the following census figures for 2013: 65.9% White, 24.6% 

African-American, 6.9% Asian, 1 .8% two or more races and the remainder composed of small percentages of 

other groups; 24.7% of the population was Hispanic. Distribution by gender is 51.5% female and 48.5% male. 

The 2013 census estimates for the State of Illinois indicate a distribution by race of 77.7% White, 14.7% Black 

or African-American, 5.1 % Asian, and the remainder composed of small percentages of other groups; 1 6.5% of 

the population was Hispanic (see http://www.lb7.uscourts.gov/documents/14c95482.pdf). 

-

FY 2016 admissions to all AbilityLab sites, including inpatient, outpatient, and day rehabilitation, were: White 

African American -Asian -with the remainder composed of small percentages of other groups.a

•aAbilityLab serveda

• Abil ityLab served aa population The age distribution for all admissions 

was 0-44 years-45-64 years-65-74 years-; and 75+ yearsMary Free Bed Rehabilitation Hospital is located in Grand Rapids, Michigan. The Grand Rapids, Michigan 2015 

census estimates indicates a demographic distribution of 1 5.6% Hispanic (see https://factfinder.census.gov/faces/tableservices/jsf/pages/productview.xhtml?src=CF). 

Of the non-Hispanic population, distribution by race was 59.0% White, 19.6% African-American, 1.9% Asian, 

and 3.9% more than one race. Distribution by gender was 51.1 % female and 48.9% male. 

For fiscal 2016, admissions to Mary Free Bed of patients with aphasia was-female and-male. The race 

distribution was-White;-African-American;-Asian; and-more than one race. 

The attached planned Inclusion Enrollment Form represents the average demographic characteristics across 

the three participating Inpatient Rehabilitation Faci lities. We will not exclude participants based on gender, race, 

or ethnicity. We expect to enroll slightly more women than men based on admissions and relevant census data. 

In Illinois, the percentage of the population that is of Hispanic or Latino origin (of any race) is 16.5%; in Cook 

County it is 24. 7%; in Grand Rapids, Ml, it is 15.6%. Since we must require participants to be premorbidly literate 

in English, Latino-Americans may be under-represented compared to the national population. 

The distribution of participants by minority status and gender may not exactly mirror the population statistics 

because the pool of available aphasic patients that receive services in the three Inpatient Rehabilitation Facilities 

is relatively small and may not be referred randomly from the population. 

Inclusion of Children 

The focus of this application is acquired aphasia in adults following stroke. Stroke in children is a rare event with 

a reported incidence of ischemic and hemorrhagic pediatric stroke ranging from 1.2 to 13 cases per 1 00,000 

children under 18 years of age.1 Language recovery takes a different form in children due to the increased 

plasticity of their central nervous system. Therefore, we will exclude children from the study. 

1. Tsze DS, Valente JH. Pediatric stroke: a review. Emerg Med Int. 2011;2011:734506. 

Page 144 

Inclusion of Women, Minorities, and Children 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Recruitment and Retention Plan 

Recruitment. Recruitment procedures that have been used successfully in previous research at each site will 

be utilized. 

We will enroll individuals with a 

primary diagnosis of stroke and 

aphasia on first admission from each 

of three Joint Commission-accredited 

IRFs: The Shirley Ryan AbilityLab, 

Alexian Brothers Rehabilitation 

Hospital in Elk Grove Village, Illinois, 

and Mary Free Bed Rehabilitation 

Hospital in Grand Rapids, Michigan, 

for a total of 300 patients followed to 

18 months. Inclusion criteria are a 

Stroke Patient Admissions with Aphasia at Participating IRFs 

and Likely Sample in Past 12 Months 

Inpatient Rehabilitation Facility ‘ Admis 

sions 

Eligi 

ble 

Likely 

to 

Conse 

nt 

Shirley Ryan AbilityLab

Alexian Brothers Rehabilitation

Hospital 

Mary Free Bed Rehabilitation 

Hospital 

Totals 

primary diagnosis of a first stroke with 

aphasia, age 21 years and older, first admission for inpatient rehabilitation, and sufficient cognitive capacity to 

provide informed consent and participate in testing. The table shows the number of stroke admissions with 

aphasia over the past fiscal year. Based on our experience recruiting stroke inpatients for a Patient-Centered 

Outcomes Research Institute-funded study requiring patient self-report capacity, as well as the percentage of 

patients who are likely to consent to participate, we expect to complete enrollment within 30 months. We will 

over-recruit by 100 patients (400 consented patients), estimating 15% attrition by 6-months and another 10% 

attrition by 18-months, taking into account the likely mortality and morbidity. 

Recruitment will be conducted by trained research assistants who are dedicated to the project at each site. The 

research assistants will review the stroke admissions on a daily basis to identify eligible participants. 

Physicians and speech-language pathologists at each site will be made fully aware of the study and will be 

notified if an eligible patient is admitted. They will inform their patients about the project and ask if a research 

assistant may contact them about the study. When patients agree, the research assistant will describe the 

purpose of the project and obtain informed consent from those who are willing to participate using an approved 

consent form and following IRB procedures. During the informed consent process, patients will be told about 

the purpose of the project, the procedures that we will use, the duration of the project, risks, benefits, 

alternative procedures, and information related to confidentiality. They will be told that participation is voluntary 

and that they can withdraw from the protocol at any time without prejudice concerning future services with the 

rehabilitation facility. 

The research assistants will be trained in human subjects research and in the use of supported conversation 

techniques for persons with aphasia so they will be able to ensure understanding by the prospective subject. 

They will be trained and supervised by research speech-language pathologist Hurwitz, with oversight by co-PI 

Cherney. 

Similar numbers of participants have been recruited successfully in past and current investigations at all project 

sites. Information about the project will be available on the respective project, laboratory, and center websites 

of each facility. 

Based on stroke patient numbers at each study site, the likelihood of enrolling the projected number of 

participants is high. We will track recruitment status weekly to ensure that recruitment goals are met. In the 

unlikely event that these goals are not being met, we will consider adding a fourth site. 

Retention. Numerous investigations have been conducted at each site that have often extended for many 

months. There have been few issues of losing participants to attrition due to the length of the protocol. The 

reasons for dropping out have included the following: death, illness, relocation, and family issues (e.g., death in 

family, new family responsibilities) rather than demands or duration of the research protocol. 

Recruitment and Retention Plan Page 145
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

We anticipate few drop-outs during the IRF stay, aside from medical complications that require transfer back to 

the acute care hospital. Depending on the cause of transfers, participants may be able to resume participation 

on readmission. They will be carefully screened to ensure that they still meet all eligibility requirements. 

Following discharge from the IRF, a research assistant will call participants weekly during the first two months 

after discharge and then monthly to review and summarize the therapy and other service information. These 

phone calls also serve to promote retention. If needed, the frequency of the phone calls can be increased for 

individual participants to keep them connected to the study and study personnel. 

In addition, participants will be assessed at 6, 12, and 18 months post-stroke with a variety of speech, 

language, cognitive-communicative, and quality of life assessments. Each of these visits will last approximately 

3-4 hours and may be completed on consecutive days if necessary.

If needed, for the 6, 12 and 18 month follow-ups, participants may be seen in their homes. Some participants 

may not be able to drive and the use of public transportation could be challenging. We have found that 

conducting research visits in subjects’ homes eases participant and family burden, increases attendance for 

scheduled sessions, and improves retention. 

Reimbursement for participation will be provided which can facilitate retention. Participants will receive 

after the inpatient rehabilitation discharge assessment. The honorarium will increase to for the 6-month 

visit, for the 12-month visit, and for the 18-month follow-up. Subjects completing all assessments will 

receive a total of . By reimbursing participation time for assessment sessions, we will be providing 

tangible acknowledgment that we value participant time. Increasing the amount reimbursed at each successive 

assessment will facilitate retention. 

We have accounted for participants lost through attrition, by planning to recruit an additional 100 participants 

(i.e., 400) with the goal of 300 participants continuing through 18 months post stroke. 

Recruitment and Retention Plan Page 146
Project Timeline 

Task Descriotion Year 1 Year 2 Year 3 Year 4 Year 5 

Aim 1: Establish a prospective cohort of stroke patients with aphasia, and define their typical patterns 

(trajectories) of linguistic, cognitive-communicative, and health-related QoL recovery 

Obtain IRB approval at 

1.1 SRALab, ABRH, 

MFBRH, set-up I I

REDCap database 

1 .2 Train research staff, 

orient therapsts I I

Consent and complete 

1.3 inpatient/outpatient I I I I I I I I I 

data collection 

Complete 6-month 

1.4 post stroke follow up I I I I I I I I I 

assessments 

Complete 12-month 

1.5 post stroke follow up I I I I I I I I I 

assessments 

Complete 18-month 

1.5 post stroke follow up I I I I I I I I I 

assessments 

1 .6 Request, extract, code 

therapy characteristics I I I I I I I I I

1.7 Data cleaning ■ ■ ■ ■ ■ ■ 

1 .8 Develop IGC models ■ ■ ■ ■ 

1 .9 Test H1 ■ ■ ■ ■ 

Aim 2. Identify factors that are associated with linguistic, cognitive-communicative, and health-related 

QoL outcomes from among: a) Patient factors, including demographic and clinical characteristics 

related to the stroke and aphasia; b) Treatment variables, including inpatient and outpatient 

aphasia therapy characteristics and other informal aphasia services; and c) Biomarkers, including 

genetic and neuroimaging biomarkers 

2.1 Data cleaning I ■ I ■ I ■ 

2.2 Develop IGC models I ■ I ■ 

2.4 Test H2a, b, c I ■ I ■ 

Aim 3: Evaluate the stability of the linguistic, cognitive-communicative, and health-related QoL 

outcomes recovery models from Aim 2 

3.1 Data cleaning I ■ I ■ I ■ I 

3.2 Test H3 using 

bootstrap methods I I I I I

3.3 Perform crossvalidation I I I I I

3.4 Disseminate findinas ■ ■ ■ 

Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4

Page 147 

Study Timeli ne 
Inclusion Enrollment Reports 

IER ID# Enrollment Location Type Enrollment Location

Study 1, IER 1 Domestic The Shirley Ryan AbilityLab (SRALab) in Chicago, Illinois; Alexian

 Brothers Rehabilitation Hospital (ABRH) in Elk Grove Village, Illinois;

 and Mary Free Bed Rehabilitation Hospital (MFBRH) in Grand

 Rapids, Michigan.

Funding Opportunity Number: PA-18-287 Received Date: Tracking Number: GRANT12670047 2018-07-05T15:37:27.000-04:00 

 Page 148
Inclusion Enrollment Report 1 

Using an Existing Dataset or Resource* : ● Yes ❍ No 

Enrollment Location Type* : ● Domestic ❍ Foreign 

Enrollment Country(ies): USA: UNITED STATES

Enrollment Location(s): The Shirley Ryan AbilityLab (SRALab) in Chicago, Illinois; Alexian Brothers Rehabilitation

 Hospital (ABRH) in Elk Grove Village, Illinois; and Mary Free Bed Rehabilitation Hospital

 (MFBRH) in Grand Rapids, Michigan.

Comments: Target enrollment is 300 participants, followed until 18 months post-onset. We will over-recruit by

 100 patients (400 consented patients), estimating 15% attrition by 6-months and another 10%

 attrition by 18-months.

Planned 

Racial Categories 

Ethnic Categories 

Not Hispanic or Latino 

Female Male 

Hispanic or Latino 

Female Male 

Total 

American Indian/ 

Alaska Native 0 0 0 0 0 

Asian 12 8 0 0 20 

Native Hawaiian or 

Other Pacific Islander 0 0 0 0 0 

Black or African 

American 33 27 0 0 60 

White 142 118 33 27 320 

More than One Race 0 0 0 0 0 

Total 187 153 33 27 400 

Cumulative (Actual) 

Racial Categories 

Ethnic Categories 

Not Hispanic or Latino Hispanic or Latino 

Unknown/Not 

Reported Ethnicity Total 

Female Male 

Unknown/ 

Not 

Reported 

Female Male 

Unknown/ 

Not 

Reported 

Female Male 

Unknown/ 

Not 

Reported 

American Indian/ 

Alaska Native 0 0 0 0 0 0 0 0 0 0 

Asian 0 0 0 0 0 0 0 0 0 0 

Native Hawaiian or 

Other Pacific Islander 0 0 0 0 0 0 0 0 0 0 

Black or African 

American 0 0 0 0 0 0 0 0 0 0 

White 0 0 0 0 0 0 0 0 0 0 

More than One Race 0 0 0 0 0 0 0 0 0 0 

Unknown or 

Not Reported 0 0 0 0 0 0 0 0 0 0 

Total 0 0 0 0 0 0 0 0 0 0 

Tracking Number: GRANT12670047 Page 149

Funding Opportunity Number: PA-18-287 Received Date: 

2018-07-05T15:37:27.000-04:00 
Section 3 - Protection and Monitoring Plans (Study 1) 

3.1. Protection of Human Subjects 1257-Cherney_HumSub narrative 2017 FINAL 2July 2018.pdf

3.2. Is this a multi-site study that will use the same protocol to ● Yes ❍ No ❍ N/A 

conduct non-exempt human subjects research at more than one

domestic site?

If yes, describe the single IRB plan 1258-Cherney_SingleIRB.pdf

3.3. Data and Safety Monitoring Plan 1259-Heinemann Cherney Data Safety Monitoring Plan.pdf

3.4. Will a Data and Safety Monitoring Board be appointed for ❍ Yes ● No 

this study?

3.5. Overall structure of the study team 1260-Cherney_Study Team.pdf

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Protection of Human Subjects 

Risks to Human Subjects 

a. Human Subjects Involvement and Characteristics: Four hundred participants with aphasia following stroke 

will be recruited upon admission to one of three inpatient rehabilitation facilities (IRF): the Shirley Ryan AbilityLab 

(SRALab) formerly the Rehabilitation Institute of Chicago, Alexian Brothers Rehabilitation Hospital (ABRH) in 

Elk Grove Village, Illinois, and Mary Free Bed Rehabilitation Hospital (MFBRH) in Grand Rapids, Michigan. Allowing for dropout, we anticipate that 300 subjects will complete all study procedures at 18 months post-stroke. 

All participants will undergo an initial screening that will include identification of demographic characteristics and 

medical history including CT/MRI review and medical complications. This review will be followed by a baseline 

assessment of speech, language, communication, and cognition skills as shown in the research plan. During the 

evaluation, subjects will be asked to complete routine speech-language tests such as name pictures, read words 

and sentences, describe a picture, repeat sentences, repeat sounds, and participate in a conversation. Specific 

tests include the NIH Stroke Scale, the Western Aphasia Battery-Revised, and the Connors Continuous Performance Test – 3. These tests will be administered at admission and/or just before discharge from the IRF. Participants will complete questionnaires about their perceptions and feelings regarding their general health, fatigue, 

sleep, mood, and communication abilities just before discharge. Their caregivers will also be asked to complete 

a questionnaire to rate communication skills in everyday situations. 

We will ask subjects to provide a saliva sample at the start of their IRF stay. DNA will be extracted from the saliva 

sample and various single-nucleotide polymorphisms (SNPs) for BDNF, APOE, IGF1, COMT, FGF2, and 

VEGFA will be investigated. Subjects who are at the SRALab and who meet the eligibility requirements for MRI, 

will receive a resting state fMRI and a high resolution anatomical scan. At ABRH and MFBRH, we will review 

their clinical MRI scans to determine the size and anatomical site of lesions. 

During the IRF stay, the IRF Patient Assessment Instrument which includes the Functional Independence Measure (FIMTM) instrument will be administered as part of routine clinical care at admission and weekly thereafter. 

We will extract IRF-PAI scores from medical records. Information about speech and language therapy sessions 

also will be extracted from medical records, including frequency and duration of treatment. In addition, the 

speech-language therapists will complete logs on their tablets during each therapy session to indicate the start 

and stop times of each treatment task and to indicate the language modality (auditory comprehension, oral expression, reading comprehension, written expression) on which the task focuses. These logs will be analyzed 

for information regarding type of speech and language therapy services. 

Following discharge from the IRF, participants are likely to seek other services such as outpatient therapy at 

hospitals and private or university clinics, aphasia conversation groups, and intensive comprehensive aphasia 

programs. Study participants and/or caregivers will complete a weekly checklist of these formal and informal 

rehabilitation services. A research assistant will call participants weekly during the first two months after discharge and then monthly to review and summarize the therapy and other service information. 

Participants will be repeat assessments at 6, 12, and 18 months post-stroke with a variety of speech, language, 

cognitive-communicative, and quality of life assessments. Each of these visits will last approximately 3-4 hours 

and may be completed on consecutive days if necessary. The assessment will include the same tests that were 

administered at discharge from the IRF except for the NIH Stroke Scale. 

Subjects will not be excluded on the basis of age, ethnic background, race, sex, or economic factors. However, 

since stroke is more prevalent in older individuals, the majority of the patients will be at least 50 years of age or 

older. 

Inclusion criteria: Men or women with diagnosis of aphasia subsequent to a first left-hemisphere infarct(s) that 

is confirmed by CT scan or MRI; first IRF admission; at least 21 years of age. 

Exclusion criteria: Any neurological condition other than cerebral vascular disease that could affect cognition 

or speech, such as Parkinson ’s disease, Alzheimer’s disease, traumatic brain injury, or the presence of righthemisphere lesions. 

Exclusion criteria for the rs-fMRI include (1) any metallic implants, tattoos on large body parts, claustrophobia, 

and (2) Pregnancy in women of child-bearing age. 

The purpose of the study is to evaluate variables that affect recovery in aphasia such as aphasia type, severity, 

lesion size and location, selected genomic biomarkers, resting state fMRI, and amount, type and duration of 

1 

Protection of Human Subjects Page 151
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Protection of Human Subjects, continued 

speech and language therapy and other services. These variables must be assessed with the person with aphasia. 

All subject data will be securely maintained at each of the facilities as described below. 

b. Sources of Materials: We will use existing patient records including MRI/CT scans to determine initial patient 

eligibility. We will evaluate subjects with the test battery for speech, language, communication, cognition and 

quality of life status at admission and discharge to the IRF, 6, 12 and 18 months post-stroke to obtain data on 

their deficits and changes that occur during recovery. We will obtain saliva samples on all subjects to evaluate 

selected polymorphisms biomarkers that affect neuroplasticity. We will conduct resting state fMRIs on a subset 

of subjects (those who are eligible for MRIs at the SRALab) and determine lesion size and site from clinical MRIs 

of other subjects. We will use existing patient records for IRF-PAI scores and to identify amount and duration of 

treatment during the IRF stay. We will obtain additional information about the type of speech and language 

therapy from logs that are completed by speech and language therapists. Participants will provide reports of their 

continued formal and informal speech and language services after discharge from the IRF. Data will be maintained in password-secured computer files and only personnel associated with the study will have access. 

c. Potential Risks: Risks associated with the speech, language, and cognitive-communicative evaluations: 

These measures are routine and generally well-accepted by patients. The quality of life measures are also routine and will be administered with aphasia-friendly supports as needed. There are no more than the usual clinical 

risks associated with these activities such as fatigue or frustration while attempting tasks that are difficult. 

Risks associated with the MRI: Only subjects who meet the MRI safety guidelines/eligibility criteria will receive 

r-s fMRIs. The main risk is one of discomfort since participants lie in a confined space with minimal head and 

body movements for about 30 minutes. 

Another potential risk may be loss of confidentiality due to participation in the study. 

Adequacy of Protection Against Risks 

a. Recruitment and Informed Consent: Admission lists at AbilityLab, ABRH and MFBRH will be reviewed daily. 

Subjects with stroke and aphasia will be informed about the project by their physician or speech-language 

pathologist and asked if a research assistant may contact them about the study. If patients agree, the research 

assistant will describe the purpose of the project and obtain informed consent from those who are willing to 

participate using an approved consent form and following IRB procedures. During the informed consent process, 

subjects will be told about the purpose of the project, the procedures that we will use, the duration of the project, 

risks, benefits, alternative procedures, and information related to confidentiality. They will be told that participation is voluntary and that they can withdraw from the protocol at any time without prejudice concerning future 

services with the rehabilitation facility. The consenting process will be carried out by personnel who are trained 

in the use of supported conversation techniques to ensure understanding by the prospective subject. The IRB 

will review the project on an annual basis to ensure patient safety and confidentiality. 

b. Protection against Risk: Participants will be offered frequent breaks between tasks to minimize risk of fatigue. 

The assessments can be administered over two test sessions on consecutive days if subjects are not able to 

tolerate the length of a single test session. Frustration with the evaluation tasks will be minimized by explaining 

the purpose of the tasks and providing frequent reinforcement for continuing to participate in them. To protect 

against fMRI risks, subjects will be carefully screened for MRI safety criteria by personnel who are thoroughly 

trained regarding safety procedures. These personnel will be trained in supported communication strategies for 

aphasia to ensure that subjects understand the safety criteria and to ensure good communication throughout the 

fMRI procedures. 

To protect against any breach in confidentiality, data collected for this project will not be a part of medical records 

and will be maintained separately. Codes instead of names of subjects will be used on videotapes, data files, 

disks, and reports. Tapes, data files, and disks will be physically secured in locked areas and only authorized 

personnel will have access to them. 

2 

Protection of Human Subjects Page 152
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Protection of Human Subjects, continued 

Potential Benefits to Human Subjects and Others 

The risks are minimal and reasonable in relation to the anticipated future benefits. While there may not be any 

benefits to the subjects who participate in the study, the findings are likely to have important implications for 

individuals with aphasia in the future. It will provide information about factors that influence positive outcomes 

including the types of services that are beneficial. It will provide information about ways to measure patientreported perceptions regarding progress during recovery and rehabilitation. 

Importance of the Knowledge to be Gained 

The knowledge gained will improve our understanding of the variables affecting recovery and rehabilitation process for individuals with aphasia such as aphasia type, severity, lesion size and location, selected genomic 

biomarkers, resting state fMRI, and amount, type and duration of speech and language treatment and other 

services. The data may lead to improved service delivery, reduced costs and effectiveness of speech-language 

services, thereby improving the communication skills and hence the quality of life of individuals with aphasia. 

Results may affect the field of neurorehabilitation since results may be applicable to other areas of deficit following stroke, and to other populations with communication problems requiring rehabilitation. 

Data and Safety Monitoring Plan 

A separate data and safety monitoring plan has been uploaded. We plan to have a Data Monitoring and Oversight Committee. All procedures will be carried out with approval of the Institutional Review Board of Northwestern University, which is the IRB for SRALab, and it will serve as the single site IRB. 

3 

Protection of Human Subjects Page 153
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Multi-Site Study Single IRB Plan 

The Northwestern University Institutional Review Board (IRB) will serve as the Single IRB (sIRB) of record. The 

Northwestern University IRB is the IRB for the lead site, the Shirley Ryan AbilityLab, and is fully accredited by 

the Association for the Accreditation of Human Research Protection Programs, Inc. The utilization of a sIRB is 

in keeping with the NIH requirement that “all sites participating in multi-site studies involving non-exempt 

human subjects research funded by the National Institutes of Health (NIH) will use a single Institutional Review 

Board (sIRB) to conduct the ethical review required by the Department of Health and Human Services 

regulations for the Protection of Human Subjects at 45 CFR Part 46”. 

The two collaborating sites (Alexian Brothers Rehabilitation Hospital in Elk Grove Village, Illinois, and Mary 

Free Bed Rehabilitation Hospital in Grand Rapids, Michigan, have agreed to rely on Northwestern University’s 

Institutional Review Board as the sIRB. If any sites are added after the award, they will rely on the sIRB. 

All participating sites will, prior to initiating the study, sign an authorization/reliance agreement that will clarify 

the roles and responsibilities of the sIRB and participating sites. 

Communication: As the lead team, the Shirley Ryan AbilityLab will be responsible for the initial submission to 

the sIRB as well as continuing review submissions. The lead team will serve as the primary liaison between the 

sIRB and collaborating study teams. Each participating site will be responsible for conveying all necessary 

information to the lead study team and will be responsible for completing all Human Research Protection 

Program requirements at their local institution. The Relying Human Research Protection Program will track the 

local study and manage all non-IRB requirements. 

The Shirley Ryan AbilityLab and the Northwestern University IRB will maintain records of the authorization and 

reliance agreements and of the communication plan. 

IRB Plan Page 154
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Data Safety Monitoring Plan 

Overview 

The proposed study is observational in which a cohort of 400 patients with stroke and aphasia are recruited on 

first admission to an Inpatient Rehabilitation Facility and followed up to 18 months after onset. Allowing for 

attrition, we anticipate a sample of 300 at 18 months. Participants will be recruited from three sites. There is no 

intervention and the risks are low. There are no more than the usual clinical risks associated with the speech, 

language, cognitive-communicative, and quality of life assessments such as fatigue or frustration while 

attempting tasks that are difficult. Risks associated with the r-s fMRIs are primarily related to physical discomfort 

as participants lie in a confined space with minimal head and body movements for about 30 minutes. There may 

be potential risks of loss of confidentiality due to participation in the study. 

Data Monitoring and Oversight Committee (DMOC) 

Based on NIDCD guidelines for observational studies, we will convene a DMOC to ensure patient safety and to 

ensure the validity and integrity of the data. DMOC membership will comprise individuals with the following 

qualifications: 

 A physician with experience in stroke rehabilitation 

 A research speech and language with experience in aphasia research 

 A neuroscientist or neurologist with experience in neuroimaging, including resting state MRIs 

 An epidemiologist with experience in health services research 

 A neuroscientist or geneticist 

 A person with aphasia and/or the family member of a person with aphasia 

Potential conflicts of interest will be assessed and documented prior to appointment on the DMOC and annually 

thereafter. The DMOC will meet at the start of the study to review the study protocol and procedures including 

the Manual of Operations and its readiness for implementation. Thereafter, the DMOC will meet annually. 

The DMOC will evaluate patient safety, determine participant burden, and provide advice on notification and 

referral of participants for any abnormal findings. Together with the Co-PIs and statistician, the DMOC will 

monitor overall study progress including recruitment and retention, adherence to study protocol, data quality 

control procedures and data quality. The DMOC will also review primary manuscripts and oral presentations that 

address the specific aims of the study. 

Additional Plans 

We plan procedures to ensure the quality and reproducibility of the collected data, including include training of 

the research assistants who will collect medical chart information and administer the speech, language, 

cognitive-communicative, and quality of life assessments. Co-PI Cherney, assisted by Research SLP Hurwitz, 

will provide initial training as well as continuous monitoring throughout the study. The project manager will 

receive weekly logs of the assessments that are scheduled and will assign 10% of them to be videotaped. 

Videos will be reviewed to ensure that the assessments are administered correctly; the assessments will be 

rescored by Research SLP Hurwitz to ensure that the test results are reliable. The research assistants will 

complete American Heart Association training and be certified to administer the NIH Stroke Scale. Research 

SLP Hurwitz has more than 10 years of experience serving as a blinded assessor for the many aphasia treat 

trials that Co-PI Cherney has conducted. 

We will provide training and continuous monitoring to the clinical speech-language pathologists at each site 

who will be logging information about their treatment sessions with study participants. Training will include 

information about aphasia treatment in general, the rationale and purpose of the study, and the treatment logs 

they will complete with study participants. Feedback on videotaped aphasia treatment sessions will allow the 

clinicians to gain practice using the treatment templates. Training will continue until clinicians achieve more 

than 90% reliability logging the start and stop times of each treatment task, and identifying the language 

modality that is the focus of each task. We expect all clinicians to achieve this level of reliability. We surveyed 

SLPs at study sites; the majority were able to identify the treatment modalities accurately. However, for 

clinicians new to the site and for clinicians who require further practice, either their treatment sessions will be 

videotaped and coded later or the research assistant will observe treatment sessions and complete the logging 

until the clinician is able to demonstrate adequate reliability. 

Data and Safety Monitoring Plan Page 155
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Dr.

every other month during the data collection period. 

Co-PIs Heinemann and Cherney, together with statistician will oversee the integrity and validity 

of the data that are entered into the REDCap database. All case report forms will be checked for completeness 

and entered into the database by the project manager. Ten percent of all case report forms will be rechecked 

by Research SLP Hurwitz or Co-PI Cherney. Based on their experience with aphasia and the outcome 

measures being used, they are able to recognize aberrant scores outside the range of responses typical of 

persons with varying types and severities of aphasia. One of the research assistants will double check data 

entry into the database from 10% of the case report forms. 

will supervise the master’s level statistician who will be responsible for cleaning the data 

The Study Team will also monitor safety. All team members will have completed IRB required training 

concerning reporting of adverse events. Any adverse event will be reported immediately by the team member 

who becomes aware of the event to the site PI, who will report the event to Co-PIs Heinemann and Cherney 

within 24 hours. They will report the event to the IRB within 48 hours of initial identification. All adverse events, 

even unrelated events, will be reported to the IRB. Unrelated events such as seizure, transient ischemic attack, 

and recurrent stroke are expected when conducting research with stroke survivors. We do not expect adverse 

events that are associated with the study procedures, but will continue to report all events, associated or not, to 

the IRB. 

Data and Safety Monitoring Plan Page 156
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Study Team Structure 

Data Collection Sites: 1) Shirley Ryan AbilityLab (Lead Site) – Chicago, IL, 2) Alexian Brothers Rehabilitation 

Hospital – Elk Grove Village, IL and 3) Mary Free Bed Rehabilitation Hospital – 

Co-PIs: Allen Heinemann, Leora Cherney (AbilityLab) 

Co-Is: Allan Kozlowski (Mary Free Bed; Site PI; statistician), Linda Foster (Alexian; Site PI, Site manager), 

Marwan Baliki (AbilityLab, Brain Imaging), Andrea Domenighetti (AbilityLab; Genetics); 

(AbilityLab & Northwestern University, biostatistician); Elliot Roth (AbilityLab; Physiatrist) 

Project Manager: TBD 

Research Speech-Language Pathologist (SLP): Rosalind Hurwitz (AbilityLab; provides training at all sites) 

Site Manager: Roberta Virva (Mary Free Bed) 

Research Assistants: TBD (AbilityLab), TBD (Alexian)*, TBD (Mary Free Bed) 

AbilityLab Site – Lead Site 

Administrative and Data Collection and Coordination Site 

Team Members: 

L. Cherney – Study Co-PI 

A. Heinemann - Study Co-PI 

M. Baliki – Co-I, Brain Imaging 

A. Domenighetti – Co-I, Genetics 

R. Hurwitz – Research SLP 

TBD – Project Manager 

TBD - Research Assistant 

R. Pichika –Research Associate Biologics Lab 

– Co-I, biostatistician 

TBD – Master’s level statistician 

Alexian Brothers Rehabilitation Hospital Mary Free Bed Rehabilitation Hospital 

Data Collection Site Data Collection Site 

Team Members: Team Members: 

L. Foster – Site PI/Manager, Co-I A. Kozlowski – Site PI, Co-I 

TBD – Research Assistant * R. Virva – Site Manager 

J. Butzer – Research Administrator 

TBD - Research Assistant 

*This research assistant will be hired by AbilityLab but will be located at ABRH 

Drs. Heinemann and Cherney will meet at least monthly (via phone conference as needed) with the entire 

team. The project manager will meet weekly with the research SLP and research assistants from all sites. The 

PI and site PI’s will have at least quarterly face-to-face meeting. 

Dr. Heinemann will work closely with AbilityLab’s research administration and the NIH project officer, obtain IRB 

approval, supervise chart extraction of therapy details, and oversee analytic and dissemination activities. Dr. 

Cherney will oversee training of all staff who interact with persons with aphasia including: informed consent; 

assessment of linguistic, cognitive-communicative, and quality of life; and weekly and/or monthly follow-up calls 

regarding formal and informal activities post-discharge from the IRF to 18 months post-stroke. She will oversee 

training of clinical speech-language pathologists at all sites in use of the treatment logs during their regular SLP 

sessions, oversee imaging and genomics activities, and assure data integrity. Together they will assure the 

quality of the research design and overall scientific conduct of the project. 

Overall Structure of the Study Team Page 157
Section 4 - Protocol Synopsis (Study 1) 

4.1. Brief Summary

4.2. Study Design

4.2.a. Narrative Study Description

4.2.b. Primary Purpose

4.2.c. Interventions

Type Name Description 

4.2.d. Study Phase

Is this an NIH-defined Phase III Clinical Trial? ❍ Yes ❍ No 

4.2.e. Intervention Model

4.2.f. Masking ❍ Yes ❍ No 

❏ Participant ❏ Care Provider ❏ Investigator ❏ Outcomes Assessor 

4.2.g. Allocation 

4.3. Outcome Measures

Type Name Time Frame Brief Description 

4.4. Statistical Design and Power

4.5. Subject Participation Duration

4.6. Will the study use an FDA-regulated intervention? ❍ Yes ❍ No 

4.6.a. If yes, describe the availability of Investigational

Product (IP) and Investigational New Drug (IND)/

Investigational Device Exemption (IDE) status

4.7. Dissemination Plan 

Funding Opportunity Number: PA-18-287 Received Date: Tracking Number: GRANT12670047 2018-07-05T15:37:27.000-04:00 

 Page 158
Delayed Onset Studies 

Delayed 

Onset 

Study# 

Study Title Anticipated Clinical 

Trial? 

Justification 

The form does not have any delayed onset studies 

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Multiple PI Leadership Plan 

Two Principal Investigators from the Shirley Ryan AbilityLab (formerly the Rehabilitation Institute of Chicago) are 

designated for this R01 application: Allen Heinemann, PhD, has expertise in health services and outcomes research and will serve as the contact PI; Leora Cherney, PhD, CCC-SLP will serve as the clinical and scientific 

expert in aphasia and speech-language pathology. Drs. Heinemann and Cherney have collaborated successfully 

on aphasia research for more than a decade and have coauthored two papers reporting the development of a 

communication confidence scale. Drs. Heinemann and Cherney have a combined 70-year history of successful 

grant management and demonstrated leadership in their respective roles, operating independently and collaboratively. 

The proposed project will define the trajectories of linguistic, cognitive-communicative, and quality of life improvement during and after inpatient rehabilitation, identify the therapy characteristics associated with gains during 

and after inpatient rehabilitation, and assess objective measures of patient-reported QoL. Dr. Heinemann will 

work closely with AbilityLab’s research administration and the NIH project officer, obtain IRB approval, supervise 

chart extraction of therapy details, and oversee analytic and dissemination activities. Dr. Cherney will oversee 

training of all staff who interact with persons with aphasia including: informed consent; assessment of linguistic, 

cognitive-communicative, and quality of life; and weekly and/or monthly follow-up calls regarding formal and 

informal activities post-discharge from the IRF to 18 months post-stroke. She will oversee training of clinical 

speech-language pathologists in use of the treatment logs, oversee imaging and genomics activities, and assure 

data integrity. Together they will assure the quality of the research design and overall scientific conduct of the 

project. 

They will use a variety of mechanisms to assure regular communication between the PIs throughout the project. 

The PIs will conduct at least monthly (or more often as needed) meetings. Communication will not be limited to 

set meetings, but conducted when and as needed. AbilityLab provides abundant “huddle spaces” for informal 

and unscheduled meetings, and Drs. Heinemann and Cherney work in close proximity to each other, making 

such meetings easy to arrange. 

The PIs have developed the proposal with the necessary care that should avoid future conflicts. However, should 

disagreements arise, the responsibilities are delineated clearly by the PI’s respective areas of scientific and

technical expertise. They report to AbilityLab’s Chief Science Officer, Rick Lieber, who can mediate conflicts

should they arise. 

Dr. Heinemann is a Professor in the Department of Physical Medicine and Rehabilitation at Northwestern University’s Feinberg School of Medicine and Director of the Center for Rehabilitation Outcomes Research at the

AbilityLab. He has over 35 years of research experience in health services research and has served as PI for 

large center grants and others involving multi-site data collection. He is a diplomate in Rehabilitation Psychology 

and a fellow of the American Congress of Rehabilitation Medicine and the American Psychological Association. 

He serves as co-Editor-in-Chief for the Archives of Physical Medicine and Rehabilitation, and is on the editorial 

boards of Rehabilitation Psychology, Journal of Head Trauma Rehabilitation, and several other journals. He is 

the author of more than 300 articles. He received the Distinguished Career Award from the Rehabilitation Psychology division of APA. Dr. Heinemann has the research, clinical, and administrative expertise to ensure the 

successful management of the clinical and scientific aspects of this R01 grant. 

Dr. Cherney is the Scientific Chair, Think and Speak Lab, at the Shirley Ryan AbilityLab and Professor in the 

Department of Physical Medicine and Rehabilitation and the Department of Communication Sciences and Disorders at Northwestern University. She has over 35 years’ clinical experience in the field of speech-language 

pathology and is Board Certified by the Academy of Neurologic Communication Disorders and Sciences. She is 

the Founder and Director of the Center for Aphasia Research and Treatment at the Shirley Ryan AbilityLab. Her 

primary research interest is treatment efficacy for patients with aphasia, she serves or has served as Principal 

Investigator on several NIDILRR, and NIH-funded grants investigating novel treatment approaches, including 

the adjuvant roles of levodopa, cortical stimulation, and transcranial direct current stimulation in aphasia treatment. Dr. Cherney has the research, clinical, and administrative expertise to ensure the successful management 

of the clinical and scientific aspects of this R01 grant. 

Multiple PD/PI Leadership Plan Page 160
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1. Cherney LR, Babbitt EM, Semik P, Heinemann AW. Psychometric properties of the communication 

Confidence Rating Scale for Aphasia (CCRSA): phase 1. Topics in stroke rehabilitation. 

2011;18(4):352-360. 

2. Babbitt EM, Heinemann AW, Semik P, Cherney LR. Psychometric properties of the Communication 

Confidence Rating Scale for Aphasia (CCRSA): Phase 2. Aphasiology. 2011;25(6-7):727-735. 

3. Kozlowski AJ, Heinemann AW. Using individual growth curve models to predict recovery and 

activities of daily living after spinal cord injury: an SCIRehab project study. Arch Phys Med Rehabil. 

2013;94(4 Suppl):S154-164 e151-154. 

4. Hart T, Kozlowski AJ, Whyte J, et al. Functional recovery after severe traumatic brain injury: an 

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Data Resource Sharing Plan 

The proposed research will include data from 400 stroke patients with aphasia who are admitted to one of 

three inpatient rehabilitation facilities (IRFs) in the Midwest; we expect 300 patients to complete an 18-month, 

post-stroke follow-up assessment. The dataset will include demographic, behavioral and self-report data 

regarding linguistic, cognitive-communicative and quality of life status obtained during the inpatient stay and at 

6, 12, and 18 months post-stroke. The dataset will also include information about therapy services including 

type, amount, and duration of treatment obtained during and after the inpatient stay. The dataset will include 

information about brain network connectivity derived from a resting state fMRI obtained at admission to the IRF 

and the presence or absence of specific genetic polymorphisms that have a role in neuroplasticity. 

We will remove personal identifiers from the dataset before release for sharing. 

We will make the REDCap data set available to users on request and only under a data-sharing agreement 

that includes (a) restrictions against efforts to identify study participants, (b) destruction of the data after 

analyses are completed, (c) reporting responsibilities, (d) restrictions on redistribution of the data to third 

parties, and (e) acknowledgement of the data source and funder. 

Resource Sharing Plan(s) Page 179