Effect of Antibiotics on Submucosal Enteric Neurons and Glia in the Lower Gastrointestinal
Phase: PHASE4
Conditions: Antibiotic Enterocolitis
Sponsor: Rockefeller University

 
Protocol including Statistical Analysis Plan 
Official Title: Effect of Antibiotics on Enteric Neurons and Glia (YAL-138) v1.2 
NCT Number - NCT05834036 
IRB approval date: November 6, 2025 

 
 
Institutional Review Board 
Sarah J. Schlesinger, MD, Chair 
Dale Miller, BA CIP  
Sr. IRB Specialist (212) 327-8411 
Vanessa Smith, BA MPS, CIM, CIP 
Sr. IRB Specialist, (212) 327-8410 
Hospital Bldg., Room 201 Box 331 
 
 
 
ClinicalTrials.gov 
National Library of Medicine 
8600 Rockville Pike 
Bethesda, MD 20894 
 
Re: Effect of Antibiotics on Enteric Neurons and Glia, NCT05834036, IRB ID YAL-1038 
Dear Representative of ClinicalTrials.gov: 
Thank you for your communication regarding project, Effect of Antibiotics on Enteric Neurons 
and Glia under NCT05834036, IRB ID: YAL-1038.  
This letter is to confirm that the uploaded Study Protocol and Statistical Analysis Plan PDF/A 
document is the original, pre-specified Study Protocol and Statistical Analysis Plan document 
approved by the Rockefeller University Institutional Review Board. Our institution utilizes an 
IRB application format, rather than a separate Protocol and/or Statistical Analysis Plan. Please do 
not hesitate to contact me if I may be of further assistance. 
Sincerely, 
 
Sarah J. Schlesinger, MD 
Chair, Institutional Review Board 
Associate Professor of Clinical Investigation 
Senior Attending Physician 
Laboratory of Chemical Biology and Signal Transduction 
The Rockefeller University 
 
 
 
 
 
 
 
 

    Study Application (Version 1.12)
1.0
General Information
*Please enter the full title of your study::
Effect of antibiotics on submucosal enteric neurons and glia in the lower gastrointestinal tract.
 
 
*Please enter the study short title:
Antibiotics effects on enteric neurons and glia.
* This field allows you to enter an abbreviated version of the Study Title to quickly identify this
study.
 
 
Is this Study using Subject Management?
Yes
No
 
 
2.0
Add departments
2.1 List departments associated with this study:
Please choose at least two labs/departments. Your main lab/dept. should be the primary
lab listed, e.g. your HOL's lab.  
All protocols must also list "Rockefeller University Hospital (RUH)" as a secondary
lab/dept.  
You may also list additional,  lab/dept(s) if appropriate to include RU collaborators.
If your lab/department is not listed in the 'Add Department' dropdown menu, please
contact RUH IT at hospital_informatics@rockefeller.edu to arrange for the new lab to be
added to the listing.
Is
Primary? Department Name
RUH - Laboratory of Mucosal Immunology (Mucida)
RUH - Research Facilitation Office (Facilitation)
 
3.0
Assign key study personnel(KSP) access to the study
3.1 * Please add a Principal Investigator for the study:
Name
Role
Training Record
Aydin, Begum, PhD
Principal Investigator
 View Training Record
3.2 If applicable, please select the Research Staff personnel:
A) Additional Investigators
Name
Role
Training Record

3.0
Assign key study personnel(KSP) access to the study
No Additional Investigators have been added
B) Research Support Staff
Name
Role
Training Record
Fry, Rebecca Stanton, MSN FNP
Facilitator
 View Training Record
3.3 *Please add a Study Contact:
Name
Role
Training Record
Aydin, Begum, PhD
Study Contact
 View Training Record
Fry, Rebecca Stanton, MSN FNP
Study Contact
 View Training Record
The Study Contact(s) will receive all important system notifications along with the Principal Investigator. (e.g. The project
contact(s) are typically either the Study Coordinator or the Principal Investigator themselves).
4.0
Rockefeller University Conflict of Interest
4.1   Investigator Financial Conflict of Interest All KSP must complete an annual certification of their Significant
Financial Interest (“SFI”) disclosures in the University’s online Research Administration System at
https://RAS.rockefeller.edu.  Disclosures also must be updated in connection with new human subjects
research protocols (“Research Certification”), and within 30 days of discovering or acquiring a new SFI.  To
avoid delays in the IRB review process, when prompted by an email from rascoi@rockefeller.edu
requesting an updated Research Certification, KSP should click on the Research Certification link contained
in that email notification, or go to https://RAS.rockefeller.edu, to (a) review and update his or her SFI
disclosures or certify that he/she has no updates, as appropriate, and (b) indicate whether any of his/her
SFI disclosures are reasonably related to the design, conduct, or reporting of the research protocol. If a
KSP discloses a SFI that might constitute a conflict of interest with respect to the proposed protocol, he or
she must e-mail a copy of the Lay Summary of the draft protocol to Teresa Solomon, Esq.
(solomot@rockefeller.edu).  Doing so will facilitate addressing COI issues in step with the development of
the study protocol.  Non-compliance or tardiness in making or updating COI disclosures will result in a
delay in IRB review.      Institutional Conflict of Interest:
 
As early as possible the PI (or a designee) preparing a clinical research protocol must review a list of
entities in which The Rockefeller University has an Institutional Financial Interest at
https://icoi.rockefeller.edu/account/login.php.  If the proposed study involves any entity on that list, the
PI (or designee) must notify Teresa Solomon, staff to the FCOI Committee, by e-mail
solomot@rockefeller.edu and Sarah Schlesinger, Chair of the IRB, by email: schless@rockefeller.edu,
provide the name(s) of the entities and a copy of the Lay Summary. Doing so will facilitate addressing
institutional COI issues in step with the development of the study protocol. Failure to take steps to review
and address potential institutional conflicts of interest will delay the IRB review process.  
5.0
External Personnel
5.1   List external personnel who will be working on the study:
Name
Institution
Telephone
E-mail
Role
Yelina Alvarez 
Janssen
Immunology 
650 269 2708 
yelina.alvarez@gmail.com Consultant

6.0
Delegation of Authority 
6.1   Enter authorized activities for all Rockefeller University personnel named on the study. 
Activity Codes:
1.   Informed consent **
11.  Participant recruitment
21.  Skin biopsy *
2.   Inclusion / exclusion criteria
12.  Perform assays 
22.  Conduct sleep study
3.   Medical/medication history *
13.  Specimen / sample analysis
23.  Diet design and preparation
4.   Perform Physical Exam *
4a. Write / Sign LIP orders *    
14.  Lumbar puncture *
24.  Nutritional assessment and
counseling
5.   Skin assessments and photos
15.  Femoral line placement *
25.  Addition of PABA to food 
6.   Study drug dispensing *
16.  Central line placement * 
26.  Data analysis
7.   Study drug administration *
17.  Insulin clamp procedure *
27.  Data review
8.   Study drug reconciliation
18.  Leukapheresis *
28.  Data management 
9.   Study drug compliance
19.  Sigmoidoscopy * 
29.  Maintain regulatory documents / files
10. Administer study questionnaire(s)
20.  Fat biopsy *
30.  Complete CRF's
Add up to three additional authorized activities specific to this study (do NOT add activities
that have previously designated codes):
31:
Facilitator
32:
33:
 Activity Codes Continued:
34.  Behavioral Testing
35.  Bod Pod
36.  Bone Marrow Aspiration *
37.  Neuropsychological Testing *
38.  Conduct Focus Group 
39.  Conduct Smell Study
40.  Genetic Counseling *
41.  Apply EEG Electrodes **
42.  Olfactometer Test
43.  Study Participant Teaching
44.  Resting Energy Expenditure 
45.  Source Document Review & Correction 
46.  Medical Photography
47.  See 4a 
48.  Adverse Event Assessment
49.  Clinical Trial Registration 
50.  Study Support Drug Dispensary
51.  Internal Monitoring 
52.  Randomization 
Enter delegation of authority for Rockefeller University Key Study Personnel:
NOTE:
*     Indicates procedures requiring the individual complete specific credentialing BEFORE the activity
may be added to their delegated activities.
**  Indicates procedures requiring the individual complete specific training BEFORE the activity may
be added to their delegated activities.

Name
Title
Authorized
Activities
Start Date
End Date
Alvarez, Yelina,
MD/PhD
PI
1, 2, 3, 4, 4a,
10, 12, 13,
19, 26, 27,
28, 30
11/14/2022
05/24/2024
Dowd,
Kathleen, BSN,
RN, CCRC
Facilitator
6,31
11/14/2022
04/17/2024
Olufeko,
Oluwatobi
Temitope, MPH,
MA, CCRC
Facilitator
31
07/18/2023
10/03/2025
Aydin, Begum,
PhD
Co-
Investigator
12, 13, 26,
27, 28, 30
04/17/2024
05/24/2024
Burgos-Rivera,
Genesis, BA
Facilitator
31
04/17/2024
10/03/2025
Aydin, Begum,
PhD
PI
12, 13,
26,27,28, 30
05/24/2024
Alvarez, Yelina,
MD/PhD
Consultant
26,27,49
05/24/2024
05/24/2024
Dowd,
Kathleen, BSN,
RN, CCRC
Facilitator
31
05/22/2024
10/03/2025
Fry, Rebecca
Stanton, MSN
FNP
Facilitator
31
10/03/2025
Enter delegation of authority for additional Rockefeller University Key Study
Personnel:
Name
Title
Authorized
Activities
Start Date
End Date
No results found
Enter the authorized activities for External Personnel:

Name
Title
Authorized
Activities
Start Date
End Date
No results found
7.0
Study Description
7.1  
Study Classification
Full Review
7.2  
* Submission Request Category
Note: For each submission, please designate the level of review, or “Submission Request Category” you are
requesting. When completing this field, please indicate the level of review you are requesting for the
specific submission you are working on.
For example, if you are submitting an Expedited Amendment request to change the Key Study Personnel on
your existing Full Board study, you should select “Expedited Review” in both the Amendment Submission
Form and Study Application. The IRB will confirm an Expedited review of the Amendment submission is
appropriate, and the overall study will remain classified as a full Board review. Please see the help bubble
for guidance.
To submit a request for a Not Human Subjects research determination, please exit this form and
select the “Not Human Subjects Research Determination” form under Create a New Study.
Exempt from Review 
Exempt with Limited Review 
Expedited Review 
Full Review 
7.3   * Lay Summary
Please provide a summary of your study in lay language that is easily understood by a non-scientist. The
summary should be no more than half a page (500 words or less) and should contain a clear statement of
the rational for the study.
Please click on the help bubble to get the information on " How to use iRIS text editor."

Please provide a summary of your study in lay language.  The summary should be no more
than a half page (500 words or less) and should contain a clear statement of the rationale for
the study. 
The interactions between bacteria and their products with the intestinal tissue are important
for maintaining a healthy and balanced system. Alterations in gut bacteria communities
have been associated with various human pathologies. Our lab and others have found that
mice treated with short and long-term antibiotics exhibit a transient yet profound loss of
neurons in the more superficial submucosal and deeper muscularis plexi in the intestine
accompanied by slow motility. Glia cells also depend on microbiota for their maintenance. In
humans, antibiotic use has been associated with disorders of gut-brain interactions (DGBI)
such as irritable bowel syndrome however whether there are changes in the enteric neurons
and glia cells remain unknown. Therefore, we propose to further characterize the neurons
and glia populations in the human distal colon after a single antibiotic course. We expect
that our study will reveal glia and neuronal subtypes that are susceptible to changes in the
bacteria populations and depend on microbial products for their maintenance. Our findings
will guide future DGBI studies to ascertain the physiological effects that such loss has on
intestinal healthy balance.
7.4  
* Public Health Impact Statement
Provide a brief plain language statement (100 words or less) of the value of the research
proposed and its potential impact on population health. Additional instructions located in
Help.
 
Anti-microbials have been associated with Disorders of Gut Brain Interactions (DGBIs).
 We propose to study the effects that antibiotic use has on the number and type of neuron
and glia cells in the gut.  A better understanding of these effects will lead to the
development of new therapeutic interventions and prevention strategies. 
8.0
Clinical Trial Registration
8.1  
Clinical Trial Registration
The types of studies listed below must be registered at Clinical Trials website before
enrolling the first participant in order to be in compliance with federal regulations and
preserve the opportunity to publish the study in journals that adhere to the ICMJE
guidelines. Please check the answer that best applies.
Study involves testing of FDA regulated drugs or biologics (See HELP) 
Study is funded by the NIH, and meets the definition of a “clinical trial” (see HELP) 
Study meets the ICMJE definition of a “clinical trial” (See HELP) 
Additional funding agency or journal requires clinical trial registration 
None of the above 

If you selected 1, 2, 3, or 4 you must register your trial with ClinicalTrials.gov through the
Rockefeller University institutional account. Please contact the Clinical Research Support
Office x7408 for assistance.
9.0
Study Overview/Summary
9.1   * Who initiated this study?
Please specify one:
Principal Investigator Initiated 
Industry Initiated 
Other 
9.2   *Are other institutions involved in the study?
No 
Yes 
9.3   * Is this a multi-site trial using a single IRB (sIRB) review arrangement? Please see help bubble for
definition.
  Yes  
  No
9.4  
* Who (What) is to be studied?
Human Subjects - including coded samples and/or data with links to Identifiers
Deidentified Samples - unable to be linked to identifiers by receiver
Data Only - unable to be linked to identifiers
Identifiable samples or data for exemptions (per 104 (s)(4))
9.5   *Study Type:
Interventional 
Observational 
9.6   The initial date of IRB approval/determination was:
12/01/2022
9.7   * What is the expected duration of the study?
7 years
9.8   * Are any of the following agents to be used in the study?

Check all that apply:
FDA Approved Drug
FDA Approved Drug for Off-Label Purpose (This might require an IND)
Investigational New Drug
Biologic Agents
Nutritional Supplements
Placebo
Vaccines
No Agents
FDA Exemption to use Study Drug
Please indicate whether your application to the FDA for use of the investigational drug is planned or
has been submitted by checking the box below. 
Include a description of the status of the FDA submission in the text box.
Planned
Submitted
9.9   * Are investigational devices to be used in the study?
  Yes  
  No
9.15   Special Research Procedures
Does the study propose to directly involve participants in the following special research
procedures?
Recombinant DNA
Gene Therapy
Fetal Tissue
Embryonic Stem Cells
Induced Pluripotent Stem Cells
CRISPR-Cas9
If any item is checked, please see Help for details.
9.16   * Radioactive Isotopes Involved
Will participants be exposed to any radiation other than routine x-rays solely for clinical care
purposes? 
  Yes  
  No
 
10.0
Interventional
10.1   *Interventional, please specify:

Open Label 
Single Blind 
Double Blind 
Other 
11.0
Study Phase:
11.1   Study Phase:
Select where applicable
Phase 0 
Phase I 
Phase I/II 
Phase II 
Phase III 
Phase IA 
Phase IB 
Phase IIA 
Phase IIB 
Phase IB/IIA 
Phase IIB/IIIA 
Phase IIIA 
Phase IIIB 
N/A 
12.0
Objectives and Rationale
12.1   * Overview
Briefly state the purpose of this study. Give enough background and rationale to provide
both scientists and lay members of the IRB and ACCTS with the basis for exposing human
participants to the risks involved.
The enteric nervous system (ENS) has been recognized as the “second brain” as it can
regulate enteric physiology without central nervous system input. Similar to the central
nervous system, it is composed of multiple neuron populations whose main functions are
gut motility, secretion, and absorption [3, 10]. In addition to the neurons, the ENS contains
glia cells whose main role is neuroprotection but also contribute to normal gut motility [11].
Several studies have demonstrated that the microbiota and the ENS have an intimate
relationship that begins in utero, and it is critical for its normal development [3]. Neurons can
recognize bacteria and their products [12, 13]. Our lab and others have shown neuronal
loss after enteric infections and antibiotic (Ampicillin) treatment in the muscularis layer, that
results in delayed transit time in animal models [5, 7]. Hence, communication between the
microbiota and the ENS is important to maintain normal gut motility. Disorders of Gut-Brain
Interactions (DGBIs) are quite common, among these are Irritable Bowel Syndrome (IBS
defined by Rome IV criteria as abdominal pain associated with a change in consistency and
frequency of bowel movements) and the constipation predominant subtype (less than 3
bowel movements per week) is the most prevalent, which is also the most common motility
disorder that our mouse models of infection and antibiotics treatment exhibit [14]. IBS has
been associated with dysbiosis and a recent study demonstrated that antibiotic use
immediately before or after screening colonoscopy increased the risk of developing IBS [9,
15]. In addition, dysfunction of submucosal neurons in IBS has been previously reported but
whether there are changes in neuron numbers or neuron characteristics has not been

explored [16]. While there have been  prospective studies that have explored the effects of
antibiotics in patients treated for Helicobacter Pylori, there have been other investigators
who have focused on the long term effects of antibiotics in healthy volunteers [17,18].
Therefore, similar to our animal models, we propose that humans experience a profound
and transient loss/alteration of neurons in the setting of antimicrobial use associated
dysbiosis that manifest as DGBIs, most notably the constipation subtypes. This proposal will
address whether antimicrobial use leads to quantitative and qualitative changes in the
populations of submucosal neurons and glia cells in human subjects. 
We will test this hypothesis in a prospective study in which healthy participants will be asked
to take the commonly used antibiotic amoxicillin twice a day for 7 days, and colon tissue
biopsies will be obtained before and after treatment. We will then process and analyze the
human tissue using techniques already established in the lab that will include confocal
microscopy to visualize structural changes, single nuclei RNA sequencing, 16S ribosomal
bacteria RNA sequencing and metabolomics analysis.
12.4   * Engaging Stakeholders: Describe any plans to engage other stakeholders (Scientists, practitioners,
patients, advocacy groups, etc.) for hypothesis generation, or feasibility purposes.  
Since this is a human subjects protocol we plan to engage the assistance of Rockefeller
Hospital Research Support Office for protocol development, and recruitment of participants.
We will need the assistance of a pharmacist to dispense the antibiotics. The hospital staff
will assist with volunteers' visits and the endoscopic procedures. In the lab, one postdoc will
assist with planning sequencing strategy.  Staff from metabolomics, genomics and
bioinformatics research support cores will also assist in this project. 
Because we will only recruit healthy participants for this study, we will not engage any
patients' groups. 
12.5   * Hypothesis
Describe the research hypothesis in a single sentence.
Antimicrobial use leads to quantitative and qualitative changes in the populations of
submucosal neurons and glia cells in human subjects.
12.6   * Aim(s)
Indicate how you will address the hypothesis (e.g., to compare groups, to estimate a
parameter, to ascertain feasibility). Since the sample size determination is usually based on
the primary aim only, the primary aim should be sufficient to justify the study.
Aim1:  Characterize the changes of submucosal neurons and glia cells before and after
course of antibiotics in humans. 
12.7   * Primary Outcome(s)
Indicate which variable(s) will be assessed to judge the primary specific aim.  Give
measurement units, if applicable.
Total number of colonic submucosal neurons and glia cells in humans before and after
course of antibiotics. 

12.8   * Secondary Outcome(s)
Indicate which additional variable(s) will be assessed to judge the secondary outcome(s).
Give measurement units, if applicable.
 
a.Gene expression profiles in the mucosa and submucosa compartments in humans
before and after course of antibiotics. 
b. Gut microbiota changes in humans after course of antibiotics. 
c. Gut metabolites changes in humans after course of antibiotics.
12.9   * Methods and Procedures
Please provide a description of the laboratory and clinical analyses and procedures that will
be performed. Include the role of external collaborators and consultants when appropriate.
Please refer to Help text for Guidance.
 
One set of samples will be studied:  Colorectal sample tissue and stool from amoxicillin-
treated participants. All samples will be collected from RUH volunteers. 
Ten 18–75-year-old participants will be divided into two groups of 5 and matched in age +/-
5 years, race, sex, and gender.
There will be five (5) study visits:
Study Visit 1 (Screening Visit) (approximately 2 hours; Out-Patient Visit)
Consent process
Medical History 
Targeted physical exam (focus on GI, cardiac and respiratory)
 HIV test
 POC Pregnancy test for women of childbearing age 
 Labs: venipuncture to collect CBC, Comprehensive metabolic panel, PT/PTT, INR for
a total of 10 ml blood (2 tsps.).
 Instructions will be provided in preparation for Visit #2. The following will be included:
a. adhere to a clear liquid diet the day prior to the scheduled flexible sigmoidoscopy. A clear
liquid diet sheet with examples will be given to each participant. 
b. The evening prior to the flexible sigmoidoscopy, participants will cleanse their bowels with
a tap water enema. A   plastic bottle and K-y jelly will be given to the participants to take
home. 
c. a sealed commercial stool collection kit (DNA Genotek) that includes specimen collection
instructions, toilet accessory, collection tubes, and spatulas will be given to the participants
to collect stool prior to the procedure. The participant will bring the stool sample during visit
#2, +/- 2 days. 
c. NPO after midnight the day of the procedure but encourage sips of water. 
Further instructions will be given to participants on how to avoid prebiotics and probiotics
during the study and to notify the PI if they need to take any antimicrobials or any new
medications, start a new diet, have enteric infections during the study as these may result in
their exclusion from the study. 

Upon review of lab results and if the participant meets eligibility criteria, the PI will contact
the study participant to schedule the flexible sigmoidoscopy. The participant will be
instructed to adhere to a clear liquid diet the day before the procedure, to self-administer the
tap water enema in the evening prior to the procedure, and not to eat or drink anything
(except sips of water) after midnight the day of the procedure. 
VISIT #2: Procedure Visit ( 2 to 21 days after screening visit) (approximately 2 hours;
Day Patient Visit)
Stool sample will be collected and stored in the refrigerator. 
Vital signs pre- and post-procedure. Post-procedure, vital signs will be taken
immediately after the procedure, then 30 minutes after the procedure, and 1hr after
the procedure. 
POC Urine Pregnancy test for women of childbearing age. 
Stool consistency and frequency questionnaire will be given to the participant to
complete.
Oral diazepam 5 mg pre-procedure will be offered and administered based on the
patient preference and PI evaluation. Oral diazepam takes 30 - 60 minutes to take
effect. 
Tap water enema upon arrival followed by additional 1 or 2, 200ml tap water enemas
if the participant still has solid debris after a bowel movement. 
Flexible Sigmoidoscopy Procedure
The sigmoidoscope is advanced to the beginning of the descending colon
(about 24 cm) and up to 20 biopsies will be obtained with Boston Scientific
Jumbo forceps (max diameter of 2.8mm), each biopsy will be 2-2.8 mm in size,
one in each quadrant, spaced 2-3cm throughout the sigmoid colon. 
Tissue specimens will be placed in sterile specimen cups containing normal
saline.
Observation for one-hour post-procedure (for signs of bleeding or distress)  and
evaluation by nursing and PI to determine when ready for discharge. 
Breakfast
Post-procedure Instruction sheet given prior to departure. 
In the event a mass, polyp, or ulceration is found, a copy of the images obtained during the
sigmoidoscopy and a letter with the examination findings will be given to the participant and
they will be instructed to follow-up with their Primary Healthcare Provider. 
The participant will be asked to return in two weeks for Visit #3 and instructions on avoiding
the addition of new probiotics, prebiotics or drastic dietary changes will be given.  In
addition, participants will be instructed to notify us if he/she starts any antimicrobial
medication including antifungals, or developed any intestinal infection. 
VISIT #3: Medication Visit (14 to 21 days after visit 2) (approximately 1 hour;
Outpatient Patient Visit)
Medical History 
Targeted physical exam (focus on GI, cardiac and respiratory)
POC Urine Pregnancy test for women of childbearing age
Participants will be randomized to receive a 7-day supply of amoxicillin
875mg capsules to be taken every 12 hours. Medication will be dispensed
and provided during the visit. 
Participants will be given a diary to record medication intake times. 
Participants will be given a plastic bottle and K-y jelly to self-apply a tap water enema
at home on the night prior to the procedure.  
A sealed commercial stool collection kit (DNA Genotek) that includes specimen
collection instructions, toilet accessory, collection tubes, and spatulas will be given to
the participants to collect stool prior to the next procedure. The participant will bring
the stool sample during Visit #4, +/- 2 days. 

Same instructions provided in preparation for Visit #2 will be provided in preparation
for Visit #4.
Same as in Visit #2 participants will be asked to avoid any new prebiotics, probiotics,
or drastic dietary changes and to notify investigators if new anti-microbial medications
were started or they developed an intestinal infection.
VISIT #4: Procedure Visit (5-9 days after initiation of antibiotics) (approximately 2
hours; Day Patient Visit)
Same as Visit #2. This visit could also occur after 5 Days of antibiotics in volunteers who
cannot tolerate a 7-day course of amoxicillin. Participants that cannot tolerate at least 5
days of antibiotics will be excluded from the study, replaced with other participants, and
provided partial compensation. 
Medication diary will be collected. 
Stool sample will be collected and stored in the refrigerator. 
Vital signs pre- and post-procedure. Post-procedure, vital signs will be taken
immediately after the procedure, then 30 minutes after the procedure, and 1hr after
the procedure. 
POC Urine Pregnancy test for women of childbearing age. 
Stool consistency and frequency questionnaire will be given to the participant to
complete.
Oral diazepam 5 mg pre-procedure will be offered and administered based on the
participant’s preference and PI evaluation. Oral diazepam takes 30 - 60 minutes to
take effect. 
Tap water enema upon arrival followed by additional 1 or 2, 200ml tap water enemas
if the participant still has solid debris after a bowel movement. 
Flexible Sigmoidoscopy Procedure
The sigmoidoscope is advanced to the beginning of the descending colon (about 24
cm) and up to 20 biopsies will be obtained with Boston Scientific Jumbo forceps (max
diameter of 2.8mm), each biopsy will be 2-2.8 mm in size, one in each quadrant,
spaced 2-3cm throughout the sigmoid colon. 
Tissue specimens will be placed in sterile specimen cups containing normal saline.
Observation for one-hour post-procedure (for signs of bleeding or distress)  and
evaluation by nursing and PI to determine when ready for discharge. 
Breakfast
Post-procedure Instruction sheet given prior to departure. 
In the event a mass, polyp, or ulceration is found, a copy of the images obtained
during the sigmoidoscopy and a letter with the examination findings will be given to
the participant and they will be instructed to follow-up with their Primary Healthcare
Provider. 
The participant will receive a sealed commercial stool collection kit (DNA Genotek)
that includes specimen collection instructions, toilet accessory, collection tubes, and
spatulas to collect stool prior to the next procedure. The participant will bring the stool
sample during visit #5, +/- 2 days.  similar to Visits #1 and # 3 to collect stool prior to
Visit #5.
Same as in Visit #3 participants will be asked to avoid any new prebiotics, probiotics,
or drastic dietary changes and to notify investigators if new anti-microbial medications
were started or they developed an intestinal infection.
Participants will be given a plastic bottle and K-y jelly to self-apply a tap water enema
at home on the night prior to the procedure.
VISIT #5: Procedure Visit (21 to 30 days after Visit #4) (approximately 2 hours; Day
Patient Visit)
Stool sample will be collected and stored in the refrigerator. 

Vital signs pre- and post-procedure. Post-procedure, vital signs will be taken
immediately after the procedure, then 30 minutes after the procedure, and 1hr after
the procedure. 
POC Urine Pregnancy test for women of childbearing age. 
Stool consistency and frequency questionnaire will be given to the participant to
complete.
Oral diazepam 5 mg pre-procedure will be offered and administered based on the
patient preference and PI evaluation. Oral diazepam takes 30 - 60 minutes to take
effect. 
Tap water enema upon arrival followed by additional 1 or 2, 200ml tap water enemas
if the participant still has solid debris after a bowel movement. 
Flexible Sigmoidoscopy Procedure
The sigmoidoscope is advanced to the beginning of the descending colon (about 24
cm) and up to 20 biopsies will be obtained with Boston Scientific Jumbo forceps (max
diameter of 2.8mm), each biopsy will be 2-2.8 mm in size, one in each quadrant,
spaced 2-3cm throughout the sigmoid colon. 
Tissue specimens will be placed in sterile specimen cups containing normal saline.
Observation for one-hour post-procedure (for signs of bleeding or distress)  and
evaluation by nursing and PI to determine when ready for discharge. 
Breakfast
Post-procedure Instruction sheet given prior to departure. 
In the event a mass, polyp, or ulceration is found, a copy of the images obtained
during the sigmoidoscopy and a letter with the examination findings will be given to
the participant and they will be instructed to follow-up with their Primary Healthcare
Provider. 
Lab Procedures
Sample processing and analysis. 
A total of 20 biopsies will be obtained per participant: 4 will be used for tissue
immunostaining and remaining 16 will be used for single nuclei sequencing. Tissue obtained
from each region will be separated: four biopsies will be pinned and fixed in 4%
paraformaldehyde overnight, followed by washing, permeabilization, and staining of the
tissue with the neuronal antibody ANNA-1 and anti-Sox10 which is a glia antibody. We will
image the samples with a confocal microscope, and we will count the neurons and glia.
Sixteen biopsies will be snap frozen in liquid nitrogen and stored in a -80C freezer. Once
several samples have been collected, we will defrost them and further process them into
single nuclei suspensions that will be utilized to generate sequencing libraries with the 10X
Chromium platform. We will sequence the nuclear RNA to determine the expression of
multiple genes in the human intestine. Of note, we do not know what the nuclei yield will be
for the pooled 16 biopsies obtained per participant, our target nuclei count will be about
20,000 in total.  We will enrich the desired populations by staining the nuclei with anti-NeuN
and anti-Sox10 to sort the neurons and glia populations respectively. We do not know what
will be the proportions of the different cell types for this particular protocol, however, based
on other studies we expect small proportion of glia and neurons thus making it necessary to
pool samples from several participants. We will not sequence the human DNA. 
We will isolate bacterial DNA from the stool and perform 16S ribosomal RNA sequencing for
which we have an optimized protocol in our lab. Moreover. we will identify and measure
stool metabolites via Liquid Chromatography- Mass Spectrometry at RU Proteomics Core. 
NOTE: 
This study will follow the NYSDOH guidelines regarding COVID-19 testing throughout the
course of the study. Any participant that reports experiencing COVID symptoms and has a
positive SARS-Cov-2 PCR test will not be able to undergo the flexible sigmoidoscopy
procedures until 5 days after symptom onset provided that symptoms are resolved. For
example, if a participant develops COVID while taking antibiotics, he/she will have to wait
until symptom resolution to undergo follow up flexible sigmoidoscopy. 

We will also follow RU COVID-19 clinic policies. 
Study is closed to enrollment as of May 24, 2024.  
12.10   * Data Analysis
Describe method(s) of data analysis. 
In this pilot study, with 10 iparticipants, we will assess the change in the outcomes between
baseline and follow up using a paired sample t-test.   While exploratory, we will be able to
detect a 1.3 standard deviation change in outcomes pre versus post, with greater than 80%
power, holding Type I Error to 5%.  
12.11   * Explain the rationale for the choice of statistical measures and the number of
participants proposed for the study, including the power calculations when applicable.
Assuming we can enroll 10 patients, we will have over 80% power to detect a 1.3 standard
deviation difference in continuous outcome measures and a 38% absolute difference in
proportions (assume base rate of 50%).  This pilot study will also provide observed effect
size for use in the design of future analysis.
12.12   * Will samples be coded?
 Yes  
 No
If Yes, Please describe coding scheme consistent with GCP.  If samples will not be coded,
please provide justification for this proposed departure from GCP practice.
 
Samples from participants seen at RUH will be coded with the alphanumeric IRB approval
followed by 
P (denotes participant), and then a consecutive number starting with 001.
For example: YAL-10xx-P-001,  YAL-10xx-P-002, YAL-10xx-P-003, etc. 
If available, upload the Data and Sample Sharing Management Plan approved by RU IT.
Version
Title
Category
Expiration
Date
Document
Outcome
View Document
No Document(s) have been attached to this form.
13.0
Participants of Study
13.1   Specify age range of participants: 
* Minimum Age:
18

* Maximum Age:
75
Please note:  If the age of participants indicated is less than 18 years old, you will be
prompted to attach a Pediatric Assent form later on in the submission process.  A link to the
Pediatric Assent form can be found in the Help link to the right, or this form can be
downloaded later on in the submission process.
 
 
13.2   * Indicate the gender(s) of the participants:
Female
Male
Unknown
Not Reported
13.3   * Indicate projected enrollment by race and ethnicity.  See Help for disease/volunteer
population demographics. 
Ethnic Category
Sex/Gender
Females
Males
Unknown or
Not Reported
Total
  Hispanic or Latino
4
2
0
6
  Not Hispanic or Latino
3
1
0
4
  Unknown
  (individuals not reporting
ethnicity)
0
0
0
0
  Ethnic Category: Total of All
Subjects*
7
3
0
10
                   Racial Categories
  American Indian/Alaska Native
0
0
0
0
  Asian
2
1
0
3
  Native Hawaiian or Other Pacific
Islander
0
0
0
0
  Black or African American
2
1
0
3
  White
3
1
0
4
  More Than One Race
0
0
0
0
  Unknown or Not Reported
0
0
0
0
  Racial Categories: Total of All
Subjects*
7
3
0
10
13.4   Exclusion of Protected Groups:
*Research involving human participants should be designed/conducted to be as broadly
inclusive as possible regarding sex, gender, race, age, and ethnicity. Exclusions regarding

these characteristics require an explanation of the rationale and justification.
Will participants of a specific sex/gender/race/ethnicity/age or other protected group
characteristic be excluded from participation?
  Yes  
  No
13.5   Vulnerable Populations
Indicate whether any of the following populations will be included in the study:
Children
Pregnant Women
Cognitively Impaired Persons
RU Employees
RU Students
Other:
13.6   *What is the total number of evaluable participants you plan to enroll at Rockefeller University Hospital
over the course of the entire study?
10
13.7   * What is the total number of participants who will need to sign consent at Rockefeller
University Hospital over the course of the entire study to result in the desired number of
evaluable participants?
20
13.8   * What is the total number of participants you plan to sign consent at Rockefeller University
Hospital in the next year?
0
13.9   * What will be the total number of evaluable participants at all sites over the course of the
entire study?
10
13.10   Inclusion Criteria
Please list participant inclusion criteria:
Order
Number
Criteria
1 
18-75 years old of different sex and races.
 
13.11   Exclusion Criteria
Please list participant exclusion criteria:
Order
Number
Criteria

1 
Rockefeller University Students and Employees
 
2 
Allergy to penicillin, amoxicillin, augmentin, ampicillin, and other antibiotics in
the penicillin family
 
3 
Pregnancy or fertility treatments
 
4 
Usage of antibiotics, antifungals or antivirals within three months prior to
participation
 
5 
Change in dietary habits within the last three months prior to participation such
as transitioning from high fat western diet to primarily plant based diet,
initiation of ketogenic, paleo or any other weight loss regimen. 
 
6 
Acute (in the past 30 days) or chronic enteric infections, including C. difficile. 
 
7 
Chronic gastrointestinal disorder including inflammatory bowel disease, celiac
disease , irritable bowel syndrome, chronic constipation or diarrhea
 
8 
Active neuropsychiatric disorder that requires anti-psychotic ie typical and
atypical antipsychotics as well as anti-epileptics, levodopa, rivastigmine or any
other neuropsychiatric medication with dopaminergic and cholinergic effects. 
 
9 
Myocardial infarction or cerebrovascular accident in the six months prior to
participation
 
10 
Coagulation disorders
 
11 
Chronic immunosuppressive medication (systemic) usage
 
12 
Anti-coagulation and anti-platelet agents such as plavix, warfarin, heparin,
direct oral anticoagulants. 
Low dose Aspirin does not constitute an exclusion criteria. 
 
13 
Prior episode of C. difficile infection. 
 
14 
Prosthetic heart valves or any other conditions that require pre-procedure
antibiotics.  
 
15 
Currently receiving chemotherapy
 
16 
Any medical, psychological or social condition, in the opinion of the
investigator, would jeopardize the health or well-being of the participant,
interfere with their participation in the study, or confound the results of the
study.
 
14.0
Schedule of Events/Study Plan
14.1  
Instructions:New Studies:

A Schedule of Events is required for all new studies involving interactions with human subjects.
The iRIS Study Plan will not be accepted for new protocols. 
A template Schedule of Events is available on the IRB Website. For any new study, populate the
template with the visits and procedures for the study. 
The content of the Schedule of Events should be consistent with any descriptions of study
procedures that may be in the protocol text and informed consent. 
Attach the completed Schedule of Events document to the Submission Form in the Schedule of
Events section.
Existing Studies: For existing studies, investigators may elect to update the existing Study Plan OR may
replace the Study Plan with a Schedule of Events, following the instructions above for new studies.
Attach the Study Plan (an option only for studies with pre-existing
Study Plans):
No Study Plan Templates have been associated.
* What is the total number of outpatient visits for all participants projected for the
next year?
0
* What is the average length of each outpatient visit (in hours)?
0
* What is the total number of Day Patient visits for all participants projected for the
next year?
0
* What is the average length of each Day Patient visit (in hours)?
0
*  What is the total number of inpatient days for all participants projected for the
next year?
0
15.0
 
Investigational and Support Medications
15.1   List all the investigational medications
See Help for link to Rockefeller University Research Pharmacy web page for additional
information.
View
Details
Drug Name
FDA Approved
IND Number
Trade Drug
Name: Amoxil
Generic Drug
Name:
Amoxicillin
Investigational
Drug Name:
Yes 
 
Trade Drug Name:
Amoxil 
Generic Drug Name:
Amoxicillin 
Investigational Drug Name:
 

Identify the name of the
manufacturer or source of
investigational drug/biologic:
USAntibiotics  
Is the Drug FDA Approved:
Yes  
Is an IND necessary
No  
IND Number
 
Who holds the IND:
N/A  
IND details:
 
Are you currently using this IND
in another research project?
No  
If yes, list the IRB Number(s):
 
Dose Range:
875mg  
Frequency:
Twice a day  
Trade Drug
Name: Valium
Generic Drug
Name:
Diazepam
Investigational
Drug Name:
Yes 
 
Trade Drug Name:
Valium 
Generic Drug Name:
Diazepam 
Investigational Drug Name:
 
Identify the name of the
manufacturer or source of
investigational drug/biologic:
Pfizer  
Is the Drug FDA Approved:
Yes  
Is an IND necessary
No  
IND Number
 
Who holds the IND:
N/A  
IND details:
 
Are you currently using this IND
in another research project?
No  
If yes, list the IRB Number(s):
 
Dose Range:
 
Frequency:
 
15.2   * Will the study involve the use of a placebo?
  Yes  
  No
15.3   Study support medications are medications that will support the conduct of the study.  Please list all
support medications to be used in the study (include all prescription drugs, over the counter drugs herbs,
and supplements).
Amoxicillin 875mg q12 hours PO
Diazepam 5mg once pre-procedure.
Fleet Enema
16.0
Consent Procedure

16.1   * This study will use the following types of informed consent:
Informed Consent Form Standard - a standard consent form with instructions for adapting it to
your study
Consent Form Genetic- a consent form designed for a study where genetic testing (as defined by
NYS law) is to be done in the CURRENT study
Consent for studies including genome wide sequencing
Pediatric Assent Form (To be used in addition to Consent) for Pediatric patients
Other (e.g., waivers, electronic informed consent)
Links to the Standard Consent, Genetic Testing Consent and the Pediatric Assent
forms can be found in the Help link to the right, or these forms can be downloaded later on in
the submission process.
16.2   * Indicate the consent process to be used.  
   (See Help for CCTS SOP)
Describe how the required information is being presented to participants (consent form,
orally, information sheet, etc.).  Attach a copy of what is being presented to participants
(usually the ICF and Assent forms).
Prior to the initiation of any study related procedures, the potential subjects will be given a
copy of the most recent IRB stamped and approved informed consent to read. Additionally,
the PI or study staff member who has been  designated to consent will discuss the specifics
of the study including but not limited to the purpose of the research, procedures, time
commitment, required tasks, test article or device, alternative treatments, benefits, risks,
confidentiality etc. in a comprehensible (non-scientific) manner, using language readily
understandable by the subject. Subjects will be told that participation is voluntary and that, if
they do not consent, they will not be penalized. The person consenting will assure the
voluntariness of the subject.
Describe the circumstances under which consent will be obtained, where the process will take
place and any waiting period between informing the prospective participant and obtaining
consent. 
A private, confidential setting will be provided for the potential subject to read and discuss
the informed consent free from coercion, undue influence or constraints of time. All
subjects will be given a chance to ask questions and express concerns. They will be given
the option to take the consent home and discuss it with family, friends, and /or health care
providers. After a subject and the person conducting the consenting signs and dates the
consent, the subject will be given a copy of the signed informed consent form. An
enrollment note will be written in the source document as to who obtained consent, how,
when, were questions asked and answered, and that a copy of the informed consent was
given to the subject.
Describe the experience of the investigators designated for this task in the DOA in obtaining
consent from participants.
Y. Alvarez has demonstrated competency in consenting subjects for participation in
research studies. This competency is based on attending a consenting class which includes
regulations, the do’s and don’ts, and didactic role-playing. It also includes observing the
consenting process as performed by an experienced consenter and then consenting a
participant to participate in a research study while being observed by the experienced
consenter.

How will it be determined that the participants or the participants' authorized representatives
understand the information presented? 
The "Teach Back" method will be used in the clinical research setting to ask research
participants to repeat or “teach back” the information, concepts and directions that the staff
member has attempted to convey to the subject. This method is used to assess
comprehension and retention of protocol requirements, adverse event information, risks and
benefits, and the subject's rights described in the Informed Consent process.
If English is not the participants' native language, how will written and/or verbal translation
be provided?
For unexpected or isolated subjects who are candidates for this study, but for whom English
is not a primary language, a translator provided through Pacific Interpreters will be used to
facilitate the explanation of the study.
Will any participants be cognitively impaired so that they may not have the capacity to give
consent?
  Yes  
  No
For participants where it has been determined that they lack the capacity to give consent,
describe the provisions for obtaining consent from the participants' legally authorized
representative.
16.3   * Based on the demographics, will this study's participant population require foreign
language consent form? 
 Yes  
 No
If Yes, please list the language(s):
Spanish
16.4   * This study's consent procedure will require the following waivers:  
(See Help for additional information.)
Waiver of one or more elements of informed consent, 45 CFR 46.116(f) 
Waiver of documentation of informed consent, 45 CFR 46.117(c) 
No waiver is requested 
16.5   Will you obtain a Certificate of Confidentiality (CoC) for this study?
 Yes  
 No
A CoC will be provided automatically as part of its funding mechanism with NIH
The PI will apply independently to NIH for a CoC
Note to Investigator: If this study has a CoC, the Informed Consent document must contain CoC
template language
16.6   * Does this study include video/audio recording, photography or other electronic recording
of human participants?
  Yes  
  No

17.0
Recruitment and Advertising
For assistance consult CRSO to create a robust Recruitment Plan see Help.
17.1   * What is the plan for recruitment?
What is the plan for recruitment?
Overview: The CRROSS seeks to prescreen 25 healthy volunteers between the ages of 18-
75 to achieve the overall goal of 15 evaluable participants. 
Feasibility and Assessment:
Incentives:1) Altruism; 2) Interest in study topic 3) Compensation 4; 3) Return of
(aggregate) results may be an incentive.
Challenges:  1) Overall impact of the Covid-19 pandemic may dissuade individuals
from voluntarily participating in research studies; 2) Number of study visits and
multiple flexible sigmoidoscopy procedures may be a deterrent.
Issues relevant to rapid accrual:
Positive:  1) Existing cohort of healthy volunteers in the repository; 2)Compensation
amount.
Negative:  1) Candidates may not be interested due to perceived discomfort and  burden of
sigmoidoscopy preparation the day before the procedure, and/or  embarrassment about the
 procedure; 2) Participants may not adhere to antibiotic treatment due to side effects 2)
Potential for post procedure bleeding may dissuade some candidates from participating.
Projected Time to Accrual Completion (PTAC):  
The research team plans to screen up to 1 day per week which translates to enrolling 2
volunteers a week. 
Factors Affecting Predicted Time to Accrual Completion
Weeks
Research team plans to screen 2 participants 1  day per
week = 2 volunteers screened per week (10 pax  Add 2 weeks for overlap with
current  study, YAL-1027 
11
Anticipated start up, add 1
2 weeks; if assay not ready, add estimated time to readiness
1
Add any vacation time when screen/visit capacity will be reduced
1
Recruitment is to occur during August? add 2 weeks due to historical slowing
N/A
Recruitment to occur across Dec Jan. time frame; add 2 wks for unit closure
N/A
Known anticipated maternity leave, other LOA of key staff –
 add est. weeks lost capacity
N/A
Staff or KSP changes – add onboarding time
N/A
Staff travel for major conferences – add weeks lost capacity
N/A
Institutional interruptions (graduation, symposium days, etc.) add team estimate
N/A
Projected Time to Accrual Completion (PTAC)
13
Recruitment Implementation:
Advertising- CRROSS will advertise on RU Classifieds, Craigslist and ResearchMatch.
Volunteers will also be drawn from the Clinical Conductor Repository.   If applicable, eligible
 participants from YAL-1027 may also be considered for this study.
Centralized Call Management – CRROSS will work with the research team to develop a
protocol-specific pre-screening script based on IRB approved protocol eligibility criteria to
prescreen volunteers who call 1800RUCARES. Potentially eligible candidates will be
scheduled for the study team for further screening. CRROSS staff will also call volunteers
based on Repository queries described above. Research teams are responsible to provide

timely updates on pre/screening outcomes by updating volunteers’ Study Status in Cerner.
The Recruitment team uses screening outcomes to review progress and strategy to keep
enrollment on target.
17.2   *From the date of final IRB approval, how long will it take to complete
enrollment of the study?
6 Months 
12 Months 
18 Months 
24 Months 
More than 2 years (specify in years) 
17.3   This Study
Involves an intervention or comparison and a defined enrollment target 
Is a natural history study with expected annual enrollment over many years 
Is an exploratory mechanistic study 
Other 
17.4   This Study will enroll:
Healthy volunteers 
Individuals affected with a specific disease/disorder 
Both 
17.5   * Do you plan on using the Research Participant Repository (RKO-0648) ?
 Yes  
 No
17.6   * Are you screening or recruiting from or through a record review of an existing patient
database of a healthcare provider? 
 
  Yes  
  No
17.7   * Please describe how the Recruitment Plan addresses recruitment of the volunteers
consistent with the demographics of the condition under study:  
Both healthy men and women of all races between the ages of  18-75 years of age will be
recruited.
17.8   * Do you plan to advertise directly to potential volunteers?  (As opposed to relying on
practitioner referrals  or flyers to practitioners)
 Yes  
 No

17.9   * Do you plan to use the free, web-based volunteer registry, ResearchMatch.org, as a
recruitment tool?
 Yes  
 No
18.0
Research Participant Repository (RKO-0648)
18.1   This protocol, will be linked with the Research Volunteer Screening/Recruitment Data Repository run by
the Recruitment staff and the Clinical Research Support Office (protocol RKO-0648-1008).   In order to
participate in the generation of the Repository the PI will enter into a Collector/Collaborator agreement
regarding the Repository. The role of Collector/Collaborator is to contribute to the Repository the name,
contact and demographic information, recruitment referral information, and screening outcome
information, as well as appropriate protocol specific screening information, of volunteers who are
screened by telephone or in person for entry into the protocol regardless of the screening outcome. In
addition to screening volunteers for the PI's current study, verbal consent will be obtained from the
volunteers regarding their willingness to be contacted in the future about possible additional research
studies. This permission may be obtained by the Recruitment office staff through the central Call Center.
 If the  PI receives calls directly from participants for initial prescreening, then the PI is responsible for
collecting the required information and conveying it to the Recruitment staff for data entry.  The consent
or withholding of permission will be recorded in the Repository as will the name of the person who
obtained the permission. A volunteer’s permission or declination will not affect their eligibility for my
current protocol, or future protocols. The Recruitment staff of the Clinical Research Support Office may
gather the Repository information and request the verbal consent of the volunteer for re-contacting on
my behalf as part of our recruitment plan.   In order to benefit from the Repository,  the PI will enter into
a Recipient/Collaborator agreement with the Repository.  The Recipient/Collaborator may receive from
the Repository pre-screened lists of potentially eligible participants for his/her study as a means to
facilitate recruitment. The Recruitment staff will prepare the Repository queries according to the protocol
eligibility requirements and available Repository information, and may re-affirm permission to re-contact
volunteers as necessary. The PI may use the information and names in the list from the Repository only
for the current study and may not save the list to use for a future study of his/her own, nor may he/she
share the list with colleagues for other studies."
19.0
Utilization of ResearchMatch.org 
19.1   Utilization of ResearchMatch.org for Recruitment
 
Basic information regarding this tool:
 
ResearchMatch.org is a national electronic, web-based recruitment tool that was created through
the Clinical & Translational Science Awards Consortium in 2009 and is maintained at Vanderbilt
University.  There is no cost for researchers at participating institutions in the ResearchMatch.org
Network to use ResearchMatch.org. The Vanderbilt IRB provides oversight for ResearchMatch.org
as a recruitment tool and this has been documented within the ResearchMatch.org IRB Letter of
Understanding which was executed by Dr. Gotschlich in October, 2009.  However, individual
requests to use ResearchMatch.org as a recruitment tool must be submitted to this institutions’
IRB.
Registration:
 
This recruitment tool may be utilized once the PI or research staff registers for recruitment access
through ResearchMatch.org and the Institutional Liaison provides approval.
The ResearchMatch.org Institutional Liaison will review the study information and evidence of IRB
approval. He/she will set the researcher’s expiration date to mirror that of the study’s IRB
approval.
Search Capability:
 
After being granted recruitment access, the researcher can search for appropriate matches
amongst the non-identifiable ResearchMatch.org Volunteer profiles in the system.  He/she can
enter study inclusion/exclusion criteria in the ResearchMatch.org Search Builder which will yield a
list of potential matches to the study’s criteria. 
Contacting ResearchMatch.org Volunteers:
 

Once yielding a list of potential matches (ResearchMatch.org Volunteers), the researcher will send
out IRB-approved content that will be the initial recruitment message that these volunteers receive
about the study through ResearchMatch.org. The study’s recruitment message will be inserted into
the standard ResearchMatch.org electronic notification that informs possible matched Volunteers
that he/she has been identified as a potential match for the study.  The secure ResearchMatch.org
clearinghouse will route this standard ResearchMatch.org email notification. These potential
matching volunteers will have the option of replying yes, no, or not respond through a set of quick
links available in this notification to the study announcement. THE CONTACT MESSAGE WILL NOT
INCLUDE THE STUDY’S DIRECT CONTACT INFORMATION (e.g. EMAIL, PHONE).  By responding yes,
the Volunteer has authorized ResearchMatch.org to release his/her contact information to the
researcher.  The researcher will be responsible for managing this contact information as called for
by this IRB-approved study protocol. 
Study Management in ResearchMatch.org:
 
Researchers (and the Liaison) can view information regarding his/her study’s status in
ResearchMatch.org (e.g. number of volunteers contacted for the study via ResearchMatch.org to
date, response rate of volunteers, etc.).  ResearchMatch.org will also be collecting aggregate data
regarding the status of ResearchMatch.org volunteers within the study. Volunteers consent to this
within the ResearchMatch.org Volunteer Agreement. This information will allow the researcher to
indicate where the Volunteer currently stands within the recruitment process and thus will help the
researcher monitor the utility and effectiveness of using this resource (e.g. Did not contact, Not
eligible, Enrolled, Completed, etc.).
20.0
Potential Benefits to Participants
20.1   * Will participation in this study provide direct benefits to the participant?
  Yes  
  No
21.0
Potential Risks to Participants
21.1  
*  Describe any potential risks: physical, psychological, social, legal or other and assess
their likelihood and seriousness. Indicate risks both to the participants and to the embryo or
fetus if the participant is or may become pregnant.  Please provide the potential risks
below:
Blood draw: Potential risks associated with venipuncture include discomfort or pain,
ecchymosis, bleeding, nerve damage, phlebitis and infection at the needle insertion site.
Additional risks include lightheadedness and a vasovagal response.
Diazepam: Potential risks associated with allergic reaction, drowsiness, loss of coordination,
drug/drug interactions with other common medications (antidepressants, other anxiolytics),
and alcohol. 
Amoxicillin: Potential risk associated with mild to severe allergic reaction, anaphylaxis or
hives, nausea, vomiting, and diarrhea (2%). Change in bowel habits and abdominal pain
<1%. Vulvovaginal infection (2%).  If participant develops vulvovaginal infection she will be
given fluconazole course and advised to follow up with gynecology. Participant will not be
able to complete last flexible sigmoidoscopy and will be given partial compensation.
Antibiotic resistance (negligible). This will not be determined until participant requires
another course of amoxicillin and even if he/she develop antibiotic resistance, it will be
difficult to know if it was due to the antibiotic course during our study or due to pre-existing
antibiotic resistance. 

Flexible sigmoidoscopy:  Potential risks include intestinal perforation, infection, and bleeding
at the biopsy sites. 
Privacy Risk:  Potential loss of privacy if there is a breach of the RU hospital computer
system. 
 
Gene expression:   Potentially the participant's identity can be unveiled. 
22.0
Procedures to Minimize Risks
22.1   * Describe the procedures for protecting against or minimizing any potential risks, and
include an assessment of their likely effectiveness. Include a discussion of confidentiality
safeguards, where relevant, and arrangements for providing medical treatment, if needed.
The sigmoidoscopy will be performed by an experienced, trained, and credentialed
physician. 
In the event of a perforation, the participant will be stabilized (placed on a stretcher, the
emergency medical response system will be activated, support therapies such as
intravenous hydration and oxygen will be provided as needed, vital signs monitored), and
the participant will be transferred to the Weill Cornell Emergency Room for further
management. The participant's Primary Care Provider will be notified of any change in the
participant's medical condition.
Blood draws will be performed by trained professionals using sterile equipment.
Participants will be asked about their medication allergies, current medications and
substance use history prior to administering diazepam and amoxicillin. 
Participants will be observed for 30-60min after procedure and advised to avoid operating a
vehicle and/or heavy machinery for the rest of the day. 
Participants who cannot tolerate taking the antibiotic will be assessed by Dr. Alvarez and
may be removed from the study.  If required, a referral to a primary care physician or clinic
will be made.
To minimize the risk of C.difficile we have selected a short antibiotic course and we will
exclude participants currently receiving chemotherapy or are taking immunosuppressive
medications. 
If any participant develops C.difficile infection and/or vulvovaginal infection, treatment will be
prescribed by Dr. Alvarez and participant will be asked to follow up with Primary Care
provider. 
Participants personal information will be maintained in password protected electronic
medical records protected in Rockefeller's network. Access of patient data from remote
computer will only be done while in Rockefeller University's VPN. 
23.0
Alternative Methods or Treatments

23.1   * Describe alternative methods or treatments for the disease(s) under study, if any, that
were considered and why they will not be used:  
There are no alternative methods or treatments that will allow the investigator to conduct the
study.
24.0
Data and Safety Monitoring
This section describes the Data and Safety Monitoring Plan (DSMP)
required of each protocol undertaken at the CCTS according to HRPP
and NIH policies Notice 98 -084 and Notice 00-038, as cited in Help
Sections below.   Depending on the level or risk and trial phase, some
protocols will need Data and Safety Monitoring Boards.
24.1   * Overall Risk Classification
An estimate of risk is necessary to evaluate the adequacy of the planned monitoring.  The
HELP section provides guidance in making the risk assessment. 
Read the risk definitions and examples of risk in the HELP section and select the risk
category that best describes the current study. 
If your assessment differs from the definitions the HELP section, describe any factors that
modify your judgment of the overall risk in the text box after the risk designation.
MINIMAL RISK 
LOW RISK 
MODERATE RISK 
SIGNIFICANT RISK 
Please provide any optional description(s):
24.2   Protocols Involving Minors
The chance of direct benefit to the child, or to understanding a disorder not otherwise
understood, may be major factors in justifying more than minimal risk in research involving
children.  
Based on the above definitions, please specify your study's risk classification below:
NOT GREATER THAN MINIMAL RISK (the risk of daily life to a healthy child living in a safe
environment) 45 CFR 46.404 
GREATER THAN MINIMAL RISK WITH DIRECT BENEFIT TO PARTICIPANT; 45 CFR 46.405 
GREATER THAN MINIMAL RISK, NO DIRECT BENEFIT, BUT BENEFIT TO UNDERSTANDING OF
PARTICPANT'S DISORDER; 45 CFR 46.406 
RESEARCH NOT OTHERWISE APPROVED PRESENTING OPPORTUNITY TO UNDERSTAND, PREVENT
OR ALLEVIATE SERIOUS PROBLEM AFFECTING CHILDREN 45 CFR 46.407 (cannot be approved by
IRB; requires public comment) 
24.3   DSMB

1. The NIH requires that all SIGNIFICANT RISK protocols have a Data and Safety
Monitoring Board and provide information about the expertise and independence of
that Board
2. Phase III trials require a Data and Safety Monitoring Board,
3. A DSMB may be appropriate for some Phase I and II protocols. (See Help for
examples.)
4. It is the investigator's responsibility to report to the IRB, the findings and
recommendations of the DSMB as they become available.
Please specify:
A DSMB is required for this study 
A DSMB is not required for this study 
Unsure 
If a DSMB is not required, but is being constituted for other reasons, please explain:
24.4   * Safety Review
Select one:
Safety Review is conducted as follows: Laboratory results for research volunteers will be reviewed
in a timely manner, usually within 24 hours of receipt by a licensed practitioner. The potential
clinical significance of any abnormal finding will be documented in the medical and research
record(s), and an appropriate plan or referral developed. The PI's review of safety issues at
research team rounds will be documented in the meeting minutes. 
Protocol Specific 
24.5   Monitoring
Monitoring Personnel:  See Help Bubble to the right.
Internal Monitoring
The PI or his/her designee shall conduct internal monitoring to assure the safe and proper
conduct of the protocol and all the elements list above in monitoring, following the general
principles of quality management.  The intensity and frequency of internal monitoring will
depend on the protocol risk to participants, the experience of the PI and research team, rate
of enrollment, and specific details of the protocol. 
Internal monitoring of informed consent and eligibility documentation will be conducted by
the research team shortly after enrollment begins.  Internal monitoring activities will be
documented by logs, meeting minutes or other systematic means.  
Specify the research team members who will conduct the internal monitoring of the study
(see Help for who may monitor):
Internal Monitoring
The PI or his/her designee shall conduct internal monitoring to assure the safe and proper
conduct of the protocol and all the elements list above in monitoring, following the general
principles of quality management.  The intensity and frequency of internal monitoring will

depend on the protocol risk to participants, the experience of the PI and research team,
rate of enrollment, and specific details of the protocol.
Internal monitoring of informed consent and eligibility documentation will be conducted by
the PI shortly after enrollment begins. Internal monitoring activities will be documented by
logs, meeting minutes or other systematic means.
Specify the research team members who will conduct the internal monitoring of the study
(see Help for who may monitor):
The PI will be shown how to perform internal monitoring. 
For new investigators:  Internal monitoring should be conducted at least monthly by new
investigators until there are essentially no findings to correct at each review.
External Monitoring
*  Is external monitoring planned for this protocol?
Yes 
No 
Unsure 
If external monitoring is planned, please specify (see Help for who may monitor):
(Significant Risk) External monitoring will occur at least every six weeks unless there is no
enrollment 
(Moderate Risk) External monitoring will occur at least quarterly 
(Low or Minimal Risk) External monitoring will occur at least annually 
If external monitoring is planned, please specify the name of the monitor:
Note that copies of external monitoring reports must be supplied to the IRB and the CRSO as soon
as they are made available
Additionally, audits of the research records of minimal, moderate or significant-risk protocols
may be performed by the CRSO staff on a random basis or as part of a prospectively
identified auditing plan. 
24.6   Adverse Event Classification
Adverse events are classified by definition, severity, and association with the investigational trial.
 
Definition of an Adverse Event
Any unfavorable or unintended sign (including abnormal lab findings), symptom or disease temporally
associated with the use of a medical treatment or procedure, or protocol,  regardless of whether it is
considered related to the medical treatment or procedure or protocol.
 
Definition of a Serious Adverse Event
Any unanticipated event that involves the following:
o   results in death
o   is life-threatening
o   requires hospitalization or prolongs existing hospitalization
o   results in persistent or significant disability/incapacity
o   is any medical event which requires treatment to prevent one of the outcomes listed above
Other events can be classified as "serious adverse events" at the discretion of the PI.
 

Definition of Anticipated/Expected Adverse Event
Any adverse event, which has been reported in the Investigator's Brochure, package insert, safety reports,
clinical protocol, consent form or listed in the NCI agent-specific Expected Adverse Event List3, is classified as
an expected adverse event.  The investigator must provide the available data of known adverse events and
toxicities that have been associated with the study drug, device, intervention, or procedures.  This information
helps to define the level of risk of the trial and enables safety monitoring.  A minimal risk trial may not have
any defined risks and a statement to that effect is sufficient to meet the DSMP requirements.
 
Definition of an Unanticipated/Unexpected Adverse Event
Any adverse event that is not consistent with the known, predicted possible effects of the research protocol. 
An unexpected adverse event varies in nature, intensity or frequency from information on the investigational
product provided in the Investigator's Brochure, package insert, safety reports, clinical protocol, or listed in
the consent form.
 
Definition of an Unanticipated Problem (UaP)
A UaP is an event or circumstance that meets all the following three criteria: [1] the nature, severity,
frequency of the event(s) or information was not expected in the descriptions in the study documents or the
characteristics of the participant population being studied; [2] there is a reasonable possibility that the
procedures involved in the research caused or are linked in a significant way to the problem; [3]the event or
information suggests that the research places particpants or others at a greater risk of harm than was
previously known or recognized (including physical, psychological, economic, or social harm.
 
 
Grade and Relatedness of Adverse Events:
Adverse Events are graded for severity and scored for relatedness to the protocol, according to a published
scale.  Several standardized AE Reporting scales are available.  (See Help for links to these scales.)  
* Please indicate the scale you intend to use:
CTC v2.0 ( http://ctep.info.nih.gov/reporting/ctc.html ) 
CTCAE v3.0 ( http://ctep.info.nih.gov/protocolDevelopment/electronic_applications/docs/ctcaev3.pdf) 
CTCAE v4.0 (http://evs.nci.nih.gov/ftp1/CTCAE/CTCAE_4.03_2010-06-14_QuickReference_8.5x11.pdf) 
CTCAE v5.0
(https://ctep.cancer.gov/protocoldevelopment/electronic_applications/docs/CTCAE_v5_Quick_Reference_8.5x11.pdf) 
AIDS Clinical Trials Group (http://aactg.s-3.com/) 
Other 
24.7   Reporting Adverse Events
All AEs will be reported to the IRB at least annually.
Reporting Serious AEs
Serious Adverse Events, (SAEs) will be reported to the IRB according to policy, within two working
days of identification of the SAE.
Select all that apply:
SAEs will be reported to the Sponsor and or ESCROW
SAEs will be reported to the sponsor within how many days of the event?
 
SAEs will be reported directly to the FDA, per 21 CFR 312

      SAEs must be reported directly to the FDA within 7 days of the event by the
investigator/sponsor.
SAEs will be reported to another entity
Describe:
Reporting Unanticipated AEs:
Select all that apply:
UAEs will be reported to the IRB
UAEs that are related and greater than moderate severity must be reported to the IRB
according to policy, within two working days of identification of the UAE. 
 
UAEs will be reported to the Sponsor
UAE will be reported to the sponsor within how many days of the event?
UAEs will be reported to the FDA, per 21 CRF 312
UAEs will be reported to the FDA, per 21 CRF 312, within 15 days.
UAEs will be reported to another entity
Describe:
24.8   Reporting Unanticipated Problems
Unanticipated problems involving risks to participants or others will be reported to the IRB and the
CRSO within five working days.
24.9   CLIA/CLEP
 
Only laboratory and research tests that are CLIA/CLEP certified or waived may be used to
determine eligibility, shared with research volunteers, and used in clinical decision making.
Select if applicable:
This study includes tests that are not CLIA/CLEP certified; the results of such tests will not be used
in clinical decision making, or to determine eligibility, or shared with participants or their health
care providers.
24.10   Tissue Repository
Human Tissue and Data Repositories collect, store, and distribute human tissue materials
and or data for research purposes. Repository activities involve three components: (i) the
collectors of tissue samples\data;  (ii) the repository storage and data management center;
and (iii) the recipient investigators.
*  Select one:

I DO NOT intend to collect, store, and distribute human tissue materials for research purposes 
I DO intend to collect, store, and distribute human tissue materials for research purposes,
therefore this protocol entails the Operation of a Tissue Repository. The IRB requires that the
protocol specify the conditions under which data and specimens may be accepted and shared, and
ensuring adequate provisions to protect the privacy of participants and maintain the confidentiality
of data. 
If you do intend to collect, store, and distribute human tissue materials, you will be asked to
upload the following documents later on in the submission:
A Sample collection protocol (for tissue collector collaborators to follow) and informed
consent document for distribution to tissue collectors and their local IRBs.
A Certificate of Confidentiality (to protect confidentiality of repository specimens and
data).
A Recipients Agreement describing the commitment of the recipient to preserve the
anonymity of the samples shared.
25.0
Toxicity Management and Stopping Rules
25.1   * Describe any drug toxicity or other conditions under which the participation of a
participant or the conduct of the study would be stopped in order to maximize safety (e.g.,
toxicity management and stopping rules):
 
If a participant develops an allergic reaction to diazepam, reaction will be immediately
treated accordingly with severity of symptoms ie if patients develops rash he/she will be
treated with Benadryl, if on the other hand patient develops anaphylactic shock, patient will
be given epinephrine intramuscular injection and stabilized (placed on a stretcher, the
emergency medical response system will be activated, other support therapies such as
intravenous hydration and oxygen will be provided as needed, vital signs monitored), and
the participant will be transferred to the Weill Cornell Emergency Room for further
management. The participant's Primary Care Provider will be notified of any change in the
participant's medical condition. 
If patients develop allergic reaction to amoxicillin, he/she will also be instructed to cease the
medication and call us and his/her PCP. He/she will be excluded from the study and advised
to follow up with PMD. 
If the participant cannot tolerate the fleet enema, he/she will be excluded. In addition, if
he/she cannot tolerate the flexible sigmoidoscopy due to pain, he/she will be excluded. 
If the participant has abnormal vital signs ie T>100.4, BP<80/50 or BP>140/90, HR<50 or
HR>100 during any of the study visits, he/she will be excluded. 
If a participant starts taking other antimicrobial medications he/she will be excluded from the
study. 
If a participant starts taking a medication that has adverse interactions with
amoxicillin, he/she will be excluded from the study. 
If a participant develops renal or liver disease that requires adjustment of
amoxicillin dose, he/she will be excluded from the study. 
* Indicate withdrawal criteria and procedures below:
If a participant cannot tolerate antibiotics he/she will receive partial compensation. If a
participant cannot undergo flexible sigmoidoscopy due to discomfort he/she will receive

partial compensation. These participants will be excluded from the study. If a participant
needs to take any other anti-microbial and/ or has an enteric infection while being in the
study, he/she will be excluded. The PI will also determine whether other medical conditions
developed during the study qualify as withdrawal criteria. 
26.0
Compensation/Costs
26.1   *Will any compensation be offered to participants in return for their participation, e.g.,
direct payment, medical care, tests, etc.?  
No 
Yes (Please describe) 
Please Describe
Participants will receive $1100 for their participation and completion of the study.
$300 for each completed sigmoidoscopy procedure
$100 for completing a 7-day course of antibiotics
Participants will receive an additional $100 for completion of all study visit requirements.  
If a participant only completes a portion of the study, they will receive partial compensation. 
26.2   * Will there be any costs to participants associated with their participation in research?
  Yes  
  No
27.0
Bibliography
27.1    Enter your bibliography below:
1. Jacobson, A., et al., The intestinal neuro-immune axis: crosstalk between neurons,
immune cells, andmicrobes. Mucosal Immunol, 2021. 14(3): p. 555-565.
2. Ye, L., et al., Enteroendocrine cells sense bacterial tryptophan catabolites to activate
enteric and vagal neuronal pathways. Cell Host Microbe, 2021. 29(2): p. 179-196 e9.
3. Joly, A., F. Leulier, and F. De Vadder, Microbial Modulation of the Development and
Physiology of the Enteric Nervous System. Trends Microbiol, 2021. 29(8): p. 686-699.
4. Heuckeroth, R.O., Hirschsprung disease - integrating basic science and clinical
medicine to improve outcomes. Nat Rev Gastroenterol Hepatol, 2018. 15(3): p. 152-167.
5. Muller, P.A., et al., Microbiota-modulated CART(+) enteric neurons autonomously
regulate blood glucose. Science, 2020. 370(6514): p. 314-321.
6. Neuvonen, M.I., et al., Intestinal Microbiota in Hirschsprung Disease. J Pediatr
Gastroenterol Nutr, 2018. 67(5): p. 594-600.
7. Vicentini, F.A., et al., Intestinal microbiota shapes gut physiology and regulates enteric
neurons and glia. Microbiome, 2021. 9(1): p. 210.

8. Kabouridis, P.S., et al., Microbiota controls the homeostasis of glial cells in the gut
lamina propria. Neuron, 2015. 85(2): p. 289-95.
9. Vajravelu, R.K., et al., Risk for Post-Colonoscopy Irritable Bowel Syndrome in Patients
With and Without Antibiotic Exposure: A Retrospective Cohort Study. Clin Gastroenterol
Hepatol, 2021.
10. Furness, J.B., et al., Intrinsic primary afferent neurons and nerve circuits within the
intestine. Prog Neurobiol, 2004. 72(2): p. 143-64.
11. Rao, M., et al., Enteric Glia Regulate Gastrointestinal Motility but Are Not Required
for Maintenance of the Epithelium in Mice. Gastroenterology, 2017. 153(4): p. 1068-
1081 e7.
12. Yarandi, S.S., et al., Intestinal Bacteria Maintain Adult Enteric Nervous System and
Nitrergic Neurons via Toll-like Receptor 2-induced Neurogenesis in Mice.
Gastroenterology, 2020. 159(1): p. 200-213 e8.
13. Obata, Y., et al., Neuronal programming by microbiota regulates intestinal
physiology. Nature, 2020. 578(7794): p. 284-289.
14. Sperber, A.D., et al., Worldwide Prevalence and Burden of Functional
Gastrointestinal Disorders, Results of Rome Foundation Global Study. Gastroenterology,
2021. 160(1): p. 99-114 e3.
15. Mars, R.A.T., et al., Longitudinal Multi-omics Reveals Subset-Specific Mechanisms
Underlying Irritable Bowel Syndrome. Cell, 2020. 182(6): p. 1460-1473 e17.
16. Wouters, M.M., et al., Histamine Receptor H1-Mediated Sensitization of TRPV1
Mediates Visceral Hypersensitivity and Symptoms in Patients With Irritable Bowel
Syndrome. Gastroenterology, 2016. 150(4): p. 875-87 e9.
17. Drokhlyansky, E., et al., The Human and Mouse Enteric Nervous System at Single-Cell
Resolution. Cell, 2020. 182(6): p. 1606-1622 e23.
18. Dethlefsen, L., et al., The pervasive effects of an antibiotic on the human gut
microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol, 2008. 6(11): p. e280.
19. Jakobsson, H.E., et al., Short-term antibiotic treatment has differing long-term
impacts on the human throat and gut microbiome. PLoS One, 2010. 5(3): p. e9836.
20. Ladirat, S.E., et al., Exploring the effects of galacto-oligosaccharides on the gut
microbiota of healthy adults receiving amoxicillin treatment. Br J Nutr, 2014. 112(4): p.
536-46.
21. Suez, J., et al., Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired
by Probiotics and Improved by Autologous FMT. Cell, 2018. 174(6): p. 1406-1423 e16

28.0
Appendices
28.1   Enter your appendices below:
None
29.0
Funding
29.1   * Do you have sufficient financial resources to support your study? 
 Yes  
 No
29.2  
If this study is/was pilot funded, please specify dates of funding:
From date:
06/01/2022
To date:
12/31/2023
29.3   Source of investigational agents:
N/A (no investigational agents) 
Provided by a pharmaceutical sponsor/partner with funding as described below 
Provided by a pharmaceutical sponsor/partner without additional funding 
Provided by investigator, participants, or other 
29.4   Specify funding by Rockefeller University, industry sponsor and/or grant:
   Search for a sponsor   
 Sponsor
Funding
Rockefeller
University
  CTSA Pilot Grant
Industry
 
Grant
 

Pilot
Award
 
29.5   List grants in which this study is named:
PHS or Non-
PHS
Program
Grant Number
Grant Name
From Date
To Date
No results found
30.0
Clinical Services
30.1   *What is the general health status of your study group(s)?
Well/Minimally Ill
Moderately Ill
Severely Ill
Other
Not Applicable
If other than Well/Minimally Ill, please describe:
30.2   * Does your study group have special care needs? 
  Yes  
  No
30.3   * Does your study have special equipment needs? 
 Yes  
 No
If Yes, please describe:
Sigmoidoscopy equipment.
30.4   * Will you require storage space on the clinical units for supplies to conduct this study?
  Yes  
  No
30.5   * Is special training of hospital staff required?
  Yes  
  No
31.0
Pharmacy Services
31.1   * Does the study require Pharmacy Services?
 Yes  
 No

If Yes, please proceed to next section.
31.2   Types of pharmacy services required:
Dispensing
Randomization
Compounding
Other
31.3   Dispensing:
Sponsor supplied drugs
Pharmacy supplied drugs
Other
31.4   Type of medication(s):
Injectable
Ophthalmic
Inhalational
Topical
Suppository
Other
If Other, please specify:
Oral
32.0
Bionutrition
32.1   * Will study require patient meals? 
 Yes  
 No
If Yes, please specify:
Type of Diet
In/Outpatient
Pack Meal
Standard
Inpatient
Outpatient
Pack Meal 
Therapeutic
Inpatient
Outpatient
Pack Meal 
Research Diet
Inpatient
Outpatient
Pack Meal 
Formula Diet
Inpatient
Outpatient
Pack Meal 

Nutrient(s) to be controlled (specify):
32.2   Will meal times be altered? 
 Yes  
 No
If Yes, please explain:
Participants have been asked to refrain from consuming any meals until the procedure is
finalized.  
32.3   Does the protocol require any of the following activities?
Food Frequency Questionnaire
Bod Pod/ Anthropometric Measurements
Diet History/ Food Records
Diet/ Nutrition Education
32.4   Will food be provided to caregiver, parent or significant other?  
  Yes  
  No
32.5   For metabolic diets, is diet homogenization required for nutrient analysis
 by independent lab?
Yes 
No 
N/A 
33.0
Clinical and Translational Research Facilitation Office
33.1   Indicate navigation assistance requested and/or received in the development of the study:
Requested
Received
Protocol Development
Protocol Implementation
Protocol Conduct
ACCTS/IRB Submission
33.2   Indicate additional education assistance requested and/or received in the development of the study:
Requested
Received

IND
IDE
Team Science Education
Study Progress Meeting
Investigator
Responsibilities
Regulatory Binder/Folder
Source Documentation
Participant Involvement in
Research
34.0
Clinical Research Support Office Resources (CRSO)
34.1   Indicate regulatory input assistance requested and/or received in the development of the study:
Regulatory Support/Design
Requested
Received
General,
Vulnerable Populations,
Minors, Group Harms
IND/IDE advice,
assistance, and referral
Informed Consent/Assent
Data Safety Monitoring
Plan
Clinical Trial Registration

Plan For Return of
Research Results
Audit/Monitoring Service,
Referrals, SOPs
34.2   Indicate recruitment assistance requested and/or received in the development of the study:  
Recruitment of Participants
Requested
Received
Recruitment Planning and/or
written Plan
Advertising Strategy, Content,
Placement
Repository/Research Match
Queries
Call
Center/Prescreening/Scheduling
Cost Sharing for Advertising
34.3   Indicate community engaging assistance requested and/or received in the development of the study:
Community Engagement
Requested
Received
PHI Statement/Engaging
Stakeholders Section
CEnR Navigation – fostering
pt/community partnership
Outreach to
community/partner/advocacy
group/CE Studio
34.4   Indicate other assistance requested and/or received in the development of the study:
Other
Requested
Received

Survey design, fielding,
validation
Data transfer and security
planning
35.0
BERD: Biostatistics, Epidemiology and Research
Design Resource
35.1   Indicate the Biostatistical assistance requested and/or received in the
development of this study:
Requested
Received
Development of
experimental design
Power analysis/Sample
size determination (# of
subjects)
Navigation (Did
Statistician participate in a
navigation meeting)
Randomization schedule
Data analysis
Development of new
statistical techniques for
data analysis (Statistical
research)
Protocol implementation
Other
35.2   If you are/will be using data analysis specify:

Exploratory
Descriptive
Hypothesis testing
Statistical modeling
Other
35.3   If you are/will be assisted with protocol implementation, specify:
Publication
Conference
Other (type of dissemination)
Grant(s)
35.4   Please select the Biostatistician on this Protocol:
Roger Vaughan, DrPH
Caroline Jiang, MS
Sandra Garcet, PhD
Adam Qureshi, MA
Other
36.0
Biomedical Informatics Resources
36.1   Indicate Bioinformatics assistance requested and/or received in the development of this study:
Requested
Received
Microarray analysis
Pathway analysis
RNA-seq analysis
Bioinformatics training
and consultation
Bioinformatics
experimental design
HPC computing
Other

36.2   If you are/will be using pathway analysis software, specify:
Ingenuity IPA
David
GSEA
Other
36.3   If you are/will be using RNAseq analysis software, specify:
Tophat
Cufflinks
Cuffdiff
CummRbund
STAR
featureCounts
DESeq2
VOOM
RNA-SeQC
If other, specify:
36.4  
Indicate Medical Informatics assistance requested and/or received in the development of this study:
Requested
Received
Data storage inside of iRIS
Redcap Database
Custom or Ad Hoc reports
Study plan creation
Specialize database or
custom software
Other
37.0
HIPAA Form
37.1   A study's specific HIPAA form signed by the volunteer is required for institutions that are
HIPAA covered entities so that they may communicate Private Health Information (PHI) to
the Investigator.  

Below, Memorial Sloan Kettering Cancer Center, New York-Presbyterian Hospital and Weill
Medical College of Cornell University are listed so that that they may report laboratory
results and X-ray readings respectively.  If you foresee that any other entity may need to
provide PHI then add them to the field highlighted in green.
37.2   Name of Study:     
Effect of antibiotics on submucosal enteric neurons and glia in the lower gastrointestinal tract.
37.3   Principal Investigator:
Begum Aydin, PhD
37.4   Industry Sponsor:
If the funding source is industry please type in the sponsor here
Who may obtain, use, and/or disclose your health information?
The following persons and organizations may obtain, use, or disclose health information about you.
The Principal Investigator(s) listed at the top of this form, and persons who assist the
Investigator(s) in carrying out the research
Each research site for this study, including The Rockefeller University, and the research
management and support staff and the medical staff at each site
Health care providers who have provided in the past, or currently provide, health care services
to you
Laboratories and other persons and organizations that will analyze your health information
and/or biological samples as part of this study, including Memorial Sloan Kettering Cancer
Center, New York-Presbyterian Hospital and Weill Medical College of Cornell University
Other entities that may need to provide PHI:
Members and staff of the Institutional Review Board and other boards and committees that
watch over research at The Rockefeller University 
Members and staff of The Rockefeller University's Office of Sponsored Research
The sponsor(s) of the research, named above, and persons who watch over the research for the
sponsor(s)
The United States Food and Drug Administration, other government agencies, regulatory entities
and Rockefeller University consultants that watch over the safety, effectiveness, and quality of
research and/or fund The Rockefeller University Hospital
Others (as described here):
What information will be obtained, used, or disclosed?   
The persons and organizations listed above may obtain, use, and disclose:  
Information about you that is created or collected during the research study (but not including
any HIV-related information) 
Health information in your medical records that is relevant to the research study (but not
including any HIV-related information)
And, if checked below:
 

___ HIV-related information (this includes any information indicating that you have had an HIV-
related test or have HIV infection, HIV-related illness, or AIDS, as well as information that could
indicate you may have been exposed to HIV) 
___ Other information (as described here):
                                                                                                                                              
                                                                                                                                              
                                                                                                                                              
                                                                                                                                               
Other information (as described here):
 
By signing this form, you give permission to the persons and organizations listed above to obtain, use
and disclose your health information noted above. 
 
 
How will your health information be used?
 
The health information noted above, as well as information shown by the boxes checked above (if
any), may be obtained, used, and disclosed: 
to conduct the research study explained to you during the informed consent process; and
to assure the quality, safety, and effectiveness of the research study 
 
Please note that the persons and organizations listed above may re-use or further disclose your
information if they are permitted by law to do so.
 
 
What are your rights?
 
It is your right to refuse to sign this authorization form.  If you do not sign this form, you will not be
able to participate in the research study.  Your health care outside the study will not be affected.  The
payment for your health care and your health care benefits will not be affected.
If you sign this authorization form, you will have the right to withdraw it at any time except to the
extent that the persons and organizations listed above:
have already taken action based upon your authorization;
need the previously collected information to complete analysis and reports of data for this
research; or
will continue to use and disclose previously collected information as permitted by the informed
consent form signed by you (except as to HIV-related information, for which disclosure to new
persons or organizations will not occur unless permitted by federal or state law). 
If you withdraw the authorization, you will not be permitted to continue taking part in the research
study.  This authorization form will not expire unless you withdraw it.  If you want to withdraw this
authorization, please write to the above named investigators. 
You have a right to see and copy your health information described in this authorization form in
accordance with The Rockefeller University's policies; in certain circumstances where the integrity of
the study will be affected, you will not be able to obtain your health records in this study until the
study has been completed.
You will receive a copy of this form after you have signed it.
 
 
Notice Concerning HIV-Related Information
If you are authorizing the release of HIV-related information, you should be aware that such
information may not be shared without your approval unless permitted by federal or state law.  You
also have a right to request a list of people who may receive or use your HIV-related information
without authorization.  If you experience discrimination because of the release or disclosure of HIV-
related information, you may contact the New York State Division of Human Rights at (212) 480-
2493 or the New York City Commission of Human Rights at (212) 306-7450.  These agencies are
responsible for protecting your rights.
 
Your signature

I have read this form, and all of my questions have been answered.  By signing below, I acknowledge
that I have read and accept all of the information above.
 
 
 
                                                           
Signature of participant or participant's legal
representative
 
                                                           
Printed name of participant
 
 
 
 
                                                           
Date
 
 
________________________________
Printed name of legal representative (if applicable)
 
 
                                    ___________
Representative's relationship to participant
 
 
 
 
 
 
THE STUDY PARTICIPANT OR HIS OR HER PERSONAL REPRESENTATIVE MUST BE PROVIDED WITH A
COPY OF THIS FORM AFTER IT HAS BEEN SIGNED.
 
38.0
End of Application Form
38.1   The study application form is complete.   
The next step in the submission  process is to gather attachments before proceeding to the
submission form. 
 
The following submission reports are generated in the Lab/Dept Reports menu, Submission
Reports section:
   - Delegation of Authority (if applicable, and if not previously generated)
   - HIPAA form (if applicable)
   - CCTS Utilization Report (required for all submissions)
   - Study Progress Report  (if the study has been managed in iRIS for a minimum of one
year, generate the Progress Report from the report menu in iRIS.  if the study has not been
managed in iRIS for one year, complete the Progress Report located on the IRB website.)
 
All other required forms can be downloaded from the corresponding sections' help links above or from
the IRB website.