April 2018

Implementation of myResearch Grants - Training and Updates

As previously announced, beginning July 1, 2018, our institutional proposal submission process will transition from COEUS to the new Grants module in myResearch. myResearch Grants is on target to go live May 15, 2018. Since COEUS will cease operation after June 30th, it is imperative that PIs and administrative staff be mindful of this transition and how it may affect sponsor deadlines. Therefore, proposal preparation and submission must be planned accordingly.

In order to provide the Office of Sponsored Programs with sufficient time to transition, all COEUS applications should be submitted by June 22nd at the latest. COEUS will no longer be accessible to the campus on July 1st, so it is strongly recommended that any important information currently stored in COEUS be downloaded and stored elsewhere.

Training for myResearch Grants will begin May 4th. The training sessions will cover the myResearch Grants proposal and endorsement process, including funding proposals, budget preparation, and credit split. Classrooms have been held for in-person training in both East and West Campus locations.

The link to register is: https://stonybrookuniversity.co1.qualtrics.com/jfe/form/SV_1Gsnw81hVhu3dVX

In addition to the in-person training, the Office of Sponsored Programs is offering the opportunity to attend two livestream sessions of the myResearch Grants training.

When: Monday, May 7th from 9-11am AND Wednesday, May 9th from 9-11am

How to access the livestream session: Click the following link: myResearch Grants Training - Livestream: https://mediaserv01.cs.stonybrook.edu:10443/room115.html

For any questions or comments related to myResearch Grants, please email us at: ovpr_myresearchgrants@stonybrook.edu.

Yimei Zhu Receives 2018 Distinguished Scientist Award from the Microscopy Society of America

The Microscopy Society of America (MSA) has selected Yimei Zhu — a Stony Brook University adjunct professor and a senior physicist at the U.S. Department of Energy’s Brookhaven National Laboratory (BNL) — to receive the 2018 Distinguished Scientist Award for physical sciences. This award annually recognizes two senior scientists, one in the physical sciences and the other in biological sciences, for their long-standing record of achievement in the field of microscopy and microanalysis.

“I am extremely humbled by this recognition, the highest honor of the society, and to be selected among the most distinguished scientists in the field worldwide,” said Zhu, who is leader of the Electron Microscopy and Nanostructure Group at BNL. “Four Nobel Laureates received the same award before winning the Nobel Prize: Ernst Ruska in 1985, Joachim Frank in 2003, Richard Henderson in 2005, and Jacques Dubochet in 2009. I strongly feel that my award is the result of not only my hard work, persistence, and curiosity about the inner world of matter but also my collaborations with colleagues and support from Brookhaven Lab and DOE over the past 30 years.”

“Yimei Zhu has made significant contributions to advancing ultrafast electron diffraction instruments and developing fast direct-electron-detectors,” said Molly McCartney, awards committee physical sciences co-chair. “Yimei’s contributions to instrumentation and methods are extensive. His most highly recognized achievement is the successful imaging, at atomic resolution, of the atomic structure of bulk catalysts by detecting the secondary electron emission.”

Zhu led the development of an ultrafast electron diffraction system that was commissioned at Brookhaven Lab in 2012 through the Laboratory-Directed Research and Development program, which promotes exploratory, mission-supported research. With an unprecedented temporal resolution 10 orders of magnitude faster than high-speed video cameras, this system is the first of its kind in the world.

“High-speed video cameras capture consecutive images at a rate less than 1000 frames per second, which is equivalent to taking a picture once every millisecond,” explained Zhu. “Our ultrafast system operates at a rate of 100 femtoseconds, or 100 quadrillionths of a second. Using a pump-probe method in which we excite a sample with laser light (the pump) and probe it with electrons while varying the time delay between the pump and probe, we can see the otherwise unobservable motion of atoms and electrons in materials.”

This capability has opened up the possibility for scientists to understand the dynamic behavior of materials—such as the intriguing transition between insulating and   superconducting phases—and to discover “hidden” states of matter beyond the solid, liquid, gas, and plasma states that are observable in everyday life.

“The bottleneck in science and technology today is the lack of materials with the desired properties for applications such as energy storage and quantum computing,” said Zhu. “Overcoming these limitations requires an understanding of the complex interactions between atoms and electrons and the exotic states of matter that are far from equilibrium. Ultrafast methods such as the pump-probe approach can provide us with the dynamic information we need to control the chemical and physical properties of materials so that we can make, for example, smaller batteries with longer cycleability and computer chips with a higher memory capacity.”

New Drugs Using the Body’s “Natural Marijuana” Could Help Treat Pain, Cancer

A new technology employing endocannabinoids for pain relief, developed by Stony Brook University researchers affiliated with the Institute of Chemical Biology and Drug Discovery (ICB & DD), has been licensed to Artelo Biosciences, Inc. Endocannabinoids are natural marijuana-like substances in the body and have potential as the basis for new medicines. Artelo has an exclusive license with the Research Foundation for the State University of New York to the intellectual property portfolio of FABP inhibitors for the modulation of the endocannabinoid system for the treatment of pain, inflammation and cancer.

Fatty Acid Binding Proteins have been identified as intracellular transporters for the endocannabinoid anadamide (AEA), a neurotransmitter produced in the brain that binds to THC receptors. Animal studies have demonstrated that elevated levels of endocannabinoids can result in beneficial pharmacological effects on stress, pain and inflammation and also ameliorate the effects of drug withdrawal. By inhibiting FABP transporters, the level of AEA is raised. Potential drugs acting in this manner would create elevated levels of AEA. The mechanism of action of such drugs would be similar to that of current antidepressants, which inhibit the transport of serotonin.

During the first year of the agreement, Artelo will collaborate with the Stony Brook research team to identify a lead FABP compound for drug development and formulation. The company will then conduct drug efficacy tests in nonclinical animal models of the compound.

The multidisciplinary research team is led by Dale Deutsch, PhD, Professor in the Department of Biochemistry and Cell Biology, and a member of the ICB & DD.  The research has been supported by a $3.8 million grant from the National Institute on Drug Abuse, an arm of the National Institutes of Health.

“The unique aspect of this research is that our focus is to investigate ways to active natural ‘marijuana’ in our bodies, the endocannabinoids,” said Deutsch. “This system has advantages over the properties of actual marijuana since endocannabinoids are not connected with dependence, potentially leading to addiction, but does act effectively against pain.”

Their research started in 2009 with the identification of the FABPs as the transporters of the endocannabinoids. When these compounds bind to the FABP they resulted in higher levels of AEA specifically. By using computational biology for virtual screening and actual assays, the researchers discovered lead compounds that bind to the FABPs and were analgesics for various types of pain.

The AEA research led to three Stony Brook University patent-covering new chemical compounds (called Stony Brook FABP Inhibitors or SB-FIs), which Artelo will investigate during its drug development plan.

“This licensing agreement gives us access to a promising intellectual property portfolio that is squarely aligned with our strategic direction as a scientific team with a proven track record of success,” said Gregory Gorgas, Chief Executive Officer of Artelo. “Working together to evaluate and identify novel FABP inhibitors based upon existing scientific data for clinical development will be complimentary to our drug pipeline and create a new opportunity for Artelo.”

In order to design the novel FABP inhibitors, members of the FABP Stony Brook research group required expertise in many disciplines, such as biochemistry, chemistry, computational biology, computer science, X-ray crystallography and medicine. The team includes Deutsch; Distinguished Professor Iwao Ojima, also the Director of the ICB & DD; Martin Kaczocha of the Department of Anesthesiology; Robert Rizzo  of the Department of Applied Mathematics and Statistics, and Huilin Li, formerly of the Department of Biochemistry and Cell Biology.

New Rapid-Fire Method Using Pathology Images, Tumor Data May Help Guide Cancer Therapies

By combining data on pathology images of 13 types of cancer and correlating that with clinical and genomic data, a Stony Brook University-led team of researchers are able to identify tumor-infiltrating lymphocytes (TILs), called TIL maps, which will enable cancer specialists to generate tumor-immune information from routinely gathered pathology slides.

Published in Cell Reports, the paper details how TIL maps are related to the molecular characterization of tumors and patient survival. The method may provide a foundation on how to better diagnose and create a treatment plan for cancers that are responsive to immune-based anti-cancer therapy, such as melanoma, lung, bladder, and certain types of colon cancer.

The gold standard for cancer diagnosis remains the pathology report from a biopsied tumor tissue. Diagnosis plays a leading role in how a patient will be treated. In certain situations and with forms of cancer treated with immune-based therapies, pathologists are also tasked with making observations on the immunologic features of the tumor tissue to determine which patients are most likely to benefit from these therapies. TILs are unleashed by immunotherapies to destroy cancer cells.

“This paper demonstrates that we can now use deep learning  methods such as artificial intelligence to extract and classify  patterns of immune cells in ubiquitously obtained pathology studies, and to relate immune cell patterns to the many other types of cancer patient molecular and clinical data,” says Joel Saltz, MD, PhD, the Cherith Chair of Biomedical Informatics at Stony Brook University and lead author of the paper, titled “Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.”

The research includes researchers from Stony Brook University, the University of Texas MD Anderson Cancer Center, Emory University, and the Institute for Systems Biology. The work stems from the efforts of The Cancer Genome Atlas (TCGA) project.

In the study, the researchers applied machine learning to digitized pathology images to characterize patterns of immune infiltration present in 4,759 TCGA patients and within 13 cancer types processing more than 5,000 digital images from the cancer types to create a “computational stain” for each. With these, they created TIL maps as a potential new guide to diagnosis and treatment planning.

TCGA is a decade long comprehensive effort spearheaded by the National Cancer Institute (NCI) and the National Human Genome Research Institute in collaboration with the cancer research community worldwide. The TIL map study is part of a cohort of 27 manuscripts published in Cell Press communicating results by the TCGA PanCancer Atlas Initiative,  which has compared and contrasted molecular features of all TCGA tumor samples from more than 10,000 cases comprising 33 different forms of cancer.

“Developing machine learning tools such as this proof of principle project to map lymphocytic infiltration patterns is important for research reproducibility in immune-oncology and will also allow these approaches to begin to be deployed as decision support for pathologists as we evaluate and report our cases for routine decision-making,” says Alexander Lazar, MD, PhD, Professor of Pathology & Genomic Medicine at MD Anderson and a co-author.

The investigators were able to develop the method and proof of concept with the assistance of data collection and calculations by way of high-performance computing systems available through Stony Brook’s Institute for Advanced Computational Science and Division of Information Technology.

Dr. Saltz and colleagues nationwide continue to investigate the use of digital archiving of pathology and the use of machine learning and artificial intelligence to enhance diagnosis and treatment of cancer.

The research was supported in part by the National Cancer Institute, the American Cancer Society, the Cancer Research Institute and the National Science Foundation

Our HRPP Standard Operating Procedures have been Updated!

For the past year, we have been preparing for our second re-accreditation with the Association for the Accreditation of Human Research Protection Programs (AAHRPP), and as a result, our SOPs have been extensively reviewed and updated.

We have posted them at this time as a single pdf here: Human Subjects Standard Operating Procedures but will create a more user-friendly format to allow for easy navigating in the near future. Please refer to these SOPs often to ensure the compliant conduct of your research activities.

Some of the more substantive changes you will notice:

1. Revisions to reflect the changes in FDA and NIH regulations over the past few years (and sent to you via this mailing and/or in Research News) including, e.g., the NIH GCP training requirement, allowance of FDA waiver of consent for minimal risk research, NIH single IRB requirement, etc.)

2. Revisions to reflect the (impending) move from IRBNet to Click as our IRB electronic management system.

3. Detailed SOPs on IRB reliance arrangements in Multi-site Research (see, in particular, Section 17.16)

4. Section (‘Recruitment of Subjects’) identifies that SBU participates in ResearchMatch (see new section 17.13) and confirms that, when recruiting patients as potential subjects, first contact must be made by someone who has a relationship (e.g., treatment etc.) with the patient; This policy protects the patient’s right to privacy.

5. Section 5.2 (‘Definitions’ within the ‘Obtaining Informed Consent’ section) provides greater detail, per the NYS Family Health Care Decisions Act, regarding the definition of a legally authorized representative who can give permission as a surrogate (in instances where an adult cannot consent for themselves).

6. Section 5.7 (‘Documentation of Informed Consent’) adds that, when using the short form procedure: In addition to receiving a copy of the (English) summary and a copy of the short form at the time of consenting, the subject must receive a copy of the summary, translated into their native language, as soon as possible after their enrollment into the study.

7. Extensive revision to Section 7.5 (‘Responsibilities for FDA-regulated Research’) to be clear regarding responsibilities of FDA regulated Clinical Investigators as well as responsibilities of those investigators who are also sponsors of INDs and IDE’s: see in particular Section (‘Additional Responsibilities When the Clinical Investigator is also the Sponsor of the IND or IDE [“Sponsor-Investigator”]’) and support services now available for Sponsor-Investigators (Section

8. Section 14 (Conflicts of Interest in Research) was revised to reflect the new annual disclosure process utilizing the electronic myResearch program.

9. Section 17.4 (‘Registration of Clinical Trials’) clarifies which research activities are subject to the clinicaltrials.gov registration requirement.

10. New Special Topics for:

a. Genomic Data Sharing (GDS) for NIH Grant Submissions (Section 17.12);

b. ResearchMatch as a Recruitment Tool (Section 17.13);

c. Conducting Research in a Clinical Setting (e.g., University Hospital): Special Considerations (Section 17.14);

d. Additional Requirements for Studies Funded by the Department of Defense (Section 17.15);

e. IRB Reliance/Single IRB (sIRB) Review (Section 17.16)

Reminder: IRB Approval does NOT mean Approval to Begin your Study!

IRB approval is just one aspect of complying with institutional requirements for the conduct of human research. Ancillary reviews and approvals are required before the commencement of studies using the facilities and patients of University Hospital, involving reviewers responsible for sign-off in the following areas:

· Pathology

· Research Pharmacy

· Radiology

· Privacy/Security (HIPAA)

· Hospital Finance/Billing

· Chair of PI’s department

· Use of research-related radiation

· Use of surgical pathology or cytology specimens

January 25th marked the implementation date for the new NIH single IRB Policy

As we have been advising you for some time now, this sIRB Policy affects multi-site studies involving non-exempt human subjects research funded by NIH, and applies to grant applications with due dates on or after January 25, 2018 and R&D contracts in response to solicitations issued on or after January 25, 2018.

A new Special Topics Section to our updated Standard Operating Procedures (SOPs)  has been added that addresses the process for IRB Reliances and NIH sIRB here at SBU.

If you have any questions about relying on an external IRB, or about having SBU be the IRB of record, for multi-site studies, please contact Ms. Lu-Ann Kozlowski in this office: lu-ann.kozlowski@stonybrook.edu, 631-632-9036.

For more information and resources directly from NIH, please go to: https://nexus.od.nih.gov/all/2017/12/07/nih-single-irb-policy-reminder/?utm_source=nexus&utm_medium=email&utm_content=nihupdate&utm_campaign=nov18

Effective and Compliance Dates of the Revised Common Rule have been postponed to July 2018 (at least)

February 9, 2018

See the federal register here: https://www.hhs.gov/ohrp/interim-final-rule-common-rule.html, and note: “Federal departments and agencies listed in the Interim Final Rule are also in the process of developing a notice of proposed rulemaking (NPRM) seeking public comment on a proposal for further delay in the required implementation of the revised Common Rule (for example, until January 21, 2019).” We will continue to monitor the situation, while concurrently working toward an easy transition for implementation of the new rule requirements when compliance with the final rule becomes required.

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