September 2017

3D Collaborations Build New Worlds for Musicians

In 2017, Stony Brook graduate student and ethnomusicologist Jay Loomis and assistant professor of computer science Roy Shilkrot teamed up to secure a grant to create 3D printed replicas of ancient wind instruments.

Assistant Professor of Computer Science Roy Shilkrot, left, and grad student and ethnomusicologist Jay Loomis collaborate on creating 3D replicas of ancient wind instruments.

The goal? To give museum-goers an opportunity to interact with rare instruments rather than merely viewing them through a glass enclosure.

Loomis had been interested in wind instruments since he was a boy in Wisconsin, when he was struck deeply by flute music wafting from his car radio. After he moved to Long Island, his thirst for playing dovetailed with an insatiable curiosity about indigenous musical instruments. He hoped to build such instruments, as a way of sharing aspects of Native American culture with the public.

In his travels as an academic, he encountered musical virtuosos, acoustic experts and computer scientists who shared his passion. That passion gained momentum when Loomis became a teaching assistant at cDACT, the Stony Brook-based Consortium for Digital Art, Culture and Technology.

Through cDACT Director Margaret Schedel, Loomis connected first with Shilkrot and later Hideo Sekino, a visiting professor from Tokyo Institute of Technology, who is associated with the Institute for Advanced Computational Science at Stony Brook.

In spring 2017, Loomis and Shilkrot developed a 3D scanner and used desktop and professional 3D printers to recreate playable replicas of wind instruments, including flutes, ceramic ocarinas and whistles of different shapes and sizes. An integral part of the process was to recreate the sound of the original instrument and mirror its physical characteristics as well.

The greatest challenge the collaborators experienced was in designing the cavity of the instrument, which was essential to recreating the authentic sound.

The results were encouraging but weren’t as precise as Loomis wanted. Schedel recommended collaborating with Sekino due to his interest in the traditional Japanese flute known as a shakuhachi. After she introduced the two musicians, Loomis was inspired to feature the instrument in an electronic piece he co-composed with Timothy Vallier.

New Computational Model of Chemical Building Blocks May Help Explain the Origins of Life

Scientists have yet to understand and explain how life’s informational molecules – proteins and DNA and RNA – arose from simpler chemicals when life on earth emerged some four billion years agoScientists have yet to understand and explain how life’s informational molecules – proteins and DNA and RNA – arose from simpler chemicals when life on earth emerged some four billion years ago. Now a research team from the Stony Brook University Laufer Center for Physical and Quantitative Biology and the Lawrence Berkeley National Laboratory believe they have the answer. They developed a computational model explaining how certain molecules fold and bind together to grow longer and more complex, leading from simple chemicals to primitive biological molecules. The findings are reported early online in PNAS.

Ken Dill
Ken Dill explains the computational model that shows how certain molecules fold and bind together in the evolution of chemistry into biology, a key step to explain the origins of life.
Previously scientists learned that the early earth likely contained the basic chemical building blocks, and sustained spontaneous chemical reactions that could string together short chains of chemical units. But it has remained a mystery what actions could then prompt short chemical polymer chains to develop into much longer chains that can encode useful protein information. The new computational model may help explain that gap in the evolution of chemistry into biology.

“We created a computational model that illustrates a fold-and-catalyze mechanism that amplifies polymer sequences and leads to runaway improvements in the polymers,” said Ken Dill, lead author, Distinguished Professor and Director of the Laufer Center. “The theoretical study helps to understand a missing link in the evolution of chemistry into biology and how a population of molecular building blocks could, over time, result in the emergence of catalytic sequences essential to biological life.”

In the paper, titled “The Foldamer Hypothesis for the growth and sequence-differentiation of prebiotic polymers,” the researchers used computer simulations to study how random sequences of water-loving, or polar, and water-averse, or hydrophobic, polymers fold and bind together. They found these random sequence chains of both types of polymers can collapse and fold into specific compact conformations that expose hydrophobic surfaces, thus serving as catalysts for elongating other polymers. These particular polymer chains, referred to as “foldamer” catalysts, can work together in pairs to grow longer and develop more informational sequences.

This process, according to the authors, provides a basis to explain how random chemical processes could have resulted in protein-like precursors to biological life. It gives a testable hypothesis about early prebiotic polymers and their evolution.

“By showing how prebiotic polymers could have become informational ‘foldamers’, we hope to have revealed a key step to understanding just how life started to form on earth billions of years ago,” explained Professor Dill.

Co-authors of the paper include Elizaveta Guseva of the Laufer Center and Departments of Chemistry and Physics & Astronomy at Stony Brook University, and Ronald N. Zuckermann of the Lawrence Berkeley National Laboratory in Berkeley, Calif.

The research was supported in part by the National Science Foundation.

New Center Will Sleuth the Subatomic Ingredients of the Universe

Despite centuries of studying the atom and the particles within it, the mysteries of matter continue to elude scientists. What are we really made of?

An Electron-Ion Collider would probe the inner microcosm of protons to help scientists understand how interactions among quarks (colored spheres) and glue-like gluons (yellow) generate the proton’s essential properties and the large-scale structure of the visible matter in the universe today.
To solve such an enigma and better understand the building blocks of our universe, Stony Brook University and the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory (BNL) have partnered to establish the Center for Frontiers of Nuclear Science, bolstered by a new $5 million grant from the Simons Foundation.

“The Center for Frontiers in Nuclear Science will bring us closer to understanding our universe in ways in which it has never before been possible,” said Samuel L. Stanley Jr., MD, President of Stony Brook University. “Thanks to the vision of the Simons Foundation, scientists from Stony Brook, Brookhaven Laboratory and many other institutions are now empowered to pursue the big ideas that will lead to new knowledge about the structure of everything in the universe today.”

Establishing the Center is a big step toward discovering the unknown essentials of matter for Stony Brook and BNL, which already have internationally renowned programs in nuclear physics. But before solving such a mystery, one must first know the clues. Here’s a quick breakdown.

Matter is any substance that has mass and takes up space. An atom is the smallest unit of matter. At an atom’s core is its nucleus, made of protons of neutrons — subatomic particles collectively called nucleons. Looking deeper, nucleons are made of elementary particles called quarks and gluons, and this is where the trail goes cold.

“The role of quarks and gluons in determining the properties of protons and neutrons remains one of the greatest unsolved mysteries in physics,” said Doon Gibbs, Ph.D., Brookhaven Lab Director.

Solving this mystery is the focus of quantum chromodynamics (QCD), a branch of theoretical physics that investigates how quarks and gluons interact as fundamental elements of matter.

Stony Brook and BNL’s new center is slated to become a leading international research and educational hub for QCD over the next several decades, uniting our faculty, students and researchers with BNL staff and scientists from around the world in an effort to crack the quantum case.

One key aspect of the Center’s launch is a proposed Electron Ion Collider (EIC), a powerful new particle accelerator that would create rapid-fire, high-resolution “snapshots” of quarks and gluons contained in nucleons and complex nuclei — crucial to QCD progress.

Abhay Deshpande, PhD, Professor of experimental nuclear physics in the Department of Physics and Astronomy in the College of Arts and Sciences at Stony Brook University
“An Electron Ion Collider would reveal the internal structure of these atomic building blocks, a key part of the quest to understand the matter we’re made of,” Gibbs said.

Abhay Deshpande, professor of experimental nuclear physics in the Department of Physics and Astronomy, has been named Director of the Center, as well as Director of Electron Ion Collider Science at BNL.

A champion of the EIC for decades, Deshpande is positioned to lead development of the collider, which was deemed highest priority for new facility construction by the National Science Foundation’s Nuclear Science Advisory Committee in an effort to strengthen and expand U.S. leadership in nuclear physics and stimulate economic benefits well into the 2040s.

Like most mysteries, collaboration is the key to success, so Deshpande is focused on uniting QCD and EIC experts from around the globe with Stony Brook students who will serve as the next generation of researchers in the field.

“Overall, I want the worldwide community of EIC enthusiasts to see the Center for Frontiers in Nuclear Science as their ‘home away from home,’ where they can come and work on EIC-related research,” Deshpande said. “My hope is that within a short time, the students at Stony Brook will have more opportunities to work with researchers at Brookhaven, and vice-versa.”

Despite the complexity of nuclear physics and related areas of study, the results of such research could reveal the most basic aspects of our very existence.

“Nuclear physics is a deep and important discipline, casting light on many poorly understood facets of matter in our universe,” said Jim Simons, chairman of the Simons Foundation. “It is a pleasure to support research in this area conducted by members of the outstanding team to be assembled by Brookhaven Lab and Stony Brook University.”

Through major funding, the Simons Foundation is bonding a partnership between Stony Brook and BNL perhaps as strong as the interaction between quarks and gluons.

“Basic science research seeks to improve our understanding of the world around us, and it can take human understanding to wonderful and unexpected places,” said Marilyn Simons, president of the Simons Foundation. “Exploring the qualities and behaviors of fundamental particles seems likely to do just that.”

— By Brian Smith

Have You Submitted Your Annual Conflict of Interest Disclosure in myResearch?

Conflict of Interest submissions went electronic on May 1st eliminating the paper forms in COEUS and IRBNet! An Annual Conflict of Interest Disclosures is required to be on file in myResearch.

This annual disclosure is then used for proposals, new awards, funded IRB protocols and PHS (NIH) award continuations!

Submissions can be completed here .

Do You Ever Wonder if You Need to Comply with Export Regulations?

Just a few examples of when export regulations may come into play are international travel, hosting visitors, purchasing items, international shipping or sharing confidential information with others. If these are things that you do, please refer to our new guidance and procedure documents for export compliance.

Message from NIH: Changing policies impact NIH-funded studies involving human subjects

Message to NIH grant applicants/awardees, contractors, researchers and research administrators:

If you are conducting NIH-funded research that involves human subjects, or are considering applying to NIH for support of such research, we want to call your attention to important changes that may affect how you:

● select the right NIH funding opportunity announcement

● write the research strategy and human subjects sections of your application

● comply with appropriate policies and regulations

First, familiarize yourself with the new PHS Human Subject and Clinical Trial Information form.

For application due dates of January 25, 2018, and beyond, you will be required to use an updated application forms package (FORMS-E), which includes the new human subject and clinical trial form. This form requests human subject and clinical trials information at the study level using discrete form fields, which is a change from current practice. Contract proposals will also require this information. Learn about the new form here .

Second, take a moment to answer these four questions about your current or proposed research:

1) Does the study involve human participants?

2) Are the participants prospectively assigned to an intervention?

3) Is the study designed to evaluate the effect of the intervention on the participants?

4) Is the effect that will be evaluated a health-related biomedical or behavioral outcome?

If the answer to all four questions is yes, then your proposed research meets the NIH definition of a clinical trial. Clarified and broadened in 2014, the definition encompasses a wide range of trial types: mechanistic, exploratory/developmental, pilot/feasibility, behavioral, and more. NIH expanded the clinical trial definition in response to widespread calls from diverse stakeholders for improved reporting of research milestones and outcomes, and for assuring maximal transparency.

Need help determining whether your study would be considered by NIH to be a clinical trial? See our webpage on the definition that includes case studies, FAQs and other resources that can help. Still unsure? Contact your NIH program official or the scientific point of contact listed on the funding opportunity announcement to which you are applying.

Third, familiarize yourself with NIH policy changes related to enhancing stewardship of clinical trials.

NIH made a number of policy changes to improve the stewardship of clinical trials across the life cycle of the trial. We encourage you to familiarize yourself with all that is changing, including:

● the requirement to apply to an FOA that specifically allows for the submission of clinical trial applications for due dates beginning January 25, 2018.

● Good Clinical Practice training expectations for NIH staff, grantees, and contractors that went into effect January 2017.

● updated peer review criteria that will be included in FOAs for clinical trial applications and solicitations for due dates on/after January 25, 2018.

● new Human Subject Information form requirements for clinical trials that will be included in updated application forms (FORMS-E) for due dates on/after January 25, 2018, and contract solicitations published as of January 25, 2018. ● use of a single IRB for non-exempt, multi-site clinical trials for application due dates on/after January 25, 2018.

● expanded registration and reporting to include all NIH supported clinical trials. Improving the design, efficiency, and transparency of clinical trials is important because it:

● respects our ethical obligation to participants to maximize the use of the knowledge from the trials in which they participate

● facilitates design of clinical trials while reducing unnecessary duplication

● promotes broad, timely, and responsible dissemination of research information and results

● fosters responsible stewardship of the public’s investment in biomedical research

We have developed a new Clinical Trial Requirements for NIH Grantees and Contractors web page to bring together all the information you need to know. Please review this information carefully. Your attention to detail will be critical to ensuring successful funding of your clinical trial awards.

We will be putting out a series of reminder policy notices, training opportunities, and other resources in the NIH Guide to Grants and Contracts , in the NIH Extramural Nexus , and on my blog. The success of clinical trials relies on the public trust in scientific rigor and ethical oversight. We all play a critical role in this process. We are most grateful to you for your help and support. Best, Michael S. Lauer, MD Deputy Director for Extramural Research, NIH One Center Drive, Building 1, Room 144 Bethesda, MD 20892

Update on the myResearch (Click) Electronic Management Program for IRB

The staff of ORC and IT (Research) have been working diligently to customize and test myResearch for IRB with the goal of making the transition from IRBNet to myResearch as seamless as possible. Once the system is ready for ‘prime time’, expected early fall, ORC will be offering in-person workshops and other training opportunities (including sending you training materials with screenshots and instructions) so that you can hit the ground running in preparing your submissions for IRB review.

We are planning a ‘phase in’ approach for use of the system such that we will first be accepting initial (new) submissions (expedited or full review) starting November 20, 2017. Then, sometime in the Spring, we will start moving over active studies that currently live in IRBNet to myResearch via the continuing review process. More on that early next year.

In the meantime, here are some little tidbits of helpful information to start building up your knowledge about the new system:

There’s some new terminology you will need to get used to. Here are three for now (and more to follow!):

● Reportable New Information (RNI): this is the term in myResearch that is what we currently refer to as, e.g., unanticipated problems involving risks to subjects or others, protocol deviations, protocol violations, non-compliance, results of audits or inspections by external agencies or study monitors etc. That sort of thing. More on that as we get closer to launch.

● Non-committee Review: is the term used to describe all reviews done outside of a convened IRB meeting, including exemption determinations, expedited reviews, and ‘Not Human Research’ and QA/QI determinations.

● Designated Reviewer: this is the individual(s) who conducts the non-committee review. If it’s anything other than an expedited review (which requires that the designated reviewer be an actual IRB member), the designated reviewer will be a member of the ORC staff.

As you know, a standard submission in IRBNet requires (in part) completion of a registration smart form, an IRB application, and an uploaded protocol. In myResearch, the smart application form you complete within the system takes the place of the registration form. There will no longer be a separate IRB application to complete. However, in its place we have created the Protocol Template for Investigator-Initiated Studies to be submitted for studies that are initiated by you ( SBU researchers ). You will note that it is much more content-intensive than our previous template in IRBNet, but it provides all the information that is required for the SBU IRBs to assess the federally mandated approval criteria. This template is a blend of the template available through the Click ‘out of box’ program, as well as templates from fellow accredited institutions.

If you would like to “test drive” this new protocol template and start using it now, please feel free to do so. If you submit a new study in IRBNet using this template, you don’t have to also complete the IRB application.

Currently, the process for using an IRB external to SBU (e,g, Chesapeake, NCI-CIRB, or other multi-center studies in which an external IRB will serve as the IRB of record for all sites) involves an administrative process for ceding that IRB review that is a blend of IRBNet and external email. With myResearch, the entire process will occur within the system. New to the submission requirements for these studies that are not SBU investigator-initiated is the need to submit a Protocol Template Supplement: SBU-Specific Information in addition to the main (external) protocol . The information will provide information on issues pertaining to the conduct of the research here, and also provide information that will be helpful for not-for-cause monitoring visits and audits that are conducted as part of ORC’s QA efforts to maintain our high quality HRPP.

Any questions pertaining to these updates may be directed to Judy Matuk at


New FDA Guidance Effective Immediately

On July 24, 2017, the FDA announced that, effectively immediately, it will now permit IRBs to waive or alter informed consent for minimal risk*  clinical investigations, so long as the IRB determines and documents that the following criteria are satisfied:
● The clinical investigation involves no more than minimal risk* to the subjects;
● The waiver or alteration will not adversely affect the rights and welfare of the subjects;
● The clinical investigation could not practicably be carried out without the waiver or alteration; and
● Whenever appropriate, the subjects will be provided with additional pertinent information after participation.

As these criteria are identical to the consent waiver criteria in the Common Rule (which doesn’t cover FDA) this is an important step in harmonization across federal agencies. Affected applications are expected to include certain registries, observational
studies, and studies using existing data and specimens.

The guidance can be accessed here.

* Minimal risk is defined as “the probability and magnitude of harm or discomfort anticipated in theresearch are not greater in and of themselves than those ordinarily encountered in daily life or during the performance of routine physical or psychological
examinations or tests.”

Wondering what’s going on with the revisions to the Final Common Rule?

Wondering what’s going on with the revisions to the Final Common Rule?

Join the club! But while we wait, our colleagues at the CITI Program have done an incredible job of creating a set of resources to help our understanding of what is changing (when it actually does, in fact, change).

Have a look:

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