De-mystifying the (NIH) Commons

NIH data scienceLarge-scale efforts are underway at NIH to tackle hurdles associated with accessing and utilizing Big Data. Making public data, especially large commonly used data sets, easily accessible in the cloud will reduce the burden and cost of individual investigators independently moving and storing data, enable the ability to compute against data sets, and permit new and novel uses across data sets. The (NIH) Commons was created as a platform to make this possible. It is a shared virtual space where scientists can engage biomedical research digital objects that will allow them to find, manage, share, use and reuse data, software, metadata and workflows. For digital objects to be in the Commons, they must have attributes that make them Findable, Accessible, Interoperable and Reusable (FAIR), i.e. they must follow the FAIR principles.

Because the Commons was only recently introduced and is still under development, many in the research community are still wondering what it’s composed of and how it works. This week, a document was released by NIH that provides a clearer description of the Commons and some of the pilot programs initiated to develop and test its various components.

The Data Science at NIH online forum, INPUT | OUTPUT, published the first in a series of blog posts describing the four main building blocks of the Commons that work together to form a complex ecosystem:

  • computing environment, such as the cloud or HPC (High Performance Computing) resources, which support access, utilization and storage of digital objects.
  • Public datasets that adhere to Commons Digital Object Compliance principles.
  • Softwareservices and tools that enable a broad array of data indexing and sharing, and connectivity between repositories and registries;
  • A set of Digital Object Complianceprinciples that describes the properties of digital objects that enables them to be findable, accessible, interoperable and reproducible (FAIR).

Each of the components are being further refined and integrated through a series of Commons pilots. Because development is ongoing, NIH hopes to foster discussion and gather input from the research community through the INPUT | OUTPUT blog. Stay tuned for future postings.

Read the full document, including details about specific pilots here.

Announcing Data Science forums for OHSU researchers

Do you have an opinion about the future of data science or research informatics at OHSU? If so, this is your chance to provide input for OHSU’s new data science initiative. OHSU will be investing in clinical and research informatics in the next several years, and the institution wants to hear from you about what is needed to succeed.

You’re invited to attend a series of three, 90-minute forums across campus to solicit input from the research community. Tim Burdick, chief clinical research informatics officer, will facilitate structured exercises to create a vision for the future of OHSU data science and research informatics. This vision will then be used to inform the strategy and investments.

The forums are open to all members of the research community and are scheduled for the following dates and times:

  • Tuesday, Nov. 3, 10 to 11:30 a.m., OHSU Hospital, 8th floor auditorium
  • Tuesday, Nov. 10, 2 to 3:30 p.m., Collaborative Life Sciences Building 1A001
  • Thursday, Nov. 19, 10 to 11:30 a.m., Montagna Auditorium (West Campus)

The tentative agenda for each session is as follows:

  • Introductions
  • Background on the OHSU Data Science Initiative
  • Small group brainstorming session: What informatics support would you want in the future to facilitate your research?
  • Small group report out: Share with the other groups in attendance what your group envisions for the future
  • Discussion

There is no need to RSVP. You can simply show up at a session prepared to participate! Snacks and drinks will be served, and OHSU merchandise will be provided for all participants.

TTBD Innovator Spotlight: Yali Jia, Ph.D.

Yali Jia, PhD

Yali Jia, PhD

Yali Jia, Ph.D., assistant professor of ophthalmology at OHSU’s School of Medicine, has been making great strides to create breakthrough optical imaging technologies that may transform the way clinicians diagnose and care for patients. As a study investigator in Center for Ophthalmic Optics and Lasers (COOL) lab of Casey Eye Institute, Jia has spent the last several years helping develop the split-spectrum amplitude-decorrelation angiography (SSADA) algorithm, which is most efficient within current available optical coherence tomography (OCT) angiography methods, and allows physicians to map out the ocular circulation down to capillary level.

Physicians currently use fluorescein angiography to test for abnormal vasculature or to view vessel leakage, which are the signs of severe macular degeneration and diabetic retinopathy. This method requires intravenous injection of a contrast dye into the blood vessels and uses infrared light waves to capture detailed cross-sectional images of the retina’s layers. However, dye-based angiography has its disadvantages. Fluorescein angiography produces a two-dimensional image and cannot be evaluated quantitatively. It can also cause adverse side effects, such as nausea and vomiting, in up to 25 percent of patients.

Jia and a team of inventors from the COOL lab developed SSADA to perform high-resolution and high-efficiency OCT angiography. Compared to fluorescein angiography, SSADA-based OCT angiography is faster, more accurate, safer, and less expensive. Furthermore, the SSADA invention is a non-invasive method that does not require dye-based injections. It can produce three-dimensional, ultra-high image resolution in three seconds, compared to the ten seconds image capture in fluorescein angiography. More importantly, it allows physicians to measure vascular density, ischemia area, and neovascularization in a quantitative manner, which is imperative for clinical diagnosis and management.

Jia’s work has brought further recognition to the COOL lab, the Casey Eye Institute, and OHSU as ophthalmologists around the world have expressed great interest in learning and using the new technology. Her interest in the optical imaging technology field stemmed from her early work in developing a new functional OCT while she was a biomedical engineering student at OHSU. As a postdoc, Jia began her work in developing the SSADA algorithm to help improve on the current OCT technology. After one-and-a-half years as a postdoc, Jia was promoted to a faculty member and now works alongside David Huang, M.D., Ph.D., a co-inventor of the first OCT system.

OHSU has filed patent applications for the SSADA invention and has exclusively licensed those patent rights to an OCT company. Since joining OHSU, Jia has submitted several invention disclosures to the office of Technology Transfer and Business Development. Now, when she writes a paper and finds that her technology is novel, she first sends it to TTBD for review. In the future, she hopes to see her inventions used widely around the world by physicians to diagnose and manage eye disease.

IRB brown bag: Navigating the new eIRB

IRB Brown BagNavigating the new eIRB

Presented by David Holmgren, IRB manager

Thursday, Nov. 12
10 to 11 a.m.
OHSU Hospital, 8th floor auditorium

Come join us for an orientation of the new eIRB system. See how UPs will trigger the RNI form, learn how to submit a Continuing Review and get an introduction to the new system in general. Bring your questions and get ready to learn!

Significant Changes to NIH Grants Policy Statement coming soon

nih-oer-logoThe NIH released a Significant Changes document this week summarizing the main grants policy changes and clarifications that will be implemented in the FY2016 NIHGPS. The revised NIHGPS, expected to be available in November, will represent an update to the March, 31, 2015 version and will be applicable across all NIH grants and cooperative agreements effective the revision date. To inform the research community of these changes immediately, the document released this week outlines the following significant changes:

  1. Genomic Data Sharing: Applications proposing to generate large-scale human and/or non-human genomic data are expected to include a genomic data sharing plan.
  2. Application Non-Compliance: Applications deemed non-compliant with NIH guidelines during the review process may be withdrawn from consideration.
  3. Clinical Trial Reporting: New Requirement Text will be added to clarify that results reporting is still required after the period of performance has ended.
  4. Change in Scope: Expands the description of change in scope from the approved involvement of human subjects and what additional approvals / changes in designation are required.
  5. Terms and Conditions language: What was formerly termed “guidance” as it relates to human fetal tissue research is now considered “regulatory requirement.”
  6. Administrative Requirement: To reduce administrative burden, NIH will allow recipients to reduce effort during a NCE without prior approval.

Read the full list of changes here.


TTBD Startup Spotlight: NeuraMedica LLC

Neuramedica logoWatertight closure of the dura mater – the membrane covering the brain and spinal cord – is a difficult and time-consuming procedure. It is typically performed using fine suture down narrow working channels using minimally-invasive surgical techniques. Repeatedly experiencing the complexity of this procedure firsthand, neurosurgeon Neil Roundy, M.D., saw an opportunity to address the problem. Roundy developed an innovative bio-absorbable clip used to close durotomy incisions during spinal surgery. But he needed support to bring his invention to market.

Neil Roundy, M.D.

Neil Roundy, M.D.

While a neurosurgery resident at OHSU, Roundy learned about the Oregon Clinical and Translational Research Institute’s Biomedical Innovation Program. He applied for a program grant and partnered with an outside contract engineer, Rachel Dreilinger, who developed the prototypes and applied for additional funding to continue development. Together, they formed NeuraMedica, LLC, in June 2014 when they licensed the technology intellectual property from OHSU. Roundy and Dreilinger were able to achieve proof-of-concept designs that led to two patent applications and additional funding.

The current goal of NeuraMedica is to bring the dural clip to market to improve upon the current standard of care – suture or metal clips – both of which have their limitations. Suture is very time consuming to perform and requires magnification in a minimally invasive environment with limited space. Metal clips or staples are occasionally used; however, metal is radiopaque, creating imaging artifacts that block the visibility of the surgical site on follow-up diagnostic imaging. Metal staples and suture penetrate the dura, creating small holes that can lead to cerebrospinal fluid leakage.

In contrast, NeuraMedica’s dural clips are quick to apply, radiolucent, bio-absorbable, and non-penetrating, providing significant clinical benefits for both the patient and the surgeon. To date, NeuraMedica has received grants from OCTRI’s Biomedical Innovation Program and Oregon Nanoscience and Microtechnologies Institute, funding administered by OHSU. NeuraMedica has also received significant support from OHSU’s Technology Transfer and Business Development office including connections to key local business advisors and other startup support services. The company is also in discussions with Madigan Army Medical Center in Tacoma, Wash. This relationship was facilitated by biomedical consultant Eric Hanson, who is also helping to prepare applications for non-dilutive funding from the Department of Defense to accelerate NeuraMedica’s pre-clinical testing.

As NeuraMedica continues down the commercialization path, it is seeking additional funding opportunities to catapult its product to market. Near-term goals include the identification of pre-clinical and clinical research partners, opportunities for future investments, and continued product preparation for launch. The NeuraMedica team sees a lot of clinical utility, cost effectiveness and patient value in this device. The team is excited to move this exciting medical device into the hands of surgeons.

OHSU Presidential Bridge Funding applications due Dec. 31

The Office of the Senior Vice President for Research has released its call for proposals for the FY16 winter OHSU Presidential Bridge Funding Program. Bridge funding is available for established investigators threatened by an imminent lapse in research support. Investigators can request up to $50,000 in funding for one year to help bridge them while they generate data to restore funding. Up to 6 awards will be made this funding cycle.

Awards will be made only to OHSU investigators. The PI must be an independent scientist. Independence is defined by: rank at the level of assistant professor or above; committed institutional support such as space and salary; a track record of first authored or senior authored publications; a recent history of federal (or similar) funding; and imminently planned or pending application for funding on a national level. Postdoctoral fellows and similar trainees are not eligible to apply.

Applications are due by 5 p.m. on Thursday, December 31, 2015. Please note, the submission process has changed – applications will now be submitted online via OHSU’s Competitive Application Portal, CAP. View guidelines and instructions here.

eIRB down time: Data migration

eIRB data migration will take place in two weeks!

The eIRB data migration is upon us! All non-pending studies from the old eIRB system will be transferring to the new eIRB (over 2,000 studies!). This means that both systems will be down and unavailable* for up to four business days. This is planned to start on Friday, Nov. 6.

About three-fourths of the studies will be moving over to the new system during this down time. The rest will be moving on a nightly basis once they have been submitted and approved.

Nightly migration: After the large data migration, all studies that are currently in a pending state will migrate once they have been submitted and approved.

This includes:

  • Mods
  • Continuing reviews
  • UPs
  • PDs

To help prepare for the move, withdraw any old items (studies, modifications, continuing reviews, reportable events) that you don’t intend on submitting/resubmitting within the next six months. These items will not be migrated to the new system. Withdrawn items, however, can still be accessed in the archive.

In the case of a needed emergency review, please contact your IRB analyst at 503 494-7887, option 1, or at

Trainings in the new system are available by registration in Compass. If you cannot attend one of the prescheduled trainings, please reach out to Dave Holmgren, IRB manager, to schedule a one-on-one training for yourself or your department.

Proposed changes to “Common Rule” now open for comment

In September of this year, the Department of Health and Human Services published proposed changes to the Federal Policy for the Protection of Human Subjects, most often referred to as the Common Rule. The Notice of Proposed Rulemaking (NPRM) is now open for public comment and includes a wide range of changes to the Common Rule with the goal of modernizing regulations to reflect current research conduct.

Some of the proposed changes include:

  • Requiring that (in most cases) research being conducted at more than one institution (multisite research) must rely on a single Institutional Review Board (IRB).
  • Applying the Common Rule regulations to all clinical trials, regardless of funding source, if they are conducted in a U.S. institution that receives funding for research involving human participants from a Common Rule agency.
  • Implementing new data security and information protection standards that would reduce the potential for violations of privacy and confidentiality.
  • Defining secondary use of non-identified biospecimens as “human subjects” for research purposes.
  • Expanding consent requirements, including written consent for use of an individual’s biological samples (blood or urine, for example) for research with the option to consent to their future use for unspecified studies.

These changes may have a significant impact on your research so make your voices heard! Comments must be submitted by December 7, 2015 via the NPRM website. For additional commentary on these proposed changes, check out this Open Mike blog entry from Deputy Director for Extramural Research, Michael Lauer.

New “Open Science Prize” competition seeks applications

open science prize
The NIH has partnered with Wellcome Trust and the Howard Hughes Medical Institute to launch a global science competition for innovative products or services that will advance “open science,” a movement to make scientific data more accessible. “Big data” generated by biomedical research is growing rapidly yet researchers’ ability to derive knowledge from that data is hindered by their ability to find, access and use it. The Open Science Prize aims to support prototyping and the development of services to overcome these hurdles and ensure data can be used to advance biomedical research discovery and innovation.

The competition consists of two phases. For the first stage, up to six teams stand to win $80,000 each to develop their ideas into a prototype or to advance an existing early stage prototype. These teams will then enter the second phase of the competition with the prototype judged to have the greatest potential to further open science receiving $230,000. The first phase of the competition is accepting applications through Feb. 29, 2016. The six winning teams will be selected based on the advice of a panel of experts  to receive the prize money to advance their ideas to prototypes, and will be required to submit their prototypes by Dec. 1, 2016. The overall winner is expected to be selected on Feb. 28, 2017.

“Research is a global, data-driven enterprise and our ability to improve health increasingly hinges on our ability to manage and make sense of the enormous amounts of data being produced by scientific research,” said NIH Director Francis S. Collins, M.D., Ph.D. “I expect the Open Science Prize to generate innovative ideas to improve data access and establish new international collaborations that will illustrate the transformative power of sharing research data.”

Because “open science” is a global movement, the prize is only open to international collaborative teams, specifically:

  • a team of two or more individuals, where at least one individual is a citizen of, or permanent resident in, the United States (US), and at least one individual is resident in a country other than the US.
  • a group of two of more public or private entities, where at least one entity is incorporated in and maintains a primary place of business in the US, and at least one entity is incorporated in and maintains a primary place of business in a country other than the US.

Learn more about the guidelines/eligibility and register your team here.

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Welcome to the Research News Blog

OHSU Research News is your portal to information about all things research at Oregon Health & Science University. Visit often for updates on events, discoveries, and important funding information.

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