2nd Semi-Annual i2b2 User Group Meeting

Make plans now to attend the 2nd semi-annual i2b2 User Group meeting, hosted by the CTSI. The meeting will take place on May 20th in the Helen Wood Hall Auditorium (1w304) from 2pm – 4pm.  All users and prospective users are invited to review new features and other improvements in i2b2.  In addition, you’ll have an opportunity to ask for and vote on future additions and changes.

But exactly what is i2b2?

i2b2 stands for “Informatics for Integrating Biology and the Bedside.” It is a system developed by Harvard University’s i2b2 Center, an NIH-funded center for biomedical computing, that integrates with eRecord to allow researchers to more easily navigate the (clunky and arcane) system.

Through i2b2, researchers can query a wide variety of information in the university’s eRecord database — as well as a handful of other local sources including data from Flowcast and HBOC — and get data within a matter of minutes.

Paul Allen, Ph.D.

Paul D. Allen, Ph.D.

“It’s really useful for answering proof of concept questions,” said Paul D. Allen, Ph.D., research assistant professor in the Department of Neurobiology and Anatomy. “When we’re working to set up resident research projects and we want to know, for example, whether there are enough newborn babies here to test for congenital CMV infection, you can go in and ask how many babies were born here in the last year, and it will spit out a number. It’s magic.”

At the CTSI, clinical research informaticist Adam Tatro, M.S., R.N., runs an i2b2 training session every month, where new users can learn the ropes.

Allen said the program has helped tremendously with study design. Recently, his group wanted to know if pediatric patients with the airway disorder laryngomalacia had more severe obstructive sleep apnea than other kids who had undergone sleep studies. Allen’s group searched for kids’ sleep studies, sorting for those with and without the disorder.

“After writing the program to read the sleep study note we answered the question in about 20 minutes – and the answer was no, these kids do just fine,” said Allen.

Additionally, the program is constantly being updated. Recently, it gained the ability to sort by prescribed medications.

“That was a really good update,” said Allen. “The caveat is we don’t know if people actually took the medications, but we can see what’s prescribed after certain treatments.”

Adam Tatro, M.S., R.N.

Adam Tatro, M.S., R.N.

Though many researchers use it to interface with eRecord, the program’s capabilities go beyond that. Christine Annis, senior health project coordinator in the Department of Neurology, is her department’s coordinator for national research studies that come through NeuroNEXT, a network for early phase neuroscience clinical trials, and uses i2b2 to pull data from Flowcast and HBOC.

By querying the various databases, Annis can respond to NeuroNEXT feasibility questionnaires in a short period of time. Site feasibility responses inform the Network as to whether there are sufficient number of specific types of patients available within the Network.

“We are asked how many people have been seen in the last year at the University of Rochester who will meet the proposals criteria, and how many of those seen we think could will enroll in the proposal if it were funded,” said Annis. “I primarily use i2b2 for those two questions.”

Annis has used i2b2 to track down data for 45 different NeuroNEXT proposals, totaling more than 1,000 different queries. By being able to run the queries on her own she does not have to ask other departments to take time out or their busy schedule to run a query on their patient databases.

“i2b2 has saved me so much time,” she said.

For more information on i2b2, contact Adam Tatro at Adam_Tatro@URMC.Rochester.edu.

Note: Thanks to Sean Dobbin, who posted the original version of this story on December 11, 2014.

Director’s Update — May 2015

Every month, the CTSI Stories Blog will post excerpts from ongoing conversations with the institute’s co-directors.

Below, Nana Bennett discusses how the CTSI has enhanced the role of its Strategic Leadership Group (SLG).NanaBennett

Tell us a little about the SLG’s role in the CTSI.

Historically, the SLG was composed of a handful of leaders from across the university. They were chosen because they were not closely involved in the CTSI, but represented leadership of relevant areas in the medical center, e.g., clinical, educational and research. The hope was that this diverse group of people, coming from a variety of backgrounds, would serve as advisers to the CTSI.

In the past, we had a less formal structure than we do now. Starting this year — and we’re emphasizing this, in particular, in the run up to the renewal — we’re presenting various aspects of the CTSI to the SLG formally, and asking them to provide feedback. In addition, we have added two new members representing the community.  This has further broadened the scope of input from the group.

What has been discussed so far?

Population health was the first area we discussed.  We discussed the meaning of population health to different constituencies and what our focus on population health could mean to the CTSI.  We talked about how, sometimes, investigators aren’t fully aware of the community engagement resources available at places like the Center for Community Health, and that it is important to consider how they’re going to engage subjects in all aspects of a study, not just during enrollment. And we talked about how the CTSI could potentially serve as a facilitator in moving research in a direction that’s based on the needs of a community. For example, two pressing problems locally are obesity and mental health, so focusing on those areas could be a good fit for the CTSI.  We discussed ways to move these research priorities forward in the medical center.

At the next meeting, we talked about our funding programs — our pilot and incubator programs. We’re expecting the renewal RFA is limit pilot funding somewhat, so we’re going to need to focus on aligning our funding with key elements of our mission and vision. We are still in the very early stages, but we discussed a few ways that we might be able to tweak those programs, such as requiring a transdisciplinary team, requiring population health alignment, and focusing on the removal of barriers to translational research.  In addition, we discussed alignment of the many pilot funding opportunities across the medical center so that investigators understand all the opportunities, and have the capacity to choose the best fit for their research.

Next, we’re going to talk about team science, and how we can better support collaboration.  It has been very helpful to have this diverse, experienced group all come together to discuss these topics.

What else has changed about the SLG?

We’ve also added two members of the Community Advisory Council – Ann Marie Cook from Lifespan and Elissa Orlando from WXXI – to the SLG. Previously, the Community Advisory Council was advising the Center for Community Health, but now that they have a presence on the SLG, providing advice to the whole CTSI.  They have a more direct voice in the decisions we make, and they keep us on track in responding to community needs.


Previous director’s updates:
April 2015 – Karl Kieburtz talks about how the leadership is preparing for the Clinical and Translational Science Award renewals.
March 2015 – Martin Zand introduces himself and discusses his interest in informatics and population-based research.
February 2015 – Nana Bennett discusses the CTSI’s Seminar Series on population health.

January 2015 – Harriet Kitzman reflects on her time as a CTSI co-director.
December 2014  – Karl Kieburtz offers his takeaways from the CTSI all-hands retreat.
November 2014 – Nana Bennett speaks to the expansion of the role of the CTSI’s Community Advisory Council.
October 2014 – Harriet Kitzman discusses the science of team science.
September 2014 – Karl Kieburtz talks about why the CTSI is beefing up its informatics team.
August 2014 – Nana Bennett discusses the new Population Health pillar.
July 2014 – Harriet Kitzman offers her takeaways from the Mini Summer Research Institute.
June 2014 – Karl Kieburtz gives an overview of the CTSI’s six pillars.

Success Stories: Trainee Pilot Program helps launch a career

The CTSI’s Trainee Pilot program offers aspiring researchers the chance to compete for a 1-year grant of up to $25,000. Courtney Jones, Ph.D., received one such award in 2012, and spoke with CTSI Stories about how the subsequent research helped shape her career.

Courtney Jones, Ph.D.

Courtney Jones, Ph.D.

Tell us a little about your research.

My dissertation centered on risk stratification of older adults with injuries. Certain hospitals, like Strong Memorial, are designated trauma centers that have specialized resources for the care of injured patients, and when we’re making a decision on where to send a patient, we want to make sure we choose the correct facility. We don’t want to send every injured patient to a designated trauma center, because then those centers may become overwhelmed. And we don’t want to send patients who are at high risk to a community hospital because they might not have the necessary resources to care for that person.

So when the ambulance arrives on the scene, it’s really about identifying where a patient should be transported. Previous research has shown that older adults are less likely to receive trauma center care than their younger counterparts, even if they have similar injuries. We really didn’t know why that was the case.

How did you come to work with the CTSI?

I was a Ph.D. student in epidemiology when I looked into the Trainee Pilot program, and it seemed really aligned with what I was doing because my research is very translational — it has the potential to really impact patient care. So the study that I proposed to the CTSI was to evaluate two hypothesized mechanisms that we thought were at play.

First, we knew there was this age based disparity in who receives trauma center care. There are national guidelines that EMS providers follow that outline things like systolic blood pressure, respiratory rate, and how the injury occurred — was it a high speed motor vehicle crash, or did they fall off a roof, for example — that determine where a patient should be transported.

The national guidelines are structured toward the most severely injured patients — the high-risk motor vehicle crashes, falls off a roof, the incidents that you might think about being on the 5:00 news. But in older adults, we know that even a simple fall can result in a pretty high risk of mortality and the need for substantial medical resources. So we’ve hypothesized that those guidelines just don’t work as well at identifying who is high risk.

We also evaluated this phenomenon where EMS providers might perceive older adults differently. There was some preliminary research done on the west coast that Identified potential reasons why older adults are more likely to be undertriaged – our goal was expand upon this previous research.

Very interesting. Can you describe your methods?

We created a quantitative survey that we administered to 600 EMS providers across the region, and we used a factorial survey method. We presented the EMS provider with a clinical scenario with different random patient characteristics. So one provider might get a vignette with a younger adult in a motor vehicle crash who had normal systolic blood pressure. And another EMS provider would have a different patient and scenario. And we’d ask: Would you take this patient to a trauma center? Then we analyzed the statistics and evaluated how they incorporated age into their decision.

The CTSI was great because it provided us the funds to do this complex, novel study in which we evaluated multiple components of decision-making, and it especially helped in recruiting the local providers to participate in the focus groups. We were able to provide food and beverages at each of the focus groups, and we provided incentives for participation, and I don’t think I would’ve had the same success — recruiting 600 EMS providers from a fairly small region — without the incentives and the support of the CTSI.

Any results you’d like to share?

What we found in the preexisting dataset is that the national guidelines don’t work as well among older adults. The sensitivity — or the ability of the national guidelines to correctly identify severely injured older adults — for individuals less than age 55 is about 80 percent, but for people over age 70, it’s only about 52 percent. And there’s a statistically significant linear decrease in sensitivity as age increases.

So that’s quite remarkable when you think about it. It has huge implications, because if the protocol they’re using in the field doesn’t work as well among older adults, then that might explain why we see that older adults are less likely to see trauma center resources.

The focus groups and factorial surveys we did with EMS providers also generated some interesting data. We failed to find a statistically significant difference in trauma center decision making between age groups, but the protocol states that age greater than 55 should be a special consideration. So if they were following the guidelines explicitly, they should’ve been more likely to transport the older patients to the trauma center. But, in fact, we failed to find such a difference.

The surveys also generated some interesting responses, such as the notion that injuries are just expected among older adults — that grandmas just fall out of bed sometimes – and as a result these injuries may not elicit the same response from providers. So that’s interesting because it speaks to what the next steps might be. Do we need to educate EMS providers? Do we need to structure the guidelines differently such that there are separate guidelines for older and younger adults?

How has your research progressed since then?

After completing the CTSI award, my primary mentor, Manish Shah, M.D. and I applied for an NIH R03 which evaluated a similar research question. We also got a CDC U01 grant that aligned perfectly with our previous research— it was an RFA for field triage decision-making for older adults taking anti-coagulants and platelet inhibitors. So in the U01 application we put a whole section of preliminary data that was essentially the findings and methodology I used in the CTSI award.

I also used the data as the basis for my future research which I outlined in NIH loan repayment award application, where they pay a portion of your student debt for you, and that was fantastic.

Overall, the CTSI was great because it was a catalyst — it was enough seed money to really show this was a worthy topic, and we got some really exciting findings which put me on a trajectory to really make this my career. We have presented the findings at numerous conferences and have manuscripts in-press and under-review.

Also, I was a Ph.D. student at the time so it was a really great opportunity for me to be a PI, if you will, before I became a faculty member. Because as a student, that’s an experience that often gets overlooked. You’re focused on your coursework and writing your dissertation, but grants management is never really part of your education. So just learning about the budgeting and the paperwork you have to fill out, that was something very complementary to my education and was a piece I wouldn’t have received otherwise.

eRecord: new search engine tool and Study Monitor changes

Changes to External Study Monitor eRecord Access

Per a new eRecord policy, external study monitor eRecord accounts will be deactivated between visits.  Notification will now need to be provided a few days before the visit so the account can be reactivated. Deactivating study monitor (ePartner) accounts in between visits complies with URMC Information Security access control policies. This information is noted on the NEW study monitor access request form available on the eRecord site under “Research,” then “External Study Monitors.”  Please note that with the new form the Principal Investigator and Program Administrator will need to sign off on the request, consistent with the request process for eRecord access for URMC research staff

To reactivate the external study monitor access, the study team’s internal contact will need to email “eRecord External Reviewer Request” at eRecordExternalReviewerRequest@URMC.Rochester.edu at least 3 days prior to the visit and include: study name (include CTO#), study monitor name(s) and dates access is needed. New request forms must be submitted for new studies and for the addition of new study monitors to existing studies. If you have any questions please contact ResearchHelp@URMC.Rochester.edu.

Find Patient Information Faster with Chart Search

A powerful new search engine lets researchers enter a keyword or keywords to search the patient chart for problems, progress notes, medications, labs, and other orders from one search bar. Users can also find and open Synopsis views, notes, and other available Hyperspace activities through this search—without needing to remember the necessary menu paths.  Click here for more information on what you can search and how it works.

Scholar Spotlight: Vankee Lin

CTSI KL2 scholar Vankee Lin, Ph.D., R.N., assistant professor in the School of Nursing and Department of Psychiatry, shares her research on Alzheimer’s Disease and memory in aging adults.

The KL2 Mentored Career Development program provides 2 years of support for new investigators interested in a career in clinical or translational research. The program is designed to support the career development of those who wish to pursue research careers in multidisciplinary clinical and translational science.

Read more about the KL2 program, and check out a list of our current and past scholars.

Director’s Update — April 2015

Every month, the CTSI Stories Blog will post excerpts from ongoing conversations with the institute’s co-directors.

Below, Karl Kieburtz talks about how the leadership is preparing for the Clinical and Translational Science Award renewals.Karl Kieburtz, M.D., M.P.H.

The new leadership structure has been in place for three months now. How are things going?

One of the great things about the change in leadership structure is it allows each of us to direct ourselves with more emphasis toward specific areas, and one of the things I’ve focused on is trying to understand what’s happening lately at NCATS. Right now, they’re very focused on the development of new methodologies and new technologies to increase the efficiency of clinical and translational research.

In research, there’s a very long window from discoveries in the lab to treatments in humans and actually influencing the health of the population. That’s often measured in decades. Can we get that down to a sub-decade measure by improving the tools we use? That’s NCATS’s big focus, and they’re demonstrating that focus by targeting their funding toward the new methodologies and technologies.

How are they targeting the funding?

The RFA for renewals for the CTSAs is coming out again soon, but they’re also having RFAs for three new structures. One is called a Recruitment Innovation Center (RIC), one is called a Trial Innovation Center (TIC), and the third is a Collaborative Innovation Network.

So the CTSA awards are the base awards, and they’re going to be reduced on the high end for institutions that had very large awards. Fortunately, we’re already among the smaller centers, so that shouldn’t affect us as much. But they’re likely going to use that reduction to pay for these new awards, and the way you grow your base award is by applying for one or more of these new structured grants.

Can you describe what they’re looking for in terms of RICs, TICs, and Collaborative Innovation Networks?

A RIC is responsible for new or more efficient ways to drive recruitment. Here, for example, through the National Center for Deaf Health Research, we’ve done a lot with the deaf community. So we’re thinking about whether that could be used as a model to recruit and engage with underserved communities, or communities with health disparities.

For the TIC, one example that would apply here is the work that Ray Dorsey has been doing with mobile technology. The mPower app, which is the Apple app that was highlighted recently, allows you to record your medications, record memory activities, there’s a voice activity, a measured gait activity. And that kind of tool is exactly the kind of methodology they’re looking for in terms of clinical trials, because it’s much more efficient than having people come into their research visits once a month.

For something like mPower, you can arrive at estimates of benefits faster. A lot of trials go on for a long period of time and are bigger because of there’s a lot variability of the data. But if you can get more data from fewer people, you can run trials faster, and you’re more efficient because there isn’t so much inter-individual variability. You often hear about certain advancements in research costing X billion dollars, but the reason for that cost is you’re actually amortizing all the failures in addition to the success. For every success, you might have 100 failures or 200 failures. But those 200 failures don’t happen early. They happen over the course of a trial or late in a trial. So one of my hopes is that by getting more accurate data early, you can fail earlier. It seems counterintuitive, but if you can cut off a line of study and save costs on something that’s ultimately going to fail, you can learn faster with more reliability. You can stop that trial and then put your energy into other things.

And then the Collaborative Innovation Network is when three or more CTSA hubs act collaboratively to develop something innovative which will improve the efficiency of trials.

mPower is a great example – what other strengths do we already possess here that could apply to the RFA?

Well what you said is important, because we want to be prepared to respond for this without chasing after something we’re not good at, or that we don’t have strong interest in, or that doesn’t tie in with our strategic aims.

But we already have an emphasis in technology and methodology as demonstrated by our clinical trial methodology pillar. We didn’t know they were going to have RICs and TICs, but we have a pre-existing emphasis on that, so that’s a big advantage.

On community engagement, which fits into the RIC side, we are ahead of the game because of the Center for Community Health and our Community Advisory Group and the efforts we’ve put in to community engagement. And structurally, we’re in a great place to look at what’s happening in the community, because we have a relatively simple and contained health care system, with two major providers, and one regional health database. Most communities aren’t that centralized.

We recently joined a large network called NIPTE where producing drugs or interventional agents can be done from basic synthesis all the way out to packaging and delivering. So that’s an additional strength.

Phil Ng and Adam Tatro have developed a tool that uses i2b2 to extract from the EMR and put into a REDcap database. They just presented that recently and it got a lot of attention because most centers don’t have that, so that could be part of an application, because we’re already developing new biomedical informatics tools to help assist in making trials more efficient.

So I think we’re going to be able to tap a few strategic domains, because they resonate well with what we’ve already been doing and what we want to improve on. And there are more that I haven’t mentioned, but that’s what Martin and Nana and I are thinking about right now: Where we are well placed to apply as a center – a RIC or a TIC – or if there’s something we should apply in to be part of an Collaborative Innovation Network.

Previous directors’ updates:

March 2015 – Martin Zand introduces himself and discusses his interest in informatics and population-based research.
February 2015 – Nana Bennett discusses the CTSI’s Seminar Series on population health.
January 2015 – Harriet Kitzman reflects on her time as a CTSI co-director.
December 2014  – Karl Kieburtz offers his takeaways from the CTSI all-hands retreat.
November 2014 – Nana Bennett speaks to the expansion of the role of the CTSI’s Community Advisory Council.
October 2014 – Harriet Kitzman discusses the science of team science.
September 2014 – Karl Kieburtz talks about why the CTSI is beefing up its informatics team.
August 2014 – Nana Bennett discusses the new Population Health pillar.
July 2014 – Harriet Kitzman offers her takeaways from the Mini Summer Research Institute.
June 2014 – Karl Kieburtz gives an overview of the CTSI’s six pillars.

URMC joins NIPTE, strengthens pharmaceutical science and engineering

The University of Rochester Medical Center has gained admission to the National Institute for Pharmaceutical Technology and Education (NIPTE), a collaborative organization dedicated to research and education in the field of pharmaceutical science and engineering.

URMC becomes the 14th member institution of NIPTE.

Cornelia Kamp, M.B.A.

Cornelia Kamp, M.B.A.

URMC’s Clinical Material Services Unit (CMSU), a core research unit of the Center for Human Experimental Therapeutics (CHET), was the key to the university’s admission. CMSU provides investigational drug and device services for many large, multi-center clinical trials conducted at URMC and elsewhere, and acts as the central pharmacy for the National Institutes of Health’s NeuroNEXT network. CMSU also works closely with the CTSI and CHET on drug development research.

“This membership in NIPTE expands the resources available to CMSU, and to researchers at the University of Rochester,” said Cornelia Kamp, M.B.A., executive director for strategic initiatives at CMSU. “A researcher can ask us a question, and if we don’t have an immediate answer, we can work on finding a solution through NIPTE.”

There is minimal overlap of expertise within the NIPTE member organizations, as each university brings something different to the table, said Kamp. Through CMSU, URMC is able to bring expertise in back-end pharmaceutical distribution — such as packaging, labeling, kitting, and drug destruction — to NIPTE. In turn, CMSU leaders hope to gain experience from other member collaborators, which could lead to gains for Rochester researchers.

Karl Kieburtz, M.D., M.P.H.

Karl Kieburtz, M.D., M.P.H.

“Through NIPTE, we have a better chance of making or procuring certain drugs that researchers might be interested in studying,” said Kamp.

The membership could also strengthen a future application that involves the Clinical and Translational Science Award program, said Karl Kieburtz, M.D., M.P.H., co-director of the CTSI, who will serve on the NIPTE Board of Directors.

“The National Center for Advancing Translational Science is developing this vision of improving the efficiency of clinical research and focusing on clinical trials,” said Kieburtz. “So we’re looking at what strengths we have that would apply towards these various centers, and CMSU’s affiliation with NIPTE is definitely one of them.”