Assessing scientific productivity: A new metric

Publication data – journal impact factors, number of first author publications, prestige of the journal – are commonly used to assess research productivity. But the metrics used to generate these data have substantial limitations. H-index, which looks at the cumulative impact of scientists’ work, disadvantages junior researchers; citation habits and dynamics can be vastly different in different research fields. Alternative methods for quantifying scientific accomplishment are under development, and though many of them have improved our understanding of citation dynamics, none have been widely adopted.

Open Mike blog, Sept. 8, 2016

Open Mike blog, Sept. 8, 2016

A group of NIH researchers is now entering this field. They developed a metric, the Relative Citation Ratio, that normalizes across different fields, institution types, and geographic regions, allowing apples-to-apples comparisons of a paper’s impact. “The goal of the Relative Citation Ratio is to quantify the impact and influence of a research article both in the context of its research field and benchmarked against publications resulting from NIH R01 awards,” according to Michael Lauer, NIH deputy director for extramural research, in his Sept. 8 Open Mike post.

The NIH researchers introduced the algorithm they developed to calculate the RCR in a recent article published in PLOS Biology. To illustrate the algorithm, an “article of interest” is cited by a number of articles. These citations can be counted over time to yield an “actual citation rate.” These citing articles also cite other articles which the authors call the “co-citation network.” This network of papers can be assumed to reflect the citation dynamics of a particular research field (or fields) of the article of interest. From these data, a “field citation rate” can be calculated that can be compared to the actual citation rate, yielding the RCR.

The authors also demonstrate using the RCR to quantify how past influence predicts future performance, but how accurate is this metric in establishing scientific quality? Three separate studies were used to compare expert peer review ratings of papers and the RCR. In all three cases, there was a strong association.

Figure 9 – RCRs correspond with expert reviewer scores. From Hutchins, et. al, (2016) Relative Citation Ratio (RCR): A New Metric That Uses Citation Rates to Measure Influence at the Article Level. PLoS Biol 14(9): e1002541. doi:10.1371/journal.pbio.1002541

RCRs correspond with expert reviewer scores. From Hutchins, et. al, (2016) Relative Citation Ratio (RCR): A New Metric That Uses Citation Rates to Measure Influence at the Article Level. PLoS Biol 14(9): e1002541. doi:10.1371/journal.pbio.1002541

The RCR measure is available here.

New research shows search and destroy function for leukemia cells

kurre-_pape-brochure-pic-2014The rapid growth of leukemia cells that “crowd out” healthy stem cells within the bone marrow has traditionally been considered the root cause for prolonged risk of infections and necessary blood transfusions. A study recently completed by a team of OHSU pediatric cancer biology researchers in the Pape Family Pediatric Research Institute – and published in the journal Science Signaling –  disputes this theory and provides the first description of leukemia cells’ ability to actively target and destroy healthy cells in bone marrow throughout the body. The identification of this process creates an opportunity for the development of new, targeted therapies to protect cells and potentially limit prolonged hospital and clinic admissions for leukemia patients.

Led by principal investigator Peter Kurre, M.D., the team discovered this process by identifying small vesicles, or exosomes, released from acute myeloid leukemia cells and their systematic study in mouse models. The leukemia vesicles circulate in the bloodstream and serve as messengers of small regulatory molecules, or microRNA. The research team showed that these vesicles act by degrading the machinery central to the function of healthy bone marrow stem cells and are unaffected by traditional cancer therapies.

Along with other studies in the field, this discovery suggests the effect of cancer may not be locally limited, but instead has the capacity to compromise healthy tissue function even before the spread of cancer cells.

 The paper, “AML suppresses hematopoiesis by releasing exosomes that contain microRNAs targeting c-MYB,” was supported in part by a grant from Hyundai Hope on Wheels. The research team included Kurre and members of his lab–Noah I. Hornick (co-first author), Ben Doron (co-first author), Sherif Abdelhamed, Kianya Huan, and Santhosh Chakkaramakkil Verghese–as well as OHSU faculty members  Christina A. Harrington and  Xiaolu A. Cambronne; and Rongkun Shen, from the College at Brockport, State University of New York.

NIH wants to hear from you

nhlbi-logo-septHelp shape the agenda of a planned future conference on coronary heart disease

In 1978, the Bethesda Conference on the Declining Mortality from Coronary Heart Disease brought together international experts from a wide range of disciplines and expertise to call attention to and illuminate the previously unappreciated and unexplained abatement of the epidemic of heart disease. Since then cardiovascular death rates have continued to decline sharply, and despite the huge growth in knowledge and advances in treatment, there remain many unresolved issues about this decline. The National Heart, Lung, and Blood Institute proposes to call another meeting to answer the big questions about the drivers of past changes and the likely trajectories in the future. To help plan this conference, the NHLBI is asking for comments and suggestions related to current and projected trends in cardiovascular disease within and between populations, modelling strategies to monitor disease burden and to examine various factors influencing disease prevalence such as socioeconomics.
Submit your comments by Dec. 31, 2016 here

niehs-logoContribute to the development of a translational research framework

The Division of Extramural Research and Training at the National Institute of Environmental Health Sciences drafted a translational research framework for environmental health sciences and is seeking input on the draft. The aim is to provide a framework that 1) represents the full spectrum of the research NIEHS grantees conduct, 2) captures all the nuances of environmental health research, especially at the more “basic” end of the research spectrum, 3) provides a common language for describing translational research in the environmental health sciences, and 4) promotes the telling of translational research stories in progress reports and other research documents. NIEHS is seeking comments on the applicability of the proposed translational research framework map to your translational research; benefits and challenges of the proposed framework, elements that are missing, other suggestions.
Submit your responses by Oct. 30, 2016 here.

NIH director to give annual Mark O. Hatfield Lecture, Oct. 24

The Director of the National Institutes of Health, Francis S. Collins, M.D., Ph.D, will be giving this year’s Mark O. Hatfield Lecture. The talk will examine recent advances in fundamental knowledge about biology—and highlight the ways in which that knowledge is serving to improve human health. Topics may include research developments at the NIH at the Mark O. Hatfield Clinical Research Center, the Precision Medicine Initiative, the Cancer Moonshot, and updates on Zika and other global health issues.

Mark O. Hatfield Lecture

Monday, Oct. 24, 2016
7 to 8 p.m.
Collaborative Life Sciences Building
1st floor lecture hall, 1A001

Add to your calendar

Collins is a physician and geneticist known for spearheading the Human Genome Project and for his landmark discoveries of disease genes. He has also written a number of books on science, medicine, and religion.

The Mark O. Hatfield Lecture is a special presentation of the Marquam Hill Lecture Series, which features a variety of experts providing free lectures on topics that greatly impact the health of Oregonians.


Grand opening of Center for Radiochemistry Research, Sept. 20

The OHSU Knight Cardiovascular Institute cordially invites you to attend the ribbon cutting of the Center for Radiochemistry Research, the newest research building on Marquam Hill since the Biomedical Research Building opened in 2005. The center will provide OHSU scientists with a new suite of powerful imaging tools and expertise, including new labs, a cyclotron for isotope generation, and advanced imaging technology for preclinical and clinical research. The the facility and its resources will give OHSU the new capacity to develop radioactive isotopes to address specific research questions using real-time imaging.

Tuesday, Sept. 20, 2016
12:30 to 1:30 p.m.
Research Courtyard
Marquam Hill

Featured speakers include:

Joe Robertson, M.D., OHSU president
Sanjiv Kaul, M.D., chief executive officer, OHSU Knight Cardiovascular Institute
Jeanne Link, Ph.D., director, Center for Radiochemistry Research

Tours of the facility will be provided immediately following the program. Refreshments will be served.

Webinar on The National Microbiome Initiative, Sept. 16

nmiIn May of this year the White House announced a collaboration with various Federal agencies and private-sector stakeholders to foster the study of microbiomes, communities of microorganisms, across different systems. The National Microbiome Initiative supports interdisciplinary research, development of platform technologies, and expansion of the microbiome workforce with the aim of protecting and restoring healthy microbiome function.


Stefano Bertuzzi

Microbiomes live on or in people, plants, soil, oceans, and the atmosphere, but how do they impact human health? Join Research!America for a webinar led by Stefano Bertruzzi, Ph.D., M.P.H., executive director and CEO of the American Society for Microbiology, who will provide an overview of the NMI, and insight about the implications and opportunities that will arise from this massive undertaking.

“The Microbiome Initiative: A closer look”

Friday, Sept. 16, 2016
10:00 – 10:30 a.m. PDT

Register today.


NRSA application workshop: Technical components, Oct. 11

If you’re planning to apply for a pre- or post-doctoral NRSA fellowship from the NIH in the near future, we encourage you to attend this workshop to learn about essential, non-research elements of your fellowship application. Topics covered include elements needed for an InfoEd proposal, how to develop a budget, how to manage reference letters, biosketches and PMCID numbers, and elements of a great training plan.

This upcoming workshop is led by Johanna Colgrove, coordinator of the MD/PhD program, Gavin Hamilton, grants and contracts administrator with the Office of Proposal and Award Management, and Rachel Dresbeck, Ph.D., director of Research Development and Academic Communications.

NRSA Application Workshop
Tuesday, Oct. 11
11 a.m. to 1 p.m.

Mackenzie Hall 2136

Open to researchers and administrators. Registration now available on Compass.

TTBD expands entrepreneur-in-residence program

After a one-year launch, Technology Transfer and Business Development is expanding its entrepreneur-in-residence program. The program has recruited two additional entrepreneurs-in-residence to provide support to inventor teams and new companies that form when they license technology intellectual property from OHSU. The current entrepreneurs-in-residence, Richard Rylander and Robert Masterson, have helped inventors by saving them time and resources, performing faculty education and outreach, providing grant support, and executing management oversight and commercialization guidance. The new entrepreneurs-in-residence will join the program to continue identifying technologies with commercial promise and provide OHSU researchers with real-world insights about the commercialization process. The new entrepreneurs-in-residence begin their residency at OHSU on Sept. 14.


Rob Arnold, new OHSU entrepreneur-in-residence

Rob Arnold is a healthcare innovation advisor at the University of Washington and partner at Quad+Aim Partners, advising emerging-growth companies on business strategy, planning, and investment. Prior to UW, Arnold was CEO of Geospiza, Inc., a leader in cloud computing solutions for genetic analysis, which was sold to Perkin Elmer in May of 2011. Before that, he was CEO of Crossport Systems, a leader in internet security solutions, which was sold to Lineo/Metrowerks, a division of Motorola. Arnold also co-founded and was CEO of ST Labs, Inc., an international leader in software quality assurance and testing, which was sold to Lionbridge.



Steve Runnels, new OHSU entrepreneur-in-residence

Steve Runnels has more than twenty-eight years of management experience in the healthcare industry. He has held the position of president and CEO of several startup biopharmaceutical companies in the US and Internationally. He was executive vice president and board member of publicly traded NeoTherapeutics, Inc. and vice president of marketing and business development at Sigma-Aldrich, a Fortune 500 company. Mr. Runnels is also an entrepreneur-in-residence at the University of Washington. Mr. Runnels holds a B.S. in cell biology and certification from the American Society of Clinical Pathology as a specialist in immunohematology. He is an M.B.A. and Ph.D. candidate in management.

To see a video of TTBD’s Lunch & Learn presentation on “How to start a company,” presented by entrepreneurs-in-residence, please click here.

For more information on the entrepreneur-in-residence program or to inquire about startup companies at OHSU, please contact Daphne Emerson at

Available now: New express rights option program for OHSU startups

948171048_ab19e27ef4_zBeginning Sept. 1, any newly formed OHSU startup company has the opportunity to obtain time-limited rights to OHSU technology through a new express option agreement program.  New startup companies with founders who are OHSU employees or students now have access to a low-cost, pre-approved agreement that can be completed quickly to secure rights in OHSU technology. This allows the new startup to focus on evaluating the technology further, conducting market research, developing a business plan, and raising funding prior to entering into a more extensive, longer-term license agreement. In general, any technology that has been disclosed to Technology Transfer and Business Development may be eligible for this program.

Benefits of the program include the following:

  • Simple, rapid access to rights to OHSU technology for new startups
  • No time and effort spent on negotiation
  • Quick agreement execution
  • Low upfront costs
  • Six-month agreement term, with the potential for term extension

The goal of the program is to encourage, foster and support the entrepreneurial culture at OHSU. For more information, please refer to the Exclusive Option Agreement for OHSU startups FAQs document or contact Andrew Watson at

Who’s new at OHSU? Fikadu G. Tafesse, Ph.D.

Fikadu G. Tafesse, Ph.D. is an assistant professor of molecular microbiology and immunology who is working to understand how pathogens utilize host cellular processes during infection. He arrived at OHSU from Boston in February, 2016.

Where are you from originally?
I was born and raised in Ethiopia and got my undergraduate degree in agriculture there, learning how to grow crops – basic farming. After graduation, I decided to go to Europe to gain more experience and ended up going to Germany for a master’s degree in horticulture. This was my first introduction to plant biotechnology and for my master’s thesis I worked on a gene family of phospholipases that modify membranes in plants.fikadu

I always wanted to go back home to Ethiopia; I never thought of staying in Europe or moving to the U.S. But during the second year of my master’s program, a friend who was getting his Ph.D. in epigenetics asked me to take pictures during his thesis defense.  Up to that point, I knew very little about his field but when I heard him talk about DNA methylation and the role it plays in cancer development, I was hooked.  In fact, I completely forgot to take pictures because I was so interested in the science! This made me want to go further with my studies before I went back home. I applied to Ph.D. programs and eventually ended up at Utrecht University in the Netherlands. There, I studied under Joost Holthuis and Gerrit van Meer, two lipid biologists. When I joined the lab, I had no idea they were world-renowned because I hadn’t been in the field. I was very fortunate to learn about lipid chemistry and biochemistry from them. I went on to do my postdoc at the Whitehead Institute at MIT and then went to the Ragon Institute at Harvard for more than a year before coming to OHSU.

Tell us about your research and what drew you to it?
Growing up in Ethiopia, I saw many people die of infectious diseases, and as a result I was naturally curious about the biology of these diseases, particularly HIV, tuberculosis, and malaria – the three main killers in developing countries. So, I decided to do my postdoc in a lab where they worked on host-pathogen interactions. That’s why I went to the lab of Hidde Ploegh at the Whitehead Institute of MIT, to work in a lab with immunologists, microbiologists, chemists, and biochemists. There, I learned about viruses, bacteria, and fungi, and my main focus was on how pathogens use the host’s lipids during infection. I then went to the Ragon Institute at Harvard to work closely with the lab of Sarah Fortune and learn about Mycobacterium tuberculosis. Little is known about the role of lipids in bacterial and viral pathogenesis, so I decided to bring what I’d learned in my postdoctoral research to this new line of work.

Human cells are surrounded by membranes, and those membranes contain lipids. Pathogens must cross membranes to infect cells, so what I’m trying to understand is how a virus such as HIV uses the host machinery, especially that of lipids, during infection. A virus doesn’t have machinery of its own, and it uses the host cellular processes for entry and replication without being detected by the immune system. If we can understand the mechanics of this, then we can design a strategy to block it. This is fundamental to combating these diseases.

What are you working on now?
The research focus in my lab is on M. tuberculosis as well as HIV and viruses from the family Flaviviridae, which includes zika, dengue, and yellow fever. M. tuberculosis is a bacteria that causes tuberculosis. If you look at deaths due to infectious disease globally, tuberculosis is one of the most devastating diseases, especially in developing countries. So I wanted to dedicate my career, in a way, to understanding tuberculosis and HIV-tuberculosis co-infections.

The main reason we don’t know much about lipids and their role in infection is because they are difficult to work with. They are not template coded – there is no DNA that really codes for lipids. They are a bi-product of a series of cellular processes such as metabolism. In research terms, you can’t overexpress it or put a tag on it, so you need a special set of skills to work with and study these metabolites. Most of the techniques we use today to study lipid biochemistry were developed in the 1970s and are very outdated. Since I have strong training in this area, I’m comfortable working on lipids and using various techniques, and I am testing out my initial hypothesis – that lipids are required for bacteria to infect host cells. Our preliminary data strongly suggest they do.

When studying the mechanics of infection by various viruses and bacteria, I ask the question, “Is there similarity between the different pathogens in terms of the way they use these lipids?” This is a very important question, because if there is a commonality, you can develop a strategy that impacts multiple diseases.  Finding the answer to that question is my goal.

In addition to my main research program, I’m also developing tools to study M. tuberculosis. The tool I’m developing uses nanobodies, single-domain antibodies that occur only in camelids and sharks. These unique antibodies are extremely small, so they penetrate tissue very well. In terms of their binding, they are as good as conventional antibodies, but they don’t require any post-translational modifications. They’re stable across a wide range of temperatures and in various pH environments. These characteristics make them very easy to work with. My technology development involves generating nanobodies that can be used not only to study the intricate interaction of the bacteria with the host but that also has the potential for diagnostic and therapeutic value. We do this by immunizing Alpaca with antigens such as M. tuberculosis virulence factors, thereby generating nanobodies that target those factors. We then evaluate whether they prevent infection in macrophages. If they have neutralizing capacity, you have a very good candidate to take to the next level of investigation. At this point we have several candidates.

I currently collaborate with folks on the east coast to do the injections, but eventually I want to have an Alpaca farm that I work with here in Oregon. This is one of the programs I really want to pursue because it has very high potential. If you can block that virulence factor, you have a cure. I just want to make a difference. I hope that what I’m doing can have an impact not only in my home country but other developing countries as well. So, I plan to establish collaborations in Ethiopia and other African countries where these diseases are epidemic. It’s important to connect the work to the place where the real problem is – that’s my long term goal.

I was aware of OHSU’s achievements before I came here, particularly in the area of infectious disease such as HIV vaccine development. And with the Oregon National Primate Research Center here, OHSU is a focal point for research into infectious disease in humans. It’s an ideal place to be. On a personal level, as soon as I got here, I really liked the city, the people, this whole region. I knew I could definitely live here, and hey, I’m from Ethiopia – those Boston winters were just too cold for me.

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