Buffalo Translational Consortium News

Davies receives KL2 Mentored Career Development Award

Posted on 09/20/17 at 01:59 pm

The UB Clinical and Translational Science Institute (CTSI) announced the appointment of Jason Davies, MD, PhD, assistant professor in the departments of Neurosurgery and Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, to the CTSA-Linked KL2 Mentored Career Development Award (MCDA) program in August.

The KL2 award provides research mentoring and career and professional development to junior faculty in health science disciplines engaged in clinical and translational research. Davies was one of three CTSI-funded scholars eligible for the KL2 Scholar position invited to apply. 

"Having CTSI-funded scholars mentored with the KL2 cohort brings together a diverse community of scholars engaged in successful interdisciplinary research, teaching, mentoring and career development in clinical and translational research, while at the same time maintaining a critical cohort of scholars in our community,” said Margarita L.  Dubocovich, PhD, SUNY Distinguish Professor in the Department of Pharmacology and Toxicology, senior associate dean for diversity and inclusion, and director of the CTSI's Workforce Development core and program lead for the KL2 Mentored Career Development Award.

The grant will support Davies’ research into finding better ways to predict who is most likely to have a stroke, and who is most likely to recover. His project has led to new predictive models that combine genetics and rich demographic, clinical and social data from electronic health records to develop personalized risk predictions. Davies received his MD and PhD at Stanford University and was a resident in the University of California San Francisco Department of Neurological Surgery program. He joined University at Buffalo Neurosurgery as a fellow in 2015 and was named assistant professor in neurosurgery a year later.

The UB Clinical and Translational Science Institute (CTSI) announced the appointment of Jason Davies, MD, PhD, assistant professor in the departments of Neurosurgery and Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, to the CTSA-Linked KL2 Mentored Career Development Award (MCDA) program in August.
The KL2 award enhances research, and  career and professional development of junior faculty in health science disciplines engaged in clinical and translational research. Davies was one of three CTSI  funded Scholars eligible for the KL2 Scholar position  who were invited to apply. 
"Having CTSI-funded scholars mentored with the KL2 cohort brings together a diverse community of scholars engaged in successful interdisciplinary research, teaching, mentoring and career development in clinical and translational research, while at the same time maintaining a critical cohort of scholars in our community,” said Margarita L.  Dubocovich, PhD, SUNY Distinguish Professor in the Department of Pharmacology and Toxicology, senior associate dean for diversity and inclusion, and director of the CTSI's Workforce Development core and program lead for the KL2 Mentored Career Development Award.
The grant will support Davies’ research into finding better ways to predict who is most likely to have a stroke, and who is most likely to recover. His project has led to new predictive models that combine genetics and rich demographic, clinical and social data from electronic health records to develop personalized risk predictions.
Davies received his MD and PhD at Stanford University and was a resident in the University of California San Francisco Department of Neurological Surgery program. He joined University at Buffalo Neurosurgery as a fellow in 2015 and was named assistant professor in neurosurgery a year lat

Clinical Research Office relaunches 'Research Roundtable' newsletter

Posted on 09/19/17 at 01:17 pm

UB's Clinical Research Office started this academic year off with the rededication of the Research Roundtable newsletter. Kim Brunton, RN, MSN, associate director of the CRO, said it's a way of keeping PIs and research coordinators in the loop. 

“There have been many changes to structure, policy and personnel since the last newsletter went out in February of 2014,” said Brunton. “By resurrecting the newsletter, we aim to communicate those changes as well as upcoming events and newsworthy items.”

The newsletter will feature items from the Institutional Review Board, contracts office, OnCore and UB’s CTSI, as well as news from the Clinical Research Office, to keep readers up to date with changing policies and procedures. 

Email Kim Brunton (.(JavaScript must be enabled to view this email address)) or Pam Anderson (.(JavaScript must be enabled to view this email address)) to be added to the mailing list.

Click here to read the August issue.

Working group seeks to extend the depth and functionality of biomedical ontologies

Posted on 09/14/17 at 12:45 pm
Illustration by Darryl Leja, NHGRI
Alexander D. Diehl, PhD

Buffalo has had an “outsized” influence in the field of biomedical ontology over the past 15 years or so, thanks in large part to the work of UB’s Barry Smith, PhD, Julian Park Distinguished Professor of Philosophy; adjunct professor of Biomedical Informatics, Computer Science and Neurology; and director of the National Center for Ontological Research.

That’s according to Alexander Diehl, PhD, associate professor in the Department of Biomedical Informatics in the Jacobs School of Medicine and Biomedical Sciences, who, along with Smith, will be among those representing UB at the 6th Annual Workshop of the Clinical and Translational Science Ontology Group at the University of Michigan on October 25 and 26. According to Diehl, Smith has been “an incredible contributor to and a leader in the field.”

Smith inaugurated the now-annual International Conference of Biomedical Ontology in Buffalo in 2009. The stated goal of the conference is “to explore new and existing uses of common ontologies to support creation, sharing and analysis of clinical data.”

Ontology, says Diehl, “was originally a philosophical discipline having to do with the enumeration or naming of things that exist in the world.” Applied ontology means using real-world categories to organize and analyze empirical data, and, through AI, to discover patterns and connections in those data that could potentially lead to practical medical advances and new therapeutics.

“What we’re really doing is trying to name entities that exist in the real world — things like objects, people or cells, but also things like processes, like walking or metabolism is a process — and we want to describe these things both in terms of what actually exists but also how they are related to each other,” he said.

In anatomy, for instance, “we talk about different parts of the brain, which parts are adjacent to other parts, how connected they are to each other,” Diel said. The main body of a neuron may lie in one layer of the brain, but its dendrites and axons may extend to other portions. Beyond a mere listing of parts, “we want to be able to describe that cell, exactly how it’s connected in the brain,” and one way to capture those connections is through applied ontology.

“The advantage of encoding all these logical connections between different entities is that then computers can use these logical statements to do inference. Say, for instance, that you have experimental evidence that a particular gene is expressed in a class of cells, a class of neurons, and then you know the parts of the brain that these neurons are found in. That gives you information about where the gene might be expressed within the brain as a whole.”

Most medical disciplines already have standards committees which sanction definitions of terms. Naming, however, is not the ultimate goal of the ontologies. “We want to use standardized names, but what we really want is interoperability between ontologies,” said Diehl.

In his own experience as an experimental immunologist in UB’s Department of Neurology, Diehl worked on ontology projects related to neurology and infectious disease, and continued his long-term work on the Cell and Gene ontologies. Currently, he is working with colleagues at Roswell Park Cancer Institute and other institutions to build out cancer ontologies for analyzing cancer data. Specifically, he plans to form a working group to develop a cancer microbiome ontology.

“All the ontologies we make are intended to be part of a larger project called the Obo (Open Biomedical Ontologies) Foundry,” Diehl said, a project that Barry Smith was instrumental in launching.

“The Obo Foundry organization specifies certain principles we follow for ontology development,” said Diehl. “The goal is to make sure these ontologies are interoperable, meaning that, for instance, when we talk about a particular type of T cell in the Gene Ontology there’s an understanding that they accept the way it’s been defined in the Cell Ontology, because the Cell Ontology is the main ontology for that domain.”

The work is inherently cross-disciplinary and collaborative, in addition to being data-driven. “The Gene Ontology Consortium is based in multiple institutions both in the U.S. and the U.K.,” Diehl says.

Diehl’s hope is that using ontologies will “enhance cancer treatment through better data analysis, both in the sense of speeding up the way we analyze how particular lymphomas and leukemias are progressing but also by improving the analysis of even older data, after it’s been collected, by looking for new patterns which the ontologies help to spot.”

Diehl’s decision to assemble a working group in cancer microbiome ontology was informed by recent trends in the field. There has been growing interest in the microbiome due to its ability to modulate the immune system and, more directly, due its role in the development of stomach cancer.

“We’re trying to model reality,” he said, “but our understanding of reality through scientific methods changes over time as we get new data.”

School of Dental Medicine teams up with CTSI to bring national researcher to Buffalo

Posted on 09/07/17 at 08:35 am
NIDCR director Martha Somerman (left) at the annual NIH Research Festival

The CTSI Seminar Series resumes on October 5 with a presentation co-sponsored by the School of Dental Medicine. Martha J. Somerman, DDS, PhD, director of the NIH National Institute of Dental and Craniofacial Research (NIDCR) will be in town to speak on her selected topic: “Guiding the Future of Oral Health Research, Together.”

The seminar is scheduled for Thursday, October 5 at 4:45 p.m. in Butler Auditorium, Farber Hall, UB South Campus. A reception will follow in Squire Hall.

Somerman’s presentation will celebrate accomplishments at UB’s School of Dental Medicine as part of the school’s 125th anniversary celebration. She plans to recognize key leaders involved in the establishment of the dental school and UB’s pioneering graduate program in oral biology.

UB’s School of Dental Medicine was established in 1892. In 1960 it launched the nation’s first Department of Oral Biology. Three years later, UB created the first PhD program in oral biology in a dental school.

Somerman will also provide an introduction to NIH and NIDCR, and an overview of NIDCR-supported research, which spans the spectrum of basic, translational, behavioral and clinical research in dental, oral and craniofacial medicine.

Through the Seminar Series, UB’s CTSI is partnering with the five health sciences schools and Roswell Park Cancer Institute to sponsor a round of visiting scholars in the forefront of their respective disciplines. 

Follow this link to read about the previous presenters in the series.

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