In this edition of Research Connections, find links to researchers in the news, updates on important deadlines, and more news for University of Rochester researchers. Email not displaying correctly?
View it in your browser.
scancollage In the image at left, the area measured by each 3D scan of a train station is shown in a different color. At right, a composite 3D model of a station after all the scans are "stitched" together with a software program.

A multidisciplinary approach to a computational challenge

The routine was the same each day. Up at 6 a.m., to bed at 11 p.m. In between, Peter Christensen, Assistant Professor of Art History, and graduate students Eitan Freedenberg and Alana Wolf-Johnson drove east from Edmonton, Alberta, Canada, finding the old train stations they had located ahead of time in the historical records — and even a few they hadn't expected.

At each station, they mounted a rented 3D scanner worth about $60,000 on a specially designed tripod, and aimed it at every surface, at every "side" of the building in succession. 12 minutes per scan. Eight to 12 scans a building. Two to three hours per building.

Eleven stations in all.

The result: a database of literally billions of points where the scanner's lasers encountered a train station's walls, windows and other features, and adjacent trees, parked cars and even a historic caboose or two.

The scans from each station are being "stitched" together to create an incredibly accurate, detailed 3D model that can be rotated in any direction on a computer screen — or the University's VISTA Collaboratory.

But then comes the challenge: Coming up with a computational model that can compare the architectural details of one station to another, to show how ostensibly similar, standardized designs were subtly altered during actual construction in ways that reflect the ethnicity and local traditions of the workers who actually built them between 1870 and 1920.

The solution will entail collaboration of a truly multidisciplinary nature.

Christensen originally envisioned adapting already available facial recognition software, until he encountered proprietary issues. In addition, after consulting with Prof. Gaurav Sharma, Professor of Electrical and Computer Engineering, Christensen realized that even if the proprietary issues could be overcome, existing facial recognition software "was not going to give us the kind of mileage we need."

So the plan is for one of Sharma's PhD students and staff in the digital humanities library to help develop a code that can flag all of the subtle but significant differences in the way two supposedly identical train stations were actually built. The challenge, Christensen adds, will be writing a code that is "smart enough to know which threshold is important, and which isn't. A millimeter difference in the size of two bricks probably is not important, but if there's a 3 mm difference in the way the corners of the bricks are cut, that is probably significant."

"This does not mean we're outsourcing art history to the computer. We're not ceding interpretive power to computers, but we are ceding a certain amount of analytical power to the computers, and then we apply a final layer of interpretation."

Freedenberg said the project illustrates how "art history and science and technology are inextricable. If you study art history, there is at some basic level a technological element. If you study Andy Warhol, you study the history of machinery. If you study architecture, you're studying structural engineering, and if you study photography, chemical processes.

"One of the ways this project can be innovative and instructive is by illuminating ways for art historians to think literally about the uses of technology to do art history."

Do you have an interesting photo or other image that helps illustrate your research? We would like to showcase it. Send a high resolution jpg or other version, along with a description of what it shows, to

Immune cells work together to fight infection

A virus or bacteria can take hold in any number of locations: the lungs, the throat, the skin, the stomach or the ear, just to name a few. How do immune cells, specifically the ones that are responsible for killing foreign invaders, know where to go?

A team of Univerity scientists has discovered that cells called neutrophils — the "first responders" of the immune system — arrive at the site of injury within an hour of infection and leave a chemical "trail" of sorts behind them. Killer immune cells called T cells use this trail to find the site of injury and subsequently destroy the invader.

"Immune cells team up and share information to get their job done, much like many types of animals take part in collective behaviors to benefit the group as a whole," said Minsoo Kim, lead author and Associate Professor of Microbiology and Immunology at the David H. Smith Center for Vaccine Biology and Immunology.

"Understanding how immune cells collaborate to arrive at the site of an infection will lead to new ways to control and improve the body's response to all types of illnesses," added David J. Topham, co-author and the Marie Curran Wilson and Joseph Chamberlain Wilson Professor of Microbiology and Immunology.

For example, in people with autoimmune disorders like multiple sclerosis and lupus, the immune system mistakenly attacks and destroys healthy body tissue. If scientists understood how to disrupt or stop immune cells' movement to healthy tissue, they may be able to improve the quality of life of people living with these devastating diseases.

Similarly, recognizing how to boost the number of immune cells that travel to fight an infection could help scientists design better vaccines for viruses like the flu.

The research is part of a $9 million National Institutes of Health Research Program Project Grant that was awarded to scientists in the School of Medicine and Dentistry in 2014. Led by principal investigator Deborah J. Fowell, Dean's Professor of Microbiology and Immunology, the goal of the five-year grant is to use cutting-edge imaging techniques to view the immune system while it is fighting infection and disease.

Kim's team used an extremely powerful technology called a multiphoton microscope to watch how various types of immune cells traveled to the trachea or windpipe of mice infected with the flu. The flu typically starts in the airways, and watching immune cells move in whole tissues in real time — as opposed to watching immune cells in a lab dish — provides a much more accurate picture of how the immune system functions.

Click here to learn more about the study, and here to learn more about the University's Multiphoton Core Facility.

Breast Cancer Coalition seeks applications for grants

The Breast Cancer Coalition of Rochester is seeking applications and proposals for its 2015-2016 Breast Cancer Research Grant Initiative. To be eligible, applicants must work in the Greater Finger Lakes Region of Western New York, including Buffalo, Ithaca, Rochester and Syracuse. The Coalition plans to fund a minimum of one $50,000 research grant. To apply, please submit all documents as required in the 2015-2016 Request For Proposals by December 31, 2015 at 5 p.m. Read more here.

Eduroam offers secure Internet connection to other institutions

University faculty, staff, and students can now connect securely to the Internet at more than 300 academic institutions using Eduroam. To access Eduroam when visiting a participating institution, login with your and your NetID password. Visiting faculty and researchers can access Eduroam at Rochester using credentials from their home institution. Read more . . .

Learn how to write a successful Data Management Plan

Need to write a data management plan for a grant? Learn the basics from noon to 1 p.m. Wednesday, Sept. 16 at 310 Carlson Library. Find out what to include, where to get help and how to write a plan that adds value to your proposal. RSVP to

Introducing a new faculty member

Catherine Kuo recently joined the Department of Biomedical Engineering and the Center for Musculoskeletal Research as an associate professor. Her research explores musculoskeletal tissue mechanobiology and developmental biology in order to inform tissue engineering and regenerative medicine approaches. A specific focus of her work is to characterize the mechanical and biochemical microenvironments of embryonic, healing, diseased, and aging tissues to provide design criteria for biomaterials and bioreactor cultures that guide stem cell differentiation and neo-tissue formation. Prior to this, Kuo was at Tufts University, where she was an assistant professor in the Department of Biomedical Engineering and in the Program of Cell, Molecular, and Developmental Biology within its Sackler School of Graduate Biomedical Sciences. She was also a visiting scientist in the Department of Chemical Engineering at Massachusetts Institute of Technology. Kuo received her BSE in materials science and engineering and PhD in biomaterials and macromolecular science and engineering from the University of Michigan. She conducted her postdoctoral training at the National Institutes of Health (NIH), specifically within the Branch of Cartilage Biology and Orthopaedics of the National Institute of Arthritis and Musculoskeletal and Skin Diseases.

UR research in the news

When asked to choose between treatments that reduced pain or would help them stand or walk, patients with a common form of lower back pain called lumbar spinal stenosis overwhelmingly chose pain relief, according to a University study. "There has long been a debate in the medical community over striking the right balance between pain relief and physical function," said lead author John Markman, Professor of Neurosurgery and Director of the Translational Pain Research Program. "While physicians have leaned toward the need to increase mobility, this study shows that patients have a clear preference for pain relief." Read more . . .

A study by graduate students Christopher Thorstenson and Adam Pazda and Prof. Andrew Elliot of the Department of Clinical and Social Sciences in Psychology is the first to show that sadness, a commonly experienced emotion, has a direct negative influence on higher-order color perception. During the study undergraduates watched videos that aroused feelings of either sadness or amusement, then took color perception tests. The results showed that sadness impairs color perception on the blue-yellow axis. This effect provides a clue that dopamine depletion may underlie the observed impairment, because research has linked retinal dopaminergic deficiencies to impeded efficiency on the blue-yellow axis. The researchers note that their study and other data support the conventional wisdom that people's emotions influence how colorful the world looks to them. Moreover, color is a factor in many standard tasks used to assess neuropsychological functioning (e.g., the Stroop test, the Wisconsin Card-Sorting Task) in clinical settings. The findings suggest that a patient's performance on such tasks is influenced by state emotion as well as enduring neuropsychological characteristics. Click here to read the study, which has been reported on by Huffington Post, Fox News, Medical Daily, and Science World Report, among others.

A pair of studies suggests that a region of the brain called the insular cortex may hold the key to treating addiction. Scientists found that smokers who suffered a stroke in the insular cortex were far more likely to quit smoking and experience fewer and less severe withdrawal symptoms than those with strokes in other parts of the brain. "These findings indicate that the insular cortex may play a central role in addiction," said lead author Amir Abdolahi, a clinical research scientist at Philips Research North America who conducted the research while an epidemiology doctoral student in Department of Public Health Sciences here. "When this part of the brain is damaged during stroke, smokers are about twice as likely to stop smoking and their craving and withdrawal symptoms are far less severe." Read more . . .

Mark your calendar

Sept. 15: Advancing Regulatory Science at the FDA. Carol Linden, Director, Office of Regulatory Science and Innovation, FDA. CTSI Seminar Series. Noon to 1 p.m., Helen Wood Hall Auditorium (1W-304).

Sept. 16: Basics of writing a Data Management Plan. Noon to 1 p.m. at 310 Carlson Library. RSVP to

Sept. 17: Retraining Damaged Brains: A Personal Journey, Krystel Huxlin, Professor of Ophthalmology and Director of Research, Flaum Eye Institute. Graduate Women in Science (GWIS) Meeting. 3-4 pm, MC 1-9576 (Case Method Room).

Sept. 18: "The Dementia Epidemic." Thomas V. Caprio, Associate Professor of Medicine, discusses managing dementia from a clinician's perspective and addressing the question of screening when no effective therapy exists. First session of the 2015-16 Public Health Grand Rounds. Noon to 1 p.m., Helen Wood Hall Auditorium (1W-304). Assorted wraps available while they last. Bring your own beverage.

Sept. 22: Regulating Science and Translational Research: Innovation to meet patients' needs. Michael Rosenblatt, Executive Vice President and Chief Medical Officer, MERCK. CTSI Seminar Series. Noon to 1 p.m., Helen Wood Hall Auditorium (1W-304).

Sept 24: Environmental Health Sciences Research Day seminar, celebrating 50 years of Environmental Health Sciences research at The University of Rochester. Various seminars on the EHSC history, new research, community impact, and a poster session. 9 a.m. to 4:30 p.m., Class of 62 Auditorium.

Sept. 30: Industry Consulting: Part One, Karl Kieburtz, CTSI director. Noon to 1 p.m., Helen Wood Hall Auditorium (1-304). Part of the series on Good Advice: Case Studies in Clinical Research, Regulation, and the Law.

Oct. 2: Applications due for a $30,000 award and a $15,000 award from the Lung Biology Strategic Plan for a high-risk project related to lung biology or disease or a nanosight technology-focused project using NS300 technology. Email Richard Phipps or Rebecca Trautman for more information. Click here to see the full RFP.

Oct. 15: Applications due no later than 5 p.m. for CFAR RNA Pilot Announcement. Click here for details.

Oct. 15-16: NIH Regional Seminar on Program Funding and Grants Administration, San Diego, CA. Click here for more information and registration.

Oct. 22: Applications due no later than 5 p.m. for CFAR Major Collaborative Pilot Announcement. Click here for details.

Oct. 30: Applications due no later than 5 p.m. for CFAR Joint Funding Opportunity in HIV/AIDS through SMD, SON and Program Of Excellence. Click here for details.

Please send suggestions and comments to Bob Marcotte. You can see back issues of Research Connections, an index of people and departments linked to those issues, and a chronological listing of PhD dissertation defenses since April 2014, by discipline.

Copyright 2013, All rights reserved.
Rochester Connections is a weekly e-newsletter for all faculty, scientists, post docs and graduate students engaged in research at the University of Rochester. You are receiving this e-newsletter because you are a member of the Rochester community with an interest in research topics.