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Michael Jarvis, Associate Professor of History, and his students are shown above on Smiths Island in Bermuda where they excavated historic sites this summer as part of an ongoing project to document the arrival of Englishmen and Africans during the early 1600s and how they adapted. Map at lower right shows the sites Jarvis and his students are studying.

A 'democratic, inclusive approach to history'

The Oven House. Smallpox Bay. Cotton Hole Bight.

These are the places where Englishmen and Africans arrived on Smiths Island in Bermuda during the early 1600s and began to adapt to life in the New World. The houses, lime kilns, wells, docks and other structures they built are gradually re-emerging from archaeological digs as three-dimensional interactive models -- thanks to Michael Jarvis, Associate Professor of History, and the hardworking University of Rochester students and Bermudian volunteers who have participated in his summer field school since 2012.

The students, many of whom have no prior training in either history or archaeology, spend five weeks digging trenches, and painstakingly sifting through one-meter square units of dirt for artifacts. By the time they leave, blisters have turned to calluses. The students have not only six academic credits under their belts -- and a memorable experience -- but all the skills they need to be hired as entry-level field archaeologists by Cultural Resource Management (contract archaeology) firms, Jarvis said.

And Jarvis will have data -- thousands of photos, and reams of documentation -- to feed into computer programs that have opened up new ways to connect and compare all this information. All this sheds new light upon the historical saga that Jarvis and his students are unearthing.

"We are taking the whole island as a microcosm of Bermudian history, of human interaction with land and sea across four hundred years," Jarvis explained. "We're investigating the very process of Americanization. What did it mean for Englishmen and Africans to arrive in this landscape and start to become something other than European and African, to become Bermudian and American?"

It is a story worth telling, he said, because "the roots of who were are today lie in the beginning of this process. We have this unbroken link of past to present. And we are still adapting -- to climate change, pollution and economic crisis -- in ways that are every bit as dynamic as when these people got off a boat on a tropical island four centuries ago."

Until recently traditional written histories have focused on wealthy, elite men because they left the lion's share of records. The Smiths Island archaeological project, by contrast, unearths evidence about the lives of women, children, enslaved Africans, Indians, and poor white farmers. It is a "democratic, inclusive approach to history," Jarvis said.

Click here to read the blog Jarvis and his students have written about their three summers doing field work. Undergraduate students interested in helping Jarvis excavate on Smiths Island next year, starting in May, can apply now by downloading an overview and application from his history department website.

Next: First the digging, then the analysis.

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

Conflicts of interest: 'Let us know and we will work with you'

A UR faculty member discloses a new technology that results in the filing of several patents by UR Ventures, the University's technology transfer office.

In this hypothetical scenario, the University determines its best path to commercialization is to license the technology to a startup company in which the faculty member has a substantial financial interest, and for which the faculty member serves as chief science officer.

Since the startup lacks its own research (e.g., bench) labs, the company wishes to sponsor further research to further the technology in the faculty member's own lab at the University.

Graduate students and post docs in the professor's lab would conduct this research.

And that raises a potential conflict of interest.

The students may feel pressured, as a result of the mentor-mentee relationship, to pursue high risk research that might benefit the professor's company, but do little the advance the students' own academic goals -- and might, in fact, limit their ability to publish findings, impacting their future careers. And the faculty member's counsel and advice to the students may be influenced by his or her financial interest in the outcome.

Does this mean the project cannot go forward?

Not necessarily. Real-life UR projects pose similar conflicts of interests or apparent conflicts every day -- and are nonetheless carried out successfully.

"We generally always find another way of doing it," said Gunta Liders, the University's Associate Vice President for Research Administration.

In our hypothetical case above, for example, one or more senior faculty with no financial interest in the company might be appointed as the major advisors or co-advisors for the students to ensure their interests are safeguarded. The university might institute a formal mechanism to review the students' progress.

Liders cannot recall a single River Campus research project being terminated over real or apparent conflict of interest issues that were disclosed to the University. Even at the Med Center -- where faculty are expressly prohibited from conducting clinical drug trials if they have an equity interest in the company that manufactures the investigational drug or device -- there is always the option of assigning the trial to another faculty member "so at least the science can go forward," Liders noted.

And that's the message Liders and other research administrators at the UR are trying to get out: conflicts of interest -- real and apparent -- are nothing that a faculty member should be defensive about, or try to hide. On the contrary, they should be as transparent as possible about them, so that:

1. The credibility of the researcher and his or her findings are not called into question.

2.The university can put a conflict of management plan in place that protects the research from bias.

3. The university can identify and head off potential, albeit unintended uses of university facilities that conflict with its not-for-profit status.

4. Intellectual property rights can be protected for the benefit of both the researcher and the university.

"Let us know what's going on," Liders said, "and we'll work with you."

"Research universities -- by their very nature -- are going to create conflicts," Liders added. At the UR, faculty members are not only allowed but encouraged to start up companies that can translate their innovations for the public good, or to consult with companies interested in their work. "We think that's a good thing," Liders said. "We want our professors engaging with industry. It benefits both sides. Industry gains knowledge. Our faculty gains knowledge."

The Council on Governmental Relations agrees: "External corporate relationships enrich faculty teaching and research, expand career and research opportunities to students, and provide the obvious mechanism for the translation of university developed inventions and discoveries into commercial ventures that benefit the public."

The university recently restructured its technology commercialization office and rebranded it as UR Ventures as part of its "commitment to facilitate the translation of our innovations for the benefit of society," said Robert Clark, the University's senior vice president for research who, along with General Counsel Gail Norris, chairs the University's Conflict of Interest committee.

"We want to get the word out that conflicts are NOT bad things, that we are committed to managing them to allow commercialization to proceed, and that the worst thing that can happen to research at this University is for researchers to not disclose a conflict so that it's not managed in a way to protect the integrity of their research."

(All faculty members and other investigators are required to submit annual financial interests reports, ordinarily in the February-March timeframe for the prior calendar year. In addition, all faculty members and investigators must disclose any additional financial interests that they acquire, within 30 days of discovering or acquiring the financial interest. School/college conflict of interest forms or reporting systems can be found here. The URMC reporting system is located at The AS&E reporting system is located at Questions? Contact the Office of Research and Project Administration (ORPA) or UR Ventures.)

Data visualization winners announced

Three University researchers reached The Big Screen -- the new VISTA Collaboratory in Carlson Library, that is -- when they were announced as the winners of the data visualization contest sponsored by the Health Sciences Center for Computational Innovation (HSCCI). They are:

1. Jim Baker, graduate student in physics, for "Evaluating the effectiveness of virus detection devices."

2. Michael Jarvis, Associate Professor of History, for "3D modeling of archaeology fieldwork" (see above).

3. Erica Kaminski, graduate student in astrophysics, and Adam Frank, Professor of Astrophysics, for "Molecular clouds and star formation."

Each of the winners' work was featured at the Grand Opening of the VISTA Collaboratory on Oct. 10 and during public tours of the VISTA during Meliora Weekend. Each researcher will also receive priority, no-cost access to the VISTA this year.

Research Connections will feature their winning entries in upcoming issues.

Glimpses of Austria before and during the Holocaust

The work of amateur filmmakers -- whose "ephemeral films" depict Jewish life in Austria before and during the Holocaust -- have until recently received little scholarly attention or systematic preservation. And yet, they contain valuable cultural and historical information, sometimes contradicting the Nazi-sponsored version of events and thus serving as a valuable corrective to the visual record.

Together with the Austrian Film Museum and the Ludwig Boltzmann Institute, the United States Holocaust Memorial Museum has designed an innovative web application that preserves both the structure and content of these films.

Learn more at the Ephemeral Films Project: National Socialism in Austria presentation, sponsored in part by the UR German Program and Department of Modern Languages and Culture, at 5 p.m., Nov. 4 in the Hawkins-Carlson Room at Rush Rhees Library.

Grantsmanship will be discussed at ASE luncheon

Lori Walters, a digital historian and professor at University of Central Florida, will discuss grantsmanship at a luncheon roundtable from noon to 1:30 p.m. Thursday, Nov. 6, in the Gamble Room of Rush Rhees Library. Walters has secured NSF, NEH, Army, and State of Florida grants for her projects, which are intended primarily to support STEM education in secondary schools. All potential Principal Investigators are welcome to attend.

Walters is visiting the School of Arts, Sciences and Engineering to discuss her digital projects and share her experiences creating them.

To attend the luncheon, RSVP to Melissa Napolitano by Monday, Nov. 3, including any dietary restrictions.

Data sharing: What to share, who to share it with, and when

(The last of three parts.)

Data sharing is required by federal funding agencies and some publishers. It's also the right thing to do, for the betterment of science and your own citation success.

"But that doesn't mean you shouldn't be strategic about what you share," notes Kathleen Fear, Data Librarian with the UR Libraries. "In general, you don't need to share everything you have with anyone who wants it."

She offered this general advice:

A good rule of thumb is to share enough of your data so that someone competent in your discipline can reproduce the results.

However, exactly what you share, and when, can vary with each project, she added. Funding agencies generally recognize that "Not all research is the same, and data isn't really a monolithic thing." Most data sharing requirements allow enough flexibility for you to determine the best way to share your data.

For many projects it makes more sense to share data in its final version, along with the scripts for publication. For other projects, it may make more sense to share raw data. If you are worried about jeopardizing intellectual property or nondisclosure agreements, consult with UR Ventures.

It is important to think about these things at the start of a project, because funding agencies will want you to outline how you plan to handle data sharing as part of your proposal or data management plan. There are many options for fine-tuning your data sharing practices, and UR library staff can help you sort through the available tools and work with you to develop a strategy that works for you and your research.

Contact Fear or, at URMC, Donna Berryman or Linda Hasman.

The Clinical and Translational Science Institute can also assist researchers through its Research Help Desk and its Office of Regulatory Support, which coordinates the University account for and provides assistance for all aspects of registration and result reporting.

For a sampling of data sharing requirements at funding agencies, visit the National Science Foundation and National Institutes of Health. Go to the Science website for that journal's description of data sharing requirements.

CTSI pilot grant supports study of new bladder cancer therapy

About 30 percent of the approximately 75,000 people diagnosed with bladder cancer each year suffer from a dangerous, muscle-invasive form of the disease that can spread to other organs. Treatment usually involves surgical removal of the organ, followed by chemotherapy. But many patients with bladder cancer are older and have other medical problems. If they are too sick for chemotherapy, then their outcomes are far worse -- these patients see their cancer returning about 50 percent of the time.

Elizabeth Guancial, Assistant Professor of Medicine, Hematology/Oncology, is working alongside Shu-Yuan Yeh, Professor of Urology, to test potential new therapies for these patients that involve targeting the estrogen receptor, which could be administered as adjuvant treatment for those at risk for developing metastatic disease after their bladders have been removed, reports the CTSI Stories blog.

Their research, which began over the summer, is supported by a CTSI Pilot Grant.

"I don't think that estrogen therapy could shrink down a tumor. I wouldn't expect it to kill any cells," said Guancial. "But it may be able to modulate the ability for bladder cancer to grow or metastasize to other sites."

Bladder cancer can be tough to study in the mouse model since the organ is so tiny, making the implantation of cancer cells challenging. But Yeh has previously studied bladder cancer in mice, and has developed a method of study that does not include the risk of perforating the organ through surgery.

"There are important strengths in this Pilot Study," said Richard Moxley, Associate Director for Funding Programs at the CTSI. "The investigative team is multidisciplinary and experienced in the methodology, the investigator has a strong mentor, and they are pursuing a very interesting hypothesis that suggests different roles for the estrogen receptor subtypes in the pathomechanism that underlies bladder cancer.

"If the mouse model and cell model data in these experiments prove promising, these findings are very likely to stimulate new therapeutic strategies in humans with bladder cancer."

Introducing a new faculty member

Wei Chen has joined the Department of Medicine, Nephrology, as an assistant professor. She has a strong interest in clinical research and medical education. Her research focus is in on metabolic acidosis, mineral metabolism and vascular calcification in patients with chronic kidney disease. She received her MD from Stony Brook School of Medicine in 2008, and joined the UR after completing a renal clinical research fellowship at the Albert Einstein College of Medicine earlier this year.

Congratulations to . . .

Mary Tantillo, Professor of Clinical Nursing, who has been awarded a Hilda & Preston Davis Foundation grant for "Reconnecting for Recovery: A Relational /Motivational Multifamily Therapy Group for Young Adults with Anorexia Nervosa Program." Multifamily Therapy Group maximizes the resources, strengths, and adaptive coping strategies of a number of patients and their family members (including "family of choice members" as defined by the patients) as they work with the therapist to eliminate Anorexia Nervosa symptoms and promote ongoing recovery.

John Tarduno, Professor of Earth and Environmental Sciences, who received the 2014 Outstanding Publication Award from the Structural Geology and Tectonics Division of the Geological Society of America at the society's Annual Meeting in Vancouver. In their 2003 Science paper on "The Emperor Seamounts: Southward motion of the Hawaiian Hotspot plume in Earth's mantle," Tarduno and co-authors used key paleomagnetic data to challenge the notion that hotspots are "fixed," changing the way that geologists perceive long-standing notions about how aspects of plate tectonics work.

A team led by Ghinwa Dumyati, Director of the Communicable Diseases Surveillance and Prevention Program at the Center for Community Health, which won a 2014 Greater Rochester Quality Council Performance Excellence Award for its work to reduce Clostridium difficile or C. diff at Rochester General Hospital, Highland Hospital, Strong Memorial Hospital and Unity Hospital. The researchers received the first-ever platinum award in the category of "Team Excellence" (only silver and gold awards have been given out in the past) for "the exhibition of excellent teamwork and results across multiple organizations." Under Dumyati's leadership, the collaborative achieved a statistically significant 19 percent decrease in the rate of C. diff developing during hospitalization in Rochester-area hospitals, which translates to a total of 65 fewer patients harmed by C. diff during the past year.

UR research in the news

Researchers at the Medical Center have launched a five-year effort to develop a comprehensive map that measures lung development from birth through childhood. The project includes researchers from several other institutions and is supported by more than $20 million from the National Institutes of Health, $6.1 million of which was awarded to the Medical Center. "We need to know more about how the lung is formed and heals normally, in order to encourage pre-term infants to develop more normally, and to help adult lungs to heal from diseases like pneumonia and emphysema," said Gloria Pryhuber, Professor of Pediatrics and Environmental Medicine and the study's lead researcher at URMC. Researchers at URMC will collect lung tissue through a multi-state organ donor network, then analyze the samples through computerized tomography (CT) scans, reconstruct the lung samples in 3D for analysis, and process the tissue for further analysis down to the individual cell and gene level. They will then dig deeper into the function and development of infection-fighting white blood cells in the lungs, while colleagues at collaborating universities will analyze other aspects of the tissue. Read more . . .

The Andrew W. Mellon Foundation has committed a matching grant of $500,000 to the University, which will establish an endowment for the University's continued partnership in the Central New York Humanities Corridor. Founded in 2006 with generous support from the Mellon Foundation, the CNY Humanities Corridor is an interdisciplinary collaboration among research institutions Syracuse University, Cornell University, and the University of Rochester -- along with the schools of the New York Six Liberal Arts Consortium -- focused on enhancing scholarship in the humanities. Read more...

The University of Rochester has been named by the Centers for Disease Control and Prevention (CDC) as the Coordinating Center for the Global and Territorial Health Research Network (GTHRN), which will develop and carry out public health research and interventions in U.S. territories in the Pacific and Caribbean. The new network will also include Yale University and the University of Illinois at Chicago as collaborating centers. "This designation builds upon Rochester's strong global health connections and track record and expertise in prevention research," said Timothy Dye, the principal investigator and director of the new Coordinating Center. "Our goal is not only to help communities in the U.S. territories address their own chronic disease challenges, but also to take the lessons that are learned and apply them to public health problems closer to home." Dye is also Professor and Associate Chair for Research in the Department of Obstetrics and Gynecology and Director of Biomedical Informatics for the Clinical and Translational Science Institute. Read more . . .

Researchers at the Aab Cardiovascular Research Institute (CVRI) have identified a gene that controls how our blood clots. Variations within this gene may explain why some people form clots more easily than others and are at greater risk of deep vein thrombosis (a blood clot that forms in a vein deep in the body and can break off and block blood flow to other parts of the body), heart attack and stroke. The study, published in the Journal of Clinical Investigation, started with scientists at the National Institutes of Health's Framingham Heart Study who analyzed the genes of more than 20,000 humans and discovered eight that were closely linked to clotting function. Senior study author Charles J. Lowenstein, Director of CVRI, explored the role of one of those genes, STXBP5, in mice and human cells. He found that STXBP5 regulates how cells release messenger molecules that spur the formation of blood clots. Read more . . .

PhD dissertation defense

Revathi Balasubramanian, Neurobiology and Anatomy, "Requirement for LIM-Homeodomain Transcription Factor LHX9 in the Differentiation of Amacrine Cell Subtypes." 1 p.m., Nov. 7, K-307 (3-6408). Advisor: Lin Gan.

Mark your calendar

Nov. 2: Applications due in several funding categories for the 2014 Pilot Award Program of the University's Center for AIDS Research. Click here to learn more.

Nov. 3: Deadline for initial abstracts for SMD Scientific Advisory Committee (SAC) "superpilot" awards. Click here to read the full RFA.

Nov. 4: Ephemeral Films Project: National Socialism in Austria. Presentation on preservation of ephemeral films that depicted Jewish life in Austria before and during the Holocaust. Sponsored in part by the UR German Program and Department of Modern Languages and Culture. 5 p.m., Hawkins-Carlson Room, Rush Rhees Library.

Nov. 6: Luncheon with Lori Walters, a digital historian and professor at University of Central Florida, to discuss grantsmanship, noon to 1:30 p.m. the Gamble Room of Rush Rhees Library. RSVP to Melissa Napolitano by Monday, Nov. 3, including any dietary restrictions.

Nov. 10: Noon deadline to apply for a Center for Community Health mini-grant to be awarded next month. Grant funding of up to $1000 is made on a quarterly basis. The application and instructions are available here.

Nov. 11: Technology Commercialization at the University of Rochester. Patrick Emmerling, Licensing Manager, UR Ventures. Noon to 1 p.m., Gowen Room, WIlson Commons. RSVP to

Nov. 13: "The Co-Evolution of Humans and Machines." Lecture by Paul Horn '72 (MA) '74 (PhD), Senior Vice Provost and Senior Vice Dean for Strategic Initiatives and Entrepreneurship, Polytechnic School of Engineering, New York University. 5 p.m., Hawkins-Carlson Room, Rush Rhees Library. Register by Nov. 3 at or with Meghan Barnhardt at (585) 275-1490.

Nov. 13: Annual Wilmot Cancer Institute Scientific Symposium. Click here for more information.

Nov. 14: Disability Studies Cluster Symposium: "Complicating Normalcy: Disability, Technology, and Society in the Twenty-First Century." Organized around the documentary film FIXED -- The Science/Fiction of Human Enhancement, which explores the meanings of "disability" and "normalcy" in contemporary times through the examination of technological and pharmacological advances designed to "fix or enhance the human body," and the bioethical implications and social tensions that arise from these scientific advances. Register here.

Nov. 19: 2014 Regional Proteomics Symposium, 9 a.m. to 5 p.m., Class of '62 Auditorium and the Flaum Atrium. Speakers from a variety of Western New York universities and institutions, and a poster session highlighting protein identification work at the University of Rochester. Register here. For more information, contact Mark D. Platt, MSRL Director at or at (585) 276-6804.

Dec. 9: How to Find Inventions, What Makes a Good Invention, and How to Find Prior Art. Reid Cunningham, IP attorney, UR Ventures. Noon to 1 p.m., Gowen Room, Wilson Commons. RSVP to

Dec. 10: Celebration of Authorship, featuring printed and electronic books, edited volumes and texts, as well as published compositions and recordings produced by University faculty and staff from all fields. 3:30 to 5:30 p.m., Hawkins Carlson Room in Rush Rhees Library. Click here for more information.

Please send suggestions and comments to Bob Marcotte. To see back issues, click here.

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.