Research Connections :: University of Rochester

The screen grab above, from the Seward Family Digital Archive, shows an example of the Text Encoding Initiative (TEI) tagging that allows readers to quickly link to additional background about people, places and items mentioned in the letters.

Researchers create their own 'index' at Seward Family Digital Archive

In the not so distant, pre-digital past, scholars interested in exploring a large collection or multi-volume compendium of letters or other documents were pretty much at the mercy of indexers.

Depending on whether certain key words or topics were included in the index, the scholar would either quickly find where to look or have to invest potentially hundreds of hours poring through documents, page by page. Or simply walk away.

This is not the case with the Seward Family Digital Archive. Its search functions "allow visitors the flexibility to follow their own research interests," the project's website notes. It is a prime example of how modern digitization and annotation techniques have made researching a collection of this scale a much easier and, ultimately, more rewarding task.

For starters, the visual presentation, featuring an elegant flat design, is compelling. A digitized image of each letter in its original handwritten form is displayed side by side with an annotated transcription. The viewer can switch back and forth, and even zoom in for a closer look at the writing.

In addition to keyword searches, other navigation tools that help researchers quickly make connections have been embedded in the archive by Project Technical Director Nora Dimmock, the assistant dean for IT, research and digital scholarship; Joshua Romphf, programmer with the Digital Humanities Center; and Camden Burd, the project's TEI and technology manager.

For example, names of many of the people, places and items are tagged in the transcriptions with Text Encoding Initiative (TEI) coding. This links the reader to a separate window with, for example, a biographical sketch of the person and a list of links to other letters in which the person is mentioned.

"Text Encoding Initiative allows you to add value to words," Burd said. "We can tag 'Lucretia Mott' and give substance to those words, and quickly find the two other letters out of the 800 where she is mentioned. It makes it easier for researchers to easily access other letters they might be interested in.

A "browse letters" function even allows researchers to quickly select all the letters exchanged between any two letter writers, by year.

This is a far cry from those pre-digital days, when navigation "tools" primarily consisted of printed indexes.

"Those editions are only as good as their indexes, and those indexes are frozen in time," says Project Director Thomas Slaughter, the Arthur R. Miller Professor of History. "In a collection numbering tens of thousands of pages you'll likely never be able to find anything that an indexer didn't think to include."

Thanks to modern digital navigation tools, "we don't have to imagine every particular purpose a researcher might have, in order to make a collection accessible," Slaughter said. "We're not frozen by our own imaginations."

browser

Researchers can quickly select all the letters exchanged between any two letter writers, by year.

The archive project, supported by a grant from the Fred L. Emerson Foundation, is a collaboration among the Department of History and the River Campus Library's Digital Humanities Center, which is supporting the website development, and Department of Rare Books and Special Collections, where most of the letters are housed. The Project also receives funds from CETL (Center for Excellence in Teaching and Learning), RCCL (Rochester Center for Community Engaged Teaching), and FURL (Friends of the University of Rochester Libraries). The project also has been awarded a two-year grant totaling over $97,000 from the National Archives Literacy and Engagement with Historical Records Program. The funding will be used to continue and expand the collaboration with volunteers from the Highlands at Pittsford retirement community and retired University staff and librarians who help transcribe, annotate, and tag letters from the Seward family. Read more here.

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 bmarcotte@ur.rochester.edu.

NSF director Córdova proposes new ideas for the agency

At a recent meeting, the National Science Board praised National Science Foundation Director France Córdova's proposed set of nine new ideas for the agency – including six "research big ideas" and three "process ideas" that she believes will lead to transformative discoveries.

The six research big ideas are:

1. Harnessing Data: A national scale initiative aimed at fundamental data science research, research data infrastructure, cyberinfrastructure, and the development of a 21st century data capable workforce.
2. Shaping the New Human Technology Frontier: Studies about how technology affects learning, human behavior and social organization and how it will affect work and productivity, the very nature of work in the future, and education.
3. The Rules of Life: Addressing our inability to predict the phenotype of a cell or organism from what we know about the genome and the environment, and understanding the rules that govern phenotypic emergence at scale.
4. Quantum Leap: Leading the Next Quantum Revolution: Exploiting quantum phenomena like superposition, entanglement, and squeezing to enable the next wave of precision sensors and more efficient computation and simulation and communication.
5. Navigating the New Arctic: Establishing an observing network of mobile and fixed platforms and tools across the Arctic to document biological, physical and social changes, and invest further in theory, modeling, and simulation of this changing ecosystem and its broader effects on the planet.
6. Windows on the Universe: the Era of Multi-Messenger Astrophysics: Explorations in the electromagnetic regime, the particle regime, and gravitational regime, using an array of ground-based observatories.

The three process ideas are:

1. Convergent Research: Merging ideas, approaches and technologies from widely diverse fields of knowledge at a high level of integration.
2. Mid-scale Research: Lowering the threshold for MREFC expenditures with appropriate modification of processes to increase the flexibility for excellent science to be done across the agency.
3. NSF 2050: Creating a breakthrough scientific pathway to NSF's centennial in 2050, including a special fund to invest in bold research questions that originate outside of any particular directorate.

Read more here.

APOBEC enzymes, our allies against disease,
can turn on us when they are not controlled

Harold C. Smith, professor of biochemistry and biophysics, became interested in epigenetics — the biological processes that alter the expression of our genes, without changing DNA sequence — long before it was a popular area.

In a recent commentary in Trends in Biochemical Sciences and in an interview with Emily Boynton at the Research@URMC blog, Smith describes his research into the APOBEC family of proteins, which play key roles in human health and disease. Their activities are regulated by genetic alterations, changes in their transcription and mRNA processing, and through their interactions with other macromolecules in the cell.

"Everyone has these enzymes and we believe that their main function is to help the body fight disease," Smith tells Boynton. "We've found that if our bodies don't control these enzymes properly, they can turn on us and cause conditions like cancer. An area where we have and continue to make major contributions is in the structure of APOBEC enzymes, which determines how they work and how they are controlled."

Smith's lab is also making progress in showing how the HIV protein dubbed "Vif" (for viral infectivity factor) tricks the body into destroying APOBEC enzymes, as if they were cellular waste. If Vif was not present, scientists have shown that APOBEC enzymes can defeat HIV by scrambling up the virus's genetic code. "We're currently looking for drugs that can target and eliminate Vif so that the APOBEC enzymes can perform their job against HIV," Smith said.

There is still much to learn about APOBEC enzymes. "We don't understand how APOBEC enzymes fine tune the expression of specific genes to help us fight disease," Smith explained. "Understanding what happens when APOBEC enzymes go awry and lead to genetic changes that cause cancer is even more difficult. So, we have a long way to go."

Stigma hinders care for HIV victims in Ghana

HIV prevalence among men who have sex with men in Ghana is 15 times higher than that of the general population. LaRon E. Nelson, an assistant professor of nursing and Dean's Endowed Fellow in Health Disparities, believes same-sex behaviors and identities that don't conform to local masculine gender norms can stigmatize the men and cause them to disengage from HIV care for fear of ridicule or mistreatment.

He has received a grant totaling more than $433,000 from the National Institutes of Health to examine the link between HIV stigma and HIV symptom frequency and distress among these men. This study continues his longstanding work with MSM in Ghana and will inform his other ongoing research on using mobile app-based peer support to help mitigate the impact of stigma on care engagement and retention.

Nelson participated in March in a White House symposium on HIV stigma. His work on HIV prevention has focused primarily on groups whose prevention needs are complicated by their socially marginalized status in their communities, with particular emphasis on Black men who have sex with men. "The results from this study can provide evidence regarding whether stigma is only a social issue or if it is also a public health issue — and what public health strategies are needed to address it," Nelson said. Read more here.

University researchers in the news

Over the past 15 years numerous studies have found that playing action video games such as "Call of Duty" helps cognitive functioning. In an article for Scientific American, Daphne Bavelier, professor of brain and cognitive sciences, and C. Shawn Green '08 (PhD), an assistant professor at the University of Wisconson-Madison, explain how shooting zombies and fending off enemy troops virtually can enhance brain skills such as visual acuity, reaction time, and multi-tasking. Read more here.

Segev BenZvi, an assistant professor of physics, and fellow scientists are looking for very energetic gamma rays and cosmic rays that enter Earth's atmosphere. When the high-energy rays interact, they create a "particle cascade" — a shower of high-energy particles — that falls to Earth. Where are they gathering this information? 13,500 feet above sea level on the side of the Sierra Negra volcano in central Mexico, where photosensors lie at the bottom of 300 giant tanks, each holding more than 50,000 gallons of purified water. As Kathleen McGarvey explains in the latest issue of Rochester Review the project is ambitious: observing gamma and cosmic rays, and contributing to the search for dark matter. Read more here.

PhD dissertation defenses

Yi-Ming Lai, Physics, "Integrated Nanophotonics with Genetically Designed Photonic Crystal Structures." 9:30 a.m., June 24, 2016. Bausch and Lomb 372. Advisor: Antonio Badolato.

Kathlyn Fillman, Chemistry, "Theoretical and Spectroscopic Studies of Mid-First Row Transition Metal Complexes." 9 a.m., June 27, 2016. 2110D Dewey. Advisor: Kara Bren.

Malik Al-Afyouni, Chemistry, "The Coordination Chemistry and Reactivity of Organometallic Cobalt, Iron and Manganese Complexes." 2 p.m., June 27, 2016. 473 Hutchison. Advisor: Kara Bren.

Sara Snell, Microbiology & Immunology, "Staphylococcus aureus Pathoadaptation and Development of Resistance." 9 a.m., June 30, 2016. K307 (3-6408). Advisor: Steven R. Gill.

Brittany Szymaniak, Genetics, "Loss of ATM induces glial cell dysfunction in a novel murine model of Ataxia-telangiectasia." 10 a.m., June 30, 2016. 1-9576 Ryan Case Method Room. Advisor: Margot Mayer-Proschel.

Lin Li, Geosciences, "Tectonic and Climatic Evolution of the Central-Northern Tibetan Plateau: Evidence from Sedimentation and Stable Isotopes." 10 a..m., July 1, 2016. Hutchison 229. Advisor: Carmala Garzione.

Enjoy the holidays

Due to the July 4 holiday, the next issue of Research Connections will be July 8.

Mark your calendar

Today: Deadline is 5 p.m. for applications for Center for AIDS Research pilot awards in Focused Topic Areas and in General HIV/AIDS. Contact Laura Enders at Laura_Enders@urmc.rochester.edu or (585)273-2939.

July 1: Deadline to submit applications for AS&E PumpPrimer II awards. Faculty in Arts & Science should refer questions to Debra Haring and those in Engineering to Cindy Gary.

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.