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.
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These brain maps show how accurately it was possible to predict neural activation patterns for new, previously unseen sentences, in different regions of the brain. The brighter the area, the higher the accuracy. The most accurate area, which can be seen as the bright yellow strip, is a region in the left side of the brain known as the Superior Temporal Sulcus. (University of Rochester graphic / Andrew Anderson)

Researchers, for first time, decode and predict
brain activity patterns of word meanings within sentences

University researchers have, for the first time, decoded and predicted the brain activity patterns of word meanings within sentences, and successfully predicted what the brain patterns would be for new sentences.

The study used functional magnetic resonance imaging (fMRI) to measure human brain activation. "Using fMRI data, we wanted to know if given a whole sentence, can we filter out what the brain's representation of a word is — that is to say, can we break the sentence apart into its word components, then take the components and predict what they would look like in a new sentence," said Andrew Anderson, a research fellow who led the study as a member of the lab of Rajeev Raizada, assistant professor of brain and cognitive sciences.

"We found that we can predict brain activity patterns — not perfectly [on average 70% correct], but significantly better than chance," said Anderson. The study is published in the journal Cerebral Cortex.

Anderson and his colleagues say the study makes key advances toward understanding how information is represented throughout the brain. "First, we introduced a method for predicting the neural patterns of words within sentences—which is a more complex problem than has been addressed by previous studies, which have almost all focused on single words," Anderson said. "And second, we devised a novel approach to map semantic characteristics of words that we then correlated to neural activity patterns." (Click here to read more about the semnatic model they used.)

The researchers say the study opens a new set of questions toward understanding how meaning is represented in the brain. "Not now, not next year, but this kind of research may eventually help individuals who have problems with producing language, including those who suffer from traumatic brain injuries or stroke," said Anderson.

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Qiang Lin, at left, assistant professor of electrical and computer engineering, and PhD student Wei Jiang, worked with researchers at the University of Victoria to show how the "optical spring" effect could enhance the detection of single particles and molecules.

Inaugural Mandel fellow continues to excel

Two years ago, the Department of Physics and Astronomy honored the late Leonard Mandel, University physicist and pioneer of quantum optics, by establishing an award to recognize exceptional achievement by a junior faculty member.

This summer, Qiang Lin, the inaugural recipient, has added to his record of achievement.

In a paper written with collaborators at the University of Victoria, Lin, an assistant professor of electrical and computer engineering, and PhD student Wei Jiang demonstrated for the first time how the so-called "optical spring" effect can be used to detect single molecules, in greater detail and at higher resolutions than is possible with conventional sensing methods. The new technology has potential applications in medical diagnostics, drug development, security screening, environmental science and other fields. (Read more here.)

Lin also received $2 million in National Science Foundation funding to lead a "dream team" of experts in developing chip-scale quantum photonics processors — using silicon carbide — that could function at or near room temperatures. Linked via fiber optics, the processors would enable long distance networks to carry out complicated functions — such as secure communications and advanced computing — more quickly and efficiently than current technologies. (Read more here.)

"People have been working in quantum optics for four or five decades now," Lin noted. "Our own Leonard Mandel was one of founders of the field. A lot of the fundamental principles have been explored; now is the time to transfer fundamental science to practical applications."

Lin received his Ph.D. in 2006 from the Institute of Optics, where he worked as a graduate student in the laboratory of Govind Agrawal, the James C. Wyant Professor of Optics and professor of physics. "He published 30 research papers before graduating, a record that is unlikely to be broken," Agrawal said when Lin received the Mandel award.

Following his doctoral work, Lin was a postdoctoral scholar in the laboratory of Oskar Painter at the California Institute of Technology. He returned to Rochester in 2011. In 2014, he received a prestigious Faculty Early Career Development award from the National Science Foundation.

Screenings may miss disabilities in refugee children

The United States takes in approximately 70,000 refugees annually, of which 30 percent are children. Refugee resettlement experiences are known to impact critical stages of a child's intellectual, social, emotional, and physical development. However, the developmental screenings recommended by the American Academy of Pediatrics don't always translate perfectly to other cultures, which can lead to a missed diagnosis of a potentially serious developmental disability, according to new Medical Center research published in the journal Pediatrics.

The research is the first known attempt to study the obstacles surrounding refugee developmental screening.

Working with the Center for Refugee Health in Rochester, researchers lead by Abigail Kroening, assistant professor of pediatrics, interviewed 29 refugee parents, community collaborators and providers, and turned up a number of cultural differences that may create barriers when identifying developmental milestones.

For example, those from cultures with multi-deity belief systems were more likely to attribute a child's disability to a generational curse or as a karmic retribution for a past transgression. Meanwhile, those with Christian or Islamic backgrounds were more likely to see a disabled child as a "gift from God." In either case, a parent may be less likely to report or engage as strongly with their child's disability.

"Here, we are inundated with baby books and milestone charts, and parents often proactively reach out to their pediatricians to say 'My child isn't talking quite as much as his peers — is that something to worry about?'" said Kroening. "That's not always the case in other cultures."

Families said that meeting with both a physician and an in-person interpreter (as opposed to a telephone interpretation) was the most ideal scenario for developmental screening. Additionally, researchers found that establishing trust between parent and provider was extremely vital to increasing a parent's engagement in terms of identifying behavioral milestones.

Kroening and her collaborators — Jessica Moore, senior instructor of psychiatry, and Therese Welch, associate professor of pediatrics — are continuing their research in the hopes of establishing a more concrete set of guidelines and resources for providers who treat refugee families and children.

Warnings raised on polymer coatings on medical devices

Rupal I. Mehta, assistant professor of pathology and laboratory medicine, warns that hydrophilic polymer coatings on catheters, guide wires, and other vascular medical devices can peel or flake off during clinical use and cause serious complications in some patients, including death.

In a recent article in Human Pathology, Mehta reviewed the cases of 32 patients with documented complications associated with polymeric coatings and showed that associated tissue changes within the brain were diverse, including structural abnormalities of small vessels (in 63 percent of patients), inflammation (38 percent), stroke (28 percent) and/or aseptic meningitis (22 percent).

Mehta was invited to present her work on this subject at the FDA Center for Devices and Radiological Health special grand rounds last fall. A recent FDA public safety communication highlights the issue and cites her work. The FDA has acknowledged important gaps in current national and international device standards, Mehta said, and the agency is working with stakeholders to better characterize and evaluate coating performance to mitigate risks of these complications in patients. Read more here.

Tips for avoiding predatory journals

So-called "predatory journals" — more interested in taking your money than in responsibly showcasing your research — have proliferated in recent years, especially with the advent of "open access" publications.

Beall's List of Predatory Publishers, for example, now lists 882 "potential, possible, or probable predatory scholarly open-access journals."

Karen Liljequist, liaison program manager with Miner Library, says it pays to be wary of scholarly journals that:

1. Send you unsolicited emails or SPAM — often containing obvious typos or grammatical errors.
2. Promise an unusually quick turnaround from article submission to publication.

Predatory journals often:

1. Do not disclose article processing charges (APC's) up front, but demand payment for publishing at a later date. "It can also be very hard to get a paper back without paying," Liljequist said.
2. Offer little nor no editorial services, and may not even be peer-reviewed, which can ultimately hurt the credibility of researchers whose work appears in them.
3. Have titles similar to legitimate journals.
4. Fabricate their journal metrics, stats and even editorial board members. "Researchers have emailed board members listed by these journals for more information, only to be told they've been trying to get the journal to remove their names," Liljequist noted.

Just because a journal or publisher appears on Beall's list does not necessarily mean it is predatory, but you may need to "gather more information before deciding to contract with them," Liljequist said.

One measure of trustworthiness is whether the journal or publisher is a member of, or listed at, the Committee on Publication Ethics, the Directory of Open Access Journals, and/or the Open Access Scholarly Publishers' Association. Click here for a checklist of additional measures of the trustworthiness of a prospective publisher or journal.

An online discussion of this topic can be found at ThinkScience.

Questions? Contact a liaison librarian at Miner Library or Justina Elmore at River Campus Libraries.

Center for AIDS Research seeks pilot award applicants

As many as two Program of Excellence Awards of up to $50,000 each will be awarded to:

1. Support a broad range of highly innovative research projects and pilot studies addressing key gaps in HIV treatment and prevention.
2. Facilitate interdisciplinary and inter-professional collaborations between the School of Medicine and Dentistry and the School of Nursing involving biomedical, clinical, epidemiological, and social/behavioral sciences.

Each application must include one co-PI from the School of Nursing and one co-PI from the School of Medicine and Dentistry. Projects will receive the highest priority if they have strong potential for followup NIH funding and create new collaborations involving multiple disciplines.

Additional information and specific application requirements can be found in the full pilot announcement and at the pilot funding opportunity page.

The pilots are jointly funded by the School of Nursing and the School of Medicine and Dentistry under the auspices of the Program of Excellence in HIV/AIDS. Applications are due no later than 5 p.m., Oct. 21, 2016. For more information about funding opportunities, contact

Sept. 26 deadline for CTSI pilot awards

The deadline is 5 p.m., Sept. 26 to submit initial project abstracts for two categories of pilot awards from the Clinical and Translational Science Institute.

The Incubator Program is an expansive pilot program that might be termed a "superpilot" award, funding two or more individual pilot projects by collaborating investigators linked to a scientific or clinical theme. The program seeks to support the development of promising clinical and translational research within the institution, where larger, carefully targeted investments can accelerate progress and create stand-alone research programs. Click here for details about the Incubator Program and to access the RFA.

The CTSI is also requesting applications for:

1. Investigator-initiated pilot studies for faculty ($50,000 maximum for one year).
2. Investigator-initiated pilot studies for trainees ($25,000 maximum for one year).
3. UNYTE Translational Research Network grants ($50,000 maximum for one year).

Click here to find out more and to access the RFA.

Workshop: Advice on Graduate Research Fellow awards

The University currently hosts more than 15 National Science Foundation Graduate Research Fellows in such disciplines as brain and cognitive sciences, chemistry, clinical and social sciences in psychology, engineering, geology, optics, and physics. To encourage more students to join this list, the AS&E Graduate Studies Office is offering a workshop for potential applicants from 4-6 p.m., Sept. 8, in the Hawkins-Carslon Room of Rush Rhees Library.

The workshop will feature an introduction to the GRFP, writing tips, and a guest panel of former winners and faculty advisers.

The Graduate Research Fellowship Program supports outstanding students pursuing research-based master's and doctoral degrees in the physical and life sciences, social sciences, engineering, STEM education, and the history and philosophy of science. Fellows benefit from a three-year annual stipend of $34,000 along with a $12,000 cost of education allowance for tuition and fees (paid to the institution), opportunities for international research and professional development, and the freedom to conduct their own research at any accredited U.S. institution of graduate education they choose.

Students interested in attending the workshop can RSVP by completing this form. Snacks will be served.

PhD dissertation defenses

Christopher Marshall, Physics, "Measurement of charged kaon production by neutrinos at MINERvA." 10 a.m., Aug. 19, 2016. Bausch and Lomb 106. Advisor: Kevin McFarland.

Brian Barnett, Philosophy, "Higher-Order Evidence: Its Nature and Epistemic Significance." 2:30 p.m., Aug. 19, 2016. Lattimore 531. Advisor: Richard Feldman.

Patrick Papadopulos, Mathematics, "On Topological Properties of Configuration Spaces of Certain Specialized Graphs." 2 p.m., Aug. 22, 2016. Hylan 1106A. Advisor: Frederick Cohen.

Mark your calendar

Sept. 1: Deadline to apply for pilot funding in support of a major initiative by the Del Monte Institute for Neuroscience to launch an Intellectual and Developmental Disabilities Research Center. Read more here.

Sept. 7: Reception in honor of Nick Vamivakas, recipient of the 2016 Leonard Mandel Faculty Fellow Award, hosted by Department of Physics and Astronomy. 5-6 p.m., 271 Bausch and Lomb.

Sept. 8: Graduate Research Fellowship Program workshop for potential applicants, including writing tips and a guest panel of former winners and faculty advisers. 4-6 p.m., Hawkins-Carlson Room, Rush Rhees Library. RSVP by completing this form.

Sept. 22-24: Department of Neurology 50th anniversary celebration, including gala banquet, department updates, and poster and platform presentations showcasing research by current faculty, alumni, fellows, and residents. Read more here.

Sept. 26: 5 p.m. deadline to submit initial abstracts for pilot awards from the Clinical and Translational Science Institute in two categories: Incubator Program and investigator-initiated and UNYTE.

Sept. 29: Identifiying journals for publication; avoiding predatory publishers. Noon to 1 p.m., Miner Classroom 1. Sign up here.

Oct. 21: 5 p.m. deadline to apply for Program of Excellence Awards of up to $50,000 each from Center for AIDS Research, for collaborative projects involving co-PIs from the School of Nursing and from the School of Medicine and Dentistry. Click here for the full pilot announcement.

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.

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Rochester Connections is a weekly e-newsletter 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.