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Max Rutter gets the lightbulb lit inside the new science classroom at Andrew Muller Primary School. File Photo by Rebecca Anzel

By Rebecca Anzel

Second-graders in Andrew Muller Primary School’s new science room were beaming with excitement Monday as teachers distributed materials for an experiment — a magnet, paperclip, battery, copper wire, rubber band and lightbulb.

The class was learning about interactions. Debbie Trelfa helped her students name each of the items in front of them and asked them to figure out how to make them interact. One table discovered the magnet attracted the paperclip, and Trelfa told her students there was another interaction they could make.

Andrew Muller Primary School second-grade teacher Debbie Trelfa teaches a new science lesson to her class. Photo by Rebecca Anzel
Andrew Muller Primary School second-grade teacher Debbie Trelfa teaches a new science lesson to her class. Photo by Rebecca Anzel

Students told one another to “persevere,” and a few minutes later another table discovered they could get the lightbulb to light up by placing it on the battery.

Miller Place school district’s two elementary schools, Andrew Muller and Laddie A. Decker Sound Beach School, adapted an available classroom each to be used as science learning and inquiry labs. Students study topics like weather and plants in an interactive way, as opposed to using textbooks.

“Having been a classroom teacher, I loved teaching science, but it’s very difficult to do in a classroom,” Andrew Muller Primary School Principal Laura Gewurz said. “Experimentation can be time consuming and complicated to set up and break down. Having a room designed for student experimentation and collaboration makes science exciting and accessible, and saves instructional time.”

These two spaces were instituted to prepare for new state science and engineering curriculum changes, which shift the focus of lessons from memorizing information presented by teachers to understanding concepts by investigating them. The updated standards are called Next Generation Science Standards, which use “three-dimensional learning.”

Instead of a teacher asking students a question with one correct answer, for example, students would instead consider an open-ended one by using evidence presented by a teacher or reading. Or, instead of students reading a textbook chapter and answering questions on a worksheet, they would read multiple sources and write reports and posters about the ideas.

“You’re seeing a lot more hands-on experiences, hearing a lot more student talk and witnessing more student collaboration.”

—Laura Gewurz

“New York State is really changing the curriculum for science, which I think is fantastic,” Gewurz said. “It has not been changed since 1996, and not only are our concepts about teaching different, the science is different.”

According to a NYS Education Department document, the proposed science learning standards will be presented to the Board of Regents this winter. It is the last step in a process that began in January 2015, when the board counseled the Education Department to begin drafting new standards. Since then, the draft was updated with results from a public survey and discussed in June 2016.

“As teachers, schools, and educational systems systemically transition to the new science standards and changes to local curriculum and instructional practice, a call for coherent professional development opportunities is vital,” the NYS Education Department said in a statement. “To this end, the Department will continue to collaborate with science education stakeholders across the state and nation to assist in building the awareness and the capacity of teachers and leaders of science.”

Miller Place is “way ahead of the game,” Assistant Superintendent Susan Hodun said, in beginning to implement science curriculum changes before the new state standards are finalized and implemented.

With cooperative learning tables for students to work with and learn from each other, separate storage areas for each grade level and science learning resources displayed, the new science labs further encourage modern teaching methods.

Anna Paesano and Kayla Martins perform the day’s experiment. Photo by Rebecca Anzel
Anna Paesano and Kayla Martins perform the day’s experiment. Photo by Rebecca Anzel

“I think it really works with the new science learning standards that New York State has developed in the sense that students have more access to authentic learning,” Gewurz said. “You’re seeing a lot more hands-on experiences, hearing a lot more student talk and witnessing more student collaboration. I think with the changes to science, it’s all coming together, which is great.”

The science room is also financially smart, she added, because instead of purchasing duplicates of materials for each classroom, the school can instead buy a wider range of materials to create a “much richer room.”

Students spend about an hour per week doing experiments that supplement the time they spend in the classroom learning about science concepts. The teachers and principal at Andrew Muller hope that hands-on experience will help their students as they get older.

“If you’re looking at college and career readiness, how would kids even know if they want to be an engineer unless they’ve had the opportunity to experiment,” Gewurz asked. “I think it’s certainly motivational and I think you will see more boys and girls interested in engineering in this country if you start to do things like this.”

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Athi Varuttamaseni. Photo couresty of BNL

By Daniel Dunaief

Athi Varuttamaseni is like an exterminator, studying ways pests can gain entry into a house, understanding the damage they can cause and then coming up with prevention and mitigation strategies. Except that, in Varuttamaseni’s case, the house he’s defending is slightly more important to most neighborhoods: They are nuclear power plants.

The pests he’s seeking to keep out or, if they enter, to expel and limit the damage, are cyberattackers, who might overcome the defenses of a plant’s digital operating system and cause a range of problems.

Varuttamaseni, an assistant scientist in the Nuclear Science & Technology Department at Brookhaven National Laboratory, started his career at BNL by modeling the failure of software used in nuclear power plant protection systems. Last year, he shifted toward cybersecurity. “We’re looking at what can go wrong with nuclear power plants” if they experience an attack on the control and protection systems, he said.

Varuttamaseni is part of a team that received a grant from the Department of Energy to look at the next generation of nuclear power plants, which are controlled and managed mostly by digital systems. A few existing plants are also looking to replace some of their analog systems with digital. “We asked what can go wrong if a hacker somehow managed to breach the outer perimeter and get in to control the system, or even if that is possible at all,” he said. By looking at potential vulnerabilities in the next generation of power plants, engineers can find a problem or potential problem ahead of time and can “go back to the drawing board to put in additional protection systems that could save the industry significant cost in the long run,” Varuttamaseni said.

Robert Bari, a physicist at BNL and a collaborator on the cybersecurity work, said Varuttamaseni, who is the lead investigator on the Department of Energy project, played “a major role” in putting together a recent presentation Bari gave at UC Berkeley that outlined some of the threats, impacts and technical and institutional challenges. The presentation included a summary and the next steps those running or designing nuclear power plants can take. Bari said it was a “delight” to collaborate with Varuttamaseni.

A colleague, Louis Chu, had recruited Varuttamaseni to work at BNL in another program, and Bari said he “recognized his abilities” and “we started to collaborate.” Varuttamaseni and Bari are going through a systematic analysis using logic trees and other approaches to explore vulnerabilities. The BNL team, which is collaborating with scientists at Idaho National Laboratory, shared the information and analysis they conducted with the Department of Energy and with an industrial collaborator.

In his second year of the work, Varuttamaseni said he is looking at the system level and is pointing out potential weaknesses in the design. He then shares that analysis with designers, who can shore up any potential problems. In the typical analysis of threats to nuclear power plants, the primary concern is of the release of radioactive material that could harm people who work at the plants or live in the communities around the facility.

Varuttamaseni, however, is exploring other implications, including economic damage or a loss of confidence in the industry. That includes the headline risk attached to an incident in which an attacker controlled systems other than a safety function and that are not critical to the operation of a plant. In addition to exploring vulnerabilities, Varuttamaseni is studying a plant’s response. Most of the critical systems are air-gapped, which means that the computer has no physical or wireless connection. While this provides a layer of protection against cyberattacks, it isn’t flawless or impenetrable. An upgrade of the hardware or patching of a hardware system might create just the kind of opening that would enable a hacker to pounce.

The Nuclear Regulatory Commission and the industry are “aware of those scenarios,” Varuttamaseni said. “There are procedures in place and mitigation steps that are taken to prevent those kinds of attacks.” Ideally, however, the power plant would catch any would-be attacker early in the process. Varuttamaseni is working on three grants that are related to systems at nuclear power plants. In addition to cyberattacks, he is also analyzing software failures in the protection system and, finally, he’s also doing statistical testing of protection systems.

Varuttamaseni, who was born in Thailand, lives in Middle Island. He appreciates that Long Island is less crowded than New York City and describes himself as an indoor person. He enjoys the chance to read novels, particularly science fiction and mysteries. He also likes the moderate weather on Long Island compared to Bangkok, although threats from hurricanes are new to him. Next June, Varuttamaseni will present a paper on cybersecurity at the American Nuclear Society’s Nuclear Plant Instrumentation, Control & Human-Machine Interface Technology Conference in San Francisco.

Varuttamaseni is “always on the lookout for insights into possible attack pathways that an attacker could come up with,” he said. “The mitigating factor of my work is that we’re looking at a longer-term problem. There’s still time to [work with] many of these potential vulnerabilities.”

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Brookhaven Town Councilwoman Jane Bonner speaks at the Organ Donor Enrollment Day kickoff event at Stony Brook University Hospital Oct. 6. Photo from Bonner’s office

By Rebecca Anzel

Registered organ donors are hard to come by in New York state compared to the rest of the United States, and for one elected official in Brookhaven, that’s not going to cut it.

Brookhaven Councilwoman Jane Bonner (C-Rocky Point) did not hesitate when her friend Tom D’Antonio said he needed a kidney. She decided right then, at the Huntington Lighthouse Music Festival in Huntington Harbor in September 2015, that she would share her spare.

She underwent comprehensive medical testing at the end of the next month to determine if she would be a viable donor — a blood test, chest X-ray, electrocardiogram, CT scan, MRI, psychological evaluation and cancer screening, to name a few.

“It’s the ultimate physical you’re ever going to have, and by the blood test alone several people were disqualified,” Bonner said. “For once in my life, it turned out that I was No. 1. And it worked out really, really well.”

Brookhaven Town Councilwoman Jane Bonner and her friend Tom D’Antonio after their surgeries to transplant her kidney into his body in April. Photo from Jane Bonner
Brookhaven Town Councilwoman Jane Bonner and her friend Tom D’Antonio after their surgeries to transplant her kidney into his body in April. Photo from Jane Bonner

The surgery was April 26, a Tuesday, at New York Presbyterian Hospital. Bonnor was home that Friday and missed only eight days of work. She said she just had her six-month checkup and she is in good health.

“Jane didn’t just save my life, she saved my family’s life,” D’Antonio said. “Donating an organ doesn’t just affect the person getting the organ — although certainly it affects them the most — it affects everyone’s life.”

Bonner said she takes every opportunity to share her story to bring awareness about the importance of being an organ donor.

“I want to be a living example to show that it can be done because it’s life changing for the recipient and only a little inconvenient for the donor,” she said.

There is a large need for organs in New York. More than 9,700 people are on the organ waiting list, and someone dies every 18 hours waiting for one, according to LiveOnNY, a federally designated organ procurement organization.

New York ranks last among the 50 states in percent of residents registered as organ donors, despite surveys showing 92 percent of New Yorkers support organ donation. Only 27 percent of New Yorkers are enrolled in the state registry, versus the average of 50 percent registered across the rest of the country.

Stony Brook Medicine and Stony Brook University hosted the Organ Donor Enrollment Day event Oct. 6, including Bonner, in a statewide effort to boost the number of registered organ donors.

“Our residents need to be reminded about the importance of organ donation,” Suffolk County Executive Steve Bellone (D) said in a statement. “Along with stressing how one organ and tissue donor can save multiple lives, understanding and debunking the social and religious myths about organ donation are also critical to turning the tides in New York as we currently rank last in registered organ donors in the nation.”

Dawn Francisquini, transplant senior specialist for the hospital, said volunteers enrolled 571 people.

“New York has a very large population, so it’s going to take a lot to get us up to where the other states are,” she said. “But we’re making progress.”

There are two ways to become an organ donor. One is to be a living donor, like Bonner. A potential donor does not have to know someone in need of an organ to donate a kidney, lobe of liver, lung or part of a lung, part of the pancreas or part of an intestine.

“I’ve been able to accomplish really amazing things, but this is a step above that. Satisfying is not even the word to describe it.”

— Jane Bonner

“Living donation is so important because not only are you giving an organ to someone, so you’ve saved that life, but you’ve also made room on the list,” Francisquini said. “So you’ve saved two lives by donating one organ.”

The most common way is by registering when filling out a driver’s license registration or renewal form to be considered as a candidate upon death. According to the U.S. Department of Health & Human Services, though, only about three in 1,000 deceased people are suitable for organ donations.

Doctors determine whether organs like kidneys, livers, bones, skin and intestines are medically viable for a waiting recipient and they typically go to patients in the same state as the donor.

Gov. Andrew Cuomo (D) signed legislation Aug. 18 allowing 16 and 17-year-olds to register as organ donors. If they die before turning 18, parents or guardians are able to reverse the decision.

“By authorizing 16 and 17-year-olds to make the selfless decision to become an organ donor, we take another significant step to grow the state’s Donate Life registry and create opportunities to save lives,” Cuomo said in a statement.

Francisquini said she thinks this new law will make a big difference. Previously, because those under-18 were not allowed to express their wishes when filling out a driver’s license form, many would not register as donors until years later when renewing their license.

Since her surgery, Bonner has shared her story in speeches, panel discussions and on social media using the hashtag #ShareTheSpare.

“I really feel like this is much better than anything I could accomplish in my professional career,” she said. “Through the support of the people that keep electing me, I’ve been able to accomplish really amazing things, but this is a step above that. Satisfying is not even the word to describe it.”

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From left, Robert Catell, chairman of the board, Advanced Energy Research and Technology Center; Vyacheslov Solovyov; Sergey Gelman, a Stony Brook engineering student; and Yacov Shamash, vice president for economic development at Stony Brook University. Photo from Stony Brook University

By Daniel Dunaief

It’s lighter, cheaper and just as strong. In the age of manufacturing the latest and greatest high-technology parts, that is a compelling combination. Indeed, the Department of Energy recently awarded the Brookhaven Technology Group, a business incubator tenant of the Advanced Energy Research and Technology Center at Stony Brook University, $1.15 million to develop a high-temperature superconductor cable with a new architecture. The grant supports the research of Vyacheslav Solovyov, an adjunct professor in the Department of Electrical Engineering at SBU and the principal investigator at Brookhaven Technology Group.

“Very few projects are funded, so we’re very excited that ours was chosen,” said Paul Farrell, the president at BTG. The potential applications for Solovyov’s Exocable, as the new architecture is called, span a wide range of uses, including in high field magnets for a new breed of accelerator. The work entails creating a high-temperature superconducting cable that is an integral ingredient in creating the superconducting machinery. The BTG process produces a high-temperature superconducting cable after removing the substrate, which is a single-crystal-like material. Solovyov transfers the superconducting layer to a supporting tape that can be engineered for strength and not for crystallinity.

This work reduces the weight of the tape by as much as 70 percent per unit length for the same current capacity. The potential for this new cable is that it can contribute to the growing field of research at Stony Brook and Brookhaven National Laboratory on superconductivity, said Jim Smith, assistant vice president of economic development at Stony Brook. “Maybe this is the next industry that replaces the Grummans and the aerospaces that have left,” he said. Semiconductors are of particular interest to manufacturers because they transmit energy with no resistance. Right now, about 6.5 percent of energy transmitted around the United States is lost in distribution wires, Smith said. Maintaining the energy that’s lost in the wires would have “tremendous benefits.”

To be sure, while the research at BTG could contribute to lower cost and improved efficiency in high-temperature superconductivity, there are hurdles to making this process and the applications of it work. For starters, the company needs to produce kilometers of ExoCable. “The challenge is to demonstrate that the properties will be as uniform as they were before the substrate removal,” explained Solovyov, who has been working in superconductivity since 1986.

Recently, Smith said he, Farrell and Solovyov met to discuss the wiring for their facility. “A lot of power and wiring will be installed in the next four to five weeks,” Smith said. Scientists who worked with Solovyov expressed admiration for his work and optimism about his results. Solovyov’s “new activity will definitely advance the long-promised practical application of superconductivity electrical power transmission, as well as in the development of high-field magnets for both industrial and scientific application,” David Welch, a former collaborator and retired senior materials scientist at Brookhaven National Laboratory, wrote in an email. Welch explained that Solovyov focused on methods for making composites of superconducting material with normally conducting metals in the form of wires, tapes and cables necessary for their practical application. “Such a combination of talents is unusual,” Welch continued. Early on, it was clear “that [Solovyov] was going to become an important member of the scientific staff at BNL.”

Solovyov started working on this process with BTG about a year and a half ago. When he first started collaborating with BTG, the company was working on a superconducting project funded by the army. When that work ended, Solovyov and BTG worked together to submit new proposals to the DOE. According to Solovyov, Stony Brook has been “very helpful in terms of providing facilities and lab space.” Stony Brook’s goal, Smith said, is to help companies like BTG succeed and measures that success in the number of new jobs created in the energy field.

Solovyov, who grew up in the Ukraine, said he has had several breakthroughs in his career. He helped develop a patented technology that can speed up the processing of superconducting materials by a factor of 10. “That has been used in production and I’m very proud of it,” Solovyov said. The professor lives in Rocky Point with his wife Olena Rybak and their two children, Natasha, 19, who attends Suffolk County Community College, and Dennis, 14, who is in high school. Solovyov said he enjoys Long Island, where he can fish for striped bass and bluefish. He pan fries what he catches.

As for his work, Solovyov has four patents and applications for three more. He and Farrell said the company is looking for opportunities for expansion. He is exploring ways to work with large-scale generators and wind turbines. Farrell explained that BTG has ambitions to become a larger company. BTG would “like to become a major contributor in this field,” Farrell said. That could include adding staff and developing more products that can be sold and used worldwide. “If our product is successful, in the sense that it improves the capability of superconductors to be used commercially, we’ll be adding people.” This work will need more funding, which the company plans to get either from the Department of Energy, from private investors or both.

“If you can improve the usefulness of superconductors and reduce the cost of the wire, there’ll be wider use than there is right now,” Farrell said.

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Alfredo Fontanini in front of a poster of a neuron in his office. Photo from Alfredo Fontanini

By Daniel Dunaief

Pull into the parking lot of your favorite restaurant and you can almost taste the onion rings, the fresh baked bread or the steamed clams. The combination of the sign, the smell of the food piped out of the familiar building, and even the familiar voice of the restaurant owner welcoming you back is a hint of the experience of eating. Indeed, when these anticipatory stimuli are a part of the dining experience, they contribute to forming flavor.

Alfredo Fontanini, an associate professor in the Department of Neurobiology & Behavior at Stony Brook University, recently conducted research on rodents in which he explored how other senses — touch, taste, smell and sight — contributed to the part of the brain responsible for taste, the gustatory cortex.

In work published recently in the journal eLife, Fontanini demonstrated that rats who heard particular sounds, smelled odors, felt a puff of air against their whiskers, or saw the flash of an LED light before they ate showed increased activity in the gustatory cortex even before they started eating. If this experiment sounds familiar, it’s because Russian scientist Ivan Pavlov demonstrated the anticipation of food in conditioning experiments with dogs, showing that their digestive systems became active when they heard a tone before they ate, associating the sound with the presentation of food.

Dr. Alfredo Fontanini looks at slides of the gustatory cortex, the part of the brain that mediates the perception of taste. Photo from Stony Brook University
Dr. Alfredo Fontanini looks at slides of the gustatory cortex, the part of the brain that mediates the perception of taste. Photo from Stony Brook University

Fontanini took this research further, however, showing that the brain regions responsible for taste can, and did, show activity prior to eating. “As we paired the stimuli in a Pavlovian task, the animal would produce mouth movements and licks in response,” Fontanini said. These movements were not there right away, but developed after three to seven days of training, suggesting that the animal could infer taste. He recorded the responses of single neurons in the gustatory cortex. Before conditioning, the neuronal response in the gustatory cortex varied according to the sense stimulated. Prior to training, neurons in the gustatory cortex showed a 16 percent response, while that went up to 33 percent after learning. “This suggested that the stimulation was predictive of taste,” Fontanini said. “More neurons were integrating between all the stimuli.”

Donald Katz, a professor of psychology at Brandeis University who oversaw Fontanini’s graduate research for five years, suggested that his former student was one of a few neuroscientists studying how anticipation of an experience, knowing what’s coming, impacts how the brain handles that experience. This study, he explained in an email, “makes perfect sense — while few researchers study how different sensory systems work together, it is well-known that taste is linked to all of the other senses. It is of great evolutionary import that this be so,” because the animal that can recognize something good to eat at the greatest distance will be the one that eats.

Katz described Fontanini’s recent work as a “wonderful finding in that it provides a substantial, natural extension” to work completed in his lab, Katz’s lab and those of other scientists. In exploring which specific senses are most important to the gustatory reflex, Fontanini said olfaction and touch are considered more relevant for food-related decisions. “These are animals that use these senses to navigate their world and explore food,” he said.

In the bigger picture, Fontanini would like to understand how the brain integrates and fuses sensory perceptions with emotions. He explained that one of the tests in animal models of depression is to look at how much a test subject still likes something sweet. “Studying taste allows us to understand how the brain creates pleasure or creates aversion that negates emotions,” he said.

Fontanini plans to extend this study to additional research. He would like to know the neurological pathways that link the visual, auditory, somatosensory and olfaction senses that contribute to forming an expectation about taste. He is also eager to understand how the anticipatory activation influences the way taste is perceived. This, he explained, would be a way to explore how expectations shape perception.

Fontanini, who grew up in the town of Brescia, Italy, which is near Milan, arrived at this particular field of research because of his interest in understanding perception and emotion. He would like to explore how the brain creates emotions. Recognizing the multisensory element to taste and eating, Fontanini suggests that understanding how olfaction and taste can interact may lead to eating sweets where the smell enhances the flavor and taste, even of a lower-calorie dessert, like a piece of chocolate cake. “If you can leverage more of the odor and less” of the taste, “you can find a way of having that richness without the need for overwhelming sweetness.”

A resident of Setauket, Fontanini lives with his wife Arianna Maffei, who is an associate professor in the Department of Neurobiology & Behavior at Stony Brook and their 11-year-old son Carlo. Relying on vocabulary of the gustatory cortex, Fontanini suggested Long Island has a “soothing sweetness” that springs from the quaint and beautiful setting his family enjoys.

As for his work, Fontanini said studying taste in the brain is challenging. “What happens when you taste chocolate: are you activating chocolate neurons or are you activating a complex pattern of activity?” The answer, he said, describing taste while borrowing from another sense, is much more like a musical ensemble during a symphonic experience than like a solo. “Understanding how taste is represented in the cortex is incredibly complex,” he said.

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Front row, from left, Liliana Dávalos, Heather Lynch and Christine O’Connell; back row, from left, Robert Harrison, IACS director and STRIDE PI, Arie Kaufman, and Janet Nye. Photo from Stony Brook University

By Daniel Dunaief

If Stony Brook University has its way, the university will stand out not only for the quality of the research its graduate students produce but also for the way those budding scientists present, explain and interpret their results to the public and to policy makers.

Pulling together faculty from numerous departments across the campus, Robert Harrison, the director of the Institute for Advanced Computational Science, created a program that will teach graduate students how to use big data sets to inform difficult decisions.

The institute recently received a $3 million grant from the National Science Foundation Research Traineeship for this effort, called Science Training & Research to Inform DEcisions, or STRIDE. The grant will be used for students in the departments of Applied Mathematics and Statistics, Biomedical Informatics, Computer Science, Ecology and Evolution and the schools of Journalism and Marine and Atmospheric Sciences.

“This is unique,” said Arie Kaufman, a distinguished professor and chair of the Department Computer Science at Stony Brook. “It’s a new kind of approach to training and adding value to Ph.D. students.” Indeed, the students who complete the STRIDE training will earn their doctorates and will also receive a certificate for their participation in this program. Students in the participating departments will need to apply for one of the 10 positions available in the program next year. The partners involved in this program expect it to expand to 30 students within five years.

Kaufman said what enabled this collaboration was the range of skill sets across Stony Brook, including the Alan Alda Center for Communicating Science, which is a growing program that already offers the type of training more typical for an actor studying improvisation techniques than for a scientist studying neurotransmitters or DNA.

The Alda Center is “creating a new course,” said Christine O’Connell, an associate director at the center and assistant professor in the School of Journalism. She is currently working on developing the course description, which will include communicating to decision makers. O’Connell, who has a doctorate in marine and atmospheric sciences, sees her work with the Alda Center and with STRIDE as the “perfect combination in bringing the decision making piece to work with scientists to help them talk about their research.”

Scientists who take courses at the Alda Center with STRIDE learn how to understand their audience through various role-playing scenarios. They will also develop their abilities to present their goals or messages in a visual way and not just talk about their work.

Heather Lynch, an associate professor in the Department of Ecology and Evolution who is also a co-principal investigator on the STRIDE grant, will help design the program, mentor students and develop courses. She’s been involved with this proposal since its inception, over three years ago. “In many ways,” she explained in an email, “my interest stems from my own difficulties communicating effectively with policy makers, and finding tools and visualizations that are compelling to a non-scientist.” Lynch recounted her frustration with presenting science to help a policy making body, such as a committee, with the kind of analysis she believed they were seeking. After she did her best to answer the question, the committee sometimes dismissed her work as not being what they wanted. “That’s frustrating because that means I failed at the outset to define the science question and that’s what I hope we can teach students to do better,” Lynch explained.

Lynch said she wishes she had the training these students will be getting. For scientists, computers are an invaluable tool that can help delve into greater breadth and depth in analyzing, interpreting and collecting information. The STRIDE effort includes a greater awareness of the way computers can inform political or social science. Researchers generate “tremendous amounts of data that can be used to analyze trends or detect diseases,” Kaufman said. “The data science is tremendous in every discipline.”

The faculty who are a part of this program said they have already benefited from the interactions they’ve had with each other as they’ve developed the curriculum. “I know a few people in Ecology and Evolution and I know more people in Marine Sciences, but these particular individuals were new to me,” said Kaufman. “We have already been communicating about ideas for how to use the Reality Deck for other projects.”

Completed in late 2012, the Reality Deck is a $2 million rectangular room in the Center of Excellence in Information Technology building. The room has hundreds of monitors that cover the wall from floor to ceiling and provides a way for researchers to study images in exquisite detail.

Other scientists in the program include Liliano Dávalos, an associate professor in the Department of Ecology and Evolution, Janet Nye, an assistant professor in the School of Marine and Atmospheric Sciences, Joel Saltz, the founding chair of the Depatment of Biomedical Informatics, Erez Zadok, a professor in the Department of Computer Science and Mighua Zhang, a professor in the School of Marine and Atmospheric Sciences.

Lynch said the program will bring in people who are working on real-world problems, including those in government, industry and nongovernmental organizations who are “in a position to take science and use it for practical purposes.” As a part of the program, the scientists will monitor the progress of the STRIDE candidates, O’Connell said.

The evaluations will check to see if “they become better communicators and better at interpreting their data for different audiences,” O’Connell said. “The evaluation piece built in will help us assess the program.”

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From left, Lorne Golub, Joseph Scaduto, Francis Johnson, Ying Gu, Hsi-Ming Lee and Maria Ryan. Photo courtesy of Stony Brook Medicine

By Daniel Dunaief

You might not be able to teach an old dog new tricks for a variety of reasons, including that your old dog might be suffering from periodontal disease. An inflammatory condition of the mouth that affects about 80 percent of dogs by the age of three, periodontal disease often starts out as gingivitis, a swelling or reddening of the gums, and then proceeds to affect the soft and hard tissues that support teeth.

Scientists and dentists at Stony Brook have developed a new treatment for periodontal disease for dogs, and, they hope, eventually for humans. The National Institute of Dental and Craniofacial Research, a unit of the National Institutes of Health, recently awarded Stony Brook University’s School of Dental Medicine and Traverse Biosciences Inc., a Long Island research company, a $1.3 million award to continue to evaluate the preclinical safety and effectiveness of TRB-NO224 to treat periodontal disease.

“The grant was approved for funding because a panel of nationally prominent dental and medical scientists agreed that our grant proposal, and our qualifications and academic records were exemplary,” Lorne Golub, a distinguished professor in the Department of Oral Biology and Pathology explained in an email. Golub, who holds 55 patents and developed Periostat and Oracea, will lead the research, along with Ying Gu, an associate professor in the Department of General Dentistry at SBU.

While periodontal disease affects dogs, it is also widely prevalent among humans, with Golub calling it the “most common chronic inflammatory disease known to mankind.” Indeed, developing effective treatments is important not only for oral health, but it has implications for other conditions that are complicated or exacerbated by the collagenase enzyme prevalent in periodontal disease.

“Some studies indicate that chronic periodontitis can increase the risk for pancreatic cancer, head and neck cancer, cardiovascular disease and others,” Golub wrote in an email. “All of these diseases result in an increase in collagenase.”

A challenge in treating periodontitis is that the enzyme that is a part of the inflammatory response, collagenase, is present, and necessary, in normal metabolism. Ridding the body of the enzyme would cause harm. Golub worked with Francis Johnson, a professor of chemistry and pharmacological sciences at Stony Brook, to develop a new treatment using a modified form of curcumin, which is a bright yellow chemical that is a member of the ginger family. Naturally occurring curcumin does provide some benefit for periodontal diseases, Golub said, although the modified version Johnson helped create is more effective. “Very little” curcumin is absorbed from the gut into the blood stream after oral administration, Golub said.

The modification Johnson and Golub made was to make their variant triketonic. With the extra ketone, which has a negative charge, the attraction for zinc and calcium, which are a part of collagenase and have positive charges, is stronger, Golub said.

In dividing the work, Gu explained that Golub will supervise personnel, coordinate and oversee all experiments and provide technical oversight for the animal experiments and biochemical analysis. Gu will work with Hsi-Ming Lee, a research assistant professor in oral biology and pathology, to perform in vivo animal experiments and the biochemical analyses of pro-inflammatory mediator levels on blood, gingival fluid and gingival tissue samples. He and Golub will perform data analysis and prepare publications together. The scientific team involved in the study of TRB-NO224, which includes Maria Ryan, the chair of the Department of Oral Biology and Pathology, intends to develop this treatment for pets first. This, Golub suggested, was in part because the approval process for pet treatments is quicker to market.

The group hopes additional research, including safety and efficacy studies, will lead them to apply to the Food and Drug Administration for human uses. Ryan, who worked as a graduate student in Golub’s lab before she became the head of the department, is pleased with the process and the track record of a department Golub helped start in 1973.

“I am proud to say that this is Department of Oral Biology and Pathology’s fourth NIDCR grant for the development of new therapeutics for the management of periodontal diseases within the past four years,” Ryan wrote in an email. “The aim of this funding mechanism is to move these novel compounds further along in the FDA drug development process.” Ryan added that the benefits of TRB-NO224 extended to other medical arenas and has led to collaborations with additional scientists. TRB-NO224 not only impacts enzymes such as collagenase, but also affects pro-inflammatory mediators, she said.

“This new compound may be useful at preventing and/or treating numerous chronic conditions,” Ryan said. Studies are currently funded to investigate indications for osteoarthritis with the director of Orthopaedic Research, Daniel Grande, at the Feinstein Institute and for acute respiratory distress syndrome with Gary Nieman at SUNY Upstate Medical University in Syracuse. Golub has worked with international collaborators for decades. Some of them praised his legacy and the work he’s continuing to do.

Golub’s patents reflect his “everlasting translational mission from molecular and biotechnological medical/dental research to doctors’ daily and every-day practice,” wrote Timo Sorsa, the Chief Dental Officer in Periodontology at the University of Helsinki Central Hospital in Finland in an email. Golub received an honorary M.D. from the University of Helsinki in 2000.

A resident of Smithtown, Golub lives with his wife Bonny, who is a travel agent. They have two children, Marlo and Michael, and four grandchildren. Golub and his wife were among the first to see a showing at the New Community Cinema in Huntington, now the Cinema Arts Centre, in their own folding chairs. They watched one of Golub’s favorite films, “Henry V,” with Sir Laurence Olivier.

Golub is optimistic about the prospects and progress on TRB-NO224. “We are beginning to see evidence of efficacy in a variety of diseases,” he offered. He also believes the treatment may have rapid acceptance because natural curcumin has been used for decades in a number of populations and is “believed to be safe and effective.”

The content in this version has been updated from the original.

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Participants at the SASI Family Fun Day held last month in Huntington. Photo by Rebecca Anzel

By Rebecca Anzel

A young scientist at Stony Brook University has received a $2.3 million grant to fund research he hopes will eventually lead to new therapies for the treatment of autism spectrum disorder.

Matthew Lerner, Ph.D., is an assistant professor of clinical psychology at Stony Brook University, and director of the Stony Brook Social Competence and Treatment Lab, the focus of which is learning to understand how children and teens with ASD form friendships.

“We use the word lab loosely, only because we collect data there,” he said. “It’s a fun space with games and activities for kids.”

“Matthew Lerner is sort of a pioneer in his thought process, and that’s what makes him special to me.”

— Priscilla Arena

His work thus far has ranged from lab-based studies — evaluating and developing tools to measure what is happening during social interactions and how the brain processes those interactions — to real-world applications. Lerner’s previous studies ask how, when and if kids make friends, and what helps them do so.

Efforts to link these two levels of analysis have never been done simultaneously — until now. Lerner won a highly competitive National Institute of Mental Health award to fund his innovative approach to studying social behaviors of children with ASD.

“It’s kind of remarkable that it really hasn’t been done in quite this way before,” he said. “We presume that these things — lab-based measures of how kids think about social interactions and real world interactions themselves — are linked, because otherwise, why would we look at them? But how they’re linked, and importantly, how we can understand how those links differ across individuals, hasn’t really been done thoroughly before.”

Priscilla Arena, the leader of a support group for parents of children with ASD, said Lerner is excited about the potential the grant gives his research.

“Matthew Lerner is sort of a pioneer in his thought process, and that’s what makes him special to me,” she said. “He sees potential in the future.”

It’s not far from her initial reaction after meeting with the Stony Brook researcher, who asked permission to speak to the parents in her group.

The Suffolk Aspergers/Autism Support and Information co-founder wanted to protect the parents, who have “already been beaten and kicked” by others looking for monetary donations and permission to study their children. But when she met Lerner, she said she knew almost immediately that he was different.

“He’s sincere, honorable, impassioned, smart and cerebral,” Arena said. “I don’t think my first impression of him has ever changed, and I think that’s why, from the get-go, I’ve had respect for him.”

The award, called Biobehavioral Research Awards for Innovative New Scientists, was created in 2009 as a way to provide younger scientists with financial support for research. It is for early-stage investigators who are on a tenure track and have no prior research project grants.

“BRAINS” is earmarked for “the most promising early investigators” and is “one of the most competitive [awards]” NIH offers, according to Lisa Gilotty, Ph.D., program officer of Lerner’s grant. Gilotty is also the chief of NIMH’s research program on autism spectrum disorder.

Matthew Lerner is enthusiastic about finding treatments for those with autism spectrum disorder. Photo from Matthew Lerner
Matthew Lerner is enthusiastic about finding treatments for those with autism spectrum disorder. Photo from Matthew Lerner

Lerner is examining how well various biological and social factors, both independently and jointly, can predict how teenagers aged 11 to 17, with and without ASD, socially interact outside of a laboratory. In the five-year project, he and his team are also studying how those factors correlate, and which best explain the resulting social behaviors.

They are hoping to use information gleaned by observing the teenagers inside and outside the lab to make precise predictions about how they make friendships.

Depending on the results, the team might be able to develop generalized patterns that can be applied to a large number of people on the spectrum and be used to create more targeted therapies.

“This is an extremely important study that will shed light on the wide variability observed in social function in ASD,” said James McPartland, director of the Yale Developmental Disabilities Clinic. “Presently, little is understood about the biological reasons for these individual differences. Dr. Lerner’s study will help us understand these differences from both behavioral and brain-based perspectives.”

Dozens of the 260 teenagers — 160 with ASD and 100 without — participating in this study are Three Village students. Lerner and his team have also connected with special educators in the area to see how participants are doing outside the lab in a classroom.

He and his team spend a lot of time in the community, at family events and meetings with parents and educators to introduce themselves, share information about their work and to learn what challenges children are experiencing. Because Lerner wants the work he does to matter to parents and community members, he calls them “stakeholders” in his research.

“The most impressive thing about him is how community-minded he is,” President and Executive Director of Asperger Syndrome and High Functioning Autism Association (AHA) Patricia Schissel said. “It is important that he’s not stuck in a lab. He’s excited to get out into the research community.”

Arena said quite a few study participants are from SASI as well — her son included. Besides hosting support groups, the program, which was co-founded by Arena with Stephanie Mendelson, provides resources and runs events and programs for special needs families.

Arena and her son were asked to complete a 500-question survey as part of the screening process, and have committed to 20 weeks of social groups.

What appealed to her about this study is Lerner’s concentration on trying to develop more effective treatments and therapies for ASD as opposed to looking for a cure.

“I always say, unless you’re going to do a lobotomy, [saying there is a cure] is baloney,” she said. “You can calm certain conditions of it down through behavior modification and therapy, but you cannot cure it. There’s no way to reverse how the brain has been formed. My son will have it forever.”

Schissel said Lerner’s study has the potential to change treatment options for those with autism as genome sequencing did for cancer.

Oncologists previously “threw the kitchen sink” at cancer and attacked tumors broadly. Once genome sequencing was developed, doctors could instead more easily treat tumors directly. Such an approach to ASD therapies would be more effective and “waste less time and enormous amounts of money,” she said.

Michael Greenberg, a social worker for outpatient child and adolescent psychiatry at Stony Brook Medicine, agreed that more specific treatments and therapies are more efficient and effective.

“It creates an opportunity to have the odds be the best the first time,” he said. “No one can predict what he’s going to find, but he’s trying to come up with something that can be replicated and benefit people more widely.”

The results from Lerner’s study might also be applicable to children without ASD. He said it is unclear whether the social patterns he and his team might uncover are unique to kids with autism. There is a potential for any treatments that stem from his findings to benefit any kid who struggles socially.

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Ivan Bozovic. Photo courtesy of BNL

By Daniel Dunaief

How long and how much work does it take to defy conventional wisdom? Often, the prevailing belief about anything has backers who support the idea and aren’t eager to change or replace what they know with something new.

Recognizing this, Ivan Bozovic, the Oxide Molecular Beam Epitaxy (MBE) group leader at Brookhaven National Laboratory, checked and rechecked his work, spending close to a decade for parts of it, repeating his steps and checking the accuracy of his data points to make sure his case, which flew in the face of what so many others believed, was airtight.

Engineers, researchers and corporations have known about so-called high-temperature superconductivity for over a century. Using objects called cuprates, which are oxides of copper, researchers have created substances that can conduct electricity with close to no resistance at temperatures that are well above the requirements for most superconductivity.

While the name high-temperature superconductivity might suggest materials that allow the passage of energy through them in a sauna, the reality is far from it, with the temperatures coming in closer to negative 163 degrees Fahrenheit. While cold by everyday standards, that is still well above the record critical temperature before cuprates, which stood at – 418 degrees F.

Up until Bozovic’s study, which was recently published in Nature, scientists believed superconductivity in these cuprates occurred because of the strength of electron pairing. Carefully and in great detail, Bozovic demonstrated that the key factor in leading to this important property was the density of electron pairs, which are negatively charged particles.

Other scientists suggested Bozovic’s study was an important result that flew against the prevailing explanation for a phenomenon that holds promise for basic science and, perhaps one day, for the transmission of energy in the future.

Bozovic’s study “shows that [the] standard picture fails quite astonishingly in copper oxides that show high temperature superconductivity,” Davor Pavuna, a professor at the Swiss Federal Institute of Technology at Lausanne, explained in an email. “We are only begining to grasp how dramatic” this latest discovery is.

Pavuna described how he was recently at an event in Corsica, France and that his colleagues believed “this is a clear signal that we will have to develop much more advanced theoretical framework for cooperative phenomena, like superconductivity.”

Bozovic’s work and his latest result “show that our physics understanding and models require some new physics framework,” Pavuna said.

Bozovic and his colleagues studied over 2,150 samples. He explained that cuprates are complex for standards of condensed matter physics because some of them have 20 to 50 atoms in unit cells. That means that when engineers synthesize them, cuprates can have a mixture of unwanted secondary phases that could “spoil the experiment.”

Ivan Bozovic with his granddaughter Vivien at Vivien’s first birthday party last year in California. PhotoPhoto by Julie Hopkins, cameracreations.net
Ivan Bozovic with his granddaughter Vivien at Vivien’s first birthday party last year in California. Photo by Julie Hopkins, cameracreations.net

The number of samples necessary to demonstrate this property is a matter of personal standards, Bozovic suggested. He made sure he kept “checking and double checking and triple checking to be sure that what we had closed all the loopholes,” Bozovic said. He wanted “no possibility of an alternative explanation.”

The way Bozovic and his colleagues approached the problem was to start with a cuprate composition. They then replaced one atom at a time by another, which provided a series of samples that were almost identical, but slightly different in chemical composition. He was able to show how the critical temperature changes with electron density in small increments.

“What’s really impressive here is [Bozovic’s] ability to use a molecular beam epitaxy system — that he designed — to place single atomic layers on to a substrate, layer by layer,” James Misewich, the associate lab director for Energy & Photon Sciences at BNL explained in an email.

Bozovic’s work is “an exciting finding that could have wide-ranging impacts on how we identify, design, and build new superconducting materials,” continued Misewich.

As with other science, Bozovic said the answer to one question leads to a series of follow up questions, which include why do small pairs of electrons form in cuprates and not in anything else.

A resident of Mount Sinai, Bozovic lives with his wife Natasha, who is a mathematician. The couple has two daughters, Dolores, a professor of Physics and Astronomy at UCLA and Marijeta, an assistant professor of Slavic Languages and Literatures at Yale, where Bozovic is an adjunct professor of Applied Physics.

Born and raised in the former Yugoslavia, Bozovic is the son of two medical doctors. His father, Bosislav Bozovic, was twice nominated for the Nobel Prize for his work on the relation between cancer and the immune system. He was also a major general in the medical corp and the head of the Medical Division of the National Academy of Sciences.

His mother, Sasha Bozovic, wrote a best-selling memoir, devoted to a daughter she lost in World War II. His mother was also a colonel in the medical corps who worked in the army until she retired as the highest ranking woman in the army. “I had some big shoes to fill,” Bozovic acknowledges.

As a teenager, Bozovic played the lead guitar in a rock band. Nowadays, he strums nursery rhymes for his granddaughter Vivien using FaceTime.

A scientist who suggests a sense of humor is extremely important, especially in a field that can include disappointments and setbacks, Bozovic jokes that he speaks “zero” languages, a conclusion he reached after listening to an online description he gave of his recent work. In reality, he can read about four languages, although he has studied more.

As for his work, Bozovic is looking forward to discussing his recent results with theorists like Gabriel Kotliar, a Rutgers Professor of Physics and Astronomy who has a part time position at BNL. Kotliar is leading a new materials theory center at BNL.

“I hope that we’ve given them new pointers about where to look and what to calculate,” Bozovic said. “I’m pretty optimistic that there will be feedback from them.”

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Tony Zador. Photo courtesy of Cold Spring Harbor Laboratory

By Daniel Dunaief

For some people, the frontier lies deep in space, further than the eye can see. For others, the frontier resides at tremendous pressure beneath the surface of the ocean. For Tony Zador, the chair of neuroscience and professor of biology at Cold Spring Harbor Laboratory, the frontier is much closer to home, in the collection of signals in our brains that enable thought and direct our actions.

Recently, Zador and his research team helped explore that frontier, developing a technological innovation that allowed them to see where nervous system cells from one important region projected into other areas.

About six years ago, Zador came up with the idea to barcode the brain. Zador and his former graduate student Justus Kebschull explored the connections between the locus coeruleus (LC) and other parts of a rodent brain. The LC is responsible for reacting to stressful situations, allowing an animal to stimulate areas that might help save its life, including those responsible for visual or auditory processing.

Researchers believed that the intercom system that connected the LC to the rest of the brain could stimulate all areas at once, like a building-wide announcement coming over the public address system. What scientists didn’t know, however, was whether that communication system could send messages to individual areas.

“People knew before our work that neurons in the locus coeruleus broadcast their signals throughout the cortex,” Zador said. “What was not known was whether there was any specificity. It was always assumed.”

Zador found that individual neurons had precise connections to different parts of the brain. While this doesn’t prove that the LC can selectively activate one area, the way a superintendent might send a signal to one wing of a building, it demonstrates the specificity of the connections, which “raises the possibility” of selective signals.

Indeed, if each neuron diffusely spread out across the entire cortex, there would be no way to achieve localized control over cortical functions through the LC system. The visual cortex, for example, would be alerted at the same time as the auditory and frontal cortex.

Ultimately, Zador is interested in the brain’s neuronal network. The way nervous system cells communicate in our brains can help us understand how we process and interact with the world around us. Down the road, he is hoping to help create something called a connectome, which will provide a map of that network.

This information, at a basic level, could provide a better understanding of neurological conditions such as autism, schizophrenia, depression and addiction.

At this stage, however, Zador is building a network called the projectome, which provides a map of the specific regions neurons go in the brain. He collects this information by inserting a deactivated virus with a unique genetic code into the brain. These viruses act as a label, allowing Zador and his colleagues to trace the areas where individual neurons go. This technique, he said, doesn’t indicate whether neuron one is connected to neuron two, three or four, but, rather, it indicates whether neuron one is connected to a bunch of neurons in regions one and two but not in three and four.

Zador “had to develop a method of bar coding each neuron so that it is unique and a technique of detecting each bar code individually,” said Bruce Stillman, the president and chief executive officer of Cold Spring Harbor Laboratory. By collecting numerous samples of where these neurons go, Zador, his collaborators and other scientists can determine the natural range of variability for animal models of individuals with typical behaviors and reactions. Once they establish that range of typical wiring, they can compare that to animal models of neurological challenges, like autism. Zador wants to “create a baseline against which we can compare neuropsychiatric models of disease.”

Stillman explained that Zador’s focus at CSHL has been on cognition — how the brain makes decisions, retains memory and pays attention to tasks at hand. Zador, Stillman suggested, is “one of the pioneers in establishing the rodent cognition area.”

To understand cognition, however, Zador needed to see what regions of the brain are connected to other areas, providing a road map of the brain. Even though he didn’t have a background in molecular biology, Zador benefited from working with specialists at CSHL to create this bar coding, Stillman explained. Stillman described Zador as “bright” and “broad thinking.”

Zador said the next step in his work will be to relate the projections to the individual cells’ function in the brain. He would also like to see their neuron-to-neuron connectivity. He said he is pursuing both goals and hopes to submit a paper in the next month or two describing such a method for the first time.

“Although we can sequence the codes” from neighboring neurons, “we still have work to do to figure out connectivity,” Zador said. “That involves significant molecular tricks that we’re refining.”

Georgio Ascoli, a collaborator with Zador and the director of the Center for Neural Informatics at the Krasnow Institute of Advanced Study at George Mason University, described Zador as an “internationally renowned, highly respected scientist,” whose best known contributions relate to the challenge of understanding how the brain can seamlessly decide which stimuli in a varied environment like a cocktail party to listen to among numerous choices.

A resident of Laurel Hollow, Zador lives with his wife Kathy Shamoun, who practices Chinese medicine at CSHL and is a childbirth educator and doula. The couple has two sons, Ronin, 10, and Bowie, 6.

As for the benefits of this bar-coding approach, Ascoli explained that the technique is “potentially revolutionary because of its inherent scalability to full mammalian brain mapping, which is currently out of reach for alternative approaches.”

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