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Daniel Dunaief

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Esther Takeuchi with photo in the background of her with President Obama, when she won the 2009 National Medal of Technology and Innovation. Photo courtesy of Brookhaven National Laboratory

By Daniel Dunaief

Pop them in the back of a cell phone and they work, most of the time. Sometimes, they only do their job a short time, discharge or generate so much heat that they become a hazard, much to the disappointment of the manufacturers and the consumers who bought electronic device.

Esther Takeuchi, a SUNY distinguished professor in the Departments of Chemistry and Materials Science and Engineering and the chief scientist in the Energy Sciences Directorate at Brookhaven National Laboratory leads a team of scientists who are exploring what makes one battery work while another falters or fails. She is investigating how to improve the efficiency of batteries so they can deliver more energy as electricity.

Esther Takeuchi with a device that allows her to test batteries under various conditions to see how they function. Photo courtesy of Brookhaven National Laboratory

The process of manufacturing batteries and storing energy is driven largely by commercial efforts in which companies put the ingredients together in ways that have, up until now, worked to produce energy. Scientists like Takeuchi, however, want to know what’s under the battery casing, as ions and electrons move beneath the surface to create a charge.

Recently, Takeuchi and a team that includes her husband Kenneth Takeuchi and Amy Marschilok, along with 18 postdoctoral and graduate students, made some progress in tackling energy storage activity in iron oxides.

These compounds have a mixed track record among energy scientists. That, Takeuchi said, is what attracted her and the team to them. Studying the literature on iron oxides, her graduate students discovered “everything from, ‘it looks terrible’ to, ‘it looks incredibly good,’” she said. “It is a challenging system to study, but is important to understand.”

This offered promise, not only in finding out what might make one set of iron oxides more effective in holding a charge without generating heat — the energy-robbing by-product of these reactions — but also in providing a greater awareness of the variables that can affect a battery’s performance.

In addition to determining how iron oxides function, Takeuchi would like to “determine whether these [iron oxides] can be useful and workable.” Scientists working with iron oxides didn’t know what factors to control in manufacturing their prospective batteries.

Takeuchi said her group is focusing on the linkage between small-scale and mesoscale particles and how that influences battery performance. “The benefit of iron oxides is that they are fairly inexpensive, are available, and are nontoxic,” she said, and they offer the potential of high energy content. They are related to rust in a broad sense. They could, theoretically, contain 2.5 times more energy than today’s batteries. “By understanding the fundamental mechanisms, we can move forward to understand their limitations,” she said, which, ultimately, could result in making these a viable energy storage material. T

akeuchi is also looking at a manganese oxide material in which the metal center and the oxygen connect, creating a tube-like structure, which allows ions to move along a track. When she started working with this material, she imagined that any ion that got stuck would cause reactions to stop, much as a stalled car in the Lincoln Tunnel leads to long traffic delays because the cars behind the blockage have nowhere to go.

Takeuchi said the ions don’t have the same problems as cars in a tunnel. She and her team believe the tunnel walls are porous, which would explain why something that looks like it should only produce a result that’s 5 percent different instead involves a process that’s 80 percent different. “These escape points are an interesting discovery, which means the materials have characteristics that weren’t anticipated,” Takeuchi said. The next step, she said, is to see if the researchers can control the technique to tune the material and make it into the constructs that take advantage of this more efficient flow of ions.

Through a career that included stops in Buffalo and North Carolina and West Virginia, Takeuchi, who has over 150 patents to her name, has collected numerous awards and received considerable recognition. She won the 2009 National Medal of Technology and Innovation, a presidential award given at a ceremony in the West Wing of the White House. Takeuchi developed compact lithium batteries for implantable cardiac defibrillators.

Takeuchi is currently a member of the National Medal of Technology and Innovation Nomination Evaluation Committee, which makes recommendations for the medal to the president. Scientists who have known Takeuchi for years applaud the work she and her team are doing on Long Island. “Dr. Takeuchi and her research group are making great advances in battery research that are very clearly promoted by the strong relationship between Stony Brook and BNL,” said Steven Suib, the director of the Institute for Materials Science at the University of Connecticut.

Indeed, at BNL, Takeuchi has used the National Synchrotron Light Source II, which became operational last year. The light source uses extremely powerful X-rays to create incredibly detailed images. She has worked with three beamlines on her research. At the same time, Takeuchi collaborates with researchers at the Center for Functional Nanomaterials at BNL.

Although she works with real-world experiments, Takeuchi partners with scientists at Stony Brook, BNL and Columbia University who focus on theoretical possibilities, offering her an insight into what might be happening or be possible. There are times when she and her team have observed some interaction with batteries, and she’s asked the theorists to help rationalize her finding. Other times, theorists have suggested what experimentalists should search for in the lab.

A resident of South Setauket, Takeuchi and her husband enjoy Long Island beaches. Even during the colder weather, they bundle up and enjoy the coastline. “There’s nothing more mentally soothing and energizing” than going for a long walk on the beach, she said.

In her research, Takeuchi and her team are focused on understanding the limitations of battery materials. Other battery experts believe her efforts are paying dividends. Suib said the recent work could be “very important in the development of new, inexpensive battery materials.”

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From left, David Tuveson with Kerri Kaplan, the executive director and chief operating officer of the Lustgarten Foundation, and Sung Poblete, the CEO of Stand Up to Cancer. Photo courtesy of the Lustgarten Foundation

By Daniel Dunaief

Even as David Tuveson was recently fishing for tautog for dinner, he conducted conference calls on a cellphone while watching the clock before an afternoon meeting. A professor at Cold Spring Harbor Laboratory and a world-renowned expert in pancreatic cancer, Tuveson describes the research of some of the students in his laboratory as having considerable bait in the water.

The director of research for the Lustgarten Foundation, Tuveson recently assumed greater responsibility for a larger boat, when he was named director of the Cancer Center at Cold Spring Harbor Laboratory, taking over a role the lab’s president Bruce Stillman held for 25 years. The Cancer Center, which is one part of CSHL, will be in “great hands since Dave Tuveson has wide respect int he cancer community because of his research accomplishments and his talents in leading others,” Stillman explained in an email.

Stillman, who will continue to run his own lab and serve as the President and CEO of CSHL, described Tuveson as a “thought leader” and a “great scientist.” Tuveson and his team of 20 in his laboratory are approaching pancreatic cancer in several directions. They are searching for biomarkers for early detection, developing and testing drugs that preferentially target cancer cells and seeking to uncover the molecular pathways that turn a mutated gene, inflammation, or an illness into a tumor.

Tuveson, who has MD and PhD degrees, focuses on finding ways to use science to help patients. He will continue the Cancer Center’s mission to understand the fundamental causes of the disease, while adding some new strategies. He plans to develop nutrition and metabolism as new areas for the Cancer Center and will recruit “ a few outstanding faculty,” he explained in an email.

CSHL will also expand its skills in immunology and chemistry. Tuveson has dedicated himself and his laboratory to taking innovative approaches to a disease that had received only one-half of 1 percent of the National Cancer Institute’s annual research budget in 1999. That is up to 2 percent today, according to the Lustgarten Foundation, which is the largest private funder of pancreatic cancer research.

Tuveson and his team have become leaders in the developing field of organoids. By taking cells from a tumor or cyst, scientists can produce a smaller copy of the tumor from inside a partial, reproduced patient pancreas. The painstaking work enables researchers to look for the specific type of tumor in a patient, while it also provides a model for testing drugs that might treat the cancer. The technique of growing organoids has become so refined that researchers can create a structure that’s a mix of normal, healthy cells blended with the tumor.

Scientists can then take the resulting structure, called a chimera, and test the effectiveness of therapies in destroying cancers, while monitoring the side effects on healthy cells. Stillman believes Tuveson’s work with pancreas cancer organoids “is at the cutting edge of research in this area.” Tuveson’s lab is using organoids to study what Tuveson, for whom metaphors roll off the tongue as often as characters break into song in Disney movies, describes as kelp-like projections. Each cell has parts that project out from the membrane. His staff is looking for changes in the kelp.

Tuveson is encouraged by work that might help find a subtle protein shift, or changes in the structure of the kelp, as a telltale sign about the type of tumor a patient who is otherwise asymptomatic might have. Doctors might one day screen for these during annual physical exams. Other scientists are so interested in the potential benefits of these organoids that they are attending a training session in Tuveson’s lab that started early this month.

A post doctoral candidate in Tuveson’s lab, Christine Chio, is studying how reactive oxygen affects the growth and stability of cancer. In general, medical professionals have recommended antioxidants to protect health and prevent disease. In pancreatic cancer, however, antioxidants are necessary to keep cancer cells alive. An abundance of reactive oxygen can cause cancer cells to shut down.

“The irony is that cancer cells make their own anti-oxidants and are very sensitive to reactive oxygen — thus we use reactive oxygen to kill cancer cells,” Tuveson explained. Chio, Darryl Pappin, a research professor at CSHL, and several other scientists published their work this summer, in which they identified protein translation as the pathway protected from reactive oxygen species in cancer cells.

At the same time that Tuveson is overseeing the work searching for biomarkers and treatments in his lab, he is also encouraging other research efforts through his work with the Lustgarten Foundation. Started in 1998 when former Cablevision executive Marc Lustgarten developed pancreatic cancer, the Foundation invested $19.4 million in 2015 to pancreatic cancer research and is projected to invest $21 million in 2016.

The mission of the Foundation is to advance research related to the diagnosis, treatment and cure of pancreatic cancer. It also offers patient advice, information and a sense of community through events. Indeed, recently, as a part of a phase 2 clinical trial at Johns Hopkins Kimmel Center, the Foundation offered to provide a free genetic test for microsatellite instability, or MSI, to anyone who might benefit from it as a part of a diagnosis and treatment. MSI occurs in about 2 percent of pancreatic cancer patients. Those with this genetic characteristic responded to a particular type of treatment, called pembrolizumab. The study is still seeking to increase enrollment.

The Foundation is encouraged by the progress scientists like Tuveson have made. “We are hopeful about the future because we know that we have the most talented cancer researchers working on this devastating disease,” Kerri Kaplan, the President and Chief Operating Officer at the Lustgarten Foundation, explained in an email. “We are particularly optimistic about the organoid project and the implications it has for more effective treatments and the work being done on our ‘earlier’ detection program.”

Still, Tuveson and the Foundation, which received donations from 62,000 people in 2015, realize there’s a long way to go. “Pancreatic cancer is an incredibly complex and difficult disease which is why we need to stay focused on funding the most promising research,” Kaplan said.

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Above, Shyamalika Gopalan. The image on the screen shows methylation levels with age. Photo by Casey Youngflesh

By Daniel Dunaief

The Museum of Natural History in New York City features a slice of a 1,400-year-old sequoia tree that was cut down in California in 1891. The cross section of the tree offers a testament to history on its inside. That’s where the tree rings that grow every year mark the passing of another year. As it turns out, humans have something in common with trees. While people may not have rings in bones that an observer can see, they do have age-related changes in their genetic material, or DNA.

Human genes go through a process called methylation in which a methyl group comprised of a carbon and three hydrogens attaches to DNA. Methylation upstream of a gene generally reduces transcription, or the copying of that gene into messenger RNA that can then begin the process of building proteins.

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Shyamalika Gopalan demonstrates how she prepares to extract DNA. Photo by Casey Youngflesh

Using broad time-based methylation changes, Shyamalika Gopalan, who is earning her doctorate at Stony Brook University in the Department of Ecology and Evolution, recently received a three-year grant from the Department of Justice to refine an understanding of methylation and aging. The DOJ would like to use this kind of analysis to gather more information from a scene at which the remaining clues include DNA that isn’t in one of its databases.

Gopalan isn’t the first scientist to study genetic methylation and aging. Other scientists have used blood, saliva and other tissues. She is starting with one type of tissue in the bone. “I’m trying to make” the analysis “more specific to bones,” she said. She doesn’t know how much variation she will find in the age-related methylation patterns depending on ethnicity and lifestyle. “It does appear that some sites are remarkably ‘clock-like,’” she said. “It is these types of sites I’m hoping to find and use in my research.”

Gopalan explained that millions of sites can be methylated. She’s hoping to hone in on those that act more like a clock and that change in a linear manner with time. She’s not sure how many sites she’ll use and said some changes in methylation involve removing methyl groups. “Some methylation increases and some decreases,” she said. “If you know the pattern with age at any site, you can start to build an estimate from those.”

Methylation occurs with age for several possible reasons. “A major theory for these changes in methylation level with age is that the epigenetic patterns are drifting from the optimum,” she said. “This may explain some, or even most, of the changes we observe, but I don’t think it is universally true for all sites in the genome.” Still, there probably is a biologically relevant reason why some of these sites are changing, she suggested.

Gopalan said we know that these methylation patterns are crucial in early development, from conception to birth and she suggested it probably doesn’t completely stop changing there. Some sites are probably regulated throughout life.

Gopalan is hoping to have the bone data prepared by this summer and then believes she’ll be able to get methylation types and start working on a computer algorithm to build a predictor for the next year. After her initial work, she will also shift to saliva and blood.

Like a scene from “Law & Order” or other crime shows, the DNA methylation test may be another clue for police officers or prosecutors to use to rule in or out potential suspects from a crime scene where DNA, but not a driver’s license, is left behind. If the genetic material is not in a database, “you could build a profile and it could be useful for narrowing down suspects,” Gopalan said. At this point, she is taking data for people of age classes but with different ethnicities and lifestyles and comparing them to people of a different age with a similar range of backgrounds and lifestyles.

Gopalan is using samples from medical schools around the New York area, borrowing from anatomy departments where people have donated their bodies to research or teaching. More broadly, she is interested in studying diverse populations, especially in Africa. She has worked with her thesis advisor Brenna Henn, exploring methylation from two different populations. These are the ‡Khomani San of South Africa and the Baka of Cameroon.

Gopalan was interested in working with methylation as a biomarker for aging when she came across this funding opportunity from the DOJ. “It was a good fit for what I had already been studying,” she said, adding that she hopes this method will be used in the future in forensics to assist in criminal investigations.

Krishna Veeramah, an assistant professor of primate genomics at Stony Brook and the chair of her thesis committee, described Gopalan as an “intellectually engaged student who is always eager to absorb information.” Veeramah explained in an email that he thinks “there is scope for this work to transition from basic research” to an application “in criminal forensics and related areas. It will certainly require more work and testing.”

Gopalan has been at SBU for over three years. She lives in Crown Heights, Brooklyn, and commutes about 90 minutes each way most days. She enjoys the beaches, farms, apple picking and the natural beauty of the area. Gopalan would like to continue to perform research after she earns her doctorate, whether that’s with a company, a research institution or with a university. She is excited about extracting and working with DNA, particularly from archeological sites. These samples “come from a field and, once you dust them off, it makes it personal. This is a part of a story.”

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Shinjae Yoo with his son Erum

By Daniel Dunaief

He works with clouds, solar radiation and nanoparticles, just to name a few. The subjects Shinjae Yoo, a computational scientist at Brookhaven National Laboratory, tackles span a broad range of arenas, primarily because his focus is using large pieces of information and making sense of them.

Yoo helps refine and make sense of searches. He develops big data streaming algorithms that can apply to any domain where data scalability issues arise. Integrating text analysis with social network analysis, Yoo did his doctoral research at Carnegie Mellon University, where he also earned a master’s degree, on creating systems that helped prioritize these electronic messages.

“If you are [traveling and] in the airport, before you get into your plane, you want to check your email and you don’t have much time,” he said. While this isn’t the main research work he is doing at the lab, this is the type of application for his work. Yoo developed his technical background on machine learning when he was at Carnegie Mellon. He said he continues to learn, improve and develop machine learning methods in various science domains. By using a statistical method that combines computational science skills, statistics and applied math, he can offer a comprehensive and, in some cases, rapid analysis of information.

Colleagues and collaborators suggested Yoo has made an impact with his work in a wide range of fields. His “contribution is not only in the academic field, but also means a lot on the industrial and academic field,” Hao Huang, a machine learning scientist at GE Global Research, wrote in an email. “He always focuses on making good use of data mining and machine learning theory on real world [areas] such as biology, renewable energy and [in the] material science domain.”

Yoo explained how a plant biologist can do stress conditioning for a plant with one goal in mind. That scientist can collect data over the course of 20 years and then they can “crunch the data, but they can’t always analyze it,” which might be too unwieldy for a bench scientist to handle. Using research from numerous experiments, scientists can study the data, which can provide a new hypothesis. Exploring the information in greater detail, and with increased samples, can also lead to suggestions for the best way to design future experiments.

Yoo said he can come to the scientist and use machine learning to help “solve their science data problem,” giving the researchers a clearer understanding of the broad range of information they collected. “Nowadays, generated data is very easy,” but understanding and interpreting that information presents bigger challenges. Take the National Synchrotron Light Source II at BNL. The $912 million facility, which went live online earlier this year, holds considerable promise for future research. It can look at the molecules in a battery as the battery is functioning, offering a better understanding of why some batteries last considerably longer than others. It can also offer a look at the molecular intermediaries in biochemical reactions, offering a clearer and detailed picture of the steps in processes that might have relevance for disease, drug interactions or even the creation of biological products like shells. He usually helps automate data analytics or bring new hypotheses to scientists, Yoo said. One of the many challenges in experiments at facilities like the NSLS II and the Center for Functional Nanomaterials, also at BNL, is managing the enormous flow of information that comes through these experiments.

Indeed, at the CFN, the transmission electron microscopy generates 3 gigabytes per second for the image stream. Using streaming analysis, he can provide an approximate understanding of the information. Yoo received a $1.9 million, three-year Advanced Scientific Computer Research grant this year. The grant is a joint proposal for which Yoo is the principal investigator. This grant, which launched this September, is about high-performance computing enabled machine learning for spatio-temporal data analysis. The primary application, he said, is in climate. He plans to extend it to other data later, including, possibly for NSLS II experiments.

Yoo finds collaborators through emails, phone calls, seminars or anywhere he meets other researchers. Huang, who started working with Yoo in 2010 when Huang was a doctoral candidate at Stony Brook, appreciates Yoo’s passion for his work. Yoo is “dedicated to his research,” Huang explained. “When we [ran] our proposed methods and got results that [were] better than any of the existing work, he was never satisfied and [was] always trying to further explore to get even better performance.”

When he works with collaborators in many disparate fields, he has found that the fundamental data analysis methodologies are similar. He needs to do some customization and varied preprocessing steps. There are also domain-specific terms. When Yoo came to BNL seven years ago, some of his scientific colleagues around the country were not eager to embrace his approach to sorting and understanding large pools of data. Now, he said other researchers have heard about machine learning and what artificial intelligence can do and they are eager to “apply those methods and publish new papers.”

Born and raised in South Korea, Yoo is married to Hayan Lee, who earned her PhD at Stony Brook and studies computational biology and specializes in genome assembly. They have a four-year old son, Erum. Yoo calls his son “his great joy” and said he “gives me a lot of happiness. Hanging around my son is a great gift.”

When Yoo was entering college in South Korea, he said his father, who had worked at the National Institute of Forest Science, played an important role. After his father consulted with people about different fields, he suggested Yoo choose computer science over chemistry, which would have been his first choice. “He concluded that computer science would be a new field that would have a great future, which is true, and I appreciate my dad’s suggestion,” Yoo said.

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Dr. Hal Walker, co-director of the New York State Center for Clean Water Technology, speaks during a symposium at Stony Brook University Thursday, June 23, 2016. Photo by Barry Sloan

By Daniel Dunaief

Water, water everywhere and Harold “Hal” Walker is making sure there’s more than a few drops on Long Island to drink. The head of the new Department of Civil Engineering at Stony Brook is one of two co-directors of the Center for Clean Water Technology. The center received a $5 million commitment from New York State to pilot test a variety of ways to remove contaminants from drinking water.

“The center will be working with water authorities and water utilities to do pilot testing of new technology to deal with emerging contaminants,” Walker said. “One goal of the testing will be to collect information needed to assess new technologies and, if they are effective, to get them approved so they can be used by water utilities.”

Contaminants the center will explore include 1,4-dioxane and perfluorinated compounds, which have “turned up in some regions of Long Island,” Christopher Gobler, the co-director of the center and an associate dean for research and professor at the School of Marine and Atmospheric Sciences, explained in an email.

’One lesson we have learned is that it is critically important to protect the environment, since the environment serves as a natural buffer to these large storms.’ — Harold Walker

The technologies the center will test likely include novel membrane processes, advanced oxidation, novel absorbents and advanced oxidation processes. The center will explore “how these compounds are removed in conventional drinking water treatments processes,” Walker said. “If they are not removed sufficiently, what do novel technologies use and are they ready for the pilot stage?” Walker acknowledges that staying ahead of the curve in being prepared to protect drinking water requires an awareness of numerous new compounds that are a part of modern manufacturing.

Gobler said the center’s findings would be made public. New York State had previously committed $3.5 million from the Environmental Protection Fund to support the center. With an additional $5 million in funding, the center will develop new technologies to improve drinking water and wastewater quality on Long Island, according to the State Department of Environmental Protection.

The center was formed originally to focus on innovative alternative individual onsite treatment systems for reduction of nitrogen and pathogens. That was broadened this year to focus on the impact of emerging contaminants on water supplies, a representative from the DEC explained in an email.

Walker has built an expertise in developing and applying membrane processes for drinking and wastewater. At Ohio State University, where he worked from 1996 until 2012, when he came to Stony Brook, he spent considerable time analyzing drinking water in the Great Lakes. Gobler appreciates Walker’s expertise.“

He has worked with many federal and state agencies on these topics across the United States,” Gobler explained. “He is also well-versed in wastewater treatment technologies.”

Jennifer Garvey, the associate director for the center, meets with Garvey and Walker at least once a week. She also connects weekly for a call or meeting to discuss administrative and strategic issues. Walker is “at the leading edge of water treatment approaches and he understands where opportunities and obstacles lie,” Garvey said. The center has a sense of urgency about the work because “there is such a clear and immense need for wastewater infrastructure improvements,” she continued. The targeted and strategic work emphasizes near-term solutions. A leading focus is a nonproprietary passive system known as a nitrogen removing biofilter that they will be piloting in Suffolk County soon. “Our hope is that we can make systems available for widespread deployment within the next two to three years,” she said.

Apart from his work at the center, which Walker estimates takes about a third of his time, he is also a professor and the founding chair of the Department of Civil Engineering, which conferred bachelor’s degrees on its inaugural 13 undergraduate students this summer. Those students have all found engineering jobs within their field of interest or continued to pursue additional schooling. The civil engineering department has 10 faculty and is at the end of the first phase of its growth and development, Walker said.

Phase II will include building out the faculty and staff, developing new research and teaching labs and enhancing the recently approved master’s of science and doctoral programs in civil engineering, Walker explained. Resiliency of the coastal communities is a major thrust of his department. He said he recently hired a number of faculty in this area and launched an Advanced Graduate Certificate in Coastal Zone Management and Engineering in partnership with the School of Marine and Atmospheric Sciences. “One lesson we have learned is that it is critically important to protect the environment, since the environment serves as a natural buffer to these large storms,” he explained.

Apart from water and the resilience of the coastal community, the civil engineering department is also involved in transportation. The department works with Farmingdale State College in a new Infrastructure, Transportation and Security Center. In that effort, the department collaborates with the Department of Computer Science, among others at Stony Brook, to bring new approaches to “improving the efficiency, sustainability and safety of our transportation system.”

For his part, Gobler welcomes the talent and expertise the civil engineering department brings to Stony Brook. “This is a tremendous asset” for Stony Brook, Gobler explained in an email. “Civil engineers solve complex problems and I have found that [Walker] and the people he has hired have the skill set and mind-set to address many environmental problems that are important on Long Island.

A resident of Port Jefferson, Walker lives with his wife Alyssa, who is a writer, and their three children, Abby, 14, Halliway, six, and Northie, who is five. They enjoy visiting the beach and traveling east to go apple and pumpkin picking. A native of Southern California, Walker started surfing at the age of 10. He was a four-year varsity letterman in surfing when he was in high school. He has surfed in Hawaii, Costa Rica, Japan, Portugal and Mexico.

As for the department, he said he feels excited by the responsibility for building only the second civil engineering program in the SUNY system. “I’d like the department to quickly become nationally recognized and be the leading source of expertise for the state on infrastructure issues, especially in the downstate area,” he said.

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Krishna Veeramah. Photo by Dean Bobo

By Daniel Dunaief

People have left all kinds of signs about their lives from hundreds and even thousands of years ago. In addition to artifacts that provide raw material for archeologists, anthropologists and historians, they also left something modern science can explore: their genes.

Genetic information locked inside their bones can add to the dialogue by providing details about what regions people might have come from and when they arrived. A group that includes Krishna Veeramah, an assistant professor of primate genomics at Stony Brook University, is using genetic information, combined with archeological evidence, to gain a better understanding of the events in Europe immediately after the fall of the Roman Empire, between the fifth and sixth centuries.

“We want to test questions that integrate historical and biological information,” said Veeramah, who is working with a multinational team of scientists. “We want to integrate archeological information.”

This is a time period in which there is some disagreement among historians about what happened after the fall of the Roman Empire. Patrick Geary, the principal investigator on a project that traces early medieval population movements through genomic research, said that this period fundamentally changed not only the demographic makeup of the populations but also the social and political constellation of Europe. These scientists are hoping to contribute their analysis of the genetic material of 1,200 people from several cemeteries to a discussion of the history of the continent.

So, how does this work? Paleogenomic data offers information from hundreds of thousands to millions of positions along the genome, which are called markers or single-nucleotide polymorphisms. Looking at the markers in total, researchers can identify small but systematic genetic differences between groups. They hope to determine where an individual’s ancestors are from based on the bones they are studying. They can only come to these conclusions, Veeramah explained, once they have sampled large numbers of people from different geographic areas during that time period. The genetic differences he is seeing are extremely small. He uses enormous pools of data that can allow him to explore subtle patterns, which emerge at the group level.

While the notion of using the genetic code to contribute information to discussions about the movement of groups of people has its proponents and practitioners, Geary and Veeramah recognize the skepticism, alarm and misdirection that comes from exploring subtle genetic differences among various groups of people. “The application of genetics to the human past is dark,” Geary said, pointing to eugenics discussions. “That’s understandable. We are emphatically opposed to such previous misuses of genetic research.” Some scientists, Geary said, are also suggesting that genetic studies will replace manuscripts or other clues. “We need all types of information,” Geary said.

Indeed, in a cemetery in Hungary that contained about 45 graves, Veeramah is studying genetic differences between two graves that are oriented in another direction from the other adult-sized graves. These two graves don’t contain any grave goods and appear to have different construction. The initial genomic analysis of a subset of individuals suggest they have a genetic profile that is different from other members of the cemetery and may show more of a connection to modern people from southern Europe rather than northern and central Europe, like the rest of the samples. The way these two graves were arranged offers intriguing possibilities, Veeramah said. This may suggest that these individuals had a distinct biological identity, which could impact some aspects of their social identity. To reach any conclusions, he hopes to collect more data from more individuals.

Geary suggested the kind of work he and Veeramah are doing, along with partners in other countries, will offer insight into the different paths of men and women. When paleogenomics first arrived as a discipline, historians were slow to embrace it. At the 2008 American Historical Association’s annual meeting, Geary gave a talk at which about 10 people attended. In January, at the 2017 American Historical Association meeting in Denver, Veeramah will discuss how a study of the Lombards offers a framework for integrating history, archeology and genomics. The president of the American Historical Association invited Veeramah and has publicized the talk as a presidential panel.

“I do believe that paleogenomics has become an important aspect of archeological work, and that the newly developed procedures for sequencing and analyzing genetic material adds a whole new dimension to work on archeological sites,” Patrick Manning, the president of the AHA and a professor of world history at the University of Pittsburgh, wrote in an email. Veeramah’s “work on the Lombards addresses an important issue in the Germanic migrations throughout Europe, long debated and now with important new information.”

Veeramah arrived at Stony Brook University in 2014 and lives in Sound Beach. He grew up outside London in Dartford and attended the same secondary school as Mick Jagger. While he likes some of the Rolling Stones songs, he’s more of a Dizzee Rascal fan. Veeramah plans to have a lab installed by next summer, when he hopes to analyze bones from archeological sites shipped from Europe.

In the meantime, he will continue to analyze genetic information coming from partners in Europe. While Veeramah and others in the field have published papers in prestigious journals like the Proceedings of the National Academy of Sciences and Science, they have struggled to receive funding from American funding agencies at the same level as their European counterparts.

“It is somewhat surprising how far behind the U.S. has gotten in this area,” Veeramah said. European grants can be more adaptable and can put more value on multidisciplinary work. “This is a systematic issue for U.S. funding. I hope it will be addressed soon.”

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Raffaella Sordella. Photo from the laboratory of Raffaella Sordella

By Daniel Dunaief

Raffaella Sordella, whose lyrical name reflects her upbringing in Italy, takes the fight against cancer personally. That’s because she underwent surgery for a tumor in her pancreas a few years ago when she, her husband Manuel Barriola and their young daughters Victoria and Alicia were living in Boston.

“The past few years I have made friends with many people who share firsthand experience with cancer,” she recalled in an email. “I have witnessed their strength and courage and they have been an incredible source of inspiration for our work, especially at times when the glass looked half-empty.”

Indeed, while she fought cancer herself, Sordella and the lab she leads as an associate professor at Cold Spring Harbor Laboratory battle against the deadly disease every day. Recently, she made a discovery about a gene that has been among the most studied and carefully combed genetic regions of the human genome. A tumor suppressor gene, p53 protects against tumor growth. An increasing number of findings, however, point toward the possibility of p53 mutants that promote tumors.

In research published in eLife, Sordella found just such a mutant. Looking at a variation in which the gene is truncated, or cut short, a range of cancers can develop and can cause greater threats to a patient’s health. “Despite four decades and all these papers, this is completely new,” Sordella said.

As many as 10 to 15 percent of tumors of the pancreas, ovaries, melanoma, head and neck and small cell lung carcinoma have this truncated version of p53, according to Sordella. “If you have these mutations, your colon cancer tends to become more metastatic,” she said.

Sordella and her colleagues studied the signaling pathway that regulates the activity of this gene. They have found a path that may become a target for drugs. Her lab is in discussions with a pharmaceutical company to start clinical trials. Sordella suggested that this type of finding addresses the notion of individualized medicine, in which doctors and scientists search for the specific genetic regions that contribute to cancer, looking for ways to block them, turn them off or slow them down.

In this truncated version of p53, the genes are active in the mitochondria, or the powerhouse of the cell, where the energy molecule adenosine triphosphate, or ATP, is produced. Sordella is studying how this mutant p53 can affect metabolism.

“The result is exciting because it was so unexpected,” Scott Lowe, the chair of the Cancer Biology & Genetics Program at the Memorial Sloan Kettering Cancer Center, wrote in an email. “The current work shows that these mutations can act as an ‘accelerator’ of tumorigenesis as well.” Lowe was a co-author on the study, who described his lab’s contributions as providing human data on the prevalence of truncated mutations in p53 in human tumors.

Researchers have dedicated considerable effort to understanding the tumor microenvironment. They are seeking to understand what a cancer might need from its immediate surroundings. Scientists studying other diseases, such as fibrosis, tissue chronic injuries, Alzheimer’s and Parkinson’s are also dedicating considerable resources to understanding the microenvironment. The recent discovery has encouraged Sordella and her colleagues to explore the role of cancer cell metabolism, cancer cells and their interaction with the tumor microenvironment, while also exploring the druggability of downstream pathways. This form of the gene is interacting with cyclophilin D, which is an inner pore permeability regulatory. Cyclophilin D, as a result, could become the target for future drug treatments.

Lowe suggested that the “current study raises the possibility that cancers with truncating mutations in p53 would be susceptible to agents that block cyclophilin D,” but added that it “should be clear that this will require much further testing.” Still, he concluded that it “is exciting as the possibility of this approach was not previously appreciated.”

Sordella came upon the discovery of the role of this form of the gene by chance. The focus of her lab is to understand the mechanism of resistance in small cell lung cancers. She generated a model in which there was resistance to a particular inhibitor. When she conducted an expression profile, she found a shift in the molecular weight of p53. Cloning and sequencing the gene demonstrated an alternative splicing, or cutting, that nobody had described.

Sordella credits partners including Edward Kastenhuber, Marc Ladanyi and Lowe at Sloan Kettering with assisting in the analysis of the gene. Sordella appreciates the financial support of Swim Across America, an organization that raises money for cancer research and that has supported her research for several years. Swim Across America takes “great pride in each new finding as these are the building blocks for achieving the ultimate goal,” Daniel Cavallo III, the beneficiary chair of the Nassau-Suffolk Chapter of Swim Across America, wrote in an email. “All you need to do is speak with Dr. Sordella for a short time and it is so clearly evident just how passionate she is about her work,” Cavallo said. “Her hard work, dedication and commitment to the cause are extraordinary — this along with her achievements are part of why we continue to fund her research.”

As a child, Sordella said she had an interest in becoming a physicist. After witnessing the suffering and strain cancer inflicted on her family, including an uncle and grandfather who succumbed to the disease when she was 13, Sordella decided that battling this disease would be her mission. Her family, she said, instilled in her the sense of finding purpose beyond the accumulation of wealth and has established a foundation with the goal of caring for the elderly and promoting education. She hopes her work contributes to her family’s legacy. “Hopefully one day soon, I will be able to celebrate with them a new great victory in the fight against cancer,” she said.

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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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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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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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