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Authors Posts by Daniel Dunaief

Daniel Dunaief

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Verbs await like a collection of colors, quivering, shaking and jumping on their palettes to define and describe the unfolding scene.

What verbs will we use to describe the future president of the United States, whose name itself can be a verb?

Well, for starters, he tweets. We know that fact through his candidacy and it’s a pattern that continues now that he is assembling a cabinet and as he awaits his turn as president. His tweets represent his direct-to-the-people message, cutting out the middle man of the media. As with pharmaceutical companies that market their products directly to consumers, sometimes Trump’s tweet messages, which crackle like thunderbolts from his fingers, should come with a warning. For example, “Don’t operate heavy equipment while listening to these tweets, which may cause shortness of breath,” or, “If you find yourself shouting approval or disapproval in response to these tweets, try not to read them in church, in a library or any place where shouting could cause a crisis.”

When he communicates with the populace, with American leaders or with foreign leaders, what verbs will fill the canvas?

He often seems to warn, to threaten and to demand. Maybe he believes American greatness starts with a tough president who insists America and its interests go directly to the front of any line.

In recent days, he has weighed in on the discussion about the election, claiming widespread voter fraud prevented him from winning the popular vote “beauty contest.”

Through his tweets, he also leveled attacks against reporters he derides for disagreeing with him.

I get it: As an agent of change, Trump may feel it’s his job not to highlight everything that’s going well with the country or to shout encouragement. That, he may believe, would be like telling a kid who has struck out continuously that he’s having a great game.

Shifting from the visuals of colors on a page to the sounds at a pep rally, will the Trump presidency repeat similar notes with a single tone? Will he continue to castigate, to criticize, to claim and to attack? Those are just a few of the verbs that describe the approach Candidate Trump took on the contentious campaign trail.

At some point, does President Trump become like a strong-willed character in a compelling novel? Will his experiences enable him to make a transition to becoming a president who emits a different tone and who leads to a symphony of greatness that comes from every part of the country?

Will the cajoling, the criticizing and the arguing transition to educating, inspiring and elevating? Yes, I know his approach and policies may help educate more Americans and may help bridge the gap between the testing levels American students reach compared with students in other nations.

Certainly, as Trump demonstrated during his campaign stops, he can and has rallied people. What actions, what verbs, will describe the way Americans and, indeed, people around the world, react to his message? As an agent of change after the polished rhetoric of President Obama, Trump may not want to compete and, indeed, may sprint away from the pontifications his predecessor proffered.

That, however, doesn’t preclude Trump from the kinds of verbs we hope we can employ to fill the pages of the next four years. Will he encourage, empower and reassure Americans about the government that supports, protects and serves them?

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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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I’m going to blend the holidays, and make a naughty and a nice list of those things for which I’m thankful. I’ll start with the nice.

I’m thankful for inspirational teachers. Every day, some teachers devote so much time and energy to their work that they ignite a passion for learning, a curiosity or a determination in their students that has the potential to pay dividends for decades. An inspired student reflects and emanates an educational light that, in turn, can have a multiplier effect, encouraging their siblings, their friends and even their parents to learn and grow.

I’m thankful for the police who patrol our streets and who protect and serve us. They can and do tackle everything from delivering a baby on the Long Island Expressway to racing toward reports of someone with a weapon.

I’m also thankful for the firefighters, who rescue people trapped in burning buildings and who suffer through cold wind, rain and snow while doing their job.

I’m thankful for all the soldiers who, regardless of which president is in office, accept their responsibility and protect America’s interests wherever they serve.

I’m thankful for the scientists who dedicate themselves, tirelessly, to the pursuit of basic knowledge about everything from quarks and neutrinos, to the researchers who are on a mission to cure cancer, to understand autism, or to defeat fungi or viruses that threaten the quality and quantity of our lives.

I’m thankful for the sanitation workers who appear during the wee hours of the morning, clear out our garbage and move on to the next house.

I’m thankful for the First Amendment. I’m grateful that our Founding Fathers decided we have the right not to remain silent. Our constitution guarantees us the kind of free speech that allows us to express our views, even if those opinions are contrary to those of our government or our neighbors.

OK, here’s the nasty list.

I’m thankful for the Internet, which prevents anyone from being wrong about anything, ever. Well, information on the Internet may also be inaccurate, but who cares? If it’s there and we repeat it, at least we’re echoing something someone else wrote, even if that person is an 8-year-old who is just learning to type and is posting something that looks like it could be right.

I’m thankful for all those people who honk at me when I don’t hit the accelerator the moment the light turns green. They remind me I should be efficient for all of our sakes and that I could be doing something much more important, like looking up stuff on the Internet rather than sitting at a light.

I’m thankful I can roll my eyes in my head. How else could I deal with those events around me that I find insufferable, from listening to our political leaders rip into each other to engaging in arguments with people who know better and can show me all the information they use to back up their arguments on the Internet.

I’m thankful for the rain and the cold and the snow. OK, so this is in between a naughty and nice one, because I believe varied weather presents something for everyone. Sure, people don’t tend to like it when the temperature falls too far, but I enjoy the cold. Besides, the winter provides a contrast to seasonable weather.

Finally, I’m thankful for prognosticators of all types, including the recent ones who seemed so sure of themselves about the results of the election. They are a reminder that sure things don’t exist in any arena, even those with a preponderance of pontificators.

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Horrible acts are now connected with the name of our President-elect Donald Trump. Yes, I’ve heard the counter argument that these acts would have been committed anyway and that the media — yes, the cursed media — is overblowing and overplaying them.

Or, is it?

My question to the president-elect is: “Why haven’t you been more forceful in showing disdain, disappointment and disgust over these acts, whether or not they might have happened even if you weren’t elected president?”

Is he worried people might think he’s being politically correct? Does he think being sensitive to others, paying attention to circumstances in which bullies run rampant or, worse, commit violent, harassing or illegal acts is a sign of weakness?

He has an opportunity to lead the nation. We owe him that, just as President Barack Obama and the defeated Hillary Clinton have said. He will be the president and, as such, he will have the attention of a world ready to react to every word he says.

Why, then, can’t he say how horrified he is by these acts? I heard that he indicated to CBS’ Lesley Stahl on “60 Minutes” that he wants people to stop. Really? That’s it? That’s the best a man who never seemed at a loss for words can offer?

He should tell those who commit hate crimes that he will come after them with the same fury and attention that he promised to send home illegal immigrants. He should make it clear that he, his administration and this country will not accept teachers who suggest they will send African-American children back to Africa, among other intolerable words and deeds.

Of course, Trump can’t be responsible for the actions of everyone in the country. But, he can and should lead by example. He can set the tone, making it clear that no matter who else he appoints to his administration or what those other people may have done or said in the past, he is the president and he has a zero-tolerance policy for the kinds of hateful actions people are committing in his name.

The media has a job to do. Reporters shine light in areas where there might otherwise be darkness. Even if the president-elect doesn’t like the news as he reads it, he can do something about what’s being reported instead of blaming the media for sharing bad news.

Even buying into his argument that nothing has changed since his election, he should push for change, for opportunity, for freedom and justice for all, and not just for those who elected him.

Look, I get it: I’m a huge Yankees fan and it sickens me when my team wins and some other Yankees fan acts out against the fans of an opposing team. I can argue that real Yankee fans wouldn’t do that and I can say, “Stop.” But the future president of the United States can and should offer more.

You want people to know they can’t connect your name and your presidency with hatred, then make it clear that you won’t tolerate it and that this is not who you are — and it is not the America you will be leading. Our president-elect had strong words for his opponents in the primaries and for his vanquished competitor in the general election. Where are those strong words now that some people in the country are acting in ways contrary to the principles on which this nation was founded?

Please, Mr. President-elect, take this moment to address those elements of this country who seem to define and justify bad acts in your name.

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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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The other day, my teenage son had a choice. No, he can’t vote and no, he wasn’t ordering a sandwich at a diner with an 18-page menu. He was with some friends who decided they wanted to get a better view of the street and, presumably, their peers who were walking below during a warm fall day.

They headed for the roof of a building, where a Private Property No Trespassing sign awaited them. They ignored the sign. When my son hesitated, they signaled for him to join them.

“Oh, come on, you’re not going to be like Joey,” they said in a complaining tone. I don’t know who Joey is, but when I heard the story I instantly wanted my son to meet him and hang out with him.“No,” he replied, “but I’m not going up there.”

What stopped him? Why didn’t he do whatever he wanted to do or, equally importantly, whatever his friends wanted? The other boys clearly expected him to fall in line, just the way our friends, our parents’ friends and our grandparents’ friends expected us and our ancestors to fall in line, too.

We send our kids to school every day to learn about differential equations, the American Revolution, the powerful prose of Ernest Hemingway and the anatomy of frogs and people, but somewhere along the lines, they have to learn to develop a set of values.

That can come from a dedicated teacher, who takes time out from a demanding schedule to teach a broader life lesson about the difficulty of making the “right” choice. It can come from a coach, a principal, a neighbor, a parent, a grandparent or anyone who goes out of his or her way to make sure that our children don’t lose theirs.

I understand that this moment isn’t the biggest challenge my son will face. Undoubtedly, someone will come up with an idea, a suggestion or a dare he feels pressure to do.

These small moments, however, lead to the bigger ones. It is the slippery slope argument. If doing something that might be a little wrong doesn’t cause problems or have any consequence, maybe doing something larger that might not be exactly right is also just fine because no one noticed or he didn’t get caught. Or, the argument that frustrates me the most, someone else did something worse, so this isn’t such a poor decision.

We all have those difficult moments, when someone whose company we enjoy encourages us to do something that might not be in our best short- or long-term interests and when, for whatever reason, that friend insists we participate to demonstrate our friendship. This is the moment when peer pressure threatens to silence the little voice in our heads that says, “This is probably a bad idea.”

We hear so many times about people who either don’t have that little voice or who have so effectively silenced it that the rules of our country don’t apply. They live with a freedom that they find exhilarating, until they get caught.

We are painfully aware of the destruction people who tumbled down that slippery slope create for themselves and society, through difficult and self-destructive habits.

There are so many other children who, thanks to the effort of the village of supporters around them who point to a true north, develop both self-control and self-confidence that allow them to say, “I’m not going to do that.”

Through any age, one of the hardest words for us to say, when those around us encourage us to join them in treading on someone else’s property or rights, is “No!”

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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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If an ounce of prevention is worth a pound of cure, what should we be preventing?

Well, we all brush our teeth. At least, we do most of the time, assuming we haven’t relaxed under the covers too long on a cold night and haven’t allowed ourselves to drift off to a wonderful, warm place where we don’t have to worry about meetings, tests, social anxiety, or delayed trains the next day.

Did we also floss? That’s a ridiculous question for those of us who have seen the 1992 movie Prelude to a Kiss. At the end of the film, Julius, played by Sydney Walker, has returned to his body after switching with Meg Ryan on her wedding day. An older man, Julius asks if he can give the young couple a piece of advice. “Floss,” he advises sagely.

Okay, so, what else do we prevent? We change the oil in our cars, or maybe a service station does that. They also probably check our brakes, realign our wheels, and check all our other fluids. That’s all good and seems necessary. How often we do that depends on our tradition and our comfort level with our vehicles.

Then, there’s our bodies. Insurance plans seem to cover the cost of an annual physical. The doctor asks us about any changes, takes some samples, and gets back to us, reminding us to eat better, to sleep better and to exercise more often. Those visits can either be a source of great pride, as we walk in noticeably lighter than we were last year, or a source of frustration, as the weight we lost the year before seems to have boomeranged back to us.

For our bodies, we can also take some preventive steps. I recently endured some lower back problems. I always thought the one advantage of being on the shorter side was that I wouldn’t have to worry about the bad backs some of the tall people of the world suffer. Wrong. My lower back was so stiff that climbing out of a car took much longer than it should, while walking down steps or a slight incline caused me to wince.

My chiropractor helped relieve that pain and gave me some back exercises, which I now do semi-regularly. Okay, well, I don’t do them as often as I brush my teeth, but I do take some time to stretch and strengthen my lower back.

When I was young and playing sports, I used to arrive at a field and play baseball, basketball or anything else and immediately start running at top speed. I barely stretched because I couldn’t wait to play.

Fast forward to today and the true weekend warrior in me, who has endured a groin strain and a partial tear of my rotator cuff, requires at least 10 to 15 minutes of stretching.

As with most life lessons, we become more aware of pitfalls and potholes after we’ve fallen into them. My experience with kidney stones means that I barely go a waking hour without drinking a cup of water. When the doctor told me that half of all kidney stone patients return within five years, I immediately decided I wanted to be in the other half, so I’m drinking water constantly.

I’m sure there are other house items we should maintain, like heaters, air conditioners, dishwashers, refrigerators and other appliances. After all, even though so many of those run for long periods of time without needing any service, they probably won’t require anything major if we give them that extra ounce of preventive attention.

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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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