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From left, Deyu Lu (sitting), Anatoly Frenkel (standing), Yuwei Lin and Janis Timoshenko. Photo from BNL

By Daniel Dunaief

What changes and how it changes from moment to moment can be the focus of curiosity — or survival. A zebra in Africa needs to detect subtle shifts in the environment, forcing it to focus on the possibility of a nearby predator like a lion.

Similarly, scientists are eager to understand, on an incredibly small scale, the way important participants in chemical processes change as they create products, remove pollutants from the air or engines or participate in reactions that make electronic equipment better or more efficient.

Throughout a process, a catalyst can alter its shape, sometimes leading to a desired product and other times resulting in an unwanted dead end. Understanding the structural forks in the road during these interactions can enable researchers to create conditions that favor specific structural configurations that facilitate particular products.

First, however, scientists need to see how catalysts involved in these reactions change.

That’s where Anatoly Frenkel, a professor at Stony Brook University’s Department of Materials Science and Chemical Engineering with a joint appointment in Brookhaven National Laboratory’s Chemistry Division, and Janis Timosheko, a postdoctoral researcher in Frenkel’s lab, come in.

Working with Deyu Lu at the Center for Functional Nanomaterials and Yuwei Lin and Shinjae Yoo, both from BNL”s Computational Science Initiative, Timoshenko leads a novel effort to use machine learning to observe subtle structural clues about catalysts.

“It will be possible in the future to monitor in real time the evolution of the catalyst in reaction conditions,” Frenkel said. “We hope to implement this concept of reaction on demand.”

According to Frenkel, beamline scientist Klaus Attenkofer at BNL and Lu are planning a project to monitor the evolution of catalysts in reaction conditions using this method.

By recognizing the specific structural changes that favor desirable reactions, Frenkel said researchers could direct the evolution of a process on demand.

“I am particularly intrigued by a new opportunity to control the selectivity (or stability) of the existing catalyst by tuning its structure or shape up to enhance formation of a desired product,” he explained in an email.

The neural network the team has created links the structure and the spectrum that characterizes the structure. On their own, researchers couldn’t find a structure through the spectrum without the help of highly trained computers.

Through machine learning, X-rays with relatively lower energies can provide information about the structure of nanoparticles under greater heat and pressure, which would typically cause distortions for X-rays that use higher energy, Timoshenko said.

The contribution and experience of Lin, Yoo and Lu was “crucial” for the development of the overall idea of the method and fine tuning its details, Timoshenko said. The teaching part was a collective effort that involved Timoshenko and Frenkel.

Frenkel credits Timoshenko for uniting the diverse fields of machine learning and nanomaterials science to make this tool a reality. For several months, when the groups got together for bi-weekly meetings, they “couldn’t find common ground.” At some point, however, Frenkel said Timoshenko “got it, implemented it and it worked.”

The scientists used hundreds of structure models. For these, they calculated hundreds of thousands of X-ray absorption spectra, as each atom had its own spectrum, which could combine in different ways, Timoshenko suggested.

They back-checked this approach by testing nanoparticles where the structure was already known through conventional analysis of X-ray absorption spectra and from electron microscopy studies, Timoshenko said.

The ultimate goal, he said, is to understand the relationship between the structure of a material and its useful properties. The new method, combined with other approaches, can provide an understanding of the structure.

Timoshenko said additional data, including information about the catalytic activity of particles with different structures and the results of theoretical modeling of chemical processes, would be necessary to take the next steps. “It is quite possible that some other machine learning methods can help us to make sense of these new pieces of information as well,” he said.

According to Frenkel, Timoshenko, who transferred from Yeshiva University to Stony Brook University in 2016 with Frenkel, has had a remarkably productive three years as a postdoctoral researcher. His time at SBU will end by the summer, when he seeks another position.

A native of Latvia, Timoshenko is married to Edite Paule, who works in a child care center. The scientist is exploring various options after his time at Stony Brook concludes, which could include a move to Europe.

A resident of Rocky Point during his postdoctoral research, Timoshenko described Long Island as “extremely beautiful” with a green landscape and the nearby ocean. He also appreciated the opportunity to travel to New York City to see Broadway shows. His favorite, which he saw last year, is “Miss Saigon.”

Timoshenko has dedicated his career to using data analysis approaches to understanding real life problems. Machine learning is “yet another approach” and he would like to see if this work “will be useful” for someone conducting additional experiments, he said.

At some point, Timoshenko would also like to delve into developing novel materials that might have an application in industry. The paper he published with Frenkel and others focused only on the studies of relatively simple monometallic particles. He is working on the development of that method to analyze more complex systems.

This work, he suggested, is one of the first applications of machine learning methods for the interpretation of experimental data, not just in the field of X-ray absorption spectroscopy. “Machine learning, data science and artificial intelligence are very hot and rapidly developing fields, whose potential in experimental research we have just started to explore.”

 

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From left, Ellen Li, Jennie Williams and Ping Ji, a technician (sitting). Photo by Daniel Irizarry

It’s a dream team tackling a nightmare scenario. While colorectal and pancreatic cancers are killers across different races, they are considerably worse for African Americans.

African Americans with colorectal cancer are about 40 percent more likely to die from it compared to those from other racial groups, according to recent data from the Surveillance, Epidemiology and End Results Program. The incidence of pancreatic cancer in African Americans is also 31 to 65 percent higher than in other racial groups.

A Stony Brook University research team led by Ellen Li, a professor of medicine and chief of the Division of Gastroenterology and Hepatology, is trying to understand the causes of these variations and, in the process, hopes to provide the kinds of clinical benefits that would help everyone.

“We think there are multiple factors,” Li said. Scientists at Stony Brook, Cold Spring Harbor Laboratory and SUNY Downstate Health Disparities Center are creating one of “the most comprehensive data sets” that people can analyze.

The team includes Jennie Williams, an associate professor in the Department of Family, Population and Preventive Medicine, Joel Saltz, the chair of Bioinformatics at Stony Brook, Richard McCombie, director of the Stanley Institute for Cognitive Genomics at Cold Spring Harbor Laboratory, David Tuveson, the director of the Lustgarten Foundation Pancreatic Research Laboratory at CSHL and several other researchers at  Downstate.

Williams said she began reading up on the response to cancer treatment by various groups in 2004. She understood that African Americans don’t respond to numerous chemotherapy prevention agents and some treatments for colon cancer. “They either don’t respond or they become resistant to chemotherapy,” she said.

When Williams started looking into this in 2008, she focused on microRNAs, which bind to messenger RNA and suppress translation. MicroRNAs are noncoding regulatory RNAs. The dysregulation of these important sequences result in the silencing of tumor suppressor proteins and the overexpression of oncogenes.

Her biggest finding was that the expression of tumor suppressor proteins inversely correlated with the overexpression of a microRNA called miR-182. This microRNA, she said, was significantly higher in tumor samples from African Americans.

With a molecular target and a potential mechanism, Williams thought she was well on her way to digging in. She ran into a significant stumbling block, however. “To do cancer chemotherapeutic studies, you need cell lines to work with,” she said.

Williams went to several companies to find colon cancer cell lines and asked, specifically, for those from African American patients. She found that the only cell lines labeled with race were those from Caucasians.

“To study chemoresponse, one needs a broad spectrum of cell lines,” Williams said.

She started generating cell lines in her lab, with three from African Americans and two from Hispanic patients, as well as some from Caucasians.

While Williams said she loves living in Stony Brook, she has found the lack of diversity among the patient population limiting in addressing cancer racial disparity. With Li’s help, she partnered with Downstate, where 75 percent of the patient population is African American.

She hopes to generate 10 African American, 10 Hispanic American and 10 Caucasian cell lines. Stony Brook and Downstate will collaborate to exchange ideas and personnel.

Williams said part of the challenge in gathering tissue samples from the African American population comes from a history of worrisome interactions with scientists.

Many African Americans have heard of the Tuskegee Institute study of African American men who came to the institute with syphilis between 1932 and 1972 but were not treated with penicillin, even after the drug became an effective and standard treatment in 1947. When the public became aware of the study, it ended and the government established strict informed consent rules about participating in scientific research.

Li said in their study on racial disparities in gastrointestinal cancers, selected staff certified in human research de-identifies everything so no one knows who each participant is. The data collection is a labor-intensive work, Li said, that is designed to provide greater insight into what might be causing these differences.

In terms of explaining the differences, Li and Williams believe it is both “genetic and epigenetic.”

In Africa, colon cancer is rare compared to its occurrence in the United States, Williams said, which suggests that diet and lifestyle contribute to the disease and its progression.

Raised in Savannah, Georgia, Williams said she was always interested in what made things change, from the tadpole in the pond to insects and birds that flew. While her parents didn’t attend college, that wasn’t an option for her: “It was never if” she went to college, “but when.”

Li, who is married to Stony Brook President Sam Stanley and has four children, said health insurance is one of numerous problems that affect individual populations. Numerous other factors could play a role in explaining the racial disparities in cancer outcomes.

Diabetes, which occurs at a higher rate in African Americans, increases the risk of colon cancer, Li said. It is unclear how much the incidence of diabetes in the African American population may contribute to the disparity, Li said.

Francis Alexander. Photo from BNL

By Daniel Dunaief

Now what? It’s a question that affects everyone from the quarterback who wins the Super Bowl — who often says something about visiting a Disney facility — to the student who earns a college degree, to the researcher who has published a paper sharing results with the scientific community.

For some, the path forward is akin to following footsteps in the snow, moving ever closer to a destination for which a path is clear. For others, particularly those developing new technology, looking to unlock mysteries, the path is more like trudging through unfamiliar terrain.

The technology at facilities like Brookhaven National Laboratory, which includes the powerful National Synchrotron Light Source II and the Center for Functional Nanomaterials, among others, enables scientists to see processes at incredibly fine scales.

While these sites offer the promise of providing a greater ability to address questions such as what causes some batteries to die sooner than others, they also cost considerable money to use, putting pressure on researchers to ask the most fruitful question or pursue research that has the greatest chance for success.

Francis Alexander. Photo from BNL

That’s where people like Francis Alexander, the deputy director of Brookhaven National Laboratory’s Computational Science Initiative, and his team at BNL can add considerable value. Alexander takes what researchers have discovered, couples it with other knowledge, and helps guide his fellow laboratory scientists to the next steps in their work — even if he, himself, isn’t conducting these experiments.

“Given our theoretical understanding of what’s going on, as imperfect as that may be, we take that understanding — the theory plus the experimental data — and determine what experiments we should do next,” Alexander said. “That will get us to our goal more quickly with limited resources.”

This approach offers a mutually reinforcing feedback loop between discoveries and interpretations of those discoveries, helping researchers appreciate what their results might show, while directing them toward the next best experiment.

The experiments, in turn, can either reinforce the theory or can challenge previous ideas or results, forcing theoreticians like Alexander to use that data to reconstruct models that take a wide range of information into account.

Alexander is hoping to begin a project in which he works on developing products with specific properties. He plans to apply his knowledge of theoretical physics to polymers that will separate or grow into different structures. “We want to grow a structure with a [particular] function” that has specific properties, he said.

This work is in the early stages in which the first goal is to find the linkage between what is known about some materials and what scientists can extrapolate based on the available experiments and data.

Alexander said the aerospace industry has “models of everything they do.” They run “complex computer simulations [because] they want to know how they’d design something and which design to carry out.”

Alexander is currently the head of a co-design center, ExaLearn, that focuses on exascale, machine-learning technologies. The center is the sixth through the Exascale Computing Project. Growth in the amount of data and computational power is rapidly changing the world of machine learning and artificial intelligence. The applications for this type of technology range from computational and experimental science to engineering and the complex systems that support them.

Ultimately, the exascale project hopes to create a scalable and sustainable software framework for machine learning that links applied math and computer science communities to create designs for learning.

Alexander “brings to machine learning a strong background in science that is often lacking in the field,” Edward Dougherty, a distinguished professor in the Department of Electrical and Computer Engineering at Texas A&M, wrote in an email. He is an “excellent choice to lead the exascale machine learning effort at Brookhaven.”

Alexander is eager to lead an attempt he suggested would advance scientific and national security work at the Department of Energy. “There are eight national laboratories involved and all the labs are on an equal level,” he said. 

One of the goals of the exascale computing project is to build machines capable of 10 to the 18th operations per second. “There’s this enormous investment of DOE” in this project, Alexander said.

Once the project is completely operational, Alexander expects that this work will take about 30 percent of his time. About 20 percent of the time, he’ll spend on other projects, which leaves him with about half of his workweek dedicated to management.

The deputy director recognizes that he will be coordinating an effort that involves numerous scientists accustomed to setting their own agenda.

Dougherty suggested that Alexander’s connections would help ensure his success, adding that he has “established a strong network of contacts in important application areas such as health care and materials.

The national laboratories are akin to players in a professional sporting league. They compete against each other regularly, bidding for projects and working to be the first to make a new discovery. Extending the sports metaphor, members of these labs often collaborate on broad projects, like players on an all-star team competing against similar teams from other nations or continents.

Alexander grew up in Ohio and wound up working at Los Alamos National Laboratory in New Mexico  for over 20 years. He came to BNL in 2017 because he felt he “had the opportunity to build something almost from the ground up.” The program he had been leading at Los Alamos was large and well developed, even as it was still growing. 

The experimental scientists at BNL have been receptive to working with Alexander, which has helped him achieve some of his early goals.

Ultimately, Alexander hopes his work increases the efficiency of numerous basic and applied science efforts. He hopes to help experimental scientists understand “what technologies we should develop that will be feasible” and “what technologies would be most useful to carry experiments out.”

Aaron Sasson. Photo courtesy of Stony Brook Medicine

By Daniel Dunaief

Thanks to the efforts of Stony Brook University School of Medicine’s Chief of Surgical Oncology Aaron Sasson and numerous doctors and researchers at Stony Brook, Long Island has its first National Pancreas Foundation Center.

A nonprofit organization, the National Pancreas Foundation goes through an extensive screening process to designate such centers around the country, recognizing those that focus on multidisciplinary treatment of pancreatic cancer. The NPF offers this distinction to those institutions that treat the whole patient and that offer some of the best outcomes and improved quality of life for people suffering with a disease who have an 8 percent survival rate five years after diagnosis.

Sasson appreciates the team effort at the medical school. “As opposed to one person leading this, there are many people here who are required to have an interest in pancreatic cancer,” he said. “We are not only looking to build a great infrastructure for the treatment of pancreatic cancer, but we’re also looking to build a team for research on pancreatic cancer.”

Sasson highlighted the research efforts led by Yusuf Hannun, the director of the Cancer Center at SBU, who has helped attract a “tremendous number of scientists” to engage in research into this disease.

The recognition by the NPF helps the university recruit physicians who are clinically interested in developing ways to improve the outcome for patients.

Pancreatic cancer presents particular challenges complicated by its biological aggressiveness, its difficulty to detect and by the many subtypes of this disease. “It’s similar to lung and breast cancer,” Sasson said. “There are many facets of those cancers. You can’t lump them all together.”

Researchers and clinicians are still trying to understand pancreatic cancer in greater detail. Once they have done that, they can advance to treating the possible subtypes.

Numerous researchers at SBU have developed collaborations with scientists at Cold Spring Harbor Laboratory. David Tuveson, the director of the National Cancer Institute-designated Cancer Center, has engaged in collaborations with SBU scientists in his work on organoids, which are model human organs grown in a lab. Scientists use organoids to test drugs and molecular pathways involved in pancreatic cancer.

Members of the Long Island community can take comfort in the continuing dedication of the numerous staff members committed to finding a cure. “Residents of Suffolk County and Long Island should be proud of what Stony Brook has been able to accomplish,” Sasson said.

Stony Brook University has been involved in several clinical efforts. The university developed a drug called CPI-613, for which Rafael Pharmaceuticals is in the early stage of clinical trials in combination with other drugs.

In early stages, the treatment increases the vulnerability of cancer cells to numerous other drugs. Newark, New Jersey-based Rafael Pharmaceuticals is testing this treatment in pancreatic cancer and in acute myeloid leukemia.

At SBU facilities, Sasson explained that researchers and clinicians are taking a multidisciplinary approach in their work. One study, he said, is exploring the effects of a kind of radiation therapy for a subpopulation of pancreatic cancer that combines expertise in radiology, gastroenterology, pathology and medical and surgical oncology.

Sasson himself is interested in screening and biomarkers. At least half of his work is related to pancreatic cancer. When he thinks about people who have battled pancreatic cancer, several patients come to mind. He had a patient who was about 80 at the time of his diagnosis. His primary doctor told him to get his affairs in order.

“We operated on him and he lived another six or seven years,” Sasson recalls. “He was grateful to see his grandchildren graduate and to see his great-grandbabies being born.”

While every patient is unlikely to have the same outcome, Sasson said surrendering to the disease and preparing for the inevitable may not be the only option, as there may be other courses of action.

Another patient had advanced pancreatic cancer for 18 months before Sasson met her. She had received no treatment and yet the cancer didn’t progress, which is “almost unheard of and unbelievable.” In fact, the case defied medical expectations so dramatically that the doctors conducted two more biopsies to confirm that she had pancreatic cancer. “She did well for many years despite having advanced pancreatic cancer.”

In another case, a patient was receiving surveillance for lung cancer every three months. In between those visits, he had developed metastatic pancreatic cancer. This patient example and the previous one show the range of cancer progression.

The value of having an integrated clinical and research program is that scientists can look for subtle clues and signals amid the reality of cancer with a wide range of outcomes. Indeed, scientists attend the weekly tumor board meeting, so they can learn about the clinical aspects of the disease. Doctors also attend research collaborations so they can hear about developments in the lab.

Rather than dictating how researchers and clinicians should collaborate, Sasson hopes to facilitate an environment that sparks these partnerships.

Sasson joined Stony Brook Medical School almost three years ago. He said he is “impressed with the caliber of physicians.” It took time to get the critical mass and organization for pancreatic cancer to match the number of basic science investigators.

“I’m hopeful for the progress we’ll be able to make to treat this terrible disease,” he said.

J. Anibal Boscoboinik. Photo courtesy of BNL

By Daniel Dunaief

It was discovered in Sweden in 1756 and its name means “boiling stone,” which suggests something that might be a part of a magic show.

All these years later, zeolites, as this class of crystalline porous aluminosilicates are known, have become a key part of many products, such as in water and air purifiers, in detergents and in petroleum refining and hydrocarbon synthesis. They are even a part of deodorizers for people’s homes.

While these rocks, which are produced naturally and synthetically, act as sieves because their contained pores are the size of small molecules, the surface science plays a role in their interactions involves some mysteries.

For researchers like associate materials scientist J. Anibal Boscoboinik, who works at Brookhaven National Laboratory in the Center for Functional Nanomaterials, the unknowns stem from the way the reactions occur inside three-dimensional pores, which is inaccessible to the typical tools of surface science.

Scientists Anibal Boscoboinik (right) with Bill Kaden from the University of Central Florida and Fernando Stavale from the Brazilian Center for Research in Physics at a Humboldt Foundation dinner in Berlin. Photo from Anibal Boscoboinik

Boscoboinik, who is also an adjunct professor of materials science and engineering at Stony Brook University, has addressed this problem by creating synthetic two-dimensional models of this versatile substance. The models, which he designed when he was at the Fritz Haber Institute of the Max Planck Society in Berlin, have the same active sites and behave chemically like zeolites.

Using the high-tech tools at BNL, including the National Synchrotron Light Source, which is the predecessor to the current NSLS II, Boscoboinik derived an unexpected result. “We found, by accident, that when we exposed [zeolites] to noble gases, they got trapped in the little cages the structure has” at room temperature, he said.

Noble gases — including argon, krypton, xenon and radon — can become enmeshed in zeolite. The only noble gases that pass directly through or enter and exit easily are helium and neon, which are too small to bind to the surface.

When a noble gas with a positive charge enters zeolite, it gains an electron immediately upon entering, so it becomes neutral. The noble gases can also get trapped even when silicates don’t have a negative charge. These gases’ ions are produced when researchers use X-rays. The ions are smaller than the neutral atom, which allows them to enter the cage.

“The energy required to get them out of the cage is high,” Boscoboinik explained. “Once they are in, it’s hard to get them out.”

This finding, which Boscoboinik and his colleagues made last year, was named one of the top 10 discoveries and scientific achievements at BNL. These zeolite cages have the potential to trap radioactive gases generated by nuclear power plants or filter carbon monoxide or other smaller molecules.

The science behind understanding zeolites is akin to the understanding of the inner workings of a battery. Zeolites and batteries are both commonly used in industry and commercial applications, even though researchers don’t have a precise understanding of the reactions that enable them to function as they do.

Indeed, scientists at BNL and elsewhere hope to gain a better understanding of the way these processes work, which offers the hope of creating more efficient, less expensive products that could be technologically superior to the current designs.

Boscoboinik, who has been at BNL for almost five years, is especially     appreciative of the opportunities to collaborate with scientists at the Department of Energy-sponsored facility and worked closely with Deyu Lu on the noble gas experiments.

He would not have learned as much only from experiments, Boscoboinik said. The theory helped explain the trapping of radon, which he didn’t work on for safety reasons because of its radioactivity.

Trapping radon gas could have significant health benefits, as the gas is often found in the ground or in basements. Radon is the second leading cause of lung cancer.

Lu, who is a physicist and theorist at the Center for Functional Nanomaterials, said in a recent email he was “impressed by the novelty of [Boscoboinik’s] research on two-dimensional zeolite.” 

The two researchers received funding starting in 2014 on a four-year collaboration. Lu said that he wanted his computational modeling to “confirm the hypothesis from the experiment that noble gas atoms prefer to enter the nano-sized pore [rather] than the interfacial area of the zeolite bi-layer.”

The two-dimensional zeolite model system “gives us a wonderful playground to learn physical insights from both theory and experiments,” he continued. Boscoboinik is “one of the few experts who can synthesize the two-dimensional zeolite film, and he is leading the field to apply synchrotron X-ray techniques to study this remarkable new material,” Lu explained.

More broadly, Boscoboinik is interested in developing a deeper awareness of the process through which zeolite breaks down hydrocarbons. He would also like to get a specific model for the way zeolite can convert methane — a gas that is increasing in the atmosphere and has been implicated in the greenhouse gas effect — into methanol, a liquid that can be converted into gasoline.

A resident of Stony Brook, Boscoboinik, who was raised in Argentina, is married and has two young children. His family enjoys going to the beach and recently visited Orient Point State Park. When he was growing up in South America and had more discretionary time, he enjoyed reading. His favorite authors are Jorge Luis Borges and Julio Cortazar.

Boscoboinik appreciates the curiosity-driven questions he gets from his children. In his work, he “tries to think like a kid. At work, I try to ask the same question my five-year old asks,” although he thinks like an adult in matters of safety.

As for his work, Boscoboinik said he knows he has a long way to go before he answers the questions he asks. “When working in this environment, you never know what you’re going to find,” he said. 

“You have to keep your eyes open for the unexpected so you don’t miss things that are really interesting, even if they are not what you were aiming at.”

Adélie penguins jump off an iceberg of one of the Danger Islands. Photo by Rachel Herman from Stony Brook University/ Louisiana State University

By Daniel Dunaief

In October of 1957 when the Soviet Union launched the satellite Sputnik, people imagined that satellites hovering over their heads could see everything and anything down below. Indeed, in the early days, some Americans rushed to close their blinds, hoping the Kremlin couldn’t see what they might be eating for dinner or watching on TV.

Satellites today collect such a wealth of information about the world below that it’s often not easy to analyze and interpret it.

That’s the case with the Danger Islands in the Antarctic. Difficult for people to approach by boat because of treacherous rocks around the islands and sea ice that might trap a ship, these islands are home to a super colony of Adélie penguins that number 1.5 million.

Nesting Adelie penguins. Photo by Michael Polito from Louisiana State University

This discovery of birds that were photographed in a reconnaissance plane in 1957 but haven’t been studied or counted since “highlights the ultimate challenge of drinking from the firehose of satellite-based information,” said Heather Lynch, an associate professor of ecology and evolution at Stony Brook University and a co-author on a Scientific Reports publication announcing the discovery of these supernumerary waterfowl.

Adélie penguins are often linked to the narrative about climate change. Lynch said finding this large colony confirms what researchers knew about Adélie biology. In West Antarctic, it is warming and the population is declining. On the eastern side, it’s colder and icier, which are conditions more suited for Adélie survival. The Danger Islands are just over the edge of those distinct regions, on the eastern side, where it is still cold and icy.

A population discovery of this size has implications for management policies. At this point, different groups are designing management strategies for both sides of the peninsula. A German delegation is leading the work for a marine protected area on the east side. An Argentinian team is leading the western delegation.

Adelie penguins on sea ice next to Comb Island. Photo by Michael Polito, Louisiana State University

This discovery supports the MPA proposal, explained Mercedes Santos, a researcher from the Instituto Antártico Argentino and a co-convener of the Domain 1 MPA Expert Group. The MPA proposal was introduced in 2017 and is under discussion in the Commission for the Conservation of Antarctic Marine Living Resources, where the United States is one of 25 members.

Said Santos in a recent email, “This publication will help us to show the importance of the area for protection, considering that decisions should be made [with the] best available information.” The location of the Danger Islands protects it from the strongest effects of climate change, as the archipelago is in a buffer zone between areas that are experiencing warming and those where the climate remains consistent over longer periods of time.

Whales and other mammals that eat krill create an unknown factor in developing fisheries plans. While penguins spend considerable time above water and are easier to monitor and count, the population of whales remains more of a mystery.

Heather Lynch with a penguin. Photo from Heather Lynch

Lynch said the more she studies penguins, the more skeptical she is that they can “stand in” as ecosystem indicators. Their populations tend to be variable. While it would be simpler to count penguins as a way to measure ecosystem dynamics, researchers also need to track populations of other key species, such as whales, she suggested. Humpback whales are “in competition with penguins for prey resources,” Lynch said.

The penguin data is “one piece of information for one species,” but MPAs are concerned with the food web for the entire region, which also includes crabeater seals. For the penguin population study, Lynch recruited members of her lab to contribute to the process of counting the penguins manually. “I figured I should do my fair share,” she said, of work she describes as “painstaking.” Indeed, Lynch and her students counted over 280,000 penguins by hand. She and her team used the hand counting effort to confirm the numbers generated by the computer algorithm.

“The counting was done to make sure the computer was doing its job well,” she said. She also wanted to characterize the errors of this process as all census counts come with errors and suggested that the future of this type of work is with computer vision.

Lynch appreciated the work of numerous collaborators to count this super colony. Even before scientists trekked out to the field to count these black and white birds, she and Matthew Schwaller from NASA studied guano stains on the Danger Islands in 2015 using existing NASA images.

The scientific team at Heroina Island in Antarctica. Photo by Alex Borowicz, Stony Brook University

This penguin team included Tom Hart from Oxford University and Michael Polito from Louisiana State University, who have collaborated in the field for years, so it was “natural that we would work together to try and execute an expedition.” Stephanie Jenouvrier, a seabird ecologist at the Woods Hole Oceanographic Institute, has considerable expertise in the modeling side, especially with the climate; and Hanumant Singh, a professor of mechanical and industrial engineering at Northeastern University has experience using drones in remote areas, Lynch said.

The penguins on the Danger Islands react to the presence of humans in a similar way to the ones elsewhere throughout the Antarctic. The birds generally don’t like creatures that are taller than they are, in part because they fear skuas, which are larger predatory birds that work together to steal an egg off a nest. Counting the penguins requires the researchers to stand, but when the scientists sit on the ground, the penguins “will approach you. You have to make sure you’re short enough.”

Lynch would like to understand the dynamics of penguin nest choices that play out over generations. She’s hoping to use a snapshot of the layout of the nests to determine how a population is changing. Ideally, she’d like to “look at a penguin colony to see whether it’s healthy and declining.” She believes she is getting close.

Above, R.C. Murphy Junior High students Gregory Garra and Gianna Raftery with Catherine Markham in Dawn Nachtigall’s seventh-grade science class last year. Photo from Three Village school district

By Daniel Dunaief

A recent study of 57 species around the world, published in the journal Science, showed that mammals moved distances two to three times shorter in human-modified landscapes.

Catherine Markham, an assistant professor in the Department of Anthropology at Stony Brook University, contributed to this research, adding information about the ranges for baboons in the Amboseli Baboon Research Project in Kenya.

Marlee Tucker, an ecologist at the Senckenberg Nature Research Society based in Frankfurt, Germany, led the effort, which involved working with 114 other scientists who are studying mammals around the world. Tucker “brought together all these research groups on a scale and scope that had not been undertaken before,” Markham said. “She evaluated in an unprecedented way what the implications of human expansion and development are for wildlife movement.”

According to Tucker, a reduction in animal movement could have ecological implications. “It is likely that ecosystem functions such as nutrients and seed dispersal will be altered,” she explained in an email. “However, whether these impacts are negative, positive or neutral requires further research.”

Tucker suggested that it is “important to maintain landscape connectivity so that animals can move freely,” which could include the creation of corridors that link natural landscapes.

While the study made it clear in a comprehensive way that mammals tend to move less when humans interact with them, it didn’t offer specific indications about the causes of that reduction. Some of that, scientists say, could come from fear, as mammals may avoid humans. Alternatively, some mammals might find a new and concentrated food source at garbage dumps and elsewhere that would reduce the need to travel.

Susan Alberts, a professor of biology at Duke University and a collaborator with Markham on baboon research, said that the “take home message” is that “this is a pervasive phenomenon and occurs on a large scale in the mammalian world.”

Markham has been studying baboons in Kenya at the Amboseli site since 2004. When Tucker reached out to her to see if she could contribute to this work, Markham saw an opportunity to collaborate using information she was already gathering.

Above, baboons with a radio collar in the Amboseli National Park in Kenya. Photo by Catherine Markham

As it turns out, baboons in the research project in Kenya live in what Markham describes as a “relatively pristine area” so they did not see “over the time period an increase in the human footprint index.”

Markham shared information about 22 baboons for about 900 days as a part of this research. Tucker’s overarching conclusion included areas where people weren’t encroaching on a mammal’s range. “When she compared the movement of animals living in relatively pristine environments — like the baboons in Amboseli — to the movement of animals living in areas of higher human encroachment, that lead to exciting conclusions,” Markham said. Tucker indicated that future research should focus on exploring the underlying mechanism of the reduction in movement.

In the meantime, Markham is continuing her studies on baboons, exploring the energetic consequences of group size. Larger groups tend to beat out smaller groups when they are competing for food and water in a particular habitat. At the same time, however, those larger groups have stress levels caused by group competition, as one baboon might find the constant proximity and rivalry with another baboon stressful. Baboon group sizes range from a low of around 20 to a high of about 100. Markham is exploring the tension within and between groups.

Over the past few years, Markham, who has been studying this competitive dynamic extensively, has used noninvasive techniques, such as gathering fecal samples, to look for levels of thyroid hormones, which can indicate an animal’s energetic condition.

Alberts explained that Markham was an important contributor to the work at Amboseli, adding that Markham “asks questions at the group level that the rest of us don’t.”

Within the community, Markham has been involved in recent efforts to inspire middle school students at R.C. Murphy Junior High school in Stony Brook to enjoy and appreciate science, working closely with science teacher Dawn Nachtigall, who has been at Murphy for 20 years.

In her second year at Murphy, Markham visits seventh-grade classes several times, discussing her work and explaining how to analyze images from camera traps set up in Kenya and at Sweetbriar Nature Center in Smithtown.

The students receive about 30 photos per pair, Nachtigall explained. Based on the pictures, the students have had to generate questions, which have included whether young deer spend more time with male or female parents, or whether hyenas come out more on full or new moons.

According to Nachtigall, Markham “has such a friendly veneer and an approachable affect” that she readily engages with the students. “She has this wonderful demeanor. She’s soft-spoken, but strong.”

Students in her class appreciate the opportunity to interact with a Stony Brook researcher. “By the end of the period, they are glad to have met her,” Nachtigall added. “Some of them want to become her.”

At the same time, Nachtigall and the other science teachers appreciate the opportunity to hear more from local scientists.

“We live vicariously through her,” Nachtigall said. “It really ignites our own passion for science. Seeing the real-world science for science teachers is just as exciting as it is for students.” Markham is working to post materials online so that teachers and parents can access the information.

A native of Rockville, Maryland, Markham, who joined Stony Brook in 2014, resides in St. James. When she was young, Markham enjoyed the opportunity to join class events in kayaks along the Potomac River. She occasionally saw beaver and bald eagles. Indeed, along the way toward working with baboons, she has also conducted research on bald eagles, monitoring their nests with remote cameras.

As for her work on the Science article, Markham said she is pleased that this kind of collaborative research can provide broad ranging insight to address questions that extend beyond the realm of any one lab or species.

Daniel Mockler in his office at Stony Brook University. Photo from SBU

By Daniel Dunaief

At first, people didn’t believe it. Now, it seems, they are eager to learn more.

Working with a talented team that included postdoctoral researchers, doctoral students and doctors, Kenneth Shroyer, the chairman of the Department of Pathology at Stony Brook University, noticed something odd about a protein that scientists thought played a supporting role, but that, as it turns out, may be much more of a villain in the cancer story.

Known as keratin 17, this protein was thought to act as a tent pole, providing structural support. That, however, isn’t the only thing it can do. The co-director of Shroyer’s lab, Luisa Escobar-Hoyos, found that this protein was prevalent in some types of cancers. What’s more, the protein seemed to be in higher concentration in a more aggressive form of the disease.

Now, working with Long Island native Daniel Mockler, a clinical assistant professor in the Department of Pathology, Shroyer and his team discovered that the presence of this particular protein has prognostic value for endocervical glandular neoplasia, suggesting the likely course of the disease.

Published in the American Journal of Clinical Pathology, the article by Mockler and his team in the Sept. 1, 2017, issue attracted the attention of pathologists around the world. It ranked as the third highest read article in the final month of 2017, according to Medscape. It was behind two other papers that were review articles, which made it the most read primary research report in pathology in December.

The response “did exceed my expectations,” Mockler stated in an email. “I would have thought [Shroyer’s earlier] paper showing that k17 can function in gene regulation would have been more popular. But I guess this [new paper] illustrates that topics that have a possible direct impact on practicing surgical pathologists will draw a lot of attention.”

To be sure, while the recent study is an early indication of the potential predictive value of this protein, there may be some mitigating factors that could affect its clinical applicability.

“It’s premature to know what the clinical utility of this marker will be,” Shroyer said. “To determine that would require a large-scale prospective clinical trial” that would involve other patient populations and other laboratories.

Still, depending on the outcome of research currently underway in Shroyer’s lab, the protein may offer a way of determining the necessary therapy for patients with the same diagnosis.

Doctors don’t want to give patients with milder version of the disease high levels of chemotherapy, which would cause uncomfortable side effects. At the same time, they want to be as aggressive as possible in treating patients whose cancers are likely a more significant threat.

“The goal of having an excellent prognostic biomarker … is to avoid over and under treatment of patients,” suggested Mockler, who is also an attending pathologist at SBU and Stony Brook Southampton.

Shroyer was delighted with the efforts of the team that put together this well-read research. “As is true of all our clinical faculty, I want to give them every opportunity to take advantage of their ability to collaborate with research faculty in our department and throughout the cancer center and the school of medicine to advance their scholarly careers and academic productivity,” he said.

Mockler’s success and the visibility of this paper is “an excellent example of how someone with a busy clinical practice can also have a major impact on translational research,” Shroyer added.

Mockler appreciated the support and work of Escobar-Hoyos, who had conducted her doctoral research in Shroyer’s lab. She has “been the main driving force, along with [Shroyer] in the initial discovery of k17 including its prognostic implications as well as its possible function in regulating gene expression,” he said.

Mockler said he spends about 80 percent of his time on patient care, with the remaining efforts divided between research and academic pursuits. His first priority is providing “excellent patient care.”

Working with Shroyer and Escobar-Hoyos, Mockler explained that they have started looking at k17 in organ systems including the esophagus, pancreas and bladder. “We are currently looking at k17 from a diagnostic point of view in regards to bladder cancer,” he said. “Discoveries that impact the daily signout of surgical pathologists by allowing us to make better and more consistent diagnoses interests me very much.”

A resident of Kings Park, Mockler, who grew up in Hicksville, lives with his fiancée Danielle Kurkowski, who is a medical technologist of flow cytometry research and development at ICON Central Laboratories in Farmingdale.

Daniel Mockler on a recent snowboarding trip to Aspen. Photo from Daniel Mockler

Outside of his work in medicine, Mockler is an avid snowboard enthusiast. He tries to get in as many trips as possible during the winter, including a vacation a few weeks ago to the Austrian Alps. A more typical trip, however, is to western mountains or to Vermont, including Killington, Okemo and Stratton.

“To blow off steam and relax, nothing is better than being on a snow-covered mountain,” he said.

Mockler is pleased with the developments in the department. He has seen the “research goals of the department change quite significantly,” adding that Shroyer has “done a tremendous amount of recruiting.”

Mockler suggests to residents that it’s “good to get involved. I always tell them that [Shroyer] has a pretty active research lab and he likes it when residents get involved.”

As for his work on k17, Mockler is pleased that he’s been able to contribute to the ongoing efforts. Shroyer “has been doing this a while and I have seen the excitement and energy he has put into k17,” he explained, “so I know that we are onto something big.”

And so, apparently, do readers of pathology journals.

Joel Saltz. Photo from SBU

By Daniel Dunaief

In the battle against cancer, doctors and scientists use targeted drugs to treat the disease. They also employ radiation, starve it of the nutrients it might need to grow, block key metabolic pathways in its development and encourage the immune system to attack these genetically misdirected cells that grow out of control. A developing field in this battle includes the use of computers, artificial intelligence and math.

Joel Saltz, the Cherith Chair of Biomedical Informatics at Stony Brook University, recently teamed up with researchers from Emory University and the University of Arkansas and won an $8 million grant from the National Cancer Institute to coordinate radiology and pathology information in the battle against cancer.

“By gathering more information, researchers can understand better what’s happening, what might happen and how best to treat cancer,” Saltz said. The grant will be divided equally among the three institutions over the course of five years. Saltz will be collaborating with Ashish Sharma at Emory and Fred Prior at the University of Arkansas.

Saltz has been working with Sharma for several years, when the two were at Ohio State and then moved together to Emory. This is Saltz’s first major grant with Prior, although the two have also known each other for years and have been working in the same NCI program.

Prior has considerable expertise in radiology, while Saltz is adding his pathology background to the mix. Radiology has used digital imaging for a long time and, until recently, pathology data was collected on glass slides. Saltz is helping bring digital pathology to this effort.

“We had been on panels for many years with NCI saying we need to do this sort of” collaboration, Saltz added, and now the trio is putting that idea to work.

Yusuf Hannun, the director of the Cancer Center at Stony Brook, sees the potential for this type of collaboration. “This is a very important effort that builds on several areas of outstanding strength” at the Cancer Center, the director explained in an email.

Exploring information from digitized radiology and pathology samples will “allow us to understand individual cancers at a much higher level. It should improve accuracy in diagnosis [and offer an] ability to provide better informed prognosis” and individual therapy, Hannun continued.

Researchers on the current grant, which is part of the Information Technology for Cancer Research, plan to expand resources for integrative imaging studies, build on the capacity to acquire high-quality data collections, dedicate resources to support reproducible research and increase community engagement.

Saltz will use the portion of the Stony Brook funds to develop new software integration tools and curation and work with researchers to analyze and understand their patient data. Over time, he will also hire additional staff to build out this expertise. He has collaborated with Kenneth Shroyer, chair of the Department of Pathology at Stony Brook, on pancreatic and ovarian cancer and on breast cancer with pathology professor Patricia Thompson, who is also director of basic science at the Cancer Center. Shroyer “plays an important role” in all his research, Saltz said.

“Digital pathology will supplement that art of surgical pathology with quantitative data, to improve diagnostic accuracy,” Shroyer wrote in an email, which will “inform decisions on how to optimize therapeutic intervention for the treatment of cancer and many other diseases.”

Shroyer interviewed Saltz before Stony Brook hired its first bioinformatics chair. “Based on his research focus, including his pioneering efforts in digital pathology, he clearly stood out as my top choice.”

Saltz and Shroyer have generated maps of patterns for immune cells in tumors. “We and others have shown that these are related to how patients respond to treatment,” Saltz said. He described his work with these scientists as “basic clinical cancer research,” in which he develops and enhances technology to understand various types of cancer.

This particular grant is “more about technology and curation,” Saltz said. “People are developing new algorithms, in artificial intelligence and machine learning.” By making this information available, scientists from around the world who have insights into the specific types of cancer can use it to predict responses to treatment and develop and refine the algorithms that underlie the computer analysis.

Using specific cancers from radiology and pathology studies is akin to sitting in a football stadium and examining a blade of grass from the bleachers, Saltz suggested, borrowing from a phrase he’d heard at a recent panel discussion with Liron Pantanowitz from the Department of Pathology at the University of Pittsburgh Medical Center.

“What we do is we create catalogs of every blade of grass and every worm and weed,” Saltz added. “It’s a huge database problem” in which he is integrating software development.

Hannun, who has been working to help Stony Brook University earn a National Cancer Institute designation, suggested that this bioinformatics work is “a critical component of our plans” and represents an area of exceptional strength.”

Cancer bioinformatics is “one of the main pillars of our research program and it integrates well with our efforts in imaging, metabolomics, improved diagnostics and improved therapeutics,” Hannun explained.

As for his department, Saltz said Stony Brook will have its first biomedical informatics Ph.D. graduate at the end of 2017. Yanhui Liang joined Stony Brook when Assistant Professor Fusheng Wang came to Long Island from Emory. Xin Chen will graduate in May of 2018.

The doctoral program, which launched last year, has five current students and “we’re hoping to get a bigger class this year,” Saltz said. “Informatics involves making techniques for better health care,” Saltz said. People with medical degrees can do fellowship training in clinical informatics.

A resident of Manhasset, Saltz lives with his wife Mary, who is an assistant clinical professor of radiology at Stony Brook University. Over the course of the next five years, Saltz said he believes this grant will continue to allow him and his collaborators to develop tools that will help provide insights into cancer research and, down the road, into personalized cancer treatment.

Richard Moffitt, who joined Stony Brook University’s Biomedical Informatics and Pathology departments at the end of July, recently contributed to an extensive study of pancreatic cancer. Photo by Valerie Peterson

By Daniel Dunaief

It may take a village and then some to conquer pancreatic cancer, which is pretty close to what The Cancer Genome Atlas project assembled.

Pulling together over 200 researchers from facilities across the United States, the TCGA recently published an article in the journal Cancer Cell in which the scientists explored genetic, proteomic and clinical information from 150 pancreatic cancer patients.

Richard Moffitt, an assistant professor in the Departments of Biomedical Informatics and Pathology at Stony Brook University who joined the institution at the end of July, was the analysis coordinator for this extensive effort.

The results of this research, which worked with pancreatic ductal adenocarcinoma, the most common form of this cancer, offered a look at specific genetic changes involved in pancreatic cancer, which is the third leading cause of death from cancer.

“The study has several immediate clinical implications for patients facing the diagnosis of pancreatic cancer,” Ralph Hruban, one of the corresponding authors on the article and the director of the Sol Goldman Pancreatic Cancer Research Center at Johns Hopkins University School of Medicine, wrote in an email.

The work “provides hope for future clinical trials in that 42 percent of patients within this cohort had cancers with at least one genetic alteration that could potentially be therapeutically targetable, and 25 percent of the patients had cancers with two or more such events.”

These genetic findings suggest a potential basis for genetic change-driven therapy trials down the road, Hruban suggested. As the analysis coordinator, Moffitt “played a critical role” Hruban continued. “He brought hard work, amazing creativity and great scientific knowledge to the project.”

Moffitt joined this effort about four years ago, after the collaboration began. The assistant professor said he pulled together the various data sets and analysis results from different teams and helped turn that into a “coherent overall story.”

Moffitt was also in charge of the messenger RNA analysis. He had been at the University of North Carolina as a postdoctoral researcher in Vice Chair of Research Jen Jen Yeh’s lab for the last five years until his recent move to Stony Brook.

Benjamin Raphael, another corresponding author on the article and a professor in the Department of Computer Science at Princeton University, suggested Moffitt played a critical part in the recent work. “In any large-scale collaboration such as this one, there tend to be a smaller number of researchers who play an outsized role in the project,” Raphael explained in an email. Moffitt “played such an outsized role. Without his dedication to the project over the past few years, it is doubtful that our analysis” would have been as comprehensive.

Members of TCGA contacted Moffitt and Yeh because the tandem were working on a new approach to studying gene expression that would eventually be published in a 2015 Nature Genetics article.

Working with Yeh, Moffitt helped tease apart the genetic signature of pancreatic cancer cells from the different types of cells around it, which also includes healthy cells and a cluster of dense cells around the tumor called the stroma.

“The proportion of cancer cells in pancreatic cancer is low so if you imagine a mix of marbles of the same color on the outside but different on the inside and only having 10 in a bag of 100, figuring out what 10 [are] ‘tumor’ colors on the inside was very challenging,” Yeh explained in an email.

The TCGA study explains subtypes of cancer Moffitt didn’t know existed just a few years ago, while exploring the possible role that micro RNA and DNA methylation — the process of adding or taking away a methyl group from a genetic sequence to turn on and off genes — has in describing those subtypes.

Researchers “need projects like TCGA that are a really well-controlled way to study almost every molecule you want to study systematically for 150 cases to reveal these networks,” Moffitt said.

Moffitt has coupled his appreciation for algorithms and math with an interest in biology and engineering. His Ph.D. was done in a dry lab, which didn’t even have a sink. When he moved to UNC to conduct his postdoctoral work, he took a different approach and worked with surgical oncologists on tissue samples.

Moffitt plans to continue working with TCGA data and also to see how the subtypes can be used to predict responses to therapies. Some time in the future, researchers hope patients can get a diagnostic biopsy that will direct them to the specific therapy they receive, he said.

Moffitt grew up in Florida and earned his bachelor’s and doctoral degrees at Georgia Tech before completing his postdoctoral research at UNC. He has been gradually drifting north. Moffitt and his wife Andrea, who just started her postdoctoral work with Michael Wigler and Dan Levy at Cold Spring Harbor Laboratory, live in Stony Brook.

A competitive water skier during his youth in Florida, Richard Moffitt, dons two skis when he’s out with friends on Lake Oconee, Georgia in 2013. Photo by Andrea Moffitt

The water on Long Island is colder than it is in Florida, where Moffitt spent considerable time on a show skiing team. This was his version of a varsity sport, where he spent about six hours a day on Saturday and Sunday during the spring and about three hours a night before tournaments performing moving pyramids, among other tricks. When he was in high school, Moffitt wrote a computer program that automates the show skiing scoring process.

Moffitt processes the world through probabilities, which figured into the way he chose stocks in high school as a part of a stock picking competition and the way he approached his picks for March Madness. His basketball bracket won a competition for bragging rights among about a dozen entrants in 2016 and he was one game away from repeating in 2017 until UNC beat Gonzaga.

As for his Stony Brook effort, Moffitt plans to collaborate with members of the Cancer Center as well. “Being in demand is a good thing.”

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