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

By Rebecca Anzel

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

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

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

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

— Priscilla Arena

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Maureen O’Leary on an expedition in Mali. Photo by Eric Roberts

By Daniel Dunaief

At their greatest depths, oceans hold onto their secrets. With layers of light-blocking water between the surface and the bottom, they hide the kind of clues that might reveal more about who, or what, lived or traveled through them.

What if a sea dried up millions of years ago? And, what if that sea left behind pieces of information — some of them small and subtle and others larger and easier to spot? That’s what happened in a part of Africa that long ago gave up any signs of flowing water. The Sahara desert was, millions of years ago, home to an inland sea called the trans-Saharan seaway.

Maureen O’Leary, a professor in the Department of Anatomical Sciences in the School of Medicine at Stony Brook University, has been to Mali, a country in the northwest of Africa, three times on expeditions, most recently in 2008. There, she collected fossils that are members of extinct groups that are part of larger evolutionary units with living members today.

O’Leary has explored and cataloged a number of remnants from the region, including a turtle and crocodile skull. She and her collaborators have also discovered sting ray fossils. Originally considered likely residents after an asteroid hit Earth that caused a massive extinction, these fossils now suggest that these sting rays lived in the area earlier than previously believed.

“This suggests that the sting rays did survive” the asteroid impact, said O’Leary. “Often extinction events are described in very broad terms but specific studies like this help us” hone in on the kind of species that survived.

She also found intriguing deposits in fossilized feces. Invertebrates burrowed through these fossilized remains, leaving a cast of the shapes of their bodies. The group that left traces of their activities in fossilized feces includes Pholadidae, which has living members. “A careful inspection of a whole fauna of fossils allows you to find invertebrates you had no record of,” said O’Leary.

Leif Tapanila, the director of the Idaho Museum of Natural History and an associate professor of geosciences at Idaho State University, joined O’Leary on an expedition to Mali in 1999, where he was the invertebrate expert. Tapanila said the feces of sharks, crocodiles and turtles have bone fragments that tend to preserve well. Some of these fossilized feces can be four- to five-feet-thick deposits. A prehistoric diver from 30 million years ago would have found that the bottom of the seaway, which was probably 50 to 70 meters at its deepest points, was covered in these hard feces, Tapanila said.

Tapanila described O’Leary as an effective collaborator who ensured scientists formed effective partnerships. “She brings people together,” Tapanila said. “One of her biggest strengths is that she finds pieces of the puzzle that are needed for a particular scientific question. She sets up the infrastructure to make a research project work.”

In one of the blocks of limestone recovered in 1999, O’Leary found a crocodile skull with well-preserved ear bones. That level of detail is unusual in a fossil because of the relatively small and fine nature of those bones. Robert Hill, who was a doctoral student in O’Leary’s lab and is now a professor at Hofstra University, noticed that the ear bones had bite marks on them. A closer examination suggested that the marks were made by a shark, either during a prehistoric battle or after the crocodile had died.

O’Leary is currently working with Eric Roberts, the head of Geoscience at James Cook University in Australia, to write a review paper on Mali that would contain some reconstructions of the region and the species. The paper would emphasize a big picture story using the specialized details she and others collected. This will not only help people see the world as it was but also may help them see the Earth as a changing place, where rising sea levels could cause another transition in a dry and arid region.

While O’Leary would like to return to Mali, she and numerous other scientists have kept their distance amid the political instability in the area. In 2008, Canadian diplomat Robert Fowler was taken hostage for 60 days. “There were some diplomats there who seemed unflappable and serious” who suggested that O’Leary and her colleagues return home during their expedition. “The American Embassy was instrumental in leaning on me to leave.” O’Leary said the politics of these areas, despite the rich story they may have to tell about the past, “can play into whether science can even be done.”

In addition to her research in Mali, O’Leary raised the money and created an online system called MorphoBank, which enables scientists studying anatomy all over the world to collect their information in one place. MorphoBank encourages those interested in anatomy of any kind to find data in one place. Tapanila credits O’Leary for creating a valuable resource. For the time, MorphoBank was “totally new. It takes a lot of effort and vision to pull that off,” he said.

O’Leary is married to Michael Novacek, an author and senior vice president and curator in the Division of Paleontology at the American Museum of Natural History. He is one of the team leaders of the joint American Museum of Natural History/Mongolian Academy of Sciences ongoing expeditions to the Gobi Desert. The duo, who collaborated on an expedition in Morocco, have co-authored papers on the philosophy of science, placental mammal evolution and a team-based study of mammal evolution that was published in the journal Science.

O’Leary watches the political scene in and around Mali from afar.“I do keep an eye on it and would love to return,” she said.

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Stony Brook’s Center for Planetary Exploration opens

Renee Schofield explains the testbed for the PIXL she built. Photo by Kevin Redding

By Kevin Redding

Although some might not think of Suffolk County as an obvious hotbed of planetary exploration, it doesn’t take long to discover just how impactful the research and work conducted on Long Island has been on the growth of space science.

Going back to the Apollo program in the early 1960s, the Grumman corporation was vital in landing astronauts on the moon by designing, assembling and testing the lunar module at its facility in Bethpage.

Even closer to home, the founder of Stony Brook University’s Department of Earth and Space Sciences, Dr. Oliver Schaeffer, became the first person to date celestial objects. He confirmed that the moon rocks brought back by Apollo astronauts were more than four billion years old.

Donald Hendrix leads a research team to help future astronauts prevent long-term illnesses. Photo by Kevin Redding
Donald Hendrix leads a research team to help future astronauts prevent long-term illnesses. Photo by Kevin Redding

Now half a century later, Stony Brook University has once again cemented Long Island’s place in innovative planetary research.

In 2014, Timothy Glotch, a professor in the department of geosciences, received a $5.5 million grant from NASA through their Solar System Exploration Research Virtual Institute program to support his research. The department eventually obtained a 6,500-square-foot, world-class facility consisting of three different labs.

On Aug. 26, the public was invited to the official opening of Stony Brook’s Center for Planetary Exploration, where faculty members and students in the department gave a tour of their labs and showcased the inspiring work that has taken place so far.

At the core of CPEX is the Stony Brook-led multi-institutional Remote, In Situ, and Synchrotron Studies for Science and Exploration Institute, one of the nine nodes of the NASA program.

“We’re trying to pave the way for future human exploration of the solar system,” Glotch said. “Right now we are doing basic science; we are doing exploration activities that are going to get humans to Mars, back to the moon, and to the moons of Mars. That work is going on right here. We’re kind of leading the way in space exploration and we’re very proud of that. ”

He stressed the importance of the overall goal: to train the next generation of solar system explorers and scientists. The students are going to be running missions in the next decade or two, he said.

“Just as Schaeffer put together a young and talented group of researchers, we now have an extraordinarily talented group of young researchers working in planetary science,” current Chair of the Department Dan Davis said.

“We’re trying to pave the way for future human exploration of the solar system.”

—Timothy Glotch

As for the three different labs, professor Joel Hurowitz runs the geochemistry lab, which includes a student-built test bed for the Planetary Instrument for X-ray Lithochemistry, which will fly on the Mars 2020 rover.

The PIXL is an X-ray microscope that looks at rock samples and builds maps of the elemental distribution in those samples to make it easier to analyze.

“From there, we can start to dig in and try to understand whether the environment that those rocks were deposited in were habitable,” Hurowitz said. “PIXL can detect things that are chemical biosignatures. It can detect biosignature in a rock on the surface of Mars. So we’re trying to place some constraints on whether or not there was ever life on Mars.”

The lab is also conducting a series of experiments to determine the damaging effects of lunar dust inhalation by future astronauts.

“What I do is I try to find minerals here on Earth that are similar to what’s found on the moon,” Donald Hendrix, a graduate student leading the research, said. “I grind them up into powders and determine what chemicals are made when they are exposed to fluid, because whenever you breathe in a mineral powder, they can produce chemicals inside your lungs that can potentially cause a lot of damage and turn into lung cancer.

Since humans are going to go back to the moon in the next 20 or 30 years, for really long periods of time, I want to know what hazards astronauts might face while they’re up there.”

Through the research he’s conducting with his team, he’s trying to figure out where astronauts could go that won’t be quite as dangerous.

Professors Joel Hurowitz, Deanne Rogers and Timothy Glotch guide their students in planetary research. Photo by Kevin Redding
Professors Joel Hurowitz, Deanne Rogers and Timothy Glotch guide their students in planetary research. Photo by Kevin Redding

Deanne Rogers runs the remote sensing facility, where faculty, students and postdoctoral researchers analyze various images and infrared data that come from Mars and the moon. From there, they incorporate observation skills and geological training to learn about the planet or moon’s environmental and climatic history.

Glotch’s spectroscopy lab is where students acquire infrared spectra of minerals and rocks for comparison to data collected by Mars and Moon orbiters. Within this lab is the Planetary and Asteroid Regolith Spectroscopy Environmental Chamber, used to re-create the conditions on the lunar surface for accurate measurements.

“I can make the moon on Earth, basically, and that’s pretty exciting,” graduate student Katherine Shirley said. “This machine is special because we can make different environments in this. Eventually we’re going to get some attachments so we can simulate the Martian surface or asteroid surface.”

The lab includes a small piece from Mars, which visitors were encouraged to hold.

Assemblyman Steve Englebright (D-Setauket), who was once a student and employee at SBU, spoke about how much the department means to him.

“I’m practically retired, but my heart is still here,” he said. “I served in this department and am proud to have been among such extraordinary researchers and wonderful human beings for 43 years. It’s a privilege now to help send resources in the direction of these extraordinary individuals who are literally writing the next chapter of our understanding of the universe and solar system. I look forward to continuing to work with you as you go forward. They say I’m technically retired, but don’t believe it. I’m just one phone call away.”

Legislator Kara Hahn (D-Setauket) presented the faculty with a proclamation from the county legislature to celebrate what this research means for the community, the university and the overall future of science.

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International students meet their host families. Director Rhona Goldman is in center of back row. Photo by Dwayne Moore

By Wenhao Ma

One local organization is helping international students adjust to American life.

An evening reception was held at the Wang Center on the Stony Brook campus Aug. 25 to introduce new international students to their host families. For 40 years, the Stony Brook Host Family Program has been providing opportunities for international students to learn about America by having them develop relationships with local volunteer families.

“It’s very difficult when you are not really comfortable with the language,” said Rhona Goldman, director of the program. “This [program] gives students a chance — off campus — to relax and interact with a family.”

Students do not live with the families, but they are invited to join them for meals or to attend events together. Goldman said some families meet with their hosted students two or three times a year, while others see each other on a regular basis.

Goldman and her husband, Dick, are hosting two new international students this year, one from Ghana and the other from China.

“There are so many international students,” Dick said. “They come in not knowing anyone. So they will gravitate to people from their own countries. The dorms, classes, study groups — everything turns out that way.”

He said a lot of international students have a difficult time adjusting to the culture. For example, they don’t know how to get a driver’s license or open a bank account. A family can ease the transition and make finding their way a much more pleasant experience, he said.

“Rhona and her husband Dick are wonderful,” said Jianing Yan, a former hosted student of theirs who graduated in May. “They helped me adapt to the life in America. They took me to shopping malls and grocery stores on the very first day I arrived. Also they helped me learn about the American culture … They really make me feel comfortable here. To me, they are my family.”

Goldman said the students are not the only ones who have benefited from the program. The families benefit, too.

David Altman became a volunteer last year. He hosted three students last semester and will host another two this fall. He said that he has traveled with his daughter to many countries and is interested in different cultures.

“I’ve studied many languages myself,” Altman said. “I know a little Chinese. [The program] helps me also. So it works both ways.”

The host family program works with the university to send out a notification to all international students after they have been admitted. To become enrolled in the program, both students and host families need to submit applications. Goldman said she matches students with families that share similar interests.

On average, about 120 students a year are assigned to 65 local families. However, according to Goldman, this year many students could not be placed simply because there are not enough hosts. She encourages families to learn more about the program and consider becoming hosts.

“We want to serve as many students as possible,” she said. “It’s a most rewarding program.”

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A drone carrying medicine and lab samples lands in a village in Madagascar. Photo courtesy of SBU

By Daniel Dunaief

Stony Brook University is taking to the skies to help people on the ground in Madagascar. Through its Global Health Institute, SBU plans to bring drones to the island nation off the southwest coast of Africa that will carry medical samples from hard-to-reach villages to its state-of-the-art research facility, Centre ValBio.

Late last month, Peter Small, the founding director at GHI, brought a drone to Madagascar, where it flew from the research station to a nearby village. The drones can fly like an airplane over 40 miles of terrain, while they take off and land like a helicopter, enabling a smooth ride to protect the samples inside the cargo area.

“Our challenge is to align the most pressing challenges that are amenable to supply chain and specimen transport and intervention,” Small said. Madagascar is dealing with “high rates of tuberculosis” among other health challenges, he said, adding that a university like Stony Brook can take complicated problems and find solutions in the real world.

The drones can provide two important functions for Madagascar: monitoring the outbreak of any unknown and potentially dangerous disease and offering health care for people who live in areas that are inaccessible by road, Small said.

A view of Madagascar from the SBU drone. Photo courtesy of SBU
A view of Madagascar from the SBU drone. Photo courtesy of SBU

“Diseases like Ebola and Zika frequently pop up in remote areas,” said Small, a medical doctor who worked at the Bill & Melinda Gates Foundation prior to joining Stony Brook University in 2015. Having sites where drones can land and collect specimens will allow village health workers to send off specimens for analysis, providing greater clarity on the incidence of specific diseases throughout the country.

Additionally, people in remote areas can send samples back to a lab to test for medical conditions, such as tuberculosis. After medical technicians run tests, the drones can return not only with drugs that can treat the condition but also with instructions on how to treat patients.

The drones can carry a special box to record whether a pill bottle is opened. The box also can carry a sound recorder that can recognize and count coughs, Small said. When the drone returns with another supply of medication, the previous medicine can make the return trip to the lab, where doctors can determine whether the cough is getting better and can see how much medicine the patient took.

Medicine is delivered to villages in Madagascar by way of drones. Photo courtesy of SBU
Medicine is delivered to villages in Madagascar by way of drones. Photo courtesy of SBU

Ideally, the drones will not require any specialized knowledge to fly. Once people in rural villages have a signal, they can request a drone, which can transport samples to a lab or bring medicine back to the village.

“We want to put these drones in the hands of the village health workers and the local health system,” said Small. He said those working with this project hoped people in the village would welcome this medical service but were unsure how it would be received. “We had no idea how people would respond to these” drones, Small said. The initial run, however, was successful. GHI plans to bring two more drones to Madagascar in the next few months.

A company in Michigan called Vayu manufactures the drones, which weigh 35 pounds, are about the size of a picnic table and can carry up to a 5-pound payload, said Daniel Pepper, the company’s chief executive officer. Using an electric, rechargeable battery, the drones can travel up to 40 miles. In the near future, Pepper hopes to increase that distance to as many as 65 miles.

Vayu has manufactured dozens of these drones. The recent Madagascar test was the first time they had used the unit in an international setting. Pepper is “speaking to partners and potential customers in over a dozen countries,” including the United States, where drones might offer a connection between medical centers in urban areas and harder-to-reach rural communities.

Pepper said the drone was the only one on the market that’s electric powered and can carry this payload over this range. “It takes off automatically and lands vertically,” he said and described the landing as “soft.”

According to Small, Madagascar could benefit from these drones, particularly in diagnosing the myriad health challenges of the area. “Madagascar is a remarkable area to start addressing some of these problems and bringing innovation,” he said.

In some villages, as many as 90 percent of people have intestinal parasites, which contributes to malnutrition and stunts growth, Small said. Small and Patricia Wright, the founder and executive director of Centre ValBio who has been working in the area for 30 years, are hoping to broaden and deepen the connection between Stony Brook and Madagascar.

The dental school has coordinated dental missions to treat hundreds of patients a day. Small said the dean of the dental school, Mary Truhlar, recently visited Madagascar to go beyond medical missions to “engage in improving the quality and training, care and health system issues.”

Small is excited with the way computational science and high-end mathematics are coming in to describe the complexities of health problems to the government of Madagascar. This will assist the government in generating medical priorities. Small has set some large goals for his role: “If life is not palpably better in five, 10 or 15 years” in Madagascar, “I will have failed at my job.”

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Dr. Kenneth Kaushansky, senior vice president for Health Sciences at Stony Brook University; said Stony Brook University President Samuel L. Stanley Jr.; and Dennis S. Charney, dean of the Icahn School of Medicine at Mount Sinai Hospital in New York City shake hands during the signing of the agreement for the two hospitals to partner. Photo from Stony Brook University School of Medicine

By Talia Amorosano

Two major medical institutions have agreed to team up, and the partnership could lead to big scientific breakthroughs.

In order to create more academic research opportunities and streamline and expand clinical care initiatives, Stony Brook Medicine and Mount Sinai Health System, in New York City, have entered into a comprehensive affiliation agreement. The change will promote inter-institution collaboration encompassing all five of Stony Brook’s Health Science schools, Stony Brook University Hospital, all 25 academic departments of the Stony Brook University School of Medicine, Mount Sinai Health System facilities and Medical School, and the Icahn School of Medicine at Mount Sinai inclusive of seven hospitals and an expanding ambulatory network.

Facilitators of the partnership believe that the expansion of clinical trials and research opportunities for both institutions will prompt research and studies that could lead to major discoveries, especially in the treatment and understanding of disease.

Dr. Kenneth Kaushansky, senior vice president for Health Sciences at Stony Brook University, noted that the alliance will make use of the strengths of each individual institution.

“What we both get out of the affiliation is enhanced possibilities for science and education,” he said. “Multiple groups of investigators [with members from each institution] work together and look at things in slightly different ways.”

In a press release, he noted Mount Sinai’s Icahn School of Medicine for its strong biomedical, clinical research and health policy expertise and Stony Brook University for its advanced mathematics, high-performance computing, and physical and chemical science departments to illustrate the point that these institutions can accomplish collaboratively more than each can do alone.

“In the long term were gonna roll out more and more in the way of clinical interactions,” said Kaushansky, who mentioned Stony Brook’s recent recruitment of two new cardiac surgeons from Mount Sinai. “We don’t do heart transplants, but Mount Sinai does.”

He emphasized the new potential for patients to easily seek services from either hospital. In fact, joint research programs ranging from fields of biomedical engineering and computer science to medicinal chemistry science, neurology, psychiatry, therapeutics and more are currently in the works.

“Stony Brook Medicine and the Icahn School of Medicine at Mount Sinai are two powerhouses of research that when partnered will definitely yield more than just the sum of their parts.”

—Lina Obeid

In terms of education, University students will now be afforded the unique opportunity to take classes offered on either or both campuses, and participate in a variety of summer programs geared toward students of all ages. The two schools plan to facilitate joint graduate and medical educational programs in a wider range of subjects than ever before, and have agreed to invest a collaborative $500,000 for the development of academically challenging pilot programs to be supervised by a joint committee.

“The joint pilots in research have immense promise to advance health at the most exciting time in the biomedical sciences, including advanced computational, bioinformatic and engineering approaches,” said Lina Obeid, MD, dean for research and vice dean for scientific affairs at Stony Brook University School of Medicine. “Stony Brook Medicine and the Icahn School of Medicine at Mount Sinai are two powerhouses of research that when partnered will definitely yield more than just the sum of their parts.”

Other leaders of each institution have already expressed similar enthusiasm about the affiliation, which was effective immediately upon signing, and many have verbalized hopes that groundbreaking research will take place as a result of this strategic partnership.

Dr. Kenneth L. Davis, president and chief executive officer of the Mount Sinai Health System, said, “Together [Mount Sinai and Stony Brook] will use our outstanding resources to create changes in medicine.”

“Each institution has so much to offer,” said Stony Brook University President Samuel L. Stanley Jr., “this is an opportunity that will prove to be beneficial to all — now and in the future — as we explore and grow this incredible collaboration.”

Looking toward the future, Kaushansky said that Stony Brook has more affiliation agreements in the works, contingent upon state approval.

“We are working very hard with our friends in the state of New York to get approval for affiliation with Southampton Hospital and Eastern Long Island Hospital in Greenport,” he said.

Also pending is a potential partnership with John T. Mather Memorial Hospital in Port Jefferson. “In April, Mather Hospital asked a number of healthcare systems — us included — whether they were interested in affiliating with Mather Hospital, and we said yes,” Kaushansky said. “We made a proposal to the Mather hospital board … and they were supposed to decide [with whom they wish to affiliate] back in June.”

About a year ago, Kaushansky said he wondered aloud how it is that the insistution could make a bigger impact on clinical medicine, education and research. He now expresses confidence that Stony Brook’s affiliation with large city medical center, Mount Sinai, and future mutually-beneficial partnerships with Long Island hospitals and medical centers, is the most surefire way to achieve such an impact.

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Dima Kozakov. Photo courtesy of Stony Brook University

A high five becomes a natural celebration after a home run because the hitter and the celebratory teammate are standing on their feet and are looking directly at each other. What if gravity didn’t keep our feet on the ground and our heads in the air? We might slap a hand into a foot or a foot into an elbow, sharing a nonverbal exchange with a different meaning.

Proteins inside our bodies don’t have the same gravitational and physical limits. They can and do come together in a soup of cytoplasm, blood, plasma and other mediums. Some of the time, those exchanges, like the high fives, communicate a message in the ordinary course of life. In other circumstances, however, those protein-protein interactions can lead to diseases like cancer.

Researchers around the world have studied these interactions using a variety of tools, trying to combat signals that contribute to damaging and life-threatening conditions.

Dima Kozakov, assistant professor in the Department of Applied Mathematics and Statistics and faculty member of the Laufer Center for Physical and Quantitative Biology at Stony Brook University, has spent several years creating a general way to model the mechanical details of how two proteins interact. This tool could become useful for researchers who are studying problematic interactions.

Leading an international team of scientists, Kozakov, who is also a faculty member at the Institute for Advanced Computational Science at SBU, created a new algorithm to model protein interactions. This algorithm accelerated how to model particular protein-protein interactions to identify harmful couplings. Kozakov and his colleagues recently published their findings in the prestigious journal, Proceedings of the National Academy of Sciences.

Applications of this technology include helping to design therapeutic proteins and speeding up vaccine design. If, for example, the interaction of a pair of proteins contributes to disease, scientists may want to design some other protein that is safe for the patient that will interact with one of the proteins. This additional coupling can avoid the more harmful protein connection.

Scientists also sometimes know that two proteins interact, but they don’t know how. Proteins often have large surfaces with many potential connections. Researchers might need to know “how two bodies come together,” Kozakov said. Proteins are flexible three-dimensional objects that consist of molecules. In modeling the interactions, Kozakov can find the three-dimensional way these proteins come together.

Computational modeling is less expensive than running experiments. At this point, the computer system needs as its starting point the three-dimensional structure of the proteins. That, Kozakov said, is much easier than determining the structure of a protein complex.

The next step is to work on methods where scientists don’t need the structure but only the chemical formula, which they can find through the amino acid sequence. Kozakov and his collaborators will use the information on the structure of similar proteins to build the models. “We’re developing a methodology that will work with the models,” Kozakov said. He described his approach as “physics based,” in which he solves a statistical mechanistic problem by using an energy function that can account for different environments.

“In principal, we can modify our energy function to account for different environments,” like changes in pH, temperature or other variables that might affect how two proteins come together. Given the way Kozakov and his colleagues designed the model, it can account for all possible configurations of two almost rigid proteins coming together.

Kozakov is also in discussions with Brookhaven National Laboratory to explore the results of small-angle X-ray scattering. The benefit of this approach is that he doesn’t need proteins in a crystalline structure, which is a requirement of crystallography. While small-angle X-ray scattering provides less information than crystallography, Kozakov said he and his colleagues can develop it in combination with other techniques where it would be equivalent.

Kozakov has been developing models since 2007 or 2008 to understand these interactions. The project in his recent paper took three years to finish. The program takes 10 to 15 minutes to run on a personal computer. Before, this kind of effort required a supercomputer.

Kozakov believes there could be other applications of this technology, where scientists could model candidate protein drugs in real time to see how the drug interacts with the protein of interest. The first version of the program came out about a year and a half ago and it took the intervening time to perfect it, he said.

Born in Eastern Europe in a region that used to be part of the Soviet Union but is now on the western border of the Ukraine, Kozakov lives in Stony Brook with his wife Olga Kozakova. The couple has a six-year old son, Platon. Kozakov’s grandparents were scientists: his grandfather, Mikhail, was a university professor and his grandmother, Nina, worked at the university. He grew up surrounded by books on physics. He “had fun, digging into antiquities books” and thought the science presented an “inspiring environment.”

As for his work, Kozakov has a big picture view of his efforts. “I want to make something useful to the community and to the world,” he said. “I want to do what I can to help.”

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Jameel Warney signs partially guaranteed deal with Mavericks

Jameel Warney dunks the ball for Stony Brook University. Photo from SBU

By Desirée Keegan

Jameel Warney’s coaches used to say the player held a basketball like a bowling ball, cupping it with his hand and wrist when driving to the basket. He holds the ball a little differently now. He’s gripping it like an NBA pro.

After competing for the Dallas Mavericks’ 2016 Summer League team from July 2 through July 8, Warney, a 6-foot, 8-inch, 260-pound forward, agreed to a partially guaranteed deal with the team, which amounts to a training camp invite.

“I always have the utmost confidence in myself and know that if I play hard, I can do whatever I think I’m capable of doing,” Warney said. “When I play well and with a chip on my shoulder, I won’t be denied. It was great to know that I can play with this level of competition.”

During five Summer League appearances, he averaged 6.5 points, 6.5 rebounds, 1.2 steals and one block per game. Dallas never ran offensive plays designed to get him open, yet Warney still shot 60 percent from the field.

Jameel Warney block a shot for the Seawolves. Photo from SBU
Jameel Warney block a shot for the Seawolves. Photo from SBU

“A lot of hard work went into this and it’s great to get some recognition, but I still have a lot of work to do,” he said. “I was happy that [Dallas] offered to bring me along to training camp, because it’s just another step toward ultimately making my dream come true.”

Although his form may not have been there from the start, the now former Stony Brook University star’s previous head coach, Steve Pikiell, said he’s proud of the player Warney has become. He noted the vast improvement he saw in Warney’s game over the 22-year-old’s four-year tenure with the Seawolves.

“Everyone says great hands, great this, great that, but he’s just a great kid,” Pikiell said. “How he handled himself on and off the court was just awesome. He’s one of the best I’ve worked with in all of my 23 years of coaching.”

Warney began his basketball career as many young players across the country now do; in the Amateur Athletic Union.

“They didn’t think he was going to make it,” his mother Denise Warney said of her son’s coaches. “They said he was very lazy, and he was struggling with the drills and it seemed like something he wasn’t interested in. That all changed in two or three months.”

Warney learned from the experience and established a newfound passion for the sport. Within months, multiple AAU teams were interested in the abnormally tall middle school standout.

From there, Warney joined the varsity basketball team at Roselle Catholic High School in New Jersey. He graduated as the school’s all-time leading scorer with 1,968 points, and averaged 17 points, 13.5 rebounds, four assists and 3.5 blocks per game as a senior.

“He’s humble and he’s hardworking. I think that’s an unbelievable combination for a kid nowadays.”

— Steve Pikiell

“For Jameel, whether he’s well, sick or tired, he plays really well,” his mother said. “He just loves the sport.”

At Stony Brook, he enjoyed much of the same success.

Warney graduated with more victories than any player in school history, and is the school’s all-time leader in points, rebounds, blocks and games played. The Associated Press All-American Honorable Mention also broke Stony Brook records for points in a season and in a single game when he scored 43 against the University of Vermont March 12.

Among all the records, Warney was also named American East Player and Defensive Player of the Year after leading the Seawolves to the American East Championship title and the first NCAA postseason berth in school history. He recorded 23 points and 15 rebounds in the first round of the tournament against the University of Kentucky on March 17, though the team fell 85-57.

“I saw something in him early on and I was able to help him bring that talent and ability out of him,” Pikiell said. “Mix that in with his hard work, and that’s how he’s gotten to the point he’s at. I know he can play at the NBA level. He has a skill set that everyone could use. He has a great motor, he’s a terrific rebounder, he has great hands, he’s a great passer, he has a tremendous physical ability and he’s an unselfish player. He has a great mind for the game of basketball, and those are attributes that bode well for him to be able to continue to play at the next level.”

Jameel Warney carries a net around his neck after the Stony Brook University men's basketball team won the America East championship. Photo from SBU
Jameel Warney carries a net around his neck after the Stony Brook University men’s basketball team won the America East championship. Photo from SBU

For Denise Warney though, it’s more than just her son’s accolades and titles. It’s about how proud she is of how far her son has come not just in the sport, but as a person. When she watches him, she can’t help but smile.

“The game for the NCAA berth, I just watch that game over and over again because it amazes me that he’s turned out to be such a great basketball player,” she said.

She is especially amazing watching him dunk the ball, because for her, it brings back a decade-old memory.

“When he was little, I remember him saying, ‘Mommy, I want a trampoline.’ I asked him why, and he said, ‘I want to put it next to the basketball hoop so I can dunk,’” she said. “We laughed about it because now when I see him dunk a ball, I go all the way back to when he was 10 years old. I get this rush watching him, I’m overcome with this emotion, and I just keep becoming prouder and prouder of him.”

Warney and his mother both appreciate those who have helped him reach such heights thus far in his career.

“The years of improving mentally and physically, being mature and proving my stuff on the court with Stony Brook after high school — I’ve learned so much,” he said. “I feel like a lot of the people I’ve come across over my years of playing basketball have influenced my life. My coaches in high school, my mom, college coaches, the rest of my family and my close friends, I’m doing this all for them because they’ve been with me through the struggles and through the highs. I’m happy to have such a nice support system with me.”

He’s influenced the lives of others as well, as young children run around Stony Brook donning his name and number on their jerseys, looking up to the professional athlete who is continuing to put in the work as he climbs his ladder toward his ultimate goal of making a roster.

“He’s humble for a player as talented as he is,” Pikiell said. “He’s humble and he’s hardworking. I think that’s an unbelievable combination for a kid nowadays. That enabled him to get better and help us do things that no Stony Brook team has ever done, I think he can make a team and stay for a long time. I think his best basketball is ahead of him.”

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Erik Muller. Photo by Yizhi Meng

By Daniel Dunaief

Diamonds may not only be a girl’s best friend, they may also be important for doctors, particularly those using radiation to treat cancer patients.

Erik Muller, a principal investigator and adjunct professor in the Department of Materials Science and Chemical Engineering at Stony Brook University, recently demonstrated that a particular type of synthetic diamond can measure the flux, position and timing of radiation beams used in cancer therapies. His research seeks to adapt diamond detectors for use with an emerging type of therapy using high-energy protons and carbon ions. “There currently does not exist a technology which can precisely measure the flux, position and timing of these proton and carbon ion beams used in radiotherapy,” Muller explained.

The diamonds Muller and his team use are more pure than any natural diamond. They contain fewer than five parts per billion of nitrogen and less boron or other impurities. They are clear with no color. Nitrogen gives diamonds a yellow or brown color and acts as a charge trap, making natural diamond unsuitable for radiation detectors.

As an SBU postdoctoral researcher, Muller joined an effort at Brookhaven National Laboratory to investigate the use of diamond as an electron source. During that study, researchers found that diamond was a valuable X-ray detector. The success of that work led to the Department of Energy funding work to develop sensors for radiotherapy.

Diamonds can provide information that enable scientists to measure in real time the development of the beam.

Once diamond growers send the product to his lab, Muller and his team screen for a defect that can lead to unwanted hot spots in the detector response to X-rays. When Muller’s lab receives the diamonds, they look like small square pieces of glass. These diamonds are bread sliced into two to three pieces that are about half the thickness of a human hair.

Partners at the Center for Functional Nanomaterials at BNL prepare, characterize, etch and pattern the diamonds in the cleanroom. The Instrumentation Division at BNL provided custom electronics, circuit design, wire bonding and assembly. “The development of the detectors, particularly the pixellated diamond X-ray detector, would not be possible without the talent and expertise” in the Instrumentation Division, Muller explained.

Muller also lauded the contribution of the Stony Brook University students who worked on the diamond effort, including Mengjia Gaowei, Tianyi Zhou, Mengnan Zou and Wenxiang Ding. In preparing a proposal for the Department of Energy to improve beam diagnostics for particle therapy, Muller met Samuel Ryu, chair of the Department of Radiation Oncology and deputy director for clinical affairs at Stony Brook University’s Cancer Center. Ryu “expressed a strong interest in using these detectors for X-ray beam therapy and we have been pursuing that as well,” Muller said.

Ryu said the existing conventional detector, which measures radiation dosage, is “limited in some sense.” He likened the radiation detector to a thermometer. If a thermometer indicates that it’s 90 degrees, it may be 91 degrees, but the thermometer may not read the temperature with enough precision to indicate the exact temperature. Similarly, the diamond detector “will improve” the precision of the radiation dose measurement. The gap in the detection of the radiation dose has been like that for more than 100 years, Ryu said.

Ryu said the addition of the diamond to the detector should be commercialized and that he and Muller are “really trying to find out how we can use these detectors in the clinic.” Ryu said he doesn’t know the time frame for when this might become available in a radiation delivery system, but he would “like to see it as soon as possible.” Ryu and his staff meet regularly with Muller and his team to analyze the data and discuss how to proceed. He described Muller as “very open-minded” and indicated that it is a “very good collaboration.”

One of the challenges in taking this diamond discovery to the next step is to ensure that the software is robust and that it has enough redundancies to turn the beam off amid any contradictory readings. Before diamonds can become a part of these carbon or ion beam treatments, researchers need to demonstrate that the radiation itself won’t damage the diamond. While Muller doesn’t expect this to happen, he said he has to prove its viability.

In the bigger picture, Muller said he and the members of his lab spend considerable time understanding the physics of radiation sensing devices in high-radiation environments. “Diamond is a very promising material in this field for continued development and is our current focus,” he suggested. “In general, I am interested in any technique and material where we can understand how the structure affects the device function.”

Residents of South Setauket, Muller lives with his wife Yizhi Meng, an assistant professor in the Department of Materials Science and Chemical Engineering at Stony Brook, and their daughter, who is in primary school. Meng, who is a graduate of Ward Melville High School, develops drug delivery materials for breast cancer and osteosarcoma, a type of bone cancer. The couple met when they were graduate students at Cornell University. They shared an interest in photography. Meng uses Nikon cameras, while Muller prefers Canon. “There’s a funny rivalry between us,” Meng said.

As for his work, Muller is optimistic that it will have an application in radiation delivery. He believes he can address the engineering challenges and is “planning to continue the commercialization of these devices.” Meng is excited by the progress Muller has been making. Muller is “working with some really great people,” she said. “It’s really exciting.”

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0 2009
Joanna Kiryluk during her trip to the South Pole in 2009. Photo from Joanna Kiryluk

By Daniel Dunaief

She traveled to a place she felt might have been as unfamiliar as visiting the moon or Mars. The project that is such a large part of her life is looking for signals sent from well beyond those relative celestial neighbors.

Joanna Kiryluk, an assistant professor of physics at Stony Brook University, didn’t travel off the planet, although she visited a remote location that was considerably different, less populated and at a higher altitude than the sandy beaches of Long Island. In 2009, Kiryluk traveled to the South Pole as a part of the aptly named IceCube project, which was completed in 2010. Kiryluk and hundreds of other physicists around the world are studying the information gathered from detectors drilled deep into the ice below the surface.

Kiryluk is studying tau and electron neutrinos, which are created as products of cosmic ray interactions and carry very high energies. Scientists do not know which sources in the universe are capable of creating such high energies. Unraveling this is one of her research goals. The neutrinos produced by collapsing stars, or supernova, typically have energies that are about a million times smaller than the high-energy neutrinos discovered by IceCube.

Neutrinos have very small masses and travel at speeds close to the speed of light, Kiryluk explained. Since they interact with matter weakly, they pass through most objects without any interactions. On rare occasions, however, these neutrinos collide with a neutron or a proton, causing a characteristic reaction that provides a clue about where they are, what energy they had when they collided, and, perhaps where they originated.

For her research, Kiryluk recently received the prestigious National Science Foundation Career Award, which provides almost $900,000 to support her work over the next five years. “It’s a great honor,” said Kiryluk. “The chances of success for such proposals are small and, in this sense, it was also a pleasant surprise.” Kiryluk said the funding will enable her to employ two graduate students per year. Part of the money will also be used for educational purposes and outreach. Kiryluk has reached out to high schools including Brentwood and Riverhead High School to involve students and teachers in research. Kiryluk is also a proponent of a Women in Science and Engineering program, or WISE, that encourages the “involvement of under-represented groups” in science, including women.

Kiryluk credits her Ph.D. advisor, Barbara Badelek, a professor at the University of Warsaw in the Department of Physics and a professor at Uppsala University, for believing in her and in her ability. She suggested that such support was critical to her success and her focus. Badelek met Kiryluk in 1994 and supervised her undergraduate and Ph.D. work. Kiryluk was “immediately recognized as a remarkably good student: hard working, trying to achieve a deep understanding of problems and very enthusiastic,” Badelek explained in an email. Badelek added that she is “very pleased to see her maturity and growing scientific prestige.”

In the IceCube project, Kiryluk is a part of an experiment that involves over 300 scientists from 48 institutions from around the world. IceCube, which took seven years to build, was manufactured as a discovery experiment to find high-energy neutrinos, which originate from astrophysical sources. People who have known Kiryluk for decades suggest that she has the right temperament for such an ambitious joint effort.

Kiryluk is “quiet and calm, but works hard and never leaves things because she finds some difficulties,” explained Ewa Rondio, the deputy director for scientific matters at the National Centre for Nuclear Research in Poland, who met Kiryluk when she was an undergraduate. Kiryluk’s goal is to measure the energy spectrum of these neutrinos. “We are interested in fluxes,” she said. These fluxes and energy spectra of high-energy neutrinos will provide insights in the sources and mechanisms of the most powerful accelerators in the universe.

A cubic kilometer of ice, IceCube, which has enough water to fill one million swimming pools, is large enough to capture more of these rare neutrino events. The key to unraveling what these signals indicate is to understand their energy and direction. The detectors don’t collect information from the neutrinos directly, but, rather from the interaction with particles in the ice. The neutrino interactions in ice produce a flash of light in the South Pole ice that the scientists measure with sensors. They study the pattern, the arrival times and the amplitude of this light at the sensors. This information can help determine the neutrino energy and direction.

Kiryluk is looking for high-energy events that are “most likely coming from outside of our galaxy,” she said. These particles are distributed all over the sky. While IceCube is capable of collecting data from the highest energy particles, it hasn’t yet gathered enough of these events to provide conclusive information at this range.

Kiryluk visited the South Pole for two weeks in 2009 before IceCube was finished. She was involved in the commissioning of the newly deployed detectors for the data acquisition system. The detectors are between 1,500 and 2,600 meters deep, which helps them “suppress any background events,” such as cosmic rays that are produced in the atmosphere. The facility is 3,000 meters high and has low humidity, which means it’s “easy to get dehydrated,” Kiryluk said. She described the working and living conditions at the South Pole as “modern.”

A native of eastern Poland, Kiryluk arrived on Long Island in 2001, when she worked at Brookhaven National Laboratory. She lives in Rocky Point. Kiryluk said the physics department is “growing.” Since her hire, nine assistant professors have joined the Department of Physics and Astronomy at Stony Brook University. As for her work, Kiryluk is inspired to understand how IceCube can be used as a “probe to study astronomy,” which enables her to be a part of the process of discovering “what is out there.”

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