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Daniel Dunaief

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Eckart Wimmer. Photo by John Griffin/SBU
Jorge Benach. Photo from SBU
Carol Carter. Photo by Jeanne Neville/SBU
David Thanassi. Photo by Jeanne Neville/SBU

By Daniel Dunaief

The American Society for Microbiology named Stony Brook University’s Department of Microbiology and Immunology a “Milestone” program on Oct. 17th, recognizing the department’s historical research contributions in fields ranging from Lyme disease to polio virus, and infection and vaccines.

Stony Brook is the 20th program to receive this distinction from the ASM, joining Cold Spring Harbor Laboratory as the second such distinguished program on Long Island, and the fourth in the state.

It’s a “shared distinction among all the friends and colleagues from the department over the years” since its inception in 1972, said Carol Carter, Distinguished Professor in the department, and recent inductee into the National Academy of Sciences.

“It’s a family-community [honor],” she continued.

The Milestone recognition from the ASM raises the profile of the department and the university, as it recognizes its historical contribution to the field, and encourages and inspires the growing staff in a department in which basic research can lead to breakthrough discoveries.

“This is not an award or discovery for the last year or year before,” said Kevin Gardner, Vice President for Research and member of the Office of the President. “This is for historical levels of achievement over a really long period of time.”

Gardner planned to join department members, politicians including Assemblymember Edward Flood (R-Port Jefferson) and executives at ASM, as part of the recognition ceremony. The ASM, which was founded in 1899, and has over 32,000 members, is a “high-quality professional society and is about as good as they get,” Gardner added.

“It’s a tremendous honor.”

Theresa Koehler, president of ASM, will give a speech on the historic microbial science accomplishments at Stony Brook and designate the site officially a Milestone program.

Professor Emeritus, Nassau Community College/ University Medical Center and ASM Member, Lorraine Findlay, will also attend.

The ASM has been recognizing Milestones in Microbiology sites since 2002, when the first such honoree, Selman Waksam’s Laboratory at Rutgers University, received the honor.

“The program celebrates groundbreaking achievements that have shaped our understanding of microbiology and inspire future generations,” ASM Archivist Colleen Puterbaugh explained in an email.

The Stony Brook Department of Microbiology and Immunology has made the kind of fundamental discoveries regarding how cells work and how DNA and RNA and the different genetic building blocks come together that have led to treatments for diseases like polio, Gardner added.

“These types of recognition really help put the word out about what we’ve done and continue to do,” said David Thanassi, Chair of the Department of Microbiology and Immunology. “It helps build morale” and aids in recruiting additional faculty.

Last year, the department added four faculty members and is in the process of searching for another person to join.

In the wake of the COVID Pandemic, universities and research facilities have emphasized the importance of microbiology, immunology and virology, which are fields that could help provide the kind of basic science that leads to early diagnosis, prevention, and treatment.

“Other places want virologists, too, because there’s a greater awareness of the need for these types of researchers,” said Thanassi.

Compelling research

In the application Carter helped prepare to submit to the ASM, she focused on three specific basic research achievements that have had an important impact on human health.

Joseph Kates, Founding Chair of the department, discovered that viruses could package enzymes required to copy themselves. His research made it possible to target viral polymerases as a type of therapy.

“Up to that point, it really wasn’t known about the basics of how viruses replicate themselves,” said Carter. “Finding this enzyme that viruses have to carry in their coat meant humans could devise a strategy for countering their ability to replicate.”

When she was considering joining the young state university, Carter interviewed with Kates in 1975. Kates “was so impressive and so much fun,” said Carter, “it was difficult to envision why you wouldn’t come and work in his department.”

Additionally, the ASM considered the research of Jorge Benach, Willy Burgdorfer and scientists from the Rocky Mountain Laboratory, who identified the cause of Lyme disease, which is a particular problem on Long Island.

This work made it possible to create antibiotic therapies.

Benach was able to “isolate the spirochetes from patients and demonstrate that they were the causative agent of Lyme,” said Carter.

Benach also characterized the form of the infection that occurs in dogs. Meanwhile, Eckard Wimmer was the first to describe the chemical synthesis of a polio virus without using a natural template. He was also the co-discoverer, with Vincent Racaniello, of the human receptor for poliovirus.

Wimmer’s work started efforts to synthesize organisms in the absence of a natural template, making it possible to develop new strategies in virus vaccine development.

Two plaques

As a part of the ceremony, the ASM will award Stony Brook two plaques. One of them will be visible in the department itself, while the other will go up in the Renaissance School of Medicine’s lobby, near the dean’s office and the library.

Carter suggested that the department continues to conduct research that is globally important.

“These days, the [discoveries] are not low-hanging fruit,” Carter said.

“The answers don’t come easily. You do feel gratified, whether you or somebody else in your unit, provides some sort of understanding that we didn’t appreciate before,” she continued.

In addition to the principal investigators who conducted research that proved important for human health, Carter added that the students who gained experience and insights at the university have gone on to develop productive careers.

“We have had fabulous students.”

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SBU's Elizabeth Watson, second from right, and her team coring.

By Daniel Dunaief

Daniel Dunaief

I used to liken the process to sitting on a highway divider where the speed limit was 70 miles per hour, holding a notebook and trying to read and record as many license plates as I could, sometimes in the pouring rain, under a bright sun, or in thick fog.

Working for a wire service, with its 24-hour news feed and its endless space for stories, was exhilarating and exhausting. My editors sometimes called me at 4 a.m. to tell me about an important story that was breaking and to encourage me to come into the office to get to work.

Oh, and every three months, when the companies I covered reported earnings, I’d arrive at work for at least a week around 7 in the morning, wait for the numbers to come out, and then spend the day reading the reports, talking with analysts and investors, getting on media conference calls with top executives and watching the stock price of the company rise and fall.

My job was to search through all that information to anticipate how people would react to piles of electronic news.

It was a great opportunity to write on deadline and to experience the absurd. One day, I helped write a few headlines and then had to use the bathroom. As I pushed the door open, my editor, following uncomfortably closely behind me, hovered.

“Can I help you?” I asked, as I stopped and turned around.

“Yeah, how long are you going to be in here?” he asked in his usual staccato, urgent tone.

“As long as it takes,” I shrugged.

“Yeah, well, there’s a headline out there and you need to send out the first version of the story within 15 minutes,” he reminded me, as if I didn’t know our rules.

“I know,” I said, “and I’m sure my system will comply with the requirements.”

Those were tough days at the office.

I’m sure everyone has difficult days at work, whether it’s a police officer dealing with someone who is in an altered, drug-induced state who may be a danger to himself or others, a teacher helping a high-stress student prepare for a standardized test, a truck driver taking a long detour around a crash site, or any of the many other possible strains or obstacles between the start of the day and the workload.

Recently, I spoke with several climate scientists who are a part of the Science on Stage free celebration at Stony Brook University’s Staller Center, which is coming up on October 28th at 4 p.m. (see related story in the Arts & Lifestyles section).

These scientists endure everything from creature discomforts, to resistance to the work they’re doing, to their own deadlines and the need to conduct their studies, publish their results and apply for funding.

Indeed, Elizabeth Watson, Associate Professor in the Department of Ecology & Evolution at Stony Brook University, shared several challenging moments.

“I’ve gotten stuck in the mud, covered with ticks, I’ve gotten Lyme, crawled across mudflats, pushed boats across mudflats, had to row our power boat back to the launch ramp more than once, [and] got forgotten about on a raft in a lagoon,” Watson wrote in an email.

Each of those challenges could have become the focal point of action for a biopic about a scientist.

Heather Lynch, Professor in the Department of Ecology & Evolution, explained that her research on penguins in Antarctica requires considerable advanced planning.

“The main challenge of working in Antarctica is really the uncertainty imposed by the weather and logistics,” she explained in an email. “It’s not enough to have Plan B, it’s more like Plan B through Plan F and then some. Covid and now avian flu have made an already difficult situation even harder.”

Still, at their most challenging moments, waiting for the weather to change, hoping someone will remember to pick them up, or living without creature comforts, these researchers find joy and derive satisfaction in doing valuable and constructive work.

“I’m like a bricklayer, adding more bricks to an enormous wall of knowledge that was started long before I started working on penguins and will continue to be built long after,” Lynch wrote.

Or, to put it another way, Watson wrote that “I love my job! No regrets.”

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Shushan Toneyan and Peter Koo at Cold Spring Harbor Laboratory. Photo by Gina Motisi/CSHL

By Daniel Dunaief

The real and virtual world are filled with so-called “black boxes,” which are often impenetrable to light and contain mysteries, secrets, and information that is not available to the outside world.

Sometimes, people design these black boxes to keep concepts, ideas or tools outside the public realm. Other times, they are a part of a process, such as the thinking behind why we do certain things even when they cause us harm, that would benefit from an opening or a better understanding.

In the world of artificial intelligence, programs learn from a collection of information, often compiling and comparing enormous collections of data, to make a host of predictions.

Companies and programmers have written numerous types of code to analyze genetic data, trying to determine which specific mutations or genetic alterations might lead to conditions or diseases.

Left on their own, these programs develop associations and correlations in the data, without providing any insights into what they may have learned.

That’s where Peter Koo, Assistant Professor at Cold Spring Harbor Laboratory, and his former graduate student Shushan Toneyan come in.

The duo recently published a paper in Nature Genetics in which they explain a new AI-powered tool they designed called CREME, which explored the genetic analysis tool Enformer.

A collaboration between Deep Mind and Calico, which is a unit of Google owner Alphabet, Enformer takes DNA sequences and predicts gene expression, without explaining what and how it’s learning.

CREME is “a tool that performs like large-scale experiments in silico [through computer modeling] on a neural network model that’s already been trained,” said Koo. 

“There are a lot of these models already in existence, but it’s a mystery why they are making their predictions. CREME is bridging that gap.”

Award winning research

Indeed, for her work in Koo’s lab, including developing CREME, Toneyan recently was named a recipient of the International Birnstiel Award for Doctoral Research in Molecular Life Sciences.

“I was genuinely surprised and happy that they selected my thesis and I would get to represent CSHL and the Koo lab at the ceremony in Vienna,” Toneyan, who graduated from the School of Biological Sciences, explained. 

Toneyan, who grew up in Yerevan, Armenia, is currently a researcher in The Roche Postdoctoral Fellowship Programme in Zurich, Switzerland.

She said that the most challenging parts of designing this tool was to focus on the “interesting and impactful experiments and not getting sidetracked by more minor points more likely to lead to a dead end.”

She credits Koo with providing insights into the bigger picture.

New knowledge

Without taking DNA, running samples in a wet lab, or looking at the combination of base pairs that make up a genetic code from a live sample, CREME can serve as a way to uncover new biological knowledge.

CREME interrogates AI models that predict gene expression levels from DNA sequences.

“It essentially replicates biological or genetic experiments in silico through the lens of the model to answer targeted questions about genetic mechanisms,” Toneyan explained. “We mainly focused on analyzing the changes in models outputs depending on various perturbations to the input.”

By using computers, scientists can save considerable time and effort in the lab, enabling those who conduct these experiments to focus on the areas of the genome that are involved in various processes and, when corrupted, diseases.

If scientists conducted these experiments one mutation at a time, even a smaller length sequence would require many experiments to analyze.

The tool Koo and Toneyan created can deduce precise claims of what the model has learned.

CREME perturbs large chunks of input sequence to see how model predictions change. It interrogates the model by measuring how changes in the input affect model outputs.

“We need to interpret AI models to trust their deployment,” Toneyan said. “In the context of biological applications, we are also very interested in why they make a certain prediction so that we learn about the underlying biology.”

Using ineffective and untested predictive models will cause “more harm than good,” added Koo.  “You need to interpret [the AI model’s] programs to trust them for their reliable deployment” in the context of genetic studies

Enhancers

Named for Cis Regulatory Element Model Explanations, CREME can find on and off switches near genetic codes called enhancers or silencers, respectively.

It is not clear where these switches are, how many there are per gene and how they interact. CREME can help explore these questions, Toneyan suggested.

Cis regulatory elements are parts of non-coding DNA that regulate the transcription of nearby genes, altering whether these genes manufacture or stop producing proteins.

By combining an AI powered model such as Enformer with CREME, researchers can narrow down the possible list of enhancers that might play an important genetic role.

Additionally, a series of enhancers can sometimes contribute to transcription. A wet lab experiment that only knocked one out might not reveal the potential role of this genetic code if other nearby areas can rescue the genetic behavior.

Ideally, these models would mimic the processes in a cell. At this point, they are still going through improvements and are not in perfect agreement with each other or with live cells, Toneyan added.

Scientists can use the AI model to aid in the search for enhancers, but they can’t blindly trust them because of their black box nature.

Still, tools like CREME help design genetic perturbation experiments for more efficient discovery.

At this point, the program doesn’t have a graphical user interface. Researchers could use python scripts released as packages for different models.

In the longer term, Koo is hoping to build on the work he and Toneyan did to develop CREME.

“This is just opening the initial doors,” he said. “One could do it more efficiently in the future. We’re working on those methods.”

Koo is pleased with the contribution Toneyan made to his lab. The first graduate student who worked with him after he came to Cold Spring Harbor Laboratory, Koo suggested that Toneyan “shaped my lab into what it is.”

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METRO photo

By Daniel Dunaief

Daniel Dunaief

Back in the day when I covered Wall Street and spoke with power-broking bankers, mergers and acquisitions experts, and traders, I often chatted with people who had little to no time.

As often as I could, I’d catch someone in the midst of an exciting transaction. I pictured them standing at their desks, staring at papers, looking closely at the clock, and envisioning various life or community-altering transactions, such as multi-billion dollar mergers.

The information would be even better, of course, if other journalists hadn’t yet heard the news, giving me the chance to be first.

Some of my sources would share juicy tidbits, about a company, a strategic move, or a new hire. The cadence of their voice was often quick and clipped and the tone was close to a conspiratorial whisper, with the volume inversely proportional to the importance of the developing story.

They would often be eager to get off the phone so they could continue to rule the world, to collect multi-million dollar fees and to prepare to help other companies keep up with the fast-merging world by moving other pieces on the financial chess board.

A few seconds after sharing the final details, they would invariably use a two word signal that meant that the conversation, whether I liked it or not, was ending.

“Gotta hop!” they’d say. It was a universally understood code for, “I’m not hanging up on you, per se, but those are the last sounds you’ll hear from me on this call.”

During busy days on Wall Street, I’d picture investment bankers in expensive suits, hopping on one foot from building to building, keeping one leg in the air as they frantically finalized details and collected signatures.

Once they reached their destination, I imagined them putting the non-hopping leg down comfortably on the ground, while massaging the one that propelled them around the lower part of Manhattan.

Wall Street hasn’t cornered the market on signals that a conversation is coming to a close.

People in the Main Street world say they “gotta run.”

Sometimes, out of politeness, someone will indicate that he or she has another important call coming in that’s related to the topic at hand.

In more personal and familiar settings, my friends and family have various codes that suggest they are preparing to end a conversation.

An audible sigh is usually the equivalent of, “okay, let’s wrap things up here.”

Then, there’s the long, slow version of “alright,” which suggests that, fun as this conversation might have been, it’s time to end the call.

I appreciate the moment when people appear to want to be sensitive to me when they’re ready to disengage. That typically includes some version of, “I’m gonna let you get back to work or whatever it is you’re doing” when, more often than not, they have to return to something.

Of course, I have been on the other side of this disengagement effort, when someone who is on a long drive is not only eager for company but is also prepared to share, stream-of-consciousness style, everything they see and comment on the driving skills of everyone around them.

“What is that red car thinking?” they’ll ask. “Did you see that?”

“No, you see, the way the phone works, I can only hear your voice. I’m not looking through a body worn camera at the road ahead of you, but I’m sure the red car did something stupid and it’s great that you’re such a skilled defensive driver.”

I sometimes try to wrap up these calls with something like, “well, it’s been nice chatting with you.”

“Yes,” they’ll reply. “It’s nice chatting with you, too. So, what do you think of the presidential election?”

“Oh, um, I think it’s a good idea every four years or so. More often than that would become too hectic and stressful for the country.”

“No, I mean, what are your top 15 issues for the election this year.”

“I’d love to share them with you, but I have to hop and I want to give you a chance to get back to driving and someone is waiting to take a run with me, so, I’m gonna go.”

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Prateek Prasanna and Chao Chen at the NCI Informatics Technology for Cancer Research meeting in St. Louis in 2022.

By Daniel Dunaief

Cancer often involves numerous small changes before it become a full blown disease. Some of these alterations are structural, as otherwise healthy cells make subtle shifts that favor out of control growth that often defies the immune system and threatens the health of tissues, organs and the entire body.

Associate Professor Chao Chen and Assistant Professor Prateek Prasanna, both in the Department of Biomedical Informatics at Stony Brook University, recently received a four-year, $1.2 million grant from the National Cancer Institute to continue to develop an enhanced breast cancer imaging tool that could detect some of those changes.

Using advanced mathematical modeling and machine learning and working with clinical collaborators in radiology, radiation oncology, surgery and pathology, the researchers are developing a tool called TopoQuant. They hope they can provide a way to look at the changes in tissue architecture that occur during the growth and development of cancer and during radiation treatment.

Receiving the grant means “other researchers also think highly about the subject,” Chen explained. “This further boosts our confidence and is an approval for our effort so far.”

By combining two-dimensional and three-dimensional data, the Stony Brook researchers, including radiation oncologist Dr. Alexander Stessin, hope to provide an analytical tool that helps doctors and patients confronting cancer all the way from the early steps the disease takes to the ways it resists various treatments.

The researchers are using tomosynthesis and MRIs, both of which are three dimensional, and conventional mammographs, which are two dimensional.

Stessin will work closely to evaluate the efficacy of the TopoQuant framework to provide a predictive and useful interpretation of breast images.

The diagnostic and prognostic tool these scientists are developing has potential applications outside the world of breast cancer. The deep learning technique could help analyze images and information for other types of cancer as well as for various neurological challenges.

“In the tools we develop, a lot of the algorithms are domain agnostic,” said Prasanna.

The approach should work as long as the researchers can get structure-rich imaging data. To be sure, while this approach has had some promising early results, it has to proceed through numerous steps to help in the clinic.

In the meantime, the researchers plan to use the funds, which will support salaries and travel budgets for researchers, to continue to develop TopoQuant.

Chen and Prasanna envision providing physicians with an explanation of why artificial intelligence is guiding them towards a particular decision.

Doctors could “place more trust in a system like this,” Prasanna said. “It lends interpretability to an analysis that is typically more opaque.”

Healthy cells

When health care technicians gather information about breast cells, they often focus on developments in and around the cancer cells.

“The premise of the work” Chen and Prasanna are doing is to look at signals “even in the normal [healthy] areas of the breast, Prasanna said. “It’s important for physicians to look at these normal areas before they begin any treatment. What our tool lets them do is extract these signals.”

The process of developing this tool started about five years ago, as the scientists shared ideas and did preliminary studies. The work became more involved and detailed around 2020.

“The challenge is to have a harmonic combination between mathematical modeling and deep learning,” Chen explained. “Incorporating principled math modeling into deep learning is important yet not trivial.”

In their work, the researchers used phantom data called VICTRE from the Food and Drug Administration. They used simulated magnetic resonance images and validated that the method can extract the tissue structure faithfully across different breast density types. They are also using data from The Cancer Imaging Archive for initial model development.

At this point, the researchers have some evidence that the alpha version of the tool has been “promising” in the context of neoadjuvant chemotherapy, which they demonstrated in a paper they published in 2021.

The results from that study indicated different topological behavior of breast tissue characterized by patients who had different responses to therapy.

The researchers plan to continue to establish that the tools are properly characterizing what is happening. After that, they will validate the effort with a Stony Brook University Hospital cohort.

Clinicians from Rutgers are working with Chen and Prasanna and will do additional testing through external data sets.

Complementary skills

Chen and Prasanna, who have joint lab meetings and discuss their research every week, work in different parts of the campus. Chen’s lab is on the west campus, while Prasanna is in the east campus.

The researchers have combined their interests and skill sets to apply a computer science driven approach to medicine and the field of bioimaging analysis.

Chen does considerable work with topological information and machine learning. Prasanna, meanwhile, is also involved in the clinical world, combining his passions for engineering and medicine.

A native of Gansu Province in China, Chen lives near New York City and commutes to the university two or three times per week, working the other days from home and meeting with students and collaborators by Zoom.

When he first joined Stony Brook in 2018, Chen was concerned about jumping into a different department.

After visiting the department and speaking with Chair Joel Saltz and other faculty, he developed greater confidence when he learned of their passion for research, their research philosophy and the chemistry within the department.

Six years later, he thinks it was “the best career decision” he made.

A native of Cuttack, India, Prasanna and his wife Shubham Jain, who is in the faculty of Computer Science at Stony Brook, have worked together professionally.

The couple enjoys hiking and has been to 47 of the 63 national parks. One of their favorite parks is Katmai National Park and Preserve in Alaska.

Prasanna’s father’s family includes many physicians and his mother’s is involved in engineering. In his career, he has combined the professional focus from both sides of his family.

Early in his career, Prasanna worked on a project that used a smart phone to obtain fundus images of the eye to predict diabetic retinopathy.

At the time, he thought “this is where I want to be,” he recalled.

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Jillian Scully on the track. Courtesy Scully family

By Daniel Dunaief

Sometimes, Jillian Scully isn’t sure whether she’s dreaming that she’s practicing or she’s awake and on the field.

That’s because the Miller Place High School senior spends so much time honing her technique and trying to increase the distance she can throw a shot put and discus.

Jillian Scully

“I’ll have dreams where I’m practicing and it’s so vivid, I think I’m there,” said Scully. “I can feel the mud on my hands and the cold ball on my neck.”

The work has paid off, as Scully, who won the New York State Outdoor State Championship in shot put by over five feet in June, and set the school record in the shot put by over 12 feet, has been recruited by Division I track and field teams around the country, from UCLA to Arizona State, Colorado State University, and the University of Michigan, to name a few.

Two weeks ago, Scully and her parents James and Despina, (who goes by “Debbie,”) got up at 3 a.m. for a flight to Colorado, where they toured Colorado State University, and just last week, they visited the University of Michigan. On her college visits, coaches have given her tours of the campus and have outfitted her in university attire. Until she chooses a school, she can’t bring any of that clothing home.

“I’m expecting when I go to these schools that I’m going to have a gut feeling,” said Scully. I have a sense that I’ll know the best fit for me as soon as I step on [the right] campus.”

Scully, who is 6 feet, 1 inch tall, has found it tough to watch others train without being able to participate.

“It’s a little difficult seeing all the throwers getting to lift and throw and me being forced to watch,” Scully explained.

Scully explained that her favorite moment in a meet is when she takes her first step into the circle, which gives her a surge of confidence.

Each time she prepares to launch the ball or discus, things go “silent in my brain, the sound stops and I just throw,” she said.

A highly valued recruit, Scully started throwing shot put and discus in middle school. Ian Dowd, who coached track and field in middle school at Miller Place, recalled how Scully could sprint the fastest, jump the furthest and, as it turns out, throw a shot put remarkably far, without any training.

“She threw [the shot put] something crazy, like 25 or 26 feet, the first time she did,” said Dowd, who now coaches basketball in the Southampton School District.

Scully’s father James, who owns and runs the construction company JFS Contracting, dabbled in track when he was in high school, including throwing shot put.

“I never thought she’d have been that good,” Scully said. “I did it because I was bored and I wanted to do something.”

The younger Scully, however, who plans to study engineering when she’s not practicing or competing in Division 1 track meets, is focused and passionate about throwing the 8.8 pound shot put as well as the 2.2 pound discus.

While shorter than her 6’3” father, Scully is taller than her 5’8” mother, Debbie, who considers herself the “small one” in the house. Debbie has never tried either sport, but has picked up her daughter’s bag to move it in the house.

“It’s no wonder you’re so strong,” Scully told her daughter. “She’s walking around with a weighted vest all day long.”

Change of life

Before she discovered track and field, where she also runs the 4×100 relay, Scully, 17, was struggling.

Scully suggested that her mother gave her the “nudge” to try track.

Jillian Scully

“I was introduced to track at a certain point in my life when I was secluded from everybody,” said Scully, who was unreceptive to people and spent her free time playing video games or being unproductive.

“The person I was for however many years is not me,” Scully recalled. “I didn’t enjoy being that person.”

When she started competing in track, she felt the experience, including the camaraderie with her teammates, “clicked” and became “a part of me.” Spinning around in a small circle and throwing objects through the air became a necessary part of her mental health, and is a large part of her personality.

Hannah Kuemmel, the Athletic Trainer at Miller Place High School, has noticed the change in Scully.

“She is a lot more confident in who she is as a person and an athlete,” said Kuemmel, who also teaches a sports medicine class in which Scully sits front and center.

When she started competing in shot put and discus, she found a way to excel. “If I’m good, I might as well keep doing it,” she said. “I love it so much.”

Good isn’t the word Bill Hiney, her personal coach who has been working with her for over two years, and who has been in the field for 36 years, would use to describe her.

“I’ve often said she’s on another planet,” said Hiney, who is the Assistant Track and Field Coach during the winter and spring seasons for Southold High School.

A good female shot put thrower can reach the mid 30 feet. At 46 feet, 11 inches, Scully is throwing 10 feet further than the best female athlete Hiney has ever worked with, which puts her “in another dimension.”

Hiney describes her athletic student as the “icing on the cake in my long career. Coaches are lucky to have someone with athleticism, size and all the elements necessary to be extraordinary.”

Five squares

And, speaking of icing, the combination of her athletic training and metabolism make Scully a voracious eater, as she consumes five square meals a day.

She typically tops it off with a pint of Haagen Dazs mint chocolate chip ice cream in the evenings.

“She eats everything under the sun,” said her father, who adds that when he brings her 20 buffalo wings, she asks for another 20 so she can have a snack later.

These days, Scully, who coaches describe as tall and lean, puts her height to use in another sport, as she is an outside hitter for the varsity volleyball team, as well.

Scully’s parents appreciate how sports has given her the self-confidence and readiness to contribute to her team.

Even during track and field competitions, when she’s preparing to do her own throwing, Scully will speak with other athletes about their technique. “When Jillian was throwing against other girls, they asked her, ‘What can I do to throw better? What am I doing wrong?’” Jim Scully said. “She takes it upon herself to help all the other throwers,” and encourages them to improve.

Athletic trajectory

As well as Scully has performed in the shot put and discus, Hiney and the head coaches from universities around the country see continued growth ahead. Scully just started weight lifting this summer. “If it was karate, she’d be a white belt,” Hiney said. Well-known coaches in the field have come to watch her throw and have been impressed. Dowd believes Scully could reach an elite level if she keeps pushing herself, even climbing as far as the Olympics.

“I would love to see her with a US banner,” Dowd said. “That would be surreal.”

As for Scully’s thoughts on the matter, she would embrace an opportunity to represent her country at the Olympic games. She recalls sitting in class, and looking up how far Olympians, who competed in this past Paris Games, threw when they were her age.

“I’m trying to compare myself and set my goals,” she said. “That would be a dream for me, going to the Olympics and competing in these events.”

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

My Aunt Maxine had Down syndrome, which means she was mentally disabled.

In so many ways, Maxine and her life defied expectations and labels.

When Maxine was born, doctors told my grandparents that she wouldn’t likely live long, so they should consider putting her in an institution.

My grandparents couldn’t imagine being away from their daughter. They took Maxine home to the Upper East Side of Manhattan, where they raised and educated her.

As she grew up, Maxine was on the shorter side, at under five feet tall, and carried the youthful, round face of Down syndrome throughout her life.

She also had facial hair that my grandmother, mother and caregivers regularly trimmed.

My aunt lacked any self-consciousness about who she was, what she was, and how she related to the world. She figured everyone was as ready to love her and interact with her as she was with them.

More often than not, she smiled, offering an energetic and enthusiastic nod whenever anyone made eye contact. Plenty of people avoided looking at her in part because she was different and, in part, because she lived in New York and the rules of sidewalk engagement limited eye contact.

When people didn’t notice or engage with her, she kept walking, singing, talking to herself, chatting with her parents or the rest of us, or whistling, which she could do by inhaling and exhaling.

She lived at a higher decibel level. Her whisper was even louder than her normal speaking voice.

“What?” she’d whisper so loudly that it could be heard in the back row of a movie theater. “You want me to be quiet? Is that what you’re telling me?”

“Yes, shhhh.”

“Don’t shush me!” she’d say, her husky whisper, like her husky voice, becoming louder and indignant.

“Sorry, Macky,” I’d say. “People are trying to watch the movie. Can you watch it, too?”

“Oh, yes, yes, yes,” she’d say, nodding vigorously. “I’ll be quiet. I will. I’ll be quiet. If that’s what you want, I can be quiet. Sure, suuuuure!”

She was spectacularly funny and knew introductions were an opportunity for comedy.

“Who is this young lady?” she’d ask anyone who walked in the door in our house. The person could be anywhere from six to 96 and she’d ask the same thing.

“How old are you?” she’d ask.

No matter the answer, she’d suggest the person was a “lovely” young lady.

“What’s your name?” she’d ask.

When the person said her name, she’d say “what” several times and then ask the person to spell it. When she slowed our guest down repeatedly and asked her to say it again, the guest would shout.

“Hey, what are you yelling for? I can hear you. Not so loud. You’re hurting my ears.”

She’d squint and a smile would fill her face as she’d scan the room, knowing the old routine had hit the mark.

More than anything else, though, Maxine was compassionate, emotionally connected, loving and supportive.

She would sing the Star Spangled Banner when she listened to Robert Merrill on the radio before a Yankees game.

“It’s so beautiful,” she’d say, as she blew her nose and wiped her eyes.

I suspect many other Americans have an aunt, sibling, distant relative, friend or neighbor for whom labels mean even less than the totality of their lives, the winsome nature of their personality, and the triumphs that define their days.

Hearing anyone use the term “disabled” as a take down misses the point, particularly for those who seek to be the country’s leader.

Maxine required but also taught a level of patience. In exchange, our family and friends appreciated her joy of life and basked in her unconditioned positive regard. She wouldn’t have resented or hated others, wouldn’t have insulted individuals or a group and would have forgiven anyone who made a mistake.

Perhaps some day, those who use words like “mental disability” as a way to dismiss others or to cast others aside will think of the Maxines of the world. We can learn so much from others whose lives are different from ours and who aren’t trying to use words to project an image, to cut others down, or to suggest that someone is limited.

I can picture Maxine sitting in a chair next to me, tilting her head and looking at me from the side.

“You’re such a silly goose,” she’d laugh.

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Ellen Pikitch at the United Nations when she spoke at the 9th International Day of Women and Girls in Science back in February. Photo from E. Pikitch

By Daniel Dunaief

Even as Covid threatened the health of people around the world, a group of 30 leading researchers from a wide range of fields and countries were exchanging ideas and actions to ensure the sustainability of ocean fisheries.

Starting in 2020, the researchers, including Stony Brook University’s Endowed Professor of Ocean Conservation Science Ellen Pikitch, spent considerable time developing operating principles to protect the oceans and specific actions that could do more than ensure the survival of any one particular species.

Earlier this week, the researchers, who come from fields ranging from biology and oceanography to social sciences and economics, published a paper titled “Rethinking sustainability of marine fisheries for a fast-changing planet” in the Nature Journal npj Ocean Sustainability, as well as a companion 11 golden rules for social-ecological fisheries.

The researchers, who were led by first author Callum Roberts, Professor of Marine Conservation at the University of Exeter, plan to share their framework with policy makers and government officials at a range of gatherings, starting with Brussel’s Ocean Week and including the United Nations Ocean Conference in Nice.

“We felt something like this was needed in order to reach these audiences effectively,” said Pikitch.

The extensive work, which included two series of workshops, outlines ways to regenerate the ocean’s health and to put people before profits.

The authors suggest that fisheries need to address their contributions to the climate crisis through activities that are polluting, such as dumping fishing gear or plastics in the ocean, carbon intensive or destructive, through the disturbance of sediment carbon stores.

The paper suggests that lost or discarded fishing gear often make up the largest category of plastic waste in the open sea. This gear is not only polluting, but leads to ghost fishing, in which fish die in abandoned or discarded nets.

The authors suggest that labelling fishing gear could encourage better stewardship of the ocean. They also argued that fisheries management has historically focused on economic output, without considering social value and effects.

“We take the view that marine life is a public asset, and its exploitation and management should work for the benefit of local communities and the public,” the authors wrote in their paper.

Pikitch described the work as an “urgent” call to action and added that the researchers will be “meeting with policy makers, retailers, fishery managers and others to discuss these results and how they can be implemented.”

The researchers engaged in this effort to find a way to compile a collection of best practices that could replace a hodgepodge of approaches that overlook important elements of sustainability and that threaten fish species as well as ocean habitats.

“Fisheries are in bad shape worldwide and are degrading rapidly with overexploitation and climate change,” Philippe Cury, Senior Emeritus Researcher at the Institute of Research for Development in Marseille, France, said in a statement. “Efficient and renewed fisheries management can really help to restore marine ecosystems and to reconcile exploitation and biodiversity.”

Pikitch anticipated that some might offer pushback to the suggestions. “If you don’t get pushback, you’re probably not saying something that is important enough,’ she said.

Ecosystem focus

Using research Pikitch led in 2004 from a paper in Science, the group constructed one of the 11 actions around developing a holistic approach to the ocean habitat.

Pikitch’s expertise is in ecosystem based fishery management.

“Fish interact with one another, feed on one another, compete with one another and share the same habitats,” Pikitch said. “For those reasons alone and more, we need to stop managing species one at a time.”

Some policies currently protect ecosystems, including the spatial and temporal management of the Canadian lobster fishery to protect whales and the no-take marine reserves to protect artisanal reef fisheries in the Caribbean.

Still, these approaches need to be applied in other contexts as well.

While some people believed that researchers didn’t know enough to create and implement holistic guidelines, Pikitch and her colleagues suggested that it’s not “necessary to know everything if we use the precautionary principle.”

Pikitch suggested that the Food and Drug Administration takes a similar approach to approving new medicines.

The FDA requires that researchers and pharmaceutical companies demonstrate that a drug is safe and effective before putting it on the market.

Fisheries are making some headway in this regard, but “much more is needed,” she said.

Subsidy problem

The authors highlighted how government subsidies are problematic.

“Many fisheries are highly carbon intensive, burning large quantities of fossil fuels often made cheaper by capacity-enhancing government subsidies,” the authors noted in the paper. “Among the worst performers in terms of fuel burned per tonne of landing gears are crustacean fisheries, fisheries that operate in distant waters, deploy heavy mobile gears like trawls, or target high value, low yield species like swordfish; most of them propped up by subsidies.”

When overfishing occurs, companies switch to catching less exploited species, even when they don’t have any data about new catches. The new species, however, soon become overfished, the authors argued.

In urging fisheries management to support and enhance the health, well-being and resilience of people and communities, the scientists add that abundant evidence of widespread human rights abuses occurs in fishing, including coercive practice, bonded, slave and child labor and unsafe, indecent and unsanitary living and working conditions.

“Abuses at sea continue and more needs to be done to stop this,” Pikitch explained.

Additionally, the authors hope to give a voice to the global south, which is “often ignored in many of these discussions about how to appropriately manage these fisheries,” she suggested.

A beginning

While the paper was published, Pikitch explained that she sees this as the beginning of change and improvement in creating sustainable fisheries policies. She anticipates that the collection of talented scientists will continue the work of protecting a critical resource for human and planetary survival.

“This group will continue to work together to try get this work implemented,” she said. “I’m enormously proud of the result.”

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

I’m getting messages every day and, often, several times a day. I must be really important.

As with snail mail, those messages could be delivering something extraordinary.

“We are writing to inform you that you’ve won a Pulitzer Prize, despite the fact that you haven’t entered anything and we haven’t yet created an extraordinarily average category.”

Or, perhaps, “we wanted to let you know that your cells are healthier than they’ve ever been and that you should keep up the good work. We’d like to study you to learn how your body is performing better than we’d expect for someone half your age.”

Then, of course, there are the realistic possibilities.

“Hey, want to go to dinner with us this weekend?”

That’s a nice message to receive from a friend or family member.

My son believes brevity is the soul of wit when it comes to messages so he’ll just write “Judge!!!!” or “Soto!!!!” or some combination of Yankee players who have performed well that day.

The most frequent messages I’m receiving are the ones from would-be political leaders, their pals, and other prominent supporters who not only want my vote, but also want me to contribute money.

I’d like to think these messages, with my name at the top, were written personally by these important people, who took the time out of their day to reach out to me.

“You know who I haven’t written to recently? Daniel Dunaief. I’ll just give him a holler to gauge his thoughts on one of the more important races.”

But, no, I know they’re not personal missives, just as I know Siri isn’t graciously saying “You’re welcome” even though she’s programmed to show appreciation in her chipper voice when I thank her.

Still, these messages have morphed from a nuisance into something else. In the frenzy and excitement of consequential races, these communiques are filled with fear and hope, often in that order. In a few short sentences, they tell me what’s at stake, what role I can play, and how these leaders will spend my money wisely.

Wouldn’t that be nice? If we donated to a campaign, wouldn’t it be great to see how our money, specifically, helped someone, as in, “this yard sign made possible by your moderately generous donation.”

If you’ve ever watched the show “Seinfeld,” George Costanza, played by Jason Alexander, suggests that he grows on people, the way ad jingles do. He is like an advertisement for Mennen deodorant. At first, you can’t stand the “byyyy Mennen” sound, but you find yourself singing it in the shower or humming it in the car.

Maybe, in some way, this unprecedented barrage of seemingly personal text messages has become like those jingles.

To be honest, I don’t read them carefully. I do, however, appreciate the earnestness with which someone sends them and I recognize that something consequential is about to happen.

Maybe it’s a bit like the December holidays. The anticipation of November 5th is exciting, even if the event itself might be lacking.

The reality of the election feels more like a gift certificate to a restaurant that serves a combination of my least favorite foods, all deep fried in a type of grease that triggers an allergic response. The election itself, as I see it, will likely have echoes from 2020, with lawyers and politicians exerting themselves, insisting that their candidate won for days or weeks after Nov. 5th.

An early riser, I grin when the message arrives an hour or so after I’ve gotten up and the person with the morning message apologizes for writing so early.

Really? Because you’re not actually sending the message and the machine that blasts them could pick any time in the day to release this particular text.

With all the money flowing into these campaigns, I wonder if the country invested all the cash both sides collected and put it in a certificate of deposit or a Treasury Bill and created scholarships, what kind of opportunities could we offer future students who one day might want to run for office.

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Photo courtesy Metro Creative Graphics

By Daniel Dunaief

While the fall provides a break from the summer heat and a respite for exhausted parents who coordinate and carpool for recreational activities, it also can trigger a return to more concentrated time indoors.

Dr. Sharon Nachman, Chief of the Division of Pediiatric Infectious Diseases at Stony Brook Children’s Hospital.
File photo

That can trigger the beginning of the flu season, as students and their families share much more than the lessons of the day and stories about teachers and classmates.

Timing shots can be a delicate balance, as the antibody coverage from these shots is typically about three months.

With the peak flu season often occurring during December and January and even into February, Dr. Sharon Nachman, Chief of the Division of Pediatric Infectious Diseases at Stony Brook Children’s Hospital, suggested that residents receive their vaccines in a few weeks.

“Getting a vaccine in October is probably the right time,” Nachman said.

Dr. Gregson Pigott, Commissioner of the Suffolk County Department of Health Services, added that the timing for Covid vaccinations is somewhat trickier.

“Because the evolution of new variants remains unpredictable, SARS-CoV2 [the virus that causes the disease] is not a typical ‘winter’ respiratory virus,” Pigott explained in an email.

The county health department recommends that residents stay up to date with their vaccinations.

“Individuals should speak with their healthcare providers for advice that is specific to them,” Pigott added.

Simultaneous shots

Doctors generally recommend receiving both shots at the same time, if people are eligible and the timing for each vaccine is right. Residents who are unsure about their eligibility should speak with their healthcare providers, Pigott explained.

Dr. Gregson Pigott, Suffolk County Health Services commissioner. File photo

The flu and Covid are viruses that change over time, creating a battle between the pharmaceutical companies that manufacture vaccinations and the viruses that attempt to evade them.

Each year, the vaccines attempt to provide the best match against the dominant or most likely strains.

The Centers for Disease Control and Prevention “determines if the vaccine will protect against a circulating virus by conducting laboratory studies on circulating flu viruses,” Pigott explained in an email. “Updated 2024-2025 flu vaccines will be trivalent” and will protect against H1N1, H3N2 and a B/ Victoria lineage virus.

Vaccine manufacturers create immunizations based on the flu strain circulating in the southern hemisphere during the recent season.

“We expect that those are what’s going to hit us in our winter,” Nachman said. “The science is there. We know generally what types will be rolling around. We could hit or miss it by a subtype.”

Nachman added that the flu vaccines represent educated guesses about the type of microbe that might cause illnesses.

“The educated guesses are still better than no vaccine, which will, for sure, not cover you at all,” Nachman said

As for the Covid immunization, doctors added that it is also likely to change as the virus that caused the pandemic mutates.

Nachman said people should plan to get the Covid shot around once a year.

“I don’t think we’re going to go to more often” than that, Nachman said.

During the summer, when an infectious strain of Covid surged across the county, state and country, Nachman said the data is not available to determine how much protection a vaccine provided.

“Only on TV do computer models work instantly,” Nachman said.

She suspects that the Covid shot offered some protection for residents, who may not have been as sick for as long as some of those who dealt with a range of symptoms.

Concussion awareness

With the start of a new school year and the beginning of contact sports like football, school districts are continuing to ensure that coaches and athletes follow concussion protocols.

“Schools have done a nice job thinking and talking about it,” said Nachman. “Coaches know you can’t throw [student athletes] out and say, ‘You’ll do fine,’” after a head injury.

Nachman suggested that area athletes may engage in activities that are not connected to the schools and that may involve head injuries that people ignore.

“We know what’s happening with school-regulated” sport, but not with those that are outside the academic umbrella, she added.

As for the emotional or psychological impacts of a divided and bitter electorate during an election year, Nachman said people are under considerable emotional stress.

“The social media echo chamber is making it worse,” she said. The abundance of misinformation on both sides is causing mental anguish.

“Election times are very stressful and I think, in particular, this election may be even more stressful,” Nachman said.

Nachman urges people to minimize their time on social media and to create down time from electronics during meals.

As students move up a grade and into new places, they also can endure stressors, peer pressure and bullying. She suggests that parents understand what their children are seeing online.

Newborn RSV protection

Children born in March or later are eligible to receive an approved shot called Beyfortus, which, in 80 percent of cases during clinical trials, prevents the development of respiratory syncytial virus, or RSV.

The Beyfortus monoclonal antibody will make a “huge difference” for newborns and their parents, Nachman said. Last year, Stony Brook had numerous hospitalizations in children under one year of age.

“We’re not going to have those children coming into the hospital,” Nachman said. “That’s amazing and is a huge step forward.”

When newborns get RSV, doctors don’t have an effective treatment for the virus and typically treat the symptoms.

The mortality rate from RSV is low, but the morbidity is high. Newborns who contract RSV can end up developing chronic asthma.

As with any shot, Beyfortus can have side effects, with the most common including rash and pain, swelling, or hardness at the site of the injection, according to AstraZeneca and Sanofi, which manufacture the antibody.

Beyfortus is covered by insurance and is under the vaccine for children program and numerous private health insurance plans. Parents can opt out of the shot. Nachman suggested they should understand what they are opting out of when they make that decision.

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