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Stony Brook University researchers Fusheng Wang and Dr. Richard Rosenthal

By Daniel Dunaief

Health care providers can use all the help they can get amid an ongoing opioid epidemic that claims the lives of 130 Americans each day.

In a cross-disciplinary effort that combines the computer science skills of Fusheng Wang and the clinical knowledge and experience of doctors including Dr. Richard Rosenthal, Stony Brook University is developing an artificial intelligence model that the collaborators hope will predict risk related to opioid use disorder and opioid overdose.

Fusheng Wang

Wang, a Professor in the Department of Biomedical Informatics and Computer Science at Stony Brook and Rosenthal, a Professor in the Department of Psychiatry and Behavioral Health in the Renaissance School of Medicine, received a $1.05 million, three-year contract from the independent funding organization Patient-Centered Outcomes Research Institute (PCORI).

“We have patients, clinical stakeholders, clinician scientists and community-based people within the system of care that have an interest at the table in the development cycle of this AI mechanism from day one,” Rosenthal said. The PCORI required that the scientists identify these stakeholders as a part of the research strategy.

The Stony Brook researchers are combining data from Cerner, a major electronic health record vendor under an institutional data usage agreement, with an awareness of the need to create a program that doctors can use and patients can understand.

Traditional public health studies rely on analyzing incidents that occurred. This approach, however, can be applied to population health management through early interventions, Wang explained.

With artificial intelligence, computer scientists typically plug enormous amounts of data into a model that searches through individual or combined factors and comes up with a prediction through a deep learning process.

The factors, which may be in the hundreds or even more, that contributed to the conclusion about a risk level aren’t always clear, which makes them difficult for doctors to explain and for patients to understand. Many of the factors may not be clinically intuitive.

Deep learning models can provide certain types of information about the prediction, such as a ranking of top factors. These factors, however, may not necessarily be clinically relevant, Wang explained.

To balance the need for data-driven analysis with the desire to create a product that people feel confident using, the scientists plan to become a part of the process.

“We are all going to educate each other,” said Rosenthal. “Patients will tell you what it means to be a patient, to be at the receiving end of some doctors telling them something they don’t know” while each group will share their lived experience.

Each participant will be a student and a teacher. Rosenthal believes this stakeholder in the loop approach will create a tool that is clinically relevant.

“There’s an opportunity to produce a highly accurate predictive mechanism that is highly acceptable based on transparency,” he said.

To be sure, people involved in this process could deemphasize a factor that doesn’t make sense to them, but that might otherwise increase the predictive accuracy of the developing model.

“This might come at the expense of the performance metric,” Rosenthal said.

Still, he doesn’t think any human correction or rebalancing of various factors will reduce the value of the program. At the same time, he believes the process will likely increase the chances that doctors and patients will react to its prognosis.

A program with a personal touch

Wang created the model the scientists are using and enhancing. He reached out to several physicians, including Director of the Primary Care Track in Internal Medicine Rachel Wong and later, Rosenthal, for his addiction research expertise.

Dr. Richard Rosenthal

Rosenthal started collaborating on grant proposals focused on big data and the opioid epidemic and attending Wang’s graduate student workgroup in 2018.

Wang recognized the value of the clinician’s experience when communicating about these tools.

“Studies show that patients have lots of skepticism about AI,” he explained. Designing a tool that will generate enough information and evidence that a patient can easily use is critical.

The kind of predictions and risk profiles these models forecast could help doctors as they seek the best way to prevent the development of an addiction that could destroy the quality and quantity of their patients’ lives.

“If we can identify early risk before the patient begins to get addicted, that will be extremely helpful,” Wang added.

If opioid use disorder has already started for a patient, the tool also could predict whether a patient has a high chance of ending treatment, which could create worse outcomes.

Refinements to the model will likely include local factors that residents might experience in one area that would be different for populations living in other regions.

Depending on what they learn, this could allow “us to frame our machine learning questions in a more context-dependent population, population-dependent domain,” Rosenthal said.

Opioid-related health problems in the northeast, in places like Long Island, is often tied to the use of cocaine. In the Southwest, the threat from opioids comes from mixing it with stimulants such as methamphetamines, Rosenthal added.

“Localization increases the accuracy and precision” in these models, he said.

Eventually, the model could include a risk dashboard that indicates what kind of preventive measures someone might need to take to protect themselves.

The scientists envision doctors and patients examining the dashboard together. A doctor can explain, using the model and the variable that it includes, how he or she is concerned about a patient, without declaring that the person will have a problem.

“Given these factors, that puts you at greater risk,” said Rosenthal. “We are not saying you’re going to have a problem” but that the potential for an opioid-related health crisis has increased.

Unless someone already has a certain diagnosis, doctors can only discuss probabilities and give sensible recommendations, Rosenthal explained.

They hope the tool they are developing will offer guidance through an understandable process.

“At the end of the day, the machine is never going to make the decision,” said Rosenthal. With the help of the patient, the clinician can and should develop a plan that protects the health of the patient.

“We’re aiming to improve the quality of care for patients,” he said.

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By Daniel Dunaief

It’s back, bigger than ever, with an added Peter-and-the-Wolf style musical debut.

This year’s version of Science on Stage at Stony Brook University, which brings together the research and life experiences of three scientists with the artistic interpretation and creative talents of three playwrights, focuses on the theme of climate change.

Before the reading of the plays at the free October 28th event at the Staller Center’s Recital Hall, a group of eight high school students and two graduate students will perform an original piece of music composed by Professor Margaret Schedel called “Carnival of the Endangered Animals” (see accompanying story below).

Christine Gilbert with graduate student Emily Gelardi. Photo by Conor Harrigan

The event, which has a seating capacity of 379, which is almost triple the potential audience size from last year, and requires advance registration, is sponsored by the Collaborative for the Earth (C4E).

The organizers of Science on Stage “want people to be thinking about [climate change] from new ways or with new perspectives,” said Heather Lynch, inaugural director of the C4E and Endowed Chair for Ecology and Evolution at Stony Brook’s Institute for Advanced Computational Science and Professor in the Department of Ecology and Evolution.

In these performances, professional actors, directed by Logan Vaughn, share a dramatic reading of the scripts, titled “Ghost Forest,” “Counterfactual,” and “Resplendence.” After the performance, the scientists and playwrights will participate in a question and answer session led by Lecturer J.D. Allen, who is managing editor of NPR affiliate WSHU.

Provost Carl Lejuez, whose office provides funding for the C4E, celebrated the ongoing collaboration between the humanities and the sciences.

“Science on Stage is one of our true interdisciplinary gems,” Lejuez explained. “In a time of such misinformation, the arts provide such a powerful vehicle to communicate science in accessible and inspiring ways.”

Indeed, in addition to hearing an original piece of music and listening to a reading of the plays, audience members will have the opportunity to share their perspectives on climate science before and after the performance.

Christine Gilbert, who holds a joint appointment at the School of Communication and Journalism and the School of Marine and Atmospheric Sciences and is one of the participating scientists, is conducting a study of the effect of the experience with audience members.

Attendees can participate in a short mobile-based survey before the plays and immediately afterwards. A social scientist, Gilbert will follow up with those members who are willing to engage in individual interviews in the weeks after the performance.

Event organizers wanted to know “what is it that’s so magical in the intersection between science, humanity and art” that drew a crowd so large last year that the fire marshal had to turn people away, said Gilbert.

By polling the audience, Gilbert, who was one of the people who couldn’t watch the show last year, hopes to explore the effect of teaching complex science in this forum.

She also hopes to assess how audience members feel after hearing more about climate change and plans to share what she learns with Stony Brook and with the broader scientific community through a published paper.

Heavy and humorous

The scientists and the playwrights appreciated the opportunity to learn from each other and to engage in a creative effort designed to use science, or the life of scientists, to appeal to audiences.

Lynch, who participated in the Science on Stage effort last year, suggested that this year’s plays are powerful and evocative.

“These are deep, adult serious issues,” she said, cautioning that the language includes some cursing and that the themes include loss, parenthood and grief. “This is not Disney.”

To be sure, the plays blend a wide range of emotions.

“With short plays that deal with heavier topics, playwrights will gravitate towards humor,” said Ken Weitzman, Founder and Associate Professor of Theater at Stony Brook, who started Science on Stage virtually in 2020. “It’s how we engage” and commune with an audience.

Counterfactual

Playwright Mat Smart

Author of the play “The Agitators,” about a true narrative describing the 45-year friendship between suffragist Susan B. Anthony and abolitionist Frederick Douglass, Smart said he has taken long Uber rides with people whose views differ from his, leading to spirited conversations.

When Smart described his experiences to Reed, they discovered they had similar interactions.

While much of the script involves a combination of conversations and ideas, Smart explained that part of the dialogue in the play came from a discussion he and Reed had about food choices and climate change. 

The interaction about cheeseburgers is “based on something [Reed] said to me,” Smart said. Reed explained the high carbon footprint of a cheeseburger, although he urged Smart to cut back rather than eliminate them from his diet.

“The play is about two people who see things very differently who choose to have a dialogue and to have a tough conversation,” said Smart. “They’re both affected by it.”

Ghost forest

Playwright Gab Reisman

Elizabeth Watson, Associate Professor in the Department of Ecology & Evolution, teamed up with Gab Reisman, who wrote “Ghost Forest.”

In this play, a climate researcher’s subjects spring to life as she writes an important grant proposal.

While it doesn’t reflect how field research or grant writing typically goes, it does capture “some things that have happened to me,” Watson said.

Her field work has involved considerable challenges, including getting stuck in the mud, being covered in ticks, crawling across mudflats, and being abandoned on a raft in a lagoon.

Watson appreciates how the artistic effort allows her to connect with people who probably aren’t the same ones who would read a publication she wrote or come to a presentation.

She also added that the world has what it needs to deal with climate change and that people need to understand the kinds of partnerships and actions that make a difference.

Resplendence

Playwright Kareem Fahmy

After speaking with Gilbert, playwright Kareem Fahmy wrote “Resplendence,” which follows three generations of a family who try to save their island off the coast of Maine.

The New England State is an important setting for playwright and scientist. 

“Maine has such a special place in my heart,” said Gilbert, who has family in the state and attended college at the University of Maine. The pull of the “wild, eastern coast of Maine is so ubiquitous.”

Gilbert appreciated how Fahmy did a “great job of personalizing the context” of the state.

The challenge of preserving destinations, particularly those close to sea level, will likely persist.

“When you do any research about climate change, you have to be aware that this is not just a problem for people living today, but for people 200 years from now,” Gilbert said.

Weitzman said the play was an epic despite its short running time and thought it was “quite touching.”

Beyond the performance

Weitzman suggested that the plays can provide an educational component beyond the confines of the Staller Recital Hall. 

While people can’t produce the plays as part of paid entertainment, teachers can read and use them in the classroom. Actors Bill Heck, April Matthis, Tina Benko, Mandi Masden and Taylor Crousore will provide dramatic reading of the plays.

In a short time, the actors are “practically off the book,” as they embrace the opportunity to bring the words to life, Weitzman said.

He suggested the plays offer a glimpse into researchers’ lives. “Here is this person on the front lines. I’m surprised at the angles that are taken” in these plays.

Stony Brook University’s Staller Center for the Arts, 100 Nicolls Road, Stony Brook will present this year’s Science on Stage: Climate Edition on Monday, Oct. 28 at 4 p.m. Doors open at 3:30 p.m. The event is free and open to the public but reservations are strongly recommended.

To register, go to: https://bit.ly/4dcDtsi or click here.

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SBU’s Margaret Schedel brings endangered species to life through musi
Margaret Schedel discusses the ‘Carnival of the Endangered Animals’ with the band and conductor Justin Stolarik during rehearsal. Photo by Heather Lynch

Science on Stage at Stony Brook University added a new dimension to the performance this year, as Margaret Schedel, Associate Professor of Music, composed “Carnival of the Endangered Animals.” The original music, which will debut on Oct. 28 at 4 p.m. at the Staller Center’s Recital Hall, is a recreation of the sounds of a wide range of animals who are in danger of becoming extinct.

“It’s melodic, interrupted by moments of trying to translate” the calls from these animals, Schedel said.

Ken Weitzman, Founder and Associate Professor at Stony Brook, appreciates how quickly music can resonate for audiences.

“Music appeals to the emotions,” said Weitzman. “I’m jealous of how quickly music can do in 10 seconds what it takes me hours to do.”

The animals featured in the piece, along with the instrument that captures their sounds, are: the Atlantic Right Whale (Marimba); the A’kikiki bird, which is a Hawaiian honeycreeper (flute); Sumatran Tiger (trumpet); sage grouse (clarinet); Bajii, which is a Yangtze river dolphin; and the Jiangtun, which is a Yangtze finless porpoise (four-hand piano); gorilla (french horn); African bush elephant (trombone); Koala (bassoon); and the penguin (oboe).

Schedel plans to share information about each piece, which eight area high school students and two graduate students will perform, with the audience through a QR code, so they can connect the sounds with the message or visuals she was conveying.

Schedel tried to use a logical progression of the instruments, mixing up the woodwinds, percussion and brass.

Threatened by land development, the sage grouse includes high and low notes from the clarinet that gets covered up by the sounds of a flute and trumpet, imitating the sounds excavators make when they back up and develop McMansions.

Endangered by the spread of avian malaria carried by mosquitoes, the Hawaiian A’kikiki bird had been able to evade these insects by traveling higher up the mountain, where the colder temperatures kills the mosquitoes. That is not happening as much because global warming is enabling the blood sucking creatures to survive at higher elevation.

The sage grouse music starts with a melodic theme on the flute and as it goes higher, the theme becomes compressed. The buzzing brass, meanwhile, gets louder and louder as the mosquito pursues its meal, infecting the bird with a lethal parasite.

Reflecting the struggle for survival these creatures face, the Yangtze river dolphin, which had about 20 members when Schedel first started composing the music, may have become extinct by the time of the performance. That is, in part, why she combined the dolphin and the finless porpoise on the four hand piano.

As for the sounds of the elephant, Schedel recalled a safari she had experienced when she had been in South Africa. Elephants charged at Schedel and her group, who had come too close to the younger ones in the herd.

The elephants growled at Schedel and her companions.

“You can feel it in your chest, the sound waves moving,” she said. “Little by little, the younger ones put up their trunks and eventually a big momma elephant with a broken tusk put up her trunk, which is a symbol of, “we are calm,’” she said. With the trombone representing the elephant, the bass drum connotes its growling sounds.

When she was growing up, Schedel listened to the Leonard Bernstein version of “Peter and the Wolf” so many times that the recording is “nearly dead,” she laughed. She hopes people enjoy her piece with the same energy and excitement, connecting the sounds and the stories with the endangered animals. 

Schedel described the experience of creating the music as a “labor of love.”

 

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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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Ron Darling will this year's keynote speaker. Photo from PSEG Long Island

Energy efficiency workshops, products and programs will provide backdrop for Darling’s personal account as player, sports commentator, author and actor

New York Mets World Series champion and recently inducted College Baseball Hall of Fame honoree, Ron Darling, will deliver the keynote address at PSEG Long Island’s Energize Long Island conference on Thursday, Nov. 7 from 7:30 a.m. to 4 p.m. The all-day event at the Hilton Long Island/Huntington, 598 Broadhollow Road, Melville will feature more than a dozen educational workshops to help attendees reduce their carbon footprint, maximize efficient energy usage and cultivate renewable energy resources. Darling’s inclusion in the program will delight baseball fans and sports enthusiasts in attendance.

“We are thrilled to have Ron Darling as our keynote speaker for the Energize Long Island conference this year as his former team makes a playoff run,” said Michael Voltz, director of Energy Efficiency and Renewables for PSEG Long Island. “I am certain attendees will enjoy hearing about his amazing career as a major league ball player, actor, author and award-winning sports commentator – even as he’s currently calling the Yankees playoff games. We’re glad to provide this value-added opportunity for our attendees. This will be the ninth year we’re providing this venue to educate people on saving money and protecting the planet through energy efficiency measures.”

Energize Long Island is geared for business owners, property managers and developers, architects, engineers, contractors, consultants and consumers interested in implementing cost-effective, proven and sustainable energy efficiency solutions. Led by industry experts, the agenda includes discussions on a wide variety of topics and best practices to benefit business owners and builders, the local economy and environment. The more than 500 expected attendees will learn about financial incentive programs, new technologies and programs that lead to reduced energy usage. Along with Ron Darling as the keynote speaker, attendees will also have the opportunity to see and learn about many products and new technologies that will be on display at a vendor showcase throughout the day.

Registration for the Energize Long Island conference is free for PSEG Long Island customers, and only $50 for all other attendees. Sponsorship and exhibiting opportunities are available. For additional information please visit www.energizelongisland.com.

 

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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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Yi-Xian Qin

Yi-Xian Qin recognized by the BMES for his groundbreaking research on bone tissue response

Yi-Xian Qin, PhD, SUNY Distinguished Professor and Chair of the Department of Biomedical Engineering in the Renaissance School of Medicine and in the College of Engineering and Applied Sciences at Stony Brook University, will receive the 2025 Biomedical Engineering Society (BMES)  Christopher Jacobs Award for Excellence in Leadership.

The annual award, established in 2019, honors the memory and contributions of Christopher R. Jacobs, PhD, co-founder and council member of the Cellular and Molecular Bioengineering (CMBE) Special Interest Group (SIG) under BMES. It recognizes individuals who demonstrate exceptional leadership excellence within the Cell and Molecular Bioengineering community. Leadership is broadly defined and includes efforts in education, service and publication/dissemination of knowledge related to the CMBE field.

Dr. Qin’s expertise and leadership at Stony Brook is broad. He is also Director of the Orthopaedic Bioengineering Research Laboratory and Co-Director of the Institute for Engineering-Driven Medicine.

An innovator whose work in the field of bone research has significantly advanced scientific  understanding of how bone tissue responds and adapts to various functional environments, bone fluid flow and regenerative responses to dynamic stimuli, Dr. Qin has published more than 180 peer-reviewed articles as well as related books and chapters and U.S. patents. His patents encompass groundbreaking technologies such as ultrasound diagnostic imaging, therapeutic applications, and mechanical stimulation for musculoskeletal diseases like osteopenia and fractures. These technologies hold promise in offering numerous clinical benefits and predicting bone loss in microgravity during long-term missions in space.

“It’s a great honor to receive this prestigious award, which allows us to enhance bioengineering and bone tissue regeneration research in mechanotransduction and translation in the Stony Brook community,” says Dr. Qi, a resident of Setauket. He described Dr. Christopher Jacobs as a pioneer in the field of cellular and molecular engineering who discovered the role of primary cilia in bone cells and its role in mechanotransduction for cell differentiation and tissue regeneration.

Dr. Qin will deliver a lecture and be honored with the award at the 2025 BMES CMBE Conference in Carlsbad, California, from January 3 to 6.

He earned both his master’s degree and PhD from Stony Brook University’s Department of Mechanical Engineering. His contributions to the field have earned him Fellowship status in several prestigious organizations, including the American Institute for Medical and Biological Engineering (AIMBE), the American Society for Bone and Mineral Research (ASBMR), the Biomedical Engineering Society (BMES), the American Society of Mechanical Engineers (ASME), the International Academy of Medical and Biological Engineering (IAMBE), and the International Academy of Astronautics (IAA). Dr. Qin also serves as Executive Editor-in-Chief for Mechanobiology in Medicine, an Elsevier journal.

Established in 1968, the BMES has more than 6,800 members and is the leading professional society for faculty, students, researchers and industry professionals in biomedical engineering. The mission of the BMES is to promote a collaborative and inclusive community to advance human health through education, discovery and translation.

 

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Ellen Pikitch, PhD, with the Explorers Club flag. Photo by Taylor Griffith

Ellen K. Pikitch, PhD, a long-time professor in the Stony Brook University School of Marine and Atmospheric Sciences (SoMAS), was recently awarded the Lowell Thomas Award for her accomplishments in field science and communication.

Presented by The Explorers Club and named for broadcast journalist and explorer Lowell Thomas, this annual award is given thematically to a group of outstanding explorers to recognize excellence in domains or fields of exploration. Pikitch was nominated for this honor by explorer Sylvia Earle. Previous winners of the Lowell Thomas Award include such luminaries as Carl Sagan, Isaac Asimov, Kathy Sullivan, Sir Edmund Hillary, Kris Thompkins, and E.O. Wilson.

“Professor Pikitch has worked tirelessly for decades on ocean conservation issues,” said School of Marine and Atmospheric Studies Dean Paul Shepson. “How gratifying that her passion and dedication in service to the world’s oceans has been recognized with this prestigious award.”

Ellen Pikitch is an endowed professor of Ocean Conservation Science and executive director of the Institute for Ocean Conservation Science. Her research primarily focuses on ocean conservation science, with emphasis on marine protected areas (MPAs), fish conservation and fisheries sustainability, ecosystem-based fishery management, and endangered fishes.

Throughout her career, Pikitch has endeavored in research activities both nationally and internationally. For seven years, Pikitch served in various roles at the Wildlife Conservation Society (WCS). During this time, she built a program to encompass field research operations in 18 countries spanning four ocean basins and spearheaded several successful ocean policy campaigns for the organization. Most recently, Pikitch served as lead investigator behind launching an eco-friendly, solar-powered, remote-controlled craft that gathers data on the species living underwater, called The DataXplorer™. Internationally, Pikitch has lent a hand in crafting public policy as Ocean Science Lead for the United Nations 10×20 Initiative and as Special Envoy to Palau. She is an active Fellow of the Explorers Club. Additionally, Pikitch is the recipient of several awards, including the Hope Spot Champion award, the Oscar E. Sette award, the Ocean Hero award, and several notable fellowships.

Founded in 1904, The Explorers Club is a multidisciplinary, professional society dedicated to the advancement of field research, scientific exploration and resource conservation. Headquartered in New York City with a community of chapters and members around the world, The Explorers Club has been supporting scientific expeditions of all disciplines, uniting our members in the bonds of good fellowship for more than a century.

 

 

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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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Heather Lynch with Emperor penguins. Photo by Evan Grant

Stony Brook University Professor Heather J. Lynch, PhD, a professor in the Department of Ecology and Evolution in the College of Arts and Sciences, and the first Endowed Chair for Ecology and Evolution at the university’s Institute for Advanced Computation Science (IACS) has been awarded the 2024 Golden Goose Award for Unconventional Research that Yielded Unexpected and Impactful Discovery.

Caption: Heather Lynch with an Adélie penguin. Photo by Ron Naveen

Professor Lynch’s project, “From Poop to Protection: Satellite Discoveries Help Save Antarctic Penguins and Advance Wildlife Monitoring” which was funded by the National Science Foundation and NASA, looks at a way “to track penguin populations via satellite imagery, leading to the discovery of 1.5 million previously undocumented Adélie penguins and a whole new way to track wildlife.“ Professor Lynch shares this award with former IACS postdoctoral fellow Christian Che-Castaldo, PhD and Mathew Schwaller, PhD. Lynch also serves as the inaugural director of Stony Brook’s Collaborative for the Earth.

The Golden Goose Award celebrates federally funded research that may at first seem obscure or unconventional but has led to major breakthroughs in science and honors the importance of basic research, which aims to investigate unknown phenomena and advance current knowledge. The awards are hosted annually by the American Association for the Advancement of Science (AAAS).

“This is a tremendous honor for Professor Lynch. The Golden Goose recognizes that scientific discovery may not always follow a conventional path. Innovation is a hallmark of Stony Brook research, and Professor Lynch’s extraordinary research and dedication to addressing climate change is a stellar example,” said Carl Lejuez, Provost and Executive Vice President

“I’m hugely honored to have our work recognized in this way, and I remain as excited about the potential of satellite imagery as I was when we started this more than a decade ago,” said Heather Lynch. “I think we’ve only just scratched the surface of its potential for research and conservation.”

Professor Lynch’s research focuses on distribution and abundance of Antarctic wildlife, particularly on the development of remote sensing approaches to monitoring Antarctica’s penguin populations. She works closely with Antarctic policymakers to make sure they have the best available science at hand when deliberating measures for the area’s protection, and her discovery (with co-awardee Mathew Schwaller) of a major population of penguins in the Danger Islands directly led to the creation of a new Antarctic Specially Protected Area. She holds a doctorate in organismic and evolutionary biology from Harvard University and earned a master’s degree in physics from Harvard University and a bachelor of arts degree in physics from Princeton University.

To see more about Professor Lynch and her collaborators’ Golden Goose award-winning research, go to YouTube.

 

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Capital projects fund review of East Beach bluff stabilization shows an estimated $800,000 budget overspend. Photo by Lynn Hallarman

By Lynn Hallarman

The final report reviewing the capital projects fund was presented to the public by CPA firm, PKF O’Connor Davies of Hauppauge, at the Village of Port Jefferson Board of Trustees Sept. 25 meeting, ending a year of uncertainty over the financial condition of the fund.

The most significant conclusion was an estimated $1.27 million in overspending on capital projects done without an identified funding source. The largest overage was the East Beach bluff stabilization project of about $800,000.

Why the review was done

One year ago, concerns were raised by then newly-appointed village treasurer, Stephen Gaffga, about the bookkeeping practices that track the village’s capital projects fund. This prompted village officials to hire PKF O’Connor Davies to give a full historical accounting of the fund’s financial recordkeeping. The review spanned from May 2016 to May 2023.

“I noticed shortly after starting my position as treasurer in September of 2023 that our capital projects fund looked like every expense account had a negative balance, which immediately raised red flags for me,” Gaffga said in an interview with TBR News Media.

Gaffga noted that best practices recommended by the Office of the New York State Comptroller were not being followed, making it difficult to track how money was being spent on individual projects.

Ideally a capital project fund ledger should give a granular view of how money flows though different projects and meticulously accounts for funding and payments related to each project, according to the OSC.

The village additionally enlisted Charlene Kagel, CPA — former commissioner of finance for the Town of Brookhaven and ex-Southampton village administrator — as an expert municipal finance consultant to assist the village as it corrects bookkeeping practices to comply with state guidelines.

Reports findings

According to PKF O’Connor Davies, the purpose of the capital projects fund review was to identify which projects have been funded, which have been overspent and what grant funds for specific projects have not yet been reimbursed to the village.

The report provided a clearer picture of the capital fund financial state, especially addressing the overall negative balance observed a year ago. PKF detailed 26 projects as having a deficit fund balance.

Reviewers also noted that “recordkeeping varied by project” — or in other words, the bookkeeping lacked a consistent approach across the ledgers.

Overall, the review revealed an $8.1 million total deficit as of May 31, 2023. “Most of this deficit, an estimated $5 million, is due to grants expected but not yet received by the village,” Gaffga said.

The estimated $1.27 million shortfall comes from spending on a few large projects, most of which, $800,000, is attributed to the bluff stabilization project.

Gaffga explained that the additional spending on the bluff project occurred incrementally over several years starting in 2017, with board members approving these expenses without first identifying a funding source.

Recommendations

Recommendations to the village boil down to one improvement: Follow bookkeeping guidance outlined by the OSC.

The report also identifies the absence of a long-term capital projects fund plan for the village.

Kagel told TBR that an excellent capital plan should include a list of proposed projects by department heads and for municipalities to assign each project a “priority ranking” year by year.

“The board ranks what projects are most important and then figures out how they are going to pay for it,” she said.

Gaffga added, “There will need to be an identified funding source to correct that $1.27 million deficit in the capital fund.”

Gaffga pointed out, however, that this amount is an unaudited estimation. The village has hired a new accounting firm, R.S. Abrams & Co. of Islandia, to finalize the numbers cited in the report before village officials will move forward with a financial plan to reimburse the capital projects fund, as required by municipal law.

“Bottom line, it’s just bad bookkeeping. The village didn’t follow the recommended practice and accounting procedures that are set forth by the state and this is what happens when you don’t,” Kagel said.

Moving forward

The treasurer for a municipality is the custodian of all capital funds, responsible for tracking the finances of each project and developing financial reports for the board and the public.

“At the same time, the board is ultimately responsible for the oversight of the village financials,” Kagel said. “It’s pretty clear that municipalities aren’t supposed to overspend their budget, according to general municipal law in New York State.”

“Stephen [Gaffga] has implemented an OSC best practice, tracking each project financial detail to be sent to the board monthly, so the board can say, ‘Hey, how come we’re in the red on this project?’” she said.

“I’m glad we are now through the most difficult part of the capital projects fund review process and we now know exactly where the village stands,” Mayor Lauren Sheprow said in an email statement to TBR News Media.

“Now the village can proceed to develop a truly transparent capital project plan with guidance from our new Budget and Finance Committee and our incredible treasurer, Stephen Gaffga,” she added.

The full report can be viewed on the Village of Port Jefferson website at www.portjeff.com, and the next Board of Trustees meeting will be held on Oct. 9, as a work session.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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