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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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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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From left, Oscar Rivera-Cruz from the University of Puerto Rico, BNL materials scientist Anibal Boscoboinik, Alexander Bailey from West Virginia State University, and Jeremy Lopez from the University of Puerto Rico. Photo courtesy of BNL

By Daniel Dunaief

It’s been a banner year for ideas and potential products that trap noble gases at Brookhaven National Laboratory. So-named for their full complement of electrons, noble gases tend to be less reactive than other atoms that can add electrons to their outer shells.

While their name sounds grandiose, these gases are anything but, particularly when people inhale the radioactive and prevalent gas radon, which can cause lung cancer or when the decay of uranium into xenon makes a nuclear reactor less efficient.

When he was studying how hydrocarbons react at the active site of zeolite models, Brookhaven National Laboratory’s material scientist Anibal Boscoboinik made an accidental discovery about a decade ago that some nanomaterials, which are incredibly small, trap these gases.

Among several other projects he’s working on, Boscoboinik has since studied these nanocages, learning about the trapping mechanism and making variations of these materials and trapping methods that can be useful for a wide range of applications. 

The Battelle Memorial Institute, which partners with Stony Brook University to form Brookhaven Science Associates and manages nine national labs across the country, named Boscoboinik an “inventor of the year” for his work developing these materials.

Battelle awards an inventor of the year to a researcher from each institution under its management, recognizing efforts that contribute to science or engineering and that can have a positive impact on society.

“It feels really good to be recognized for the work,” said Boscoboinik, who is proud of the many people who made this progress possible directly and indirectly. “It would be amazing if we get to see something that stemmed from an accidental discovery doing very basic fundamental research becoming a real-life application that can benefit society.”

At the same time, three students from minority serving institutions were selected to receive seed grants as a part of MSI (for Minority Serving Institutions) Connect at BNL, in which they seek to commercialize a way to remove radon from the air.

They may work in a business to business model to supply other companies that can incorporate their materials into products.

The students, Jeremy Lopez Flores and Oscar Rivera-Cruz from the University of Puerto Rico and Alexander Bailey from West Virginia State University, will enter phase 2 in the process. The next phase of funding comes from other sources, such as FedTech. Boscoboinik will advise the students as they develop the company and any potential products.

These undergraduate students are looking to remove radon from the air at a concentration of four picocuries per liter, which is equivalent to smoking eight cigarettes a day.

“I am certainly pleased that the value of our collective output was recognized,” said Bailey, who is from St. Albans, West Virginia, in an email. Bailey, a sophomore double majoring in chemistry and math, plans to attend graduate school after completing his undergraduate studies.

Rivera-Cruz, who is a senior majoring in Cellular and Molecular Biology, appreciated the guidance from Boscoboinik, whom he described in an email as an “incredible resource for the team” and suggested that the team was “extremely grateful and lucky” to have Boscoboinik’s support.

In other research

As a staff member at the Center for Functional Nanomaterials, Boscoboinik spends half his time working with scientists from around the world who come to the CFN to conduct experiments and half his time working on his own research.

The process of granting time to use the facilities at BNL is extremely competitive, which means the projects he works on with other scientists are compelling. “While I help them with their research, I get to learn from them,” he said.

Boscoboinik regularly works with the group of Professor Guangwen Zhou from Binghamton University. In recent work, they explored the dynamics of peroxide formation on a copper surface in different environments.

In his own work, Boscoboinik is also interested in trying to help the nuclear energy community.

During the breakdown of radioactive uranium, the process heats up water in a tank, moving a turbine that produces energy.

The breakdown of uranium, however, produces the noble gas xenon, which is a neutron absorber, making reactors less efficient.

Boscoboinik anticipates that any new product that could help the field of nuclear energy by removing xenon could be a decade or more away. “This is a highly regulated industry and changes in design take a very long time,” he explained.

Boscoboinik is also collaborating with researchers from Johns Hopkins University on metal organic frameworks. Some molecules pass through these frameworks more rapidly than others, which could enable researchers to use these frameworks to separate out a heterogeneous collection of molecules.

Additionally, he is developing processes to understand dynamic conditions that affect different types of reactions. At this point, he has been looking at the oxidation of carbon monoxide, which he called the “drosophila” of surface science for its widespread use and versatility, to develop the methodology. In oxidation, carbon monoxide mixes with oxygen to make carbon dioxide.

In his work, Boscoboinik has collaborated with Qin Wu, who deploys artificial intelligence to interpret the data he generates in his experiments.

The long-term plan is to develop complex-enough algorithms that suggest experiments based on the analysis and interpretation of data.

Outside the lab

Boscoboinik is a part of a collaborative effort to combine science and music. “We use music as a way to enable conversations between scientists and the general public” to help make the sometimes complex and jargon-laden world of science more accessible, he said.

In Argentina, research groups have taken famous musicians to the lab to perform concerts while encouraging conversations about science. During the course of their visits, the musicians speak with scientists for the benefit of the public. In prior seasons, the musicians used popular songs to relate to the research the scientists they interview do. Part of the plan is to make new songs related to the research.

Boscoboinik is part of a collaboration between Music for Science, the network of Argentinian scientists abroad, and the Argentinian diplomatic missions, including the embassies and the consulates. At some point in the future he may create a show that relates noble gases and music.

As with his some of his scientific work, the connection between music and research is a developing proof of concept that he hopes has broader appeal over time.

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Minghao Qiu presenting at the American Geophysical Union Conference in San Francisco last year. Photo courtesy of M. Qiu

By Daniel Dunaief

When Minghao Qiu woke up in Beijing on Jan. 12, 2013  during his freshman year in college, he couldn’t believe what he was seeing or, more appropriately, not seeing. The worst air pollution day in the history of the city mostly blocked out the sun, making it appear to be closer to 8 p.m. than a typical morning.

Minghao Qiu

While Qiu’s life path includes numerous contributing factors, that unusual day altered by air pollution had a significant influence on his career.

An Assistant Professor at Stony Brook University, Qiu straddles two departments that encapsulate his scientific and public policy interests. A recent hire who started this fall, Qiu will divide his time equally between the School of Marine and Atmospheric Sciences and the Renaissance School of Medicine’s Program in Public Health.

Qiu studies fundamental questions in atmospheric sciences as they influence human health.

He is part of several new hires who could contribute to the climate solutions center that Stony Brook is building on Governors Island and who could provide research that informs future policy decisions.

Noelle Eckley Selin, who was Qiu’s PhD advisor at the Massachusetts Institute of Technology and is Professor in the Institute for Data, Systems and Society and the Department of Earth, Atmospheric and Planetary Sciences, suggested Qiu is a valuable scientific, policy and educational asset.

“Stony Brook is doing a lot to address climate in a serious way with great research,” Selin said. Qiu joining the institution “could really help out the university’s broader climate efforts and make them more impactful.”

Selin appreciated how Qiu was eager to dive deeper into questions, wanting to ensure that conclusions were valid and asking how to use data to test various ideas.

As a mentor, Qiu has proven inspirational.

“A lot of my current students will go and talk to him and come back to me and say, ‘[Qiu] had five excellent ideas on my project,’” Selin said. “That’s characteristic of how he works. He’s really generous with his time and is always thinking about how to look at problems.”

Policy focus

Using causal inference, machine learning, atmospheric chemistry modeling, and remote sensing, Qiu focuses on environmental and energy policies with a global focus on issues involving air pollution, climate change and energy transitions.

Qiu would like to address how climate change is influencing the air people breathe. Increasing heat waves and droughts cause people to use more energy, often through air conditioning. The energy for the electricity to power temperature controls comes from natural gas, coal, or fossil fuels, which creates a feedback loop that further increases pollution and greenhouse gases.

“Our work tries to quantify this,” Qiu said.

He also analyzes the impact of climate change on wildfires, which affects air quality.

In a research paper published last year, Qiu joined several other scientists to analyze the impact of wildfires on air quality.

The study, published in the journal Nature, found that since at least 2016, wildfire smoke eroded about a quarter of previous decades-long efforts to reduce the concentration of particulates above 2.5 microgram in several states.

Wildfire-driven increases in ambient particulates are unregulated under air pollution laws.

The authors showed that the contribution of wildfires to regional and national air quality trends is likely to grow amid a warming climate.

In his research, Qiu seeks to understand how to use energy and climate policy to address air pollution and greenhouse gases.

“Renewable energy and climate policy in general provides potential benefits,” Qiu said.

He uses publicly available data in his models.

New York pivot

While wildfires have been, and likely will continue to be, an area of focus for his work, Qiu plans to shift his focus to the kind of pollution that is typically more prevalent in New York.

In large urban cities, pollution often comes from a concentration of traffic, as people commute to and from work and drive to the city for entertainment and cultural events.

“We are going to pivot a little bit, especially to factors that are more relevant” to the Empire State, he said.

While climate change is a broad category that affects patterns across the world, air pollution and its impacts are more regional.

“The biggest impact of air pollution happens locally” particularly in terms of health effects, Qiu said.

From Beijing to MIT

Born and raised in Beijing, Qiu began connecting how climate or energy policy influences air pollution at MIT.

“When I started my PhD, there was not much real world data analysis” that linked how much renewable energy helps air quality, Qiu said. “We have historical data to do that, but it’s a lot more complex.”

After he graduated from MIT, Qiu moved to Stanford, where he shifted his focus to climate change.

“There, I got to collaborate more directly with people in the public health domain,” he said, as he focused on wildfires.

Personal choices

Despite studying air pollution and climate change, Qiu does not have HEPA filters in every room and, by his own admission, does not live a particularly green life. He does not have an electric car, although he plans to get one when he needs a new vehicle. He urges people not to sacrifice the living standards to which they are accustomed, which can include eating their preferred foods and traveling to distant points in the world.

Qiu believes there are choices individuals can make to help, but that the kind of decisions necessary to improve the outlook for climate change come from centralized government policy or large enterprises.

“I have great respect for people who change their personal behavior” but he recognizes that “this is not for everyone.”

A resident of Hicksville, Qiu lives with his wife Mingyu Song, who is a software engineer. The couple met when they were in high school.

When he’s not working on climate models, he enjoys playing basketball and, at just under six feet tall, typically plays shooting guard.

As for his research, Qiu does “rigorous scientific research” that draws from historical data.

“I feel a sense of urgency that we would like to get the answers to many of the scientific evidence as quickly as possible to communicate to policy makers,” he said.

He wants his research to be impactful and to help policy makers take “appropriate measures.”

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Suffolk County Community College recently completed its Summer High School Offshore Wind Turbines course, designed to introduce high school students to the burgeoning field of wind energy. Photo courtesy of SCCC

Suffolk County Community College has announced the successful completion of its recent Summer High School Offshore Wind Turbines course, designed to introduce high school students to the burgeoning field of wind energy. The college held two separate summer sessions and provided students with a comprehensive, hands-on learning experience.

The first camp was comprised solely of participants from the South Huntington School District. The second camp welcomed students, including those from the South Huntington School District, as well as participants from the New York State STEP (Science and Technology Entry Program) grant program

The program is sponsored by a grant awarded by the Offshore Wind Training Institute, an organization administered by SUNY Farmingdale and Stony Brook University. The grant is titled “Strengthening the Wind Energy Education Pipeline (SWEEP).”

The offshore wind turbines course is part of Suffolk County Community College’s broader effort to prepare students for careers in the renewable energy sector. This grant also enabled the college to expand its welding and composites training programs. Since the launch of these programs, students have successfully completed both the welding and Introduction to Basic Composite Technology courses, with a majority of students passing the American Welding Society (AWS) certification exam.

As part of the students’ comprehensive training experience, all students in the welding and basic composite technology programs also participated in career exploration workshops. These workshops featured guest speakers from the National Offshore Wind Training Center, the Building and Construction Trades Council of Nassau and Suffolk Counties, and Community Offshore Wind, offering valuable insights into the industry and future career paths. As a result, a number of students have already interviewed with labor unions for potential pre-apprenticeship opportunities in the Building and Construction Trades Council of Nassau and Suffolk Counties.

Additional students are scheduled to participate in these programs throughout 2024 and 2025. An inaugural cohort of a 60-hour composites course, leading to a national certification by CertTEC, is scheduled for Spring 2025. The college has also developed offshore wind career exploration modules in collaboration with the Institute for Workforce Advancement. These modules aim to engage underrepresented populations and post-high-school students by providing insights into wind energy fundamentals, local projects, and career opportunities. To date, three workshops have been held, with 12 more planned throughout the remainder of the grant project. Portable simulations will be used to enhance engagement at career fairs, libraries, and community venues

About Suffolk County Community College

Suffolk County Community College is the largest community college in the State University of New York (SUNY) system, enrolling approximately 21,000 students at its three campuses in Selden, Brentwood and Riverhead. Suffolk offers the Associate in Arts (A.A.), Associate in Science (A.S.), and Associate in Applied Science (A.A.S.) degrees, as well as a variety of certificate programs. Offering affordable college tuition, a highly respected Honors program, workforce training programs, extensive extracurricular activities, championship athletic teams, and numerous transfer programs, Suffolk is a first-choice college for Long Island students. Visit us online at sunysuffolk.edu.

Research/Work reported in this press release was supported by SUNY System Administration under SUNY Offshore Wind Training Institute.

STEP is funded by the New York State Education Department (NYSED) Project # 0516-24-0041Office of Access, Equity and Community Engagement Services (OAECES) & Office of Postsecondary Access, Support and Success (OPASS).

 

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