CLOSE
Tags Posts tagged with "Daniel Dunaief"

Daniel Dunaief

by -
0 1102
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.”

by -
0 791
METRO photo

By Daniel Dunaief

Daniel Dunaief

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

by -
0 1192
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.

by -
0 967
Jillian Scully on the track. Courtesy Scully family

By Daniel Dunaief

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

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

Jillian Scully

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Change of life

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

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

Jillian Scully

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

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

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

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

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

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

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

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

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

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

Five squares

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

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

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

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

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

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

Athletic trajectory

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

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

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

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

by -
0 605
Pixabay photo

By Daniel Dunaief

Daniel Dunaief

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

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

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

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

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

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

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

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

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

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

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

“Yes, shhhh.”

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

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

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

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

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

“How old are you?” she’d ask.

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

“What’s your name?” she’d ask.

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

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

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

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

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

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

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

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

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

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

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

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

by -
0 1043
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.”

by -
0 584
Pixabay photo

By Daniel Dunaief

Daniel Dunaief

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

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

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

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

Then, of course, there are the realistic possibilities.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

by -
0 656
Photo courtesy Metro Creative Graphics

By Daniel Dunaief

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

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

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

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

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

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

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

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

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

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

Simultaneous shots

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Concussion awareness

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

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

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

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

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

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

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

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

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

Newborn RSV protection

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

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

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

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

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

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

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

by -
0 729
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.

by -
0 564
Pixabay photo

By Daniel Dunaief

Daniel Dunaief

I hadn’t been to Los Angeles in over 30 years. On our trip last week, I traveled with my wife, worked remotely, visited with our nephew, and purchased tickets to attend my first home Dodgers game.

During a visit that only lasted a few days, my wife and I stayed on Eastern Standard Time, which meant we were awake between 5:30 and 6:30 a.m. local time and were at work by 7 a.m..

My wife walked across a street to her office and I sat at a desk on the 17th floor of a hotel, laptop in front of me with my cell phone at the ready.

At around 7:30 a.m. on Thursday, I felt as if the desk in front of me were shaking.

At first, I figured it had to be some neurological quirk. After all, the older I get, the more inexplicable my sometimes random body signals are to me.

When the desk shook a second time, I made an announcement to the empty room.

“That’s an earthquake!” I declared, as if naming it and knowing what it was gave me some small measure of control. I walked around in circles and wondered what I should grab, where I should go, and what I should do.

I knew my wife was in meetings that morning, but called her immediately anyway.

She picked up in that hushed tone she uses when she’s on a phone or a zoom call.

“What’s happening?” she whispered.

“Did you feel the earthquake?” I asked. “What are you doing about it over there?”

“Earthquake? What earthquake? No,” she said, as she quickly typed into her computer.

Sure enough, within seconds of the quake, she had found something online confirming the event.

“What do you want to do?” she asked. 

I was staring out the window, which probably isn’t the right place to go, and watched people casually walking along the sidewalk, cars navigating through crowded streets and birds flying between the buildings.

“I’m going to call the lobby,” I said. I told her I’d get back to her immediately if there was anything we should do.

“Hi,” I stammered, “is this the front desk?”

“Yes,” the woman said. “How can I help you?”

“I’m on the 17th floor and I just felt an earthquake,” I announced.

Silence. I suspect the woman in the lobby was thinking something along the lines of, “You’re not from around these parts, are you?”

“What should I do?” I asked.

“Oh,” she sighed. “Well, if you’re worried or if things are falling from the ceiling, you can take shelter.”

“Shelter? Where? What should I do?”

“You can go under your desk or wait in a door frame. We also have a communication system on every floor and we can let you know if you need to evacuate.”

“So, what do I do?” I asked again.

“Whatever makes you comfortable,” she sighed. “Can I help you with anything else?”

“No,” I said, hanging up the phone. I grabbed my wallet, put on my shoes, and made sure I had everything I might need. I stood in the middle of the room in earthquake sensing mode. I had become a human seismometer, with my arms out, my feet spread apart and my palms pointing down to sense any vibrations.

I kept checking online, where I read coverage of an earthquake that didn’t seem to have caused any damage.

My wife and I traded texts and decided to continue working.

Later that day, we discussed the quake with friends and strangers, triggering all kinds of stories about earlier quakes and the ones people felt at different times.

I’m sure people in New York don’t hear honking taxis, people in the southeastern United States barely register screeching cicadas, and people in Phoenix somehow adjust to the searing heat.

I don’t think I’ll ever be enough of a Californian or a would-be Californian not to worry about the Earth moving under my feet.

Oh, and I did get to the Dodgers game the night before. The stadium was magnificent, the sushi was remarkably good, and the fans were delighted by the other-worldly performance of Shohei Ohtani, who crushed a home run and stole a base. 

The explosive sounds of a thrilled crowd of close to 50,000, the excitement of people jumping out of their seats, and the celebratory flashing lights were far more familiar than the shaking desk I felt the next morning.

Prev1...101112...87Next Page 11 of 87
TBR News Media is your local news and entertainment website.
We provide you with the latest breaking news and information for your community.
Contact us: [email protected]

Most Viewed

©