Stony Brook University

Clare Flynn conducts a census count of gentoo penguins at Neko Harbour in Antarctica in January 2023.

By Daniel Dunaief

Humans may have nothing on penguins when it comes to viral marketing. Almost immediately after the Covid pandemic shut down tourism in parts of Antarctica, some gentoo penguins likely altered their choice of nesting sites.

Clare Flynn with her award- winning poster at the Pacific Seabird Group annual meeting in Feb. 2023. Photo by William Kennerly

As if the penguins got an avian email alert indicating that tourists eager to send a post card from the only post office in Antarctica weren’t coming, these flightless birds quickly divvied up desirable real estate, which, for a gentoo penguin, means bare rock on which they make nests out of pebbles.

“Antarctica is seen as a mostly pristine place where humans have very little impact,” said Clare Flynn, a PhD student in the lab of Heather Lynch, the Institute for Advanced Computational Sciences Endowed Chair for Ecology & Evolution at Stony Brook University.

Flynn used a combination of ground counts from researchers and drone footage to tally the nests during the Covid years. Based on these numbers, she concluded that tourism has been “depressing the population sizes at Port Lockroy” and nearby Jougla Point.

The study suggests that even limited human visits to remote locations can alter decisions by wildlife, affecting the kind of reproductive choices that could, over time and with greater numbers of people coming, affect population sizes.

Pomona College Biology Professor Nina Karnovsky, who is an undergraduate thesis advisor and mentor for Flynn but didn’t participate in this research, suggested that this kind of analysis highlights the need for greater awareness of human influence.

“It shows that people even visiting the colony can have impacts,” Karnovsky said. “Tourism is a double-edged sword. You want people to experience Antarctica and see how precious life there is.” At the same time, researchers don’t want any such visits to have negative side effects.

Nest numbers

The number of penguin nests in Port Lockroy surged to 978 in the 2021/ 2022 breeding season. That is considerably higher than the 535 nesting pairs in the 2018/2019 season, according to data compiled and analyzed by Flynn. What’s more, when the post office returned to normal operations, bringing back tourists in 2022 and 2023, the nest number at Port Lockroy returned to its earlier levels, at 529.

The overall number of nesting gentoo penguins didn’t change dramatically in a cluster of gentoo penguin colonies around Wiencke Island during Covid, as many of these birds likely shifted their breeding locations from nearby sites that don’t have as much human activity, such as Damoy Point.

“It’s shocking how quickly [the changed nesting sites] happened,” Flynn said, occurring over the course of two years, not generations. “Tourism is just ramping up when the penguins are choosing nesting sites.” The shifting nest sites accounted for most of the increase in Port Lockroy and Jougla Point. Some of the gentoo penguins who may have skipped a breeding season, however, also might have decided to give it a go amid the pandemic closure.

Post office attraction

Flynn and Lynch have a few theories about what caused these nesting patterns.

Flynn suggested the nesting sites at Damoy Point and Dorian Beacon, where the number of nesting colonies declined during the lockdown, may have been close to carrying capacity, which means that prospective penguin parents found the equivalent of No Vacancy signs when they searched for places to build their nest.

Sites near the post office were not at carrying capacity prior to the pandemic. From visual inspection of the drone images, these sites had available bare rock, which is a limiting factor for gentoo penguins.

Flynn believes that pedestrian traffic may have dissuaded penguins from creating nests.

Human disturbance

Boat traffic may also be dissuading gentoo penguins from nesting. While there is a limit to the number of people who can land at any given time, people often cruise around the area in zodiacs, which increases the noise and could create a physical barrier for swimming penguins.

Last month, Lynch brought Flynn’s analysis of nesting numbers during the pandemic to the Antarctic Treaty Consultative Meeting in Finland. Policy makers are considering implementing a no-wake zone in Port Lockroy harbor as a first step to reduce disturbance.

While the number of nests typically varies by year at these sites, the dramatic increases and decreases lie outside that normal range, Flynn said. She called the numbers “eye popping,” as Port Lockroy had the largest population size ever recorded in 2021/ 2022 and Jougla Point saw the largest population size in 2021/2022 in over 20 years. Damoy Point and Dorian Beacon, by contrast, had huge drops.

Understanding the effects of tourism is becoming increasingly important, particularly as the appetite for travel to this area increases.

While gentoo penguins are doing well overall, an increase in the kind of tourism that exists at Port Lockroy could affect their breeding success.

“We need to understand how increasing levels of tourism affect these species so that the effects in conjunction with climate change effects don’t cause a disaster” for several penguin species, Flynn added.

Rewarding pivot

Flynn hadn’t intended to study the effects of Covid on the gentoo penguin. Instead, she was using drone images to identify whether penguins nested in the same place from one year to the next.

While Flynn was annotating images from 2018 through 2021, Lynch noticed the changes at Port Lockroy during those years. After Flynn took a deeper dive into the numbers, she made a new poster just one week before presenting her results at the Pacific Seabird Group annual meeting in February.

The “exhausting” effort, as Flynn put it, paid off, as she won runner up honors for best PhD poster at the conference. She has since sent the results out to Biological Conservation for publication.

Ecology spark

Flynn grew up near Baltimore and attended Pomona College, where she anticipated exploring her interest in math. She switched her focus to ecology. An ecology and evolution class she took with Karnovsky cemented her decision and brought her into the world of seabirds.

Karnovsky recalled how Flynn “loved collecting data,” which, in Southern California is “not a walk in the park, literally.” Flynn had to contend with cactus and poison ivy on an owl project.

Karnovsky believes her former student could “go on and do great things in this field.”

At one point about five years ago, Karnovsky told Flynn she might “go to Antarctica one day to study penguins,” Flynn recalled. At the time, Flynn thought the idea sounded “crazy.”

Karnovsky’s suggestion about Flynn’s future was less crazy than it was prescient.

When she’s not following her research calling, Flynn enjoys following recipes. She makes baked goods and is particularly fond of a blueberry muffin recipe she found in Bon Appétit magazine. Instead of putting in too many blueberry, which sink in the muffin, she makes a blueberry compote and sprinkles lemon zest sugar on top.

As for her future, Flynn hasn’t decided on a post PhD plan. This could include becoming a professor or pursuing a data science career.

“I could see her becoming a really wonderful professor because she also sees mentoring as really important,” Karnovsky said.

Jacqueline Castaldo

Stony Brook University Director of Business in Finance & Administration (F&A) Jacqueline Castaldo has been awarded the State University of New York  (SUNY) Chancellor’s Award for Excellence in Professional Service.  

Castaldo’s responsibilities include oversight of the finances and budget within several University areas including Budget, Financial Planning & Analysis; Enterprise Risk Management; Facilities & Services; Finance; Human Resource Services; Marketing & Communications and Government & Community Relations. She also collaborates on financial matters for the Division of Information Technology. 

The Chancellor’s Awards for Excellence are System-level honors conferred to acknowledge and provide recognition for consistently superior professional achievement and to encourage the ongoing pursuit of excellence. Individuals nominated for these awards must meet all prescribed eligibility criteria and must be individuals of achievement, committed to the State University and its students, respected by the campus community and worthy of emulation by colleagues and students on the home campus and across SUNY. 

“I congratulate Jackie on this well-deserved achievement,” said Jed Shivers, Senior Vice President, F&A. “Her responsibilities have grown significantly since joining the university and she has definitely demonstrated excellence in her efforts.  We have worked on a number of projects together and I have been impressed with her dedication to detail and ensuring that financial statements are accurate as well as actionable.”

Castaldo joined Stony Brook University seven years ago in the Office of Procurement as a Business Analyst Lead. After working in Procurement for almost two years, the Bayport resident transitioned into a new role in F&A, serving as a Senior Financial Analyst where she was responsible for data analytics within the University, developing key metrics to enhance business processes and expanding upon University initiatives. In 2021, she was promoted to Assistant Director of Finance, a post she held for approximately one year before being appointed to Director of Business Operations for F&A. 

By Daniel Dunaief

This is part 2 of a two-part series.

Cancers not only compromise human health, but they can also suppress the body’s immune response. A little studied small protein called cystatin C, which is secreted by numerous cells, may render the immune system less effective in its response to tumors.

Sam Kleeman, a PhD student in Cold Spring Harbor Laboratory Assistant Professor Tobias Janowitz’s lab, recently published results in the journal Cell Genomics that demonstrate a link between elevated levels of this protease inhibitor, the suppression of the immune system, and the development of cancer.

Kleeman was able to demonstrate a potential role “Cystatin C might play in damping down the immune response to tumors,” he said.

Cystatin C is a known cysteine protease inhibitor, but the biological and organ-level relevance of this has not been characterized in detail. This protein could be one of many mechanisms by which glucocorticoids can reduce the effectiveness of the immune system.

Cystatin C could drive the progression of the disease, which could explain why Kleeman has found evidence that higher levels coordinate with worse outcomes.

Starting with the data

Pursuing an interest in data- driven research, Kleeman, who has a Bachelor of Medicine and Surgery from New College at the University of Oxford, searched the UK Biobank, which provides health data for numerous people in the United Kingdom. 

In this Biobank, Kleeman, who joined Cold Spring Harbor Laboratory in August of 2020, found that cystatin C was the best prognostic indicator of cancer deaths.

“I was a little surprised by this,” Kleeman said as he had heard of cystatin C as a marker of kidney function, but was not aware of any association with cancer mortality. Some studies had found evidence for this previously, but those were in small cohorts and were poorly understood, he explained.

A healthy kidney clears most proteins quickly, pumping it out into urine. A kidney that’s not functioning optimally, however, allows it to accumulate.

In his research, Kleeman removed cystatin C selectively in cancer cells, causing the tumors to grow more slowly. The main changes in the architecture of the tumor was that it reduced the frequency of macrophages with expression of a protein called Trem2. While the exact mechanism is not known, it’s likely that immune control of the tumor increases without cystatin C.

Kleeman also demonstrated a similar effect on the connection between levels of Covid-19 and mortality in a paper published in iScience.

The biological mechanism explaining the correlation is nuanced. Patients with higher levels of glucocorticoids can be associated with poor outcomes. It is not a simple relationship, he said, which makes causality difficult to assess.

Kleeman believes cystatin C secretion in response to glucocorticoids has context dependency. Not all cells posses inducible cystatin C secretion.

The research primarily found that only macrophages and cancer cells can secrete cystatin C in response to glucocorticoids.

He describes a “two hit” model, by which glucocorticoids plus an inflammatory stimulus recruit macrophages. The model applies to all inflammatory stores, but is co-opted in the case of cancer.

At this point, drugs aren’t available to inhibit or reduce cystatin C. Instead, Kleeman suggested that a viable research target route might involve creating a specific antibody.

Some researchers have created so-called knockout mice, which don’t have this protein. These mice can survive without it, although eliminating all cystatin C creates other problems.

Kleeman speculated that the protein could play a role in preventing significant immune reaction against sperm.

Indeed, this protein is secreted at high levels in the testes. Males without it have lower sperm function and production.

Kleeman hopes this work acts as a starting point to understand the mechanism better by which glucocorticoids modify immune response to cancer, and to investigate cystatin C as a possible therapeutic target.

Long standing partnership

As an undergraduate, Kleeman took a class with Janowitz, which kicked off a mentorship that now spans two continents.

Kleeman appreciates the comfort level Janowitz has in working on higher-risk, higher-reward topics or on ideas that haven’t already attracted considerable attention from other scientists.

“There’s a tendency in science towards group think,” Kleeman said. In the history of medicine and science, many widely accepted theories turn out to be wrong. “Patients undoubtedly benefit from a diversity of thought in science and medicine,” he explained.

When he completes his PhD, Kleeman said it would be a “dream to have a dual appointment” in which he could conduct research and work in the clinic with patients. To get there, he knows he needs to establish his research profile that includes a genuine track record of achievement while demonstrating that he can function as a reliable and effective clinician.

Kleeman’s thesis research lies outside the field of cystatin C, which started out as a curiosity and developed into the recent publication. He wanted to “understand what UK Biobank could teach us about cancer patients.” With Janowitz and Cold Spring Harbor Laboratory Professor Hiro Furukawa, Kleeman is working to understand how a specific type of cancer could cause an auto-immune disease.

A resident of Forest Hills, Kleeman lives about 45 minutes from the lab. Outside of work, he enjoys visiting national parks. He has visited 10 so far, including Yosemite National Park, Zion and Rocky Mountain National Park. 

Professionally, Kleeman feels it is a privilege to be a PhD student. He appreciates that he can explore his interests without too many restrictions and is eager to make the most of the opportunity.

Vanessa Aleksander and Ignacy Liss in a scene from March ‘68. Photo courtesy of Staller Center

Stony Brook University’s Staller Center  for the Arts turns into a movie lover’s mecca when new independent films screen at the Stony Brook Film Festival on evenings and weekends from Thursday, July 20 to Saturday, July 29. The popular festival, now in its 28th year, will become a hub for some of the best filmmakers working today, a meeting ground for favorite actors and rising stars, and a showcase of new masterpieces as it pairs memorable short films with an array of features you won’t see anywhere else.

Presented by Island Federal, this year’s lineup offers 36 films from over 26 countries. The Festival kicks off with the U.S. premiere of the Dutch film Sea of Time. Led by Sallie Harmensen (SkyTV’s Devils), Reinout Scholten van Aschat, and of Danish stage and screen fame Elsie De Brauw, the harrowing, heartbreaking, and ultimately hopeful film is anchored by the powerhouse performances that examine enduring love in times of hardship.

Many international films in this year’s Festival are threaded by this theme of love overcoming life’s difficulties. Whether it is the blossoming young love against all odds in the Polish period drama March ’68, the touching Japanese film Trapped Balloon (starring Toko Miura of the 2022 Oscar-winning film Drive My Car), the gorgeous and romantic love story of My Sailor, My Love with Scottish film icon James Cosmo (Game of Thrones, His Dark Materials) and Tony-Award Winner Bríd Brennan (Dancing at Lughnasa), or the hilarious, music-infused road trip feature Grandpa Goes South from Slovenia.

Continuing on this shared theme of overcoming is Martha, a film that tells the true story of Martha Liebermann, wife to famed painter Max Liebermann, as she faces the Third Reich on own her terms. 

At the same time, the powerful documentary Radioactive, directed by Stony Brook University professor Heidi Hutner, recounts the saga about four housewives from Three Mile Island facing down the nuclear industry Goliath for over forty years, and The Grandson tells the story of a man’s refusal to allow heartless scammers to get the best of his grandfather in this tight Hungarian thriller.

There is no shortage of independent cinema in this year’s lineup, including the Serbian puzzle piece Where the Road Takes You, which takes the Western trope of the stranger in town who saves the girl and flips it on its head. From Canada comes the quirky comedy I Like Movies about the reformation of a crabby, awkward teenage cinephile. 

Also providing comic relief is the scenic and quietly riotous American indy Friends From Home, shot on the cheap during Covid, and from Italy, the strangely compelling Amanda, about a young woman who suddenly decides that an acquaintance from her very young childhood is now her best friend.

Rounding out a host of stellar independent offerings is the wild Yes, Repeat, No, set in a studio where three actors are all auditioning for the same role. This courageous and unforgettable film zeroes in on questions of conflicting identity while managing to surprise at every turn.

Some recognizable faces also show up in this year’s lineup, including Richard Kind, Karen Allen, and Peter Reigert in Hit Man: Secrets of Lies and the wickedly hilarious Two Chairs, Not One, starring Caitlin Reilly (HBO’s Hacks), whose wildly popular TikTok account has amassed hundreds of millions of views.

The closing night feature tells an extraordinary tale of overcoming. Divertimento shares the true story of sisters Zahia and Fettouma Ziouani, a conductor and a cellist, who, despite being Algerian immigrants from the wrong part of Paris, managed to create a world-class professional orchestra with little more than respect, determination, and sheer talent. Opening and closing with the insistent rhythm of Ravel’s Bolero, the film makes its hopeful message equally insistent: family and community can make the impossible possible.

“We are very excited to have filmmakers from all over the world join us for their premiere screenings. Our audiences can gather in a huge theater with Long Island’s largest screen, to see movies the way they were meant to be seen,” says Festival Director Alan Inkles. 

“Not only are these films not available on any streaming format, but you also get to hear directly from the filmmakers themselves, ask them a question at our live Q&A, and even vote for your favorite,” he said.

Additional sponsors for the Stony Brook Film Festival include Campolo, Middleton & McCormick, LLP; Suffolk County; Altice Media; and WLIW/PBS.

FILM SCHEDULE

OPENING NIGHT

Thursday, July 20 at 8 p.m.

Feature: Sea of Time

Short: The Red Suitcase

Friday, July 21 at 7 p.m.

Feature: Exodus

Short: Hit Friends

Friday, July 21 at 9:30 p.m.

Feature: I Like Movies

Short: Chipper

Saturday, July 22 at 7 p.m.

Feature: My Sailor, My Love

Short: The Countryman

Saturday, July 22 at 9:30 p.m.

Feature: Grandpa Goes South

Short: Two Chairs, Not One

Sunday, July 23 at 7 p.m.

Feature: Martha

Short: Stuck

Sunday, July 23 at 9:30 p.m.

Feature: Friends From Home.

Short: At A Glance

Monday, July 24 at 7 p.m.

Feature: Trapped Balloon

Short: Healer

Monday, July 24 at 9:30 p.m.

Feature: A Fleeting Encounter

Short: Winter’s Passing

Tuesday, July 25 at 7 p.m.

Feature: Elik & Jimmy

Short: The Third Defector

Tuesday, July 25 at 9:30 p.m.

Feature: Amanda

Short: Mahogany Drive

Wednesday, July 26 at 7 p.m.

Feature: Radioactive: The Women of Three Mile Island

Short: Queen Moorea

Wednesday, July 26 at 9:30 p.m.

Feature: Where the Road Leads

Short: Hit Man: Secrets of Lies

Thursday, July 27 at 7 p.m.

Feature: March ‘68

Short: The Father, The Son and The Rav Kalmenson

Thursday, July 27 at 9:30 p.m.

Feature: Yes Repeat No

Short: Demon Box

Friday, July 28 at 7 p.m.

Feature: The Grandson

Short: Death By Puppies

Friday, July 28 at 9:30 p.m.

Feature: First Snow of Summer

Short: Voices

CLOSING NIGHT

Saturday, July 29 at 8 p.m.

Feature: Divertimento

Short: The Basics of Love

CLOSING NIGHT AWARDS

10:30 p.m. Presented on stage.

——————————————-

Ticket information

All screenings are held at Stony Brook University’s Staller Center for the Arts, 100 Nicolls Road, Stony Brook in the 1,000-seat Main Stage theater. 

Festival goers can choose from a Gold Pass “VIP” ($250), Regular Pass ($100), new! Flex Pass ($75), or Individual Pass of $15, $13.50 seniors. To learn about the different membership levels and their benefits, call 631-632-2787 or visit www.stonybrookfilmfestival.com.

This article first appeared in Summer Times, a seasonal guide supplement by TBR News Media.

By Melissa Arnold

Spending any amount of time in a hospital setting is bound to be taxing, not just physically but emotionally. Sometimes, a little reminder that you’re being thought of and supported can make all the difference. 

Since 2008, the Stony Brook Stitchers have volunteered their time and skill to knit, crochet and sew gifts for patients that could use a pick-me-up.

Melissa Shampine

In the neonatal intensive care unit (NICU), families might receive a cute knit cap for their little one. In difficult situations where a baby passes away, a special wrap for the baby can be used to take treasured photos, and parents are given a memory pouch to hold mementos like a lock of hair. Patients in other departments, such as the cancer center or pediatric hospital, might curl up with an afghan, lap blanket or prayer shawl during their stay. Residents at the nearby Long Island State Veterans Home receive donations as well.

The project is a grassroots effort that began with hospital staff who wanted to brighten patients’ days.

Stitchers co-director Melissa Shampine grew up attending a small parochial school in Manhattan, where the boys were taught chess and the girls learned to crochet. 

“Even though it was mandatory, I found that I actually liked it, and eventually learned to knit as well,” she recalled. “I really enjoyed being creative in that way.”

Shampine now works as a teaching hospital staff assistant at Stony Brook University Hospital. One of her former coworkers, Shakeera Thomas, was also a knitter, and together they began to brainstorm ways they could use their talents to benefit patients.

The idea spread through word of mouth, first among hospital staff, then across the street to the university. Nurse directors and health care providers identified patients who might want a gift. Students and employees from both campuses began donating yarn and got to work. Their numbers grew, and over time, even the surrounding communities got involved.

Jan Tassie

While the project is united under the Stitchers title, there are no official members or meetings. Some people work together at their churches, libraries or other small group settings, but countless others simply knit at home when they have the time. 

In 2015, Jan Tassie responded to an email from Shakeera Thomas, inviting hospital employees to learn to crochet. 

“I always wanted to learn to crochet, and someone tried to teach me years ago when I was pregnant with my first son, but it didn’t work out,” said Tassie, who recently retired from the university’s Office of Financial Aid and Scholarship Services. “When I met Shakeera, she promised that when she was done with me, I’d be able to crochet. And at the end of one day, I could.”

Thomas relocated shortly thereafter, and Tassie stepped into the role as co-director for the Stitchers.

“In the hospital and university settings, you always have people who come and go, so the numbers wax and wane. But Jan is motivated — she is the kind of person who will chat up people in the yarn aisle at craft stores, or through networking, so there are always hands to help. Our website is a labor of love for her, too. She’s done so much,” Shampine said.

The Stitchers come from all walks of life and skill levels. Some have been knitting for decades, while others learned recently with the intent of supporting the project.

Among them is Jack Domaleski, a 24-year-old from New Suffolk who took up knitting during the pandemic quarantine.

Jack Domaleski with two knitted baby hats.

“During COVID, I taught myself to knit by watching videos on YouTube because I was bored and looking for something to do. It was easy to learn,” said Domaleski, who works in the restaurant industry. “My mom did it when I was younger, and it’s nice to end up with a finished product that you can share with others. I thought that it would be nice to donate to the hospital in some way, and when I wrote to them, they told me about the Stitchers.”

He was also inspired to knit by his own story. Domaleski was born several months premature, and spent nearly 90 days at Stony Brook’s NICU before he was strong enough to go home.

Today, he knits baby hats while thinking of other families going through similar circumstances.

“It helps me to feel connected to my own story, and anything you take the time to make is especially meaningful for the people that receive it,” he said. 

For information about volunteering or donating yarn or handmade items to the Stony Brook Stitchers, visit www.stonybrookstitchers.com or send an email to Jan Tassie at [email protected].

From left, Allison McLarty, MD, Marc Goldschmidt, MD, Hal Skopicki, MD, PhD. Photo from Stony Brook Medicine

In 2010, Stony Brook Heart Institute’s Ventricular Assist Device (VAD) Program was established on Long Island to implant this life saving device. A VAD, also often called a left ventricular assist device or LVAD, is a surgically implanted, battery powered pump that, by supporting the lower left ventricle (the heart’s main pumping chamber), helps a failing heart to do its job more efficiently. The VAD can be used as an intermediary step before heart transplantation or, in patients who, due to advanced age or medical condition are not transplant candidates, as a long-term “destination” device. 

VAD patient Joseph Cerqueira and his wife.

Now 10+ years later, patients, their families and medical staff from the Heart Institute gathered on June 15, to celebrate the anniversary of this life saving heart device and program. (The 10-year event was postponed in 2020 due to Covid-19.) 

“Nobody knew when we began putting in heart pumps 13 years ago that they would be this durable and reliable,” says Allison McLarty, MD, Surgical Director of the VAD program. “This amazing device has revolutionized the management of advanced heart failure.”  

“For the VAD team, there is the immense reward of seeing these extraordinary individuals return to their homes and families with a much better quality of life,” added Marc Goldschmidt, MD, Director, Heart Failure and Cardiomyopathy Center and Medical Director, Ventricular Device Program.

“A VAD program at Stony Brook Heart Institute has been a tremendous asset for both the community and the hospital. Patients with the most complex heart conditions have access right here, close to home, to all the state-of-the-art services they need,” said Hal Skopicki, MD, PhD, Co-Director, Stony Brook Heart Institute and Chief of Cardiology.  

Among the patients who attended today’s event was Joseph Cerqueira, 63, who received a VAD in 2017 and a heart transplant the following year. Following his surgery, Joseph returned to his work as a corporate chef. 

“Everybody went the extra mile to make me comfortable and knowledgeable on how to adapt to every aspect of life with a VAD,” said Cerqueira. “Now my quality of life is perfect. I still get tired and I know my limitations, but besides that I do whatever has to be done.”

To learn more about the Ventricular Assist Device Program, visit https://heart.stonybrookmedicine.edu/services/vad.

Benjamin Martin. Photo by Jeanne Neville/Stony Brook Medicine

Benjamin Martin, PhD, Associate Professor in the Department of Biochemistry and Cell Biology at Stony Brook University, and member of the Stony Brook University Cancer Center, has received a $2 million grant from the National Institutes of Health’s National Institute of General Medical Sciences (NIGMS) to conduct research to understand the molecular and cell biology of neuromesodermal progenitors. The grant term, effective June 1, 2023, is five years.

The Martin Lab uses zebrafish embryos as a model system. The grant enables Martin and colleagues to carry out research designed to more clearly define and observe neuromesodermal progenitors, stem cells that contribute to spinal cord or skeletal muscle development. The overall goal of the lab is to advance an understanding of the vertebrate body plan via the zebrafish embryos and provide insights to understand stem cell biology and mechanisms of cancer metastasis.

This image captured by the Martin lab shows three different time points of a developing zebrafish to demonstrate how differentiated neurons and muscle expand as the embryos grow. The image shows the zebrafish reporter transgenes that label skeletal muscle (magenta color) and neurons (green color). Image from Benjamin martin

Martin and colleagues observe zebrafish to demonstrate how differentiated neurons and muscle expand as embryos grow. Neuromesodermal progenitors exist in all vertebrate embryos, so zebrafish are used as a common model to these cells’ development to better define how the embryonic body plan is formed and how spinal cord and skeletal muscle are induced from this population.

Martin’s NIGMS grant is called the Maximizing Investigators’ Research Award (MIRA), under the category of supporting established scientific investigators. This distinction recognizes the importance of the lab’s research, and reinforces their efforts to reach a breakthrough in this area of cell biology.

NIGMS supports fundamental studies that shed light on biological processes and catalyze advancements in the diagnosis, treatment and prevention of diseases. It also leads efforts to train the next generation of scientists, promote diversity in the workforce, and expand research capacity nationwide.

 

 

From left, Dr. Richard Rugen, Chairman, WMHO; Gloria Rocchio, President, WMHO; Chris Richey, Trustee, WMHO; Dr. Taylor Evans, Stony Brook University School of Marine and Atmospheric Sciences; Kathleen Mich, Trustee, WMHO; Deborah Boudreau, Education Director, WMHO; Charles Napoli, Trustee, WMHO. In attendance virtually: Jamie Parker, The Fullwood Foundation; Nicole Sarno, Business Manager Director, Business Banking, Webster Bank; Jon Dilley, President, Mill River Wetland Committee. Not pictured: The Frey Family Foundation. Photo from WMHO

The Ward Melville Heritage Organization (WMHO) hosted its third Long  Island Sound Connections Summit last week. This virtual, hands-on collaborative learning program connects  students across Long Island Sound and allows them to conduct their own research to better understand the water  systems in their environment.  

Long Island Sound Connections is the first program to connect both shores with students from New York and  Connecticut — with virtual class check-ins, “summits” where students present their findings, an ongoing collection of  data, and an analysis on that information. The Long Island Sound Connections program was designed to help  students learn about the Long Island Sound and to inspire them to become ‘citizen scientists’ and protect their  environment. The program is offered via distance learning from the WMHO’s Erwin J. Ernst Marine Conservation  Center (EMCC), where students have front row seats to one of the most pristine natural resources in New York  State.  

Dr. Taylor Evans and WMHO Education Director Deborah Boudreau sharing information with classes about different species (such as horse shoe crabs) that have survived in the Long Island Sound, some for over 445 million years. Photo from WMHO.

WMHO collaborated with Stony Brook University’s Ecology and Evolution Distinguished Professor Jeffrey  Levinton, and Dr. Taylor Evans of Stony Brook University’s School of Marine and Atmospheric Sciences to  develop a system of data collection parameters for monitoring and analyzing West Meadow Creek’s water quality  and species counts. 

Professor Levinton and Dr. Evans will continue to support WMHO in developing this  multipronged project that seeks to educate the public by providing data representing the creek’s health over time to  the public and researchers. They will also assist participating classes to in continuing to learn about the Long Island  Sound environment on an ongoing basis.  

The third “summit” of classes in this program was between Ms. Michelle Miller and Ms. Doreen Barry’s 6th grade  Science class from Selden Middle School and Ms. Jess Castoro’s 6th grade Science class from Achievement First  Bridgeport Academy Middle School, who worked in collaboration with Mill River Wetland Committee. 

The 2023  “summit” participants have been researching the Sound for six months, and with assistance from professionals in the  field, have learned the environmental impact of industrialization, recent achievements on mitigating the effects, and  how to utilize their data in the future by monitoring the Sound. 

Each class created specialized newscasts to showcase  their findings on the relationships between water quality, animal and plant species, and even with human impact. In  this cross sectional study of the Sound, students compared and contrasted their two environments (suburban and  urban) and presented it to their partner class. 

In addition, the study is longitudinal and seeks to track changes over  time. Data will be added into the WMHOs software to create a data map and timeline to assist environmental  researchers of all ages to understand and appreciate similarities and differences across the Long Island Sound.  

With grants provided by the Fullwood Foundation, the Frey Family Foundation and Webster Bank, this program  was offered to participating classes free of charge. All costs associated with the program were sponsored by these  organizations.  

For more information about the WMHO, on the Long Island Sound Connection program, other historic,  environmental and scientific programs that the WMHO offers, please call 631-751-2244 or visit wmho.org. 

Ali Khosronejad in front of the Santa Maria Cathedral, which is considered the first modern cathedral in Madrid.

By Daniel Dunaief

An approaching weather front brings heavy rains and a storm surge, threatening to inundate homes and businesses with dangerous water and potentially undermining critical infrastructure like bridges.

Once officials figure out the amount of water that will affect an area, they can either send out inspectors to survey the exact damage or they can use models that take time to process and analyze the likely damage.

Ali Khosronejad

Ali Khosronejad, Associate Professor in the Department of Civil Engineering at Stony Brook University, hopes to use artificial intelligence to change that.

Khosronejad recently received $550,000 from the National Science Foundation (NSF) for four years to create a high-fidelity model using artificial intelligence that will predict the flood impact on infrastructure.

The funds, which will be available starting on June 20, will support two PhD students who will work to provide an artificial intelligence-based program that can work on a single laptop at a “fraction of the cost of more advanced modeling approaches,” Khosronejad said during an interview in Madrid, Spain, where he is on sabbatical leave under a Fulbright U.S Senior Scholar Award. He is doing his Fulbright research at Universidad Carlos III de Madrid.

Stony Brook University will also provide some funding for these students, which will help defray the cost of expenses related to traveling and attending conferences and publishing papers.

In the past, Stony Brook has been “quite generous when it comes to supporting graduate students working on federally funded projects,” Khosronejad explained and he hopes that continues with this research.

Khosronejad and his students will work with about 50 different flooding and terrain scenarios, which will cover about 95 percent of extreme flooding. These 50 possibilities will cover a range of waterways, infrastructure, topography, and coastal areas. The researchers will feed data into their high fidelity supercomputing cluster simulations to train artificial intelligence to assess the likely damage from a flood.

As they build the model, Khosronejad explained that they will collect data from floods, feed them into the computer and test how well the computer predicts the kind of flooding that has can cause damage or threaten the stability of structures like bridges. Over the next four years, the team will collect data from the Departments of Transportation in California, Minnesota and New York.

Nearly six years ago, his team attempted to use algorithms available in ChatGPT for some of his AI development. Those algorithms, however, didn’t predict flood flow prediction. He tried to develop new algorithms based on convolutional neural networks. Working with CNN, he attempted to improve its capabilities by including some physics-based constraints.

“We are very enthusiastic about this,” Khosronejad said. “We do think that this opportunity can help us to open up the use of AI for other applications in fluid mechanics” in fields such as renewable energy, contaminant transport predictions in urban areas and biological flow predictions, among others.

Planners working with groups such as the California Department of Transportation could use such a program to emphasize which infrastructure might be endangered.

This analysis could highlight effective mitigation strategies. Artificial intelligence can “provide [planners and strategists] with a tool that is not that expensive, can run on a single laptop, can reproduce lots of scenarios with flooding, to figure out which infrastructure is really in danger,” Khosronejad said.

Specifically, this tool could evaluate the impact of extreme floods on bridge foundations. Floods can remove soil from around the foundation of a bridge, which can cause it to collapse. Civil engineers can strengthen bridge foundations and mitigate the effect of future floods by using riprap, which is a layer of large stones.

This kind of program can reduce the reliance on surveying after a flood, which is expensive and sometimes “logistically impossible and unsafe” to monitor areas like the foundations of bridges, Khosronejad said. He plans to build into the AI program an awareness of the changing climate, so that predictions using it in three or five years can provide an accurate reflection of future conditions.

“Floods are getting more and more extreme” he said. “We realize that floods we feed into the program during training will be different” from the ones that will cause damage in subsequent years.

Floods that had a return period of every 100 years are now happening much more frequently. In one or two decades, such a flood might occur every 10 years.

Adding updated data can allow practitioners to make adjustments to the AI program a decade down the road, he suggested. He and his team will add data every year, which will create a more versatile model.

What it can’t do

While the AI programs will predict the damage to infrastructure from floods, they will not address storm or flood predictions.

“Those are different models, based on the movement of clouds” and other variables, Khosronejad said. “This doesn’t do that: if you give the program a range of flood magnitudes, it will tell you what will happen.”

High fidelity models currently exist that can do what Khosronejad is proposing, although those models require hundreds of CPUs to run for five months. Khosronejad has developed his own in house high fidelity model that is capable of making similar predictions. He has tested it to examine various infrastructures and used it to study various flooding events. These models are expensive, which is why he’s trying to replace them with AI to reduce the cost while maintaining fidelity.

AI, on the other hand, can run on a single CPU and may be able to provide the same result, which will allow people to plan ahead before it happens. The NSF approved the single principal investigator concept two months ago.

Khosronejad has worked with Fotis Sotiropoulos, former Dean of the College of Engineering and Applied Sciences at Stony Brook and current Provost at Virginia Commonwealth University, on this and other projects.

The two have bi-weekly discussions over the weekend to discuss various projects.

Sotiropoulos was “very happy” when Khosronejad told him he received the funds. Although he’s not a part of the project, Sotiropoulos will “provide inputs.”

Sotiropoulos has “deep insights” into fluid mechanics. “When you have him on your side, it always pays off,” Khosronejad said.

Dr. Justice Achonu. Photo by Jeanne Neville/ Stony Brook Medicine

Justice Achonu, MD, an orthopaedic surgery resident at Stony Brook Medicine, is one of four orthopaedic surgeons in the U.S. to be selected for the American Board of Orthopaedic Surgery’s (ABOS) Resident Advisory Panel. Responsible for providing insight into the resident experience, the panel collaborates with multiple other committees within the ABOS to support the interests of residents throughout the country. His two-year term on the panel begins July 1, 2023.

According to the ABOS, each applicant to the panel is reviewed by at least two ABOS Board members who are all accomplished leaders in their field. Applicants practice in all regions of the country. Dr. Achonu’s panel cohort is the third ever selected by the ABOS. Every year, the panel is tasked with identifying and completing a project that will benefit orthopaedic residents across more than 200 accredited training programs nationwide.

Panelists are encouraged to provide the ABOS with recommendations, several of which have been adopted by the Board, including an official Residency to Retirement Roadmap.

Dr. Achonu received a B.S. in neuroscience from the University of Pittsburgh in 2015 and graduated from the Renaissance School of Medicine at Stony Brook University in 2020. He resides in Holbrook.

Stony Brook’s Department of Orthopaedics provides full-service patient care and sub-specialty resident and faculty training in all areas of Orthopaedics. The department includes a comprehensive Orthopaedic Research Program featuring clinical and laboratory facilities and resources for investigation of molecular, biologic, and biomechanical research topics.