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Daniel Dunaief

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Above, a humpback whale breaks the surface of the water. Photo from Eleanor Heywood/National Marine Fisheries Service permit no. 21889

By Daniel Dunaief

The waters off the South Shore of Long Island have become a magnet, attracting everything from shipping vessels, recreational boaters, fishermen and women, potential future wind farms, and humpback whales.

While the commercial component of that activity can contribute to the local economy, the whale traffic has drawn the attention of scientists and conservationists. Whales don’t abide by the nautical rules that guide ships through channels and direct traffic along the New York Bight, a region from the southern shore of New Jersey to the east end of Long Island.

Left, Julia Stepanuk with a drone controller. Photo by Kim Lato

Julia Stepanuk, a PhD student at Stony Brook University in the laboratory of Lesley Thorne, Assistant Professor in the School of Marine and Atmospheric Sciences, is focusing her research efforts on monitoring the humpback whale’s use of this habitat.

“This can help us understand how we focus our energy for monitoring and conservation,” she explained in an email. If the whales are traveling, it helps to know where to minimize human impact.

Ultimately, the work Stepanuk, who also earned her Master’s degree at Stony Brook in 2017, does provides ecological context for how whales use the waters around New York and how old the whales are that are feeding in this area.

In her dissertation, Stepanuk is “looking at the biological and ecological drivers, the motivators of where the whales are, when they’re there, specifically, from the lens of how human activity might be putting whales at risk of injury or mortality.”

Each summer, whales typically arrive in the area around May and stay through the end of October.

When she ventures out on the water, Stepanuk uses drones to gather information about a whale’s length and width, which indicates the approximate age and health of each individual. Since 2018, she has been gathering information to monitor activity in the area to track it over time.

With the research and data collected, she hopes to help understand the ecology of these whales, which will inform future policy decisions to manage risk.

Stepanuk’s humpback whale work is part of a 10-year monitoring study funded by the New York State Department of Environmental Conservation, which includes four principal investigators at the School of Marine and Atmospheric Sciences. The study looks at carbonate chemistry, physical oceanography, fish distribution, and top predator abundance, distribution and body condition, Thorne explained.

“My lab is leading the seabird and marine mammal aspect of this project,” said Thorne.

The grid over the whale demonstrates how members of Thorne’s lab measure the size of the whale from drone images. Photo by Julia Stepanuk

By documenting the ecological ranges of whales of different ages, Stepanuk may provide insight into the age groups that are most at risk. Many of the humpback whales that travel closer to shore are juveniles, measuring below about 38 feet.

Stepanuk has seen many of these whales, either directly or from the drones she flies overhead. She has also gathered information from events in which whales die after boats hit them.

Mortality events off the east coast have been increasing since 2016 as numerous whales have washed up along the coast. About half of the humpbacks in these mortality events have evidence of human interaction, either ship strike or entanglement, Stepanuk said.

“There have been many more strandings than usual of humpback whales along the east coast” in the last five years, Thorne explained.

Humpback whales likely have appeared in larger numbers in New York waterways due both to the return of menhaden in nearshore waters, which comes from changes in the management of this fish stock and from environmental management more broadly, and from an overall increase in the humpback whale population after 40 years of protection, Thorne suggested.

Ultimately, Stepanuk said she hopes to use the scientific inquiry she pursued during her PhD to help “bridge the gap between academic, policymakers, conservationists, interested parties and the public.” 

A part of Stony Brook’s STRIDE program, for science training and research to inform decisions, Stepanuk received training in science communication, how to present data in a visual and accessible way, and how to provide science-based information to policymakers.

For Thorne, this study and the analysis of the vessel strikes on humpback whales could be helpful for understanding similar dynamics with other cetaceans.

Julia Stepanuk and Matt Fuirst, a previous master’s student in Lesley Thorne’s lab, release a drone. Photo by Rachel Herman

“Understanding links between large whales and vessel traffic could provide important information for other studies, and could provide methods that would be useful for studies of other species,” said Thorne.

Stepanuk offers some basic advice for people on a boat in the New York Bight and elsewhere. She suggests driving more slowly if visibility is limited, as people would in a car in foggy weather. She also urges people to pay close attention to the water. Ripples near the surface could indicate a school of fish, which might attract whales.

“Slow down if you see dolphins, big fish schools and ripples,” she said. “There’s always a chance there could be a whale.”

If people see a whale, they shouldn’t turn off their engines: they should keep the engine in neutral and not approach the whale head on or cut them off. For most species, people can’t get closer than 300 feet. For North Atlantic right whales, which are critically endangered, the distance is 1,500 feet.

She suggests people “know the cues” and remember that whales are eagerly feeding.

Stepanuk has been close enough to these marine mammals to smell their pungent, oily fish breath and, when they exhale, to receive a residue of oil around her camera lens or sunglasses. She can “loosely get an idea of what they’re feeding on in terms of how bad their breath is.”

When she was younger, Stepanuk, who saw her first whale at the age of eight, worked on a whale watching boat for six years in the Gulf of Maine. An adult female would sometimes leave her calf near the whale watching boat while she went off to hunt for food. The calf stayed near the boat for about 45 minutes. When the mother returned, she’d slap the water and the calf would race to her side.

“Experiences like that stuck with me and keep me excited about the work we do,” Stepanuk said.

Video: Humpback whale lunge feeding off the south shore of Long Island

 

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Clinical Assistant Professor of Medicine at Stony Brook Medicine, Dr. Miguel Saldivar, wants residents to make vaccine decisions based on scientific information, rather than Internet speculation. Saldivar, who joined Stony Brook just months before the pandemic hit Long Island, sees improvement in the overall infection numbers, which have declined in recent weeks to about two to three percent from closer to five to six percent. In a wide-ranging interview (which can be seen online at tbrnewsmedia.com), Saldivar answered a host of questions.

TBR: Do you have any concerns about the number or percentage of people who are not lining up for vaccination?

Saldivar: In general, what we are more concerned about is the amount of misinformation that is out there. If you go on social media — if you go just on the internet, period — there’s a lot of people who are spreading lot of information that is really frankly inaccurate.

TBR: What are Stony Brook and others trying to do to counter misinformation?

Saldivar: There are a number of things we hear fairly frequently, probably the more common one I personally have heard, because Pfizer and Moderna are based on mRNA technology, everybody hears the term RNA and is worried that it’s going to change my genetic code and turn me into a mutant or cause a disease down the line. The first thing to understand about that, the way both of those vaccines work, it’s a set of instructions being given to the body cells, the moment it’s been delivered, the mRNA dissolves. It has no way of getting into the deeper part of the cells to change your genetic code.

TBR: Black and brown communities have a distrust of the federal government after some well known problems regarding Tuskegee Experiment and other issues. Is there broader acceptance now compared with a month or two ago?

Saldivar: Statistically, if you compare how this disease has affected minority communities, the risk of a severe outcome, hospitalization intubation and death is almost universally higher among minority communities. That has a number of factors, not just the disease itself. It’s also the fact that within those communities, it is more frequent to find some of the risk factors, meaning diabetes, obesity, preexisting pulmonary disease so on and so forth … What I have been personally involved with is reaching out to the community, we have found a lot of community centers have been very ready and willing to engage in a conversation. We have found places of worship to be wonderful places to have that conversation

TBR: What does the data tell you about the pandemic?

Saldivar: The last numbers I heard from the meeting this morning were between two to three percent positivity. We’ve been there for a week. Before that, we were staying pretty stable at like five to six percent or thereabouts. It looks like finally, this may be the effect of the vaccine, the numbers are finally starting to little by little trend their way down. We’ve been cautiously optimistic. There seems to be a little bit of a light at the end of the tunnel.

TBR: You have a bachelor’s degree in classical guitar performance. How did you wind up in infectious disease?

Saldivar: Through the nonprofit circle, I landed a job with the medical center at UCLA. That’s where I met a very, very good friend and mentor. She was key to helping me shape the path. I feel incredibly lucky to be part of this profession.

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Photo by Pixabay

By Daniel Dunaief

Daniel Dunaief

I have two friends whose sons are contemplating important choices. The first son, Matt, is trying to decide where to attend college.

He has gained admission to two elite schools. He can’t go wrong, as his parents have told him repeatedly, with either choice. Making this decision in a normal year would be hard. In a pandemic year, it’s almost impossible.

Matt can’t stay over at each school for a weekend or even attend a few classes. He can’t get much of a feeling for the “vibe” of the school because he can’t go into most of the buildings, even with a mask and with his letter of admission.

He can compare the national rankings from U.S. News and World Report, check college guides, talk with his guidance counselor, chat with graduates from his high school who attend each school and stroll around each campus. 

He can’t, however, fully try on the school, the way he might a tailored suit. Masks cover the faces of most of the people at each school, which makes it impossible to search for smiles on the faces of his potential future classmates.

He recently found himself leaning toward school A. The same day, his father spoke with a friend of his whose daughter was attending school B.

His father showed a picture of his friend’s daughter to Matt. The friend’s attractive daughter caused Matt to rethink his tentative decision.

That brings me to my other friend’s son, Eric. In his mid-20s, Eric has been caught in the same social world that has limited the options for everyone else.

Eric has been dating a woman for over two years and is considering the future of the relationship. He is not sure whether it’s the appropriate time to consider living together or getting married.

Eric is incredibly attached to his girlfriend, who has been one of the few people he sees regularly in real life during the pandemic.

Eric is not sure how long this altered reality, in which he works from home, speaks with family and friends virtually most of the time, and sees his girlfriend during his limited social hours, will last. In the meantime, he’d like something in his life to move forward.

Matt and Eric are weighing their options. For Matt, the choice of college may well come down to the last picture of another student he sees before he pushes a button.

Choosing a college can, and likely should, involve more significant factors. Then again, both of the colleges line up so well that he is likely to have a similar experience, albeit with different people around him, at each school.

Eric’s decision, however, isn’t so interchangeable. It involves a leap of faith that those of us who are married have made that relies on our own criteria. We can consult family, friends, and counselors as we weigh the pros and cons, but, ultimately, the responsibility and opportunity rest with us.

Coming up with his own questions and his own scale to evaluate the relationship is challenging, particularly when everything seems somewhere between good and great right now. He can’t possibly know what life will look like in two, five, 10 or 20 years from now.

I don’t envy either Matt or Eric as they contemplate these decisions. I do, however, agree with Matt’s parents: he can’t go wrong. For Eric, the decision has more significant longer-term ramifications and likely reflects variables that are difficult to imagine, particularly amid the uncertainty of the present.

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From left, atmospheric scientists Andrew Vogelmann, Edward Luke, Fan Yang, and Pavlos Kollias explored the origins of secondary ice — and snow. Photo from BNL

By Daniel Dunaief

Clouds are as confounding, challenging and riveting to researchers as they are magnificent, inviting and mood setting for artists and film makers.

A team of researchers at Brookhaven National Laboratory and Stony Brook University recently solved one of the many mysteries hovering overhead.

Some specific types of clouds, called mixed-phase clouds, produce considerably more ice particles than expected. For those clouds, it is as if someone took an empty field, put down enough seeds for a thin covering of grass and returned months later to find a fully green field.

Ed Luke, Atmospheric Scientist in the Environmental Sciences Department at Brookhaven National Laboratory, Andy Vogelmann, Atmospheric Scientist and Technical Co-manager of the BNL Cloud Processes Group, Fan Yang, a scientist at BNL, and Pavlos Kollias, a professor at Stony Brook University and Atmospheric Scientist at BNL, recently published a study of those clouds in the journal Proceedings of the National Academy of Sciences.

“There are times when the research aircraft found far more ice particles in the clouds than can be explained by the number of ice nucleating particles,” Vogelmann wrote in an email. “Our paper examines two common mechanisms by which the concentrations of ice particles can substantially increase and, for the first time, provides observational evidence quantifying that one is more common” over a polar site.

With a collection of theoretical, modeling and data collecting fire power, the team amassed over six years worth of data from millimeter-wavelength Doppler radar at the Department of Energy’s Atmospheric Radiation Measurement facility in the town of Utqiagvik, which was previously called Barrow, in the state of Alaska.

The researchers developed software to sort through the particles in the clouds, grouping them by size and shape and matching them with the data from weather balloons that went up at the same time. They studied the number of secondary ice needles produced under various conditions.

The scientists took about 100 million data points and had to trim them down to find the right conditions. “We culled the data set by many dimensions to get the ones that are right to capture the process,” Luke explained.

The dataset required supercooled conditions, in which liquid droplets at sub-freezing temperatures came in contact with a solid particle, in this case ice, that initiated the freezing process.

Indeed, shattering ice particles become the nuclei for additional ice, becoming the equivalent of the venture capitalist’s hoped for investment that produces returns that build on themselves.

“When an ice particle hits one of those drizzle drops, it triggers freezing, which first forms a solid ice shell around the drop,” Yang explained in a press release. “Then, as the freezing moves inward, the pressure starts to build because water expands as it freezes. That pressure causes the drizzle drop to shatter, generating more ice particles.”

Luke described Yang as the “theory wizard on the ice processes and nucleation” and appreciated the opportunity to solve the mechanism involved in this challenging problem.

“It’s like doing detective work,” said Luke. The pictures were general in the beginning and became more detailed as the group focused and continued to test them.

Cloud processes are the biggest cause for differences in future predictions of climate models, Vogelmann explained. After clouds release their precipitation, they can dissipate. Without clouds, the sunlight reaches the surface, where it is absorbed, particularly in darker surfaces like the ocean. This absorption causes surface heating that can affect the local environment.

Energy obtained from microscopic or submicroscopic processes, such as the absorption of sunlight at the molecular level or the energy released or removed through the phase changes of water during condensation, evaporation or freezing, drive the climate.

“While something at microscales (or less) might not sound important, they ultimately power the heat engine that drives our climate,” said Vogelmann.

To gather and analyze data, the group had to modify some processes to measure particles of the size that were relevant to their hypothesis and, ultimately, to the process.

“We had to overcome a very serious limitation of radar,” Kollias said. They “started developing a new measurement strategy.”

When the cost of collecting large amounts of data came down, this study, which involved collecting 500 times more data points than previous, conventional measures, became feasible.

Luke “came up with a very bright, interesting technique of how to quantitatively figure out, not if these particles are there or how often, but how many,” Kollias said.

Luke found a way to separate noise from signal and come up with aggregated statistics.

Kollias said everyone in the group played a role at different times. He and Luke worked on measuring the microphysical properties of clouds and snow. Yang, who joined over two and a half years ago and was most recently a post doctoral research associate, provided a talented theoretical underpinning, while Vogelmann helped refine the study and methodology and helped write up the ideas.

Kollias said the process begins with a liquid at temperatures somewhere between 0 and 10 degrees below zero Celsius. As soon as that liquid touches ice, it explodes, making it a hundred times more efficient at removing liquid from the cloud.

Kollias described the work as a “breakthrough” because it provided real measurements, which they can use to test their hypotheses.

In the next few months, Kollias said the group would make sure the climate modeling community sees this work.

Luke was hoping the collaboration would lead to an equation that provided the volume of secondary ice particles based on specific parameters, like temperature and humidity.

From the data they collected, “you can almost see the equation,” Luke said. “We wanted to publish the equation. That’s on the to-do list. If we had such an equation, a modeler could plug that right in.”

Even though they don’t yet have an equation, Luke said that explicit descriptions of the dataset, in the form of probability density functions, are of value to the modeling community.

The group would like to see how broadly this phenomenon occurs throughout the world. According to Kollias, this work is the “first step” and the team is working on expanding the technique to at least three more sites.

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County Executive Steve Bellone, center, speaks at the April 20 press conference. Police Chief Stuart Cameron, left, and Suffolk County Police Department Commissioner Geraldine Hart were also in attendance. Photo from Suffolk County

In response to the 50 mass shootings that have occurred throughout the country in the last month, the Suffolk County Police Department is enabling supermarkets and big box retailers to connect to a camera system set up to provide the police with video access to schools.

Using a resource called SHARE, which stands for Sharing to Help Access Remote Entry, businesses can plug their closed-circuit systems to the police department’s Real-Time Crime Center. The connection, which will have no cost for businesses, is designed to provide critical, up-to-the-minute information to police in the event of an active shooter.

“We know from previous active shooter events that seconds matter,” said SCPD Commissioner Geraldine Hart at a press conference on Tuesday announcing the initiative at the Suffolk County Police Department Headquarters in Yaphank. “Seconds can save lives.”

The ability to see inside a building would give the police intelligence that they could pass along to first responding officers, providing a description and updated location of a person or people who had weapons.

“One of the things that keeps me up as county executive is the idea that we could have one of these shootings here in our county in Long Island,” said County Executive Steve Bellone (D) at the press conference. The SCPD, which has been “at the forefront of efforts to address the possibility of mass shootings is, once again, announcing a continuation of these efforts.”

The collaboration between these stores and the police could go a step further, giving the police access to electronic controls that would allow them to open electronic doors remotely for emergency responders, helping them get to victims sooner and giving them a chance to maneuver around a perpetrator.

“We value partnerships with the community,” Hart said. “The goal is to keep people safe.”

Since 2016, the Suffolk County Police Department has done 420 active shooter presentations. On May 2, the SCPD will hold an active shooter drill at a King Kullen in Middle Island, which is the first time the police will conduct such an exercise in a supermarket.

The SCPD has also held 67 stop the bleed training classes for residents, which teaches people to treat wounds and practice applying tourniquets.

The SCPD will have the “ability to see inside those stores if, God forbid, an active shooter situation arises,” Bellone said.

In 2019, Bellone, Hart and Police Chief Stuart Cameron announced the SHARE program at West Babylon high school, which gave police the ability to tap into closed circuit TVs at area schools.

“This is one of the best things we can do to help save lives in an active shooter situation,” Bellone said. “We’re going to do everything we can on a local level to deal with the possibility of mass shootings.”

Bellone called the number of mass shootings in the country, which exceeds one per day, “insane,” and urged Congress to adopt “common-sense gun safety measures.” Rather than wait for a provision that might solve or prevent all the problems, Bellone urged Congress to take action immediately to reduce the risk of events that rob families and the community of loved ones amid senseless violence.

The police would only access cameras in the event of an emergency or a potentially dangerous situation.

Last month, the Village of Port Jefferson — which has had cameras hooked up to the Suffolk County Real-Time Crime Center for over two years — was able to help police find and arrest Joseph Garcia of Port Jefferson Station for the alleged shooting of David Bliss Jr. on Main Street. 

“We were proud to partner with the Suffolk County Real-Time Crime Center a few years ago to take advantage of this program that keeps our streets safe,” said Mayor Margot Garant. “It’s proven to create a quick response and help reduce crime in our village.”

Businesses and Suffolk County residents can gather more information at: SCPDShield.org.

Additional reporting by Julianne Mosher

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

About 16 years ago, I stood on the warning track and held my then one-year old son high in my arms above the blue, outfield fence in right center field of the old Yankee Stadium. We asked him to extend his glove as if he had leapt in the air to catch a home run.

Now, as he prepares to graduate from high school, my wife and I are pondering the end of an era filled with the numerous triumphs and challenges of youth sports.

In the last few weeks, while we have awaited the time outs, batting glove adjustments, pauses to look for signs from the catcher, and warm up tosses by each pitcher, we have been replaying our own montage from his years on a baseball field.

A few years after his Yankee Stadium debut, our son donned a baggy uniform that hung from his slight four-year old frame, standing with his left arm out, hoping to catch a ball I tossed with a slight arc toward him.

As the years advanced, his skill set and intensity for the game grew more rapidly than the developmental rules of the sport.

Station-to-station baseball was an abomination for him. When he was six, he caught a ball at shortstop, tagged the runner jogging from second and stepped on third for, what he considered, an unassisted triple play. He tossed the ball to the mound and jogged off the field, only to hear that everyone hadn’t batted so he had to stay on the field. I can still see the disappointed look on his face as all the runners moved to the next base.

Every moment wasn’t athletic heaven. He struggled to find the strike zone when he was pitching, swung and missed at pitches he knew he could hit and suffered through the inconsistent coaching and advice of everyone from his father to the parents of his teammates to semi-professionals eager to give back to the community.

Despite playing a game of failure, he continued to venture to fields close and far for another opportunity to compete, get some exercise and join teammates who have become long-time friends.

He learned how to pick up his friends after their moment in the spotlight didn’t end the way they wanted.

He took us to places way off a tour guide’s map of the eastern United States, as we drove from single traffic-light towns, with their one gas station and one diner, all the way up to Cooperstown.

We paced along frigid sidelines, hoping darkness or snow would grant us a reprieve from frozen bleachers and numb toes. We drove on roads in which the car thermometer read 113 degrees.

When he was old enough, he stood on a 90-foot diamond, looking from third to first as if he needed binoculars to see his teammate and a strong wind to help his throw reach the target.

As he got taller and stronger, the distance became more manageable. 

As parents, we made our share of errors on the sidelines and in the stands. While we told him it was the effort that mattered, not the result, he could see the joy in our faces after a win and the slumped shoulders after a tough loss.

While he’ll undoubtedly play other games down the road, that road won’t be as close as the ones we’ve traveled together. 

In a recent game, our son raced back and caught a ball against the wall, in a place on the field similar to the one where he extended his tiny glove at Yankee Stadium. We have shared such a long and inspired journey between those two mirrored moments.

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Dr. Kenneth Kaushansky
Stony Brook, NY; Stony Brook University: School of Medicine 2018 Convocation Photo by Arthur Fredericks
Stony Brook, NY; Stony Brook University Medical Center: The White Coat Ceremony in the Student Activities Center. (8/14/2016)
Stony Brook, NY; Stony Brook University MART & Children's Hospital Pavilion: MART ribbon cutting, November 1, 2018. Left to right: New York State Assemblyman Steve Englebright; SUNY Trustee and Stony Brook Foundation board member Cary Staller; Stony Brook University President Samuel L. Stanley Jr., MD; New York State Senator Kenneth P. LaValle; SUNY Chancellor Kristina Johnson; Jim and Marilyn Simons; New York State Senate Majority Leader John Flanagan; Kevin Law, President of the Long Island Association and Chair of the Stony Brook Council; Kenneth Kaushansky, MD, Senior Vice President for Health Sciences and Dean of the School of Medicine; Director of the Stony Brook University Cancer Center Yusuf Hannun, MD; representing Governor Andrew Cuomo, Marta Santiago-Jones, Consultant Nurse Hospital Services Administrator at the New York State Department of Health.
Stony Brook, NY; Stony Brook University Medical Center: Donors David and Cynthia Lippe and Dean, School of Medicine and Senior Vice President of Health Sciences Ken Kaushansky outside of the garden area of the MART/Hospital Pavilion
Stony Brook, NY; Stony Brook University Hospital: Stony Brook Medicine rolled out new Mobile Stroke Units on March 18, 2019, to treat people who are having a stroke. Left to right: Kimberly Noel, MD, Director, Telehealth, Stony Brook Medicine, Michael Guido III, MD, Neurologist, Director, Stony Brook Neurology Stroke Program, Ken Kaushansky, MD, Dean, Renaissance School of Medicine at Stony Brook University, David Fiorella, MD, PhD, Neurointerventionalist, Director, Stony Brook Cerebrovascular Center, Trevor Marshall, MD and Eric Niegelberg, Associate Director, Operations, Emergency Services and Internal Medicine
Stony Brook, NY; Stony Brook University: Chancellor Jim Malatras and Stony Brook University President McInnis Announce Partnership with SUNY Upstate Medical University to Launch Pooled Surveillance Testing for COVID-19. Stony Brook to Test 5200 Students Each Week. Testing Expansion Follows FDA Approval of Groundbreaking Saliva Swab Test Developed at Upstate Medical University

By Daniel Dunaief

Like so many others, Ken Kaushansky had to alter his plans when the pandemic hit last March. Kaushansky had expected to retire after over 10 years as Dean of the Renaissance School of Medicine at Stony Brook University and the Senior Vice President of Health Sciences, but the public health needs of the moment, particularly on Long Island which became an early epicenter for the disease, demanded his attention.

“Now that COVID hopefully is coming under control, it seems more logical” to retire this year, Kaushansky said in a wide-ranging interview about the pandemic, his career, and the medical school. In January, he stepped down as the dean, while he plans to retire as Senior Vice President of Health Sciences at the end of June.

Views on the Pandemic

Dr. Kenneth Kaushansky

Looking back at the immediate challenges in the first few months, Kaushansky said SBU did “extremely well” in caring for patients who were battling COVID-19 and was gratified by the school’s effort to catalog and understand the disease. “I’m very proud that we’ve been able to study this infection on all sorts of levels and make a real impact that has helped others,” he said.

Early on, as the medical team at Stony Brook met, Kaushansky urged the hospital to study COVID “to the hilt” and to “extract every little bit of data we can. We must keep all that data on all these patients.”

Indeed, Stony Brook has created a database that continues to grow of close to 10,000 people, which includes 3,000 inpatients, 4,000 who weren’t sick enough for hospital admission, and around 3,000 who thought they had the disease, but had other illnesses. “We’ve learned a ton from that, and it’s not just learning for learning’s sake,” Kaushansky said. The demand for the use of the database is so high that a steering committee is reviewing proposals. 

Stony Brook had heard from doctors in Italy that COVID patients were having problems with blood clotting. This symptom was particularly meaningful to Kaushansky, who is a hematologist.

SBU studied the symptoms and “did a trial to see if aggressive anticoagulants would produce better outcomes” than the standard of care at the time, he said. “Our [intensive care unit] patients who were on this more aggressive anticoagulation protocols had half the mortality” of other patients, so the hospital “quickly adopted all of our care” to the more effective approach.

The hospital preemptively used biomarkers to determine who should and should not get aggressive anticoagulation. A subsequent study using the database confirmed the school’s early conclusion. Stony Brook published over 150 papers on the structure of the virus, clinical observations, sociological interventions, and a host of other areas, according to Kaushansky.

Carol Gomes, Chief Executive Officer of Stony Brook University Hospital, appreciated Kaushansky’s hands on approach, which included participating in daily calls as part of the hospital incident command center.

She likened Kaushansky to an orchestra leader, coordinating the research and patient care, making sure there was “no duplication of effort.”

Kaushansky believes federal research funding agencies and policy makers will recognize the importance of gathering information about this pandemic to treat future patients who might battle against variants and to provide a playbook for other health threats. “We really do need to prepare for the next one” as this is the third and deadliest of three coronaviruses, including SARS and MERS, he said.

Vaccines

As for vaccines, Kaushansky said Stony Brook was making it as “convenient as we can” to get a vaccination for health care workers. As of about a month ago, over 80 percent of Stony Brook’s health care workers had been vaccinated.

The black and brown communities have benefited from seeing leaders and role models receiving the vaccine. “This is beginning to erode the mistrust,” said Kaushansky, which developed as a byproduct of the infamous Tuskegee experiment, in which black men with syphilis did not receive penicillin despite its availability as an effective treatment.

Kaushansky added that a concern he’s heard from a range of people is that the vaccine was developed too quickly and that the side effects could be problematic. He cited the simultaneous steps doctors, pharmaceutical companies and others took to accelerate a process that didn’t leave out any of those steps.

Kaushansky participates in a group email interaction with prominent European hematologists. Looking at the data for the Astrazeneca vaccine, these researchers have calculated that anywhere from one in 500,000 to one in a million have developed blood clots.

“Not a single person on this mass email believes that they should stop the Astrazeneca vaccines for that kind of incident,” he said.

What He Helped Build

Kaushansky has been such a supporter of expanding the facilities and expertise at Stony Brook that he said the campus developed a joke about him.

“What’s the dean’s favorite bird?” he asked. “A crane.”

Fixtures on the campus for years, those cranes — the construction vehicles, not the birds — have changed the university, adding new teaching, research and clinical space on the campus.

That includes the Medical and Research Translational building and Bed Tower, which started in 2013 and opened in 2018, and the Hospital Pavilion, which has an additional 150 beds. Those extra beds were especially important a year after the pavilion opened, providing much-needed space for patients battling against COVID.

Gomes appreciated what Kaushansky built physically, as well as the interactive collaborations among different parts of the university. “An active collaboration and communication between researchers, clinicians and academics is a very different model” from the typical separation among those groups, she said. The work “reaped great rewards on the front end with the ability to collaborate to bring new ideas forward.”

As for the type of care patients received at Stony Brook, Kaushansky recalled a discussion over six years ago about central line infections. The data came from a 12 month period, starting six months prior to the meeting and going back to 18 months earlier.

“How are we going to know why all those central line infections occurred by looking at data” from so much earlier, Kaushansky recalled asking. The hospital created real time dashboards, which is an effort that has “paid huge dividends.”

Kaushansky cited the hospitals’ top 100 health grade for three years running. These grades assess whether patients survive a procedure, have complications or need to be readmitted.

“You’re going to get the best care possible when you come to Stony Brook,” Kaushansky said, as the top 100 rating puts Stony Brook in the top 2 percent of hospitals in the country.

Apart from the buildings Kaushansky helped develop, he’s proud of the program he helped build for medical school students.

About six years ago, Stony Brook instituted a new medical school curriculum that had translational pillars. The school starts students in the clinical realm considerably earlier than the classic program that involves two years of basic studies, followed by two years of clinical work.

Stony Brook provides basic science, followed by earlier exposure to the clinic, with a return to basic science after that

“It’s much more effective if you teach the basic science after the student has witnessed the clinical manifestation,” Kaushansky said. These approaches are part of translational pillars in areas such as cancer, physiology and infectious diseases.

As for what he’ll miss after he leaves, Kaushansky particularly appreciated the opportunity to speak with students. He used to hold a monthly breakfast with four or five students, where he learned about each student, their career goals and their medical journey.

A former colleague at the University of California at San Diego, John Carethers, who is the Chair in the Department of Internal Medicine at the University of Michigan, visited Kaushansky as a speaker twice at Stony Brook.

Carethers saw “first hand the wonderful impact he had on students — knowing their names, and providing wonderful advice,” he wrote in an email.

The Next Steps

For a decade, Kaushansky said he wanted to create a course about the future of medicine.

“There are a lot of great innovations in medicine that are fascinating from a scientific and clinical perspective,” Kaushansky said.

He will work on a course for use at Stony Brook in the main campus, the medical campus and for whichever program is interested in sharing these innovative medical and scientific steps in medicine.

He also plans to continue to be the lead editor of the primary textbook in hematology, called Williams Hematology. The textbook has gone through 10 editions.

Kaushansky and his wife Lauren, who is an author and education professor at Stony Brook, aren’t likely to remain on Long Island in the longer term. The couple has a getaway home in Santa Fe and may go there.

Kaushansky’s hobbies include wood working and running. He made a sofa when he was an undergraduate at UCLA, while his second significant work was a 16-foot sailboat he made as a second-year resident. He estimates he has made 40 pieces of furniture.

Kaushansky runs four miles a day four to six times a week. In 1990, he ran the Seattle Marathon which was the Goodwill Games Marathon, finishing in a time of around three hours and twenty-five minutes.

Culturally, Kaushansky hopes the school continues to embrace his focus on generosity.

“You’ve got to be generous with your time,” he said. 

“No more can you say that you are too busy to talk. You have to be of a personality that takes pride and that gets the endorphins going from seeing the people you have brought, the people you have entrusted in leadership roles, succeed.”

Photos courtesy of Stony Brook University

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F. William Studier

By Daniel Dunaief

People around the world are lining up, and in some cases traveling great distances, to get vaccinations to COVID-19 that will provide them with immune protection from the virus.

An important step in the vaccinations from Pfizer-BioNTech and Moderna, the two messenger RNA vaccinations, originated with basic research at Brookhaven National Laboratory in the 1980’s, close to 40 years before the pandemic infected millions and killed close to three million people.

At the national laboratory, scientists including F. William Studier, Alan Rosenberg, and the late John Dunn, among others, worked on another virus, called the T7 bacteriophage, which infects bacteria. T7 effectively corrupts a bacteria’s genetic machinery, turning it into a machine that makes copies of itself.

From top graphic, the T7 virus uses RNA polymerase and a promoter to start a process inside a bacteria that makes copies of itself; researchers use copies of the promoter and the polymerase to insert genes that code for a specific protein; the mRNAs are injected into our arms where human ribosomes make COVID-19 spike proteins. Those spike proteins train the attack dog cells of our immune system to recognize the virus if it attempts to invade.

Back in the 1980’s, Studier and Dunn in BNL’s Biology Department were trying to do something no one else had accomplished: they wanted to clone the T7 RNA polymerase. The use of this genetic region, along with a promoter that starts the process of transcription, enabled scientists to mimic the effect of the virus, directing a cell to make copies of genetic sequences or proteins.

The BNL researchers perfected that process amid a time when numerous labs were trying to accomplish the same molecular biological feat.

“Although there were several labs that were trying to clone the T7 RNA polymerase, we understood what made its cloning difficult,” said Alan Rosenberg, who retired as a senior scientist at BNL in 1996. The patented technology “became the general tool that molecular biologists use to produce the RNA and proteins they want to study.”

The scientists who worked on the process, as well as researchers who currently work at BNL, are pleased that this type of effort, which involves a desire for general knowledge and understanding before policy makers and funders are aware of all the implications and benefits, led to such life-saving vaccinations.

“This is an excellent example of the value of basic science in that the practical applications were quite unanticipated,” John Shanklin, Chair of BNL’s Biology Department, wrote in an email. 

“The goal of the work Studier and his team did was to understand fundamental biological principles using a virus that infects bacteria. Once discovered, those principles led to a transformation of how biochemists and biomedical researchers around the world produce and analyze proteins in addition to providing a foundational technology that allowed the rapid development of mRNA vaccines,” he wrote.

Shanklin described Studier, who recruited him to join BNL 30 years ago from Michigan, as a mentor to numerous researchers, including himself. Shanklin credits Studier for helping him develop his career and is pleased that Studier is getting credit for this seminal work.

“I am tremendously proud that the basic research done in the Biology Department has been instrumental in accelerating the production of a vaccine with the potential to save millions of lives worldwide,” Shanklin wrote. “I couldn’t be happier for [Studier] and his team being recognized for their tremendous basic science efforts.”

Steve Binkley, Acting Director of the Department of Energy’s Office of Science, acknowledged the importance of the earlier work.

“The fact that scientific knowledge and tools developed decades ago are now being used to produce today’s lifesaving mRNA vaccines for COVID-19 is a great example of how the Department of Energy’s long-term investments in fundamental research at our National Laboratories can improve American lives today and into the future,” Binkley said in a statement.

Studier explained that his interests were more modest when he started studying this particular virus, which infects the bacteria E. coli.

“T7 was not a well-studied bacteriophage when I came to Brookhaven in 1964,” Studier, who is a senior biophysicist Emeritus, said in a statement. “I was using it to study properties of DNA and decided also to study its molecular genetics and physiology. My goal, of course, was to understand as much as possible about T7 and how it works.”

In an email, Studier said he did not realize the connection between his work and the vaccinations until Venki Ramakrishnan, a Nobel-Prize winning structural biologists from the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, told him.

“I am pleased that our work with T7 is relevant for fighting this world-wide pandemic,” Studier wrote. “History shows that some of the most useful discoveries come from basic research that could not have been predicted.”

While BNL is one of 17 Department of Energy facilities, it has conducted scientific research in numerous fields.

Several translational achievements originated at BNL, Shanklin wrote, including the thalium stress test for evaluating heart function, the development of Fluoro Deoxy Glucose for Positron Emission Tomography and the first chemical synthesis for human insulin, which allowed human insulin to replace animal insulin.

As for the effort that led to the T7 discoveries, Studier worked with Parichehre Davanloo, who was a postdoctoral fellow, Rosenberg, Dunn and Barbara Moffatt, who was a graduate student.

Rosenberg appreciated the multi-national background of the researchers who came together to conduct this research, as Moffatt is Canadian and Davanloo is Iranian.

Rosenberg added that while the group had “an inkling” of the potential usefulness of the processes they were perfecting, they couldn’t anticipate its value over the next 40 years and, in particular, its current contribution.

“Nobody really understood or thought just how widely spread its use would be,” Rosenberg said. “We certainly had no idea it would be an important element in the technology” that would lead to the Pfizer and Moderna vaccinations.

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Pixabay photo

By Daniel Dunaief

Daniel Dunaief

After a year filled with various kinds of losses in 2020, many residents are coping with emotional burdens, including a calendar filled with anniversaries of painful memories.

Called the anniversary effect, people who have been grieving losses are approaching and, in some cases have passed, the one year anniversary of the death of a family member, the last time they saw a family member in person, or the day they dropped a friend who couldn’t breathe off at a hospital.

“It’s good to acknowledge an anniversary is coming up,” said Mandi Zucker, a licensed social worker with a certificate in grief recovery and in thanatology, which is the study of death and dying. Those who feel comfortable offering their support might want to ask someone who is grieving what they are doing, if they have any plans and how they might spend the day.

Zucker, who is the founder of Inner-Harbor, a center that helps young adults who are grieving, cautioned that reaching out to someone only as an anniversary approaches might backfire.

If the anniversary is the only time someone reaches out, “that might feel disingenuous,” Zucker cautioned. People who are grieving might wonder “where you’ve been for the past year, if you are reaching out as if the other 364 days have not been difficult.”

People eager to provide support to the many residents who are dealing with the symptoms and after effects of grief should first make sure they are comfortable enough with their own lives to respond to their family and friends.

“Don’t ask if you’re not ready to hear it,” Zucker suggested. “If you’re going through something yourself and you’re in a hurry and don’t have the time, don’t ask.”

Support often takes the form of listening, rather than interrupting or talking. Zucker suggests people encourage those who are grieving to speak, without interrupting them, sharing their own anecdotes or judging them.

While it might not sound like long, two minutes is considerably longer than most people can offer their thoughts and feelings, as others typically interrupt well before then.

“There is nothing we can say that’ll fix” grief, Zucker said. “Our goal to be supportive is to let them say more. When you’re talking with them, think about why you are talking.”

Commenting on someone’s experience, by acknowledging that their description sounds sad, scary or painful, gives them an opening to continue to share.

When someone says, “It’s been rough with COVID,” almost everyone can offer their own experiences with the virus, the losses of freedom, and opportunity that they’ve felt, she said. Even though a supporter might want to share their experience to relate, the person who is grieving is likely better off having an opening to continue to share and experience their feelings, Zucker suggested.

Sometimes, just allowing the person to tell you to go away gives people control over a life that seems out of control.

“You can give them space, [but] you can also send an email or text saying that you are still thinking about them,” Zucker said. “You don’t have to imply that they must respond.”

Zucker is a fan of handwritten notes, which provide a material connection when someone doesn’t feel like talking, but can see a physical reminder of their connection to others.

If people notice that someone who is grieving isn’t getting dressed or showering, they can comment on it, letting them “know you see them.”

Zucker has a contrary view to the comment people often receive about being strong. For her, people show strength by being vulnerable, not by masking their feelings.

People who might be experiencing grief might also need to diversify their sources of support and strength. That could include meditating or going for walks.

 

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Michael Frohman. Photo from SBU

By Daniel Dunaief

Bringing together researchers and clinicians from six countries, including scientists scattered throughout the United States, a team of scientists co-led by Stony Brook University’s Michael Frohman linked mutations in a gene to congenital heart disease.

Frohman, Chair of the Department of Pharmacological Sciences in the Renaissance School of Medicine at SBU, has worked with the gene Phospholipidase D1 (or PLD1), for over 25 years. Researchers including Najim Lahrouchi and Connie Bezzina at the University of Amsterdam Heart Center linked this gene to congenital heart disease.

“The current study represents a seminal finding in that we provide a robust link between recessive genetic variants of PLD1 and a rather specific severe congenital heart defect comprising right-side valvular abnormalities,” Bezzina wrote in an email. 

Michael Frohman at Glymur Falls in Iceland.

The international group collected information from 30 patients in 21 unrelated families and recently published their research in the Journal of Clinical Investigation.

A number of other genes are also involved in congenital heart disease, which is the most common type of birth defect. People with congenital heart disease have a range of symptoms, from those who can be treated with medication and/or surgery for pre-term infants to those who can’t survive.

The discovery of this genetic link and congenital heart disease suggests that PLD1 “needs to be screened in cases with this specific presentation as it has implications for reproductive counseling in affected families,” Bezzina explained.

Bezzina wrote that she had identified the first family with this genetic defect about five years ago.

“We had a strong suspicion that we had found the causal gene, but we needed confirmation and for that, we needed to identify additional families,” she said. “That took some time.

Bezzina described the collaboration with Frohman as “critical,” as she and Lahrouchi had been struggling to set up the PLD1 enzymatic assay in their lab, without any success. Lahrouchi identified Frohman as a leading expert in the study of PLD1 and the team reached out to him.

His work was instrumental in determining the effect of the mutations on the enzymatic activity of PLD1, Bezzina explained.

The timing in connecting with Frohman proved fortuitous, as Frohman had been collaborating with Michael Airola, Assistant Professor in the Department of Biochemistry & Cell Biology at Stony Brook University, on the structure of the PLD1 catalytic domain.

“Together, they immediately saw that the mutations found in the patients were located primarily in regions of the protein that are important for catalysis and this provided detailed insight into why the mutations caused the PLD1 enzyme to become non-functional,” Bezzina wrote.

These findings have implications for reproductive counseling, the scientists suggested.

A couple with an affected child who has a recessive variation of PLD1 could alert parents to the potential risk of having another child with a similar defect.

One of the variants the scientific team identified occurs in about two percent of Ashkenazi Jews, which means that 1 in 2,500 couples will have two carriers and a quarter of their conceptions will be homozygous recessive, which virtually guarantees congenital heart disease. This, however, is about three times less frequent than Tay-Sachs. “This has, in our view, clinical implications for assessing the risk of congenital heart defects among individuals of this ancestry,” said Bezzina.

The mutation probably arose among Ashkenazi Jews around 600 to 800 years ago. There are about 20 known disease mutations like Tay-Sachs in this population that are found only rarely in other groups.

Lahrouchi and Bezzina specialize in the genetics of congenital heart disease, which occurs worldwide in 7 out of every 1,000 live births.

With 56 coauthors, Frohman said this publication had the largest number of collaborators he’s ever had in a career that includes about 200 papers. While this is unusual for him, it’s not uncommon among papers in clinical research.

The lead researchers believed a comprehensive report with a uniform presentation of clinical data and biochemical analysis would provide a better resource for the field, so they brought together research from The Netherlands, the Czech Republic, Israel, France, Italy and the United States.

Previous research that involved Frohman revealed other patterns connected to the PLD1 gene. 

About a dozen years ago, Frohman helped discover that mice lacking the PLD1 gene, or that were inhibited by a drug that blocked its function, had platelets that are less easily activated, which meant they were less able to form large blood clots.

These mice had better outcomes with strokes, heart attacks and pulmonary embolisms.

The small molecule inhibitor was protective for these conditions before strokes, but only provided a small amount of protection afterwards. Technical reasons made it difficult to use this inhibitor in clinical trials.

The primary work in Frohman’s lab explores the link between PLD1 and cancer. He has shown that loss of PLD1 decreases breast cancer tumor growth and metastasis.

As for what’s next, Frohman said he has a scientific focus and a translational direction. On the scientific front, he would like to know why the gene is required for heart development. He is launching into a set of experiments in which he can detect what might go wrong in animal models early in the development of the heart. 

Clinically, he hopes to explore how one bad copy of the PLD1 gene combines with other genes that might contribute to cause enough difficulties to challenge the survival of a developing heart.

A resident of Old Field, Frohman lives with his wife Stella Tsirka, who is in the pharmacology department and is Vice Dean for Faculty Affairs in the Renaissance School of Medicine. The couple has two children, Dafni, who is a first-year medical student at Stony Brook and Evan, who is a lawyer clerking with a judge in Philadelphia.

Outside of work, Frohman, who earned MD and PhD degrees, enjoys hikes in parks, kayaking and biking.

Having a medical background helped him learn a “little bit about everything,” which gave him the opportunity to prepare for anything new, which included the medical implications of mutations in the PLD1 gene.

Bezzina hopes to continue to work with Frohman, on questions including how the mutation type affects disease severity. “An interplay with other predisposing genetic factors is very interesting to explore as that could also help us in dissecting the disease mechanism further,” she wrote.

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