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Daniel Dunaief

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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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Photo from Pexels

By Daniel Dunaief

Daniel Dunaief

When I was in college, I learned an important lesson in class that had nothing to do with the subject I was studying. Many years ago, I attended an early morning anthropology lecture.

Pacing at the front and bottom of a semicircular stage, the professor shared details about the hungry ghost festival. In various parts of Asia and India, people practice a ritual in which they relieve the suffering of their deceased relatives by providing food. During this time, the professor said, people prepare meals and leave empty seats for ghosts, who ritualistically consume the food.

Seated next to a friend from our dorm, I was busily taking notes, not only because I wanted to do well on a future test, but because I also found the description fascinating.

That’s when the professor became distracted. Someone from the audio visual department was quietly packing up equipment at the back of the room.

“Excuse me,” the professor yelled to the man. “What are you doing?”

“I’m sorry,” the man said.

“Well, you should be,” the professor barked back.

The man continued to try to pack up the materials quietly. The noise, which I barely heard from a seat that was much closer to the back of the room, was still too much for my professor.

“You’re sorry, but you’re still disrupting my class!” he shouted.

“I’m packing up the material. I work for the university. One of the other classes needs it now,” the man replied. “I’ll keep it down.”

“No, this is ridiculous,” the professor said through gritted teeth. “I won’t tolerate this. You will leave.”

The man stood still, unsure of what to do. In that moment, I felt like I had a choice: I could either say something to support the man in the back of the room or walk out of the class. By doing and saying nothing, which is what I did, I felt like I was accepting the professor’s behavior.

When the man spent one more minute doing his work, the professor demanded to know where he worked so he could show up and bother him while he was trying to concentrate.

All these years later, I still think of that small moment. These types of incidents require a readiness to think, speak or act, especially to something that disturbs or distresses us. It’s akin to what coaches say all the time in sports: know what you’re going to do with the ball before it comes to you. If you have to think too much about your next move, it’s going to be too late.

A recent anti-Asian incident in New York City, in which security guards watched as a man knocked down and kicked a 65-year-old woman on her way to church, reminded me of the need to be prepared to do the right thing, even when someone wrongs someone else.

We are more likely to act when we are prepared to help, even if the moment creates discomfort for us.

Nowadays, we all have an opportunity to support each other, particularly amid anti-American attacks on members of the Asian American community. These cowardly verbal and physical assaults will become less prevalent if perpetrators know we’re all prepared to stand up for our friends and neighbors who have become the target for random anger during the pandemic. Asian Americans are not an enemy of the rest of us any more than our heart is the enemy of our body. We should stand with, and for, each other.

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Peter Koo Photo from CSHL

By Daniel Dunaief

The goal sounds like a dystopian version of a future in which computers make critical decisions that may or may not help humanity.

Peter Koo, Assistant Professor and Cancer Center Member at Cold Spring Harbor Laboratory, would like to learn how to design neural networks so they are more interpretable, which will help build trust in the networks.

The neural networks he’s describing are artificial intelligence programs designed to link a molecular function to DNA sequences, which can then inform how mutations to the DNA sequences alter the molecular function. This can help “propose a potential mechanism that plays a causal role” for a mutation in a given disease, he explained in an email.

Researchers have created numerous programs that learn a range of tasks. Indeed, scientists can and have developed neural networks in computer vision that can perform a range of tasks, including object recognition that might differentiate between a wolf and a dog.

Koo when he received a COVID vaccination.

With the pictures, people can double check the accuracy of these programs by comparing the program’s results to their own observations about different objects they see.

While the artificial intelligence might get most or even all of the head-to-head comparisons between dogs and wolves correct, the program might arrive at the right answer for the wrong reason. The pictures of wolves, for example, might have all been taken during the winter, with snow in the background The photos of dogs, on the other hand, might have cues that include green grass.

The neural network program can arrive at the right answer for the wrong reason if it is focused on snow and grass rather than on the features of the animal in a picture.

Extending this example to the world of disease, researchers would like computer programs to process information at a pace far quicker than the human brain as it looks for mutations or genetic variability that suggests a predisposition for a disease.

The problem is that the programs are learning in the same way as their programmers, developing an understanding of patterns based on so-called black box thinking. Even when people have designed the programs, they don’t necessarily know how the machine learned to emphasize one alteration over another, which might mean that the machine is focused on the snow instead of the wolf.

Koo, however, would like to understand the artificial intelligence processes that lead to these conclusions.

In research presented in the journal Nature Machine Intelligence, Koo provides a way to access one level of information learned by the network, particularly DNA patterns called motifs, which are sites associated with proteins. It also makes the current tools that look inside black boxes more reliable.

“My research shows that just because the model’s predictions are good doesn’t mean that you should trust the network,” Koo said. “When you start adding mutations, it can give you wildly different results, even though its predictions were good on some benchmark test set.”

Indeed, a performance benchmark is usually how scientists evaluate networks. Some of the data is held out so the network has never seen these during training. This allows researchers to evaluate how well the network can generalize to data it’s never seen before.

When Koo tests how well the predictions do with mutations, they can “vary significantly,” he said. They are “given arbitrary DNA positions important scores, but those aren’t [necessarily] important. They are just really noisy.”

Through something Koo calls an “exponential activation trick,” he reduces the network’s false positive predictions, cutting back the noise dramatically.

“What it’s showing you is that you can’t only use performance metrics like how accurate you are on examples that you’ve never seen before as a way to evaluate the model’s ability to predict the importance of mutations,” he explained.

Like using the snow to choose between a wolf and a dog, some models are using shortcuts to make predictions.

“While these shortcuts can help them make predictions that [seem more] accurate, like with the data you trained it on, it may not necessarily have learned the true essence of what the underlying biology is,” Koo said.

By learning the essence of the underlying biology, the predictions become more reliable, which means that the neural networks will be making predictions for the right reason.

The exponential activation is a noise suppressor, allowing the artificial intelligence program to focus on the biological signal.

The data Koo trains the program on come from ENCODE, which is the ENCyclopedia Of DNA Elements.

“In my lab, we want to use these deep neural networks on cancer,” Koo said. “This is one of the major goals of my lab’s research at the early stages: to develop methods to interpret these things to trust their predictions so we can apply them in a cancer setting.”

At this point, the work he’s doing is more theoretical than practical.

“We’re still looking at developing further tools to help us interpret these networks down the road so there are additional ways we can perform quality control checks,” he said.

Koo feels well-supported by others who want to understand what these networks are learning and why they are making a prediction.

From here, Koo would like to move to the next stage of looking into specific human diseases, such as breast cancer and autism spectrum disorder, using techniques his lab has developed.

He hopes to link disease-associated variance with a molecular function, which can help understand the disease and provide potential therapeutic targets.

While he’s not a doctor and doesn’t conduct clinical experiments, Koo hopes his impact will involve enabling more trustworthy and useful artificial intelligence programs.

Artificial intelligence is “becoming bigger and it’s undoubtedly impactful already,” he said. “Moving forward, we want to have transparent artificial intelligence we can trust. That’s what my research is working towards.”

He hopes the methods he develops in making the models for artificial intelligence more interpretable and trustworthy will help doctors learn more about diseases.

Koo has increased the size and scope of his lab amid the pandemic. He current has eight people in his lab who are postdoctoral students, graduate students, undergraduates and a master’s candidate.

Some people in his lab have never met in person, Koo said. “I am definitely looking forward to a normal life.”

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Photo from Pixabay

By Daniel Dunaief

Daniel Dunaief

No matter how much uncertainty and anxiety clouds our lives, the passion that inspires us can  penetrate the haze.

My retired neighbors, whom I see regularly on our walks, have shared their lives with us over the last year, offering news updates about their two grown children as well as their pursuit of vaccinations. Amid all the other news, they shared a development in their backyard that has completely captivated their attention.

Andrea and Bob said they were doing their usual gardening, trimming their bushes and reseeding their lawn, when they noticed something new next to their grill. Two mallards had decided to nest in a nearby bush.

The presence of this nest has captivated them to such a degree that it’s clear that the first place they look when they return from their walks is in the direction of the nest. They are eager to see whether their visitors, whom they assure us will take about the same 28 days to hatch that it takes between each of the two Moderna vaccinations for COVID, have pushed their way out of their eggs.

Each day, the parent mallards swim in their pool, taking short breaks from their early parenting duties to wade back and forth in a water body that Andrea and Bob assure us won’t have any chemicals or even salt until later in the summer.

They seem so thrilled to host their new guests that the bird droppings or other germs that might clog their filter or encourage bacterial growth don’t seem to concern them.

Indeed, they are so focused on these duck eggs that they have told anyone who ventures in their backyard, including insect control experts, not to spray or go near the nest.

Just to make sure the nest remains undisturbed from human activities, they have also put sawhorses — the kinds of temporary fencing police use to control crowds and building managers use to keep people away from exclusive entrances and exits to buildings — on either side of the nest.

Once the ducks hatch, they plan to take pictures from their window or around their yard, sharing them with friends and family.

The excitement this nest has created not only speaks to the Groundhog Day nature of our lives, but also to the core passion some people feel for nature.

When the right kind of animals appear, and I suspect a young raccoon or a nest of vultures wouldn’t make the cut, people will go well out of their way to support those creatures and to encourage the safety of their young.

Perhaps the arrival of spring and the renewal and hope it brings offers a fitting backdrop for the affection and appreciation of this collection of eggs.

After all, this spring in particular is unlike any other, as people hope to get vaccinated, emerge from their versions of hibernations and plan, tentatively, for the next steps over the next few months and year.

We will hopefully see friends and family we haven’t seen in months or even a year and, in some cases, will also visit with extended friends and family fortunate enough to have added new life to their ranks as well. Despite the baby bust, two sisters in my wife’s extended family gave birth to baby girls within weeks of each other. They will have their own stories to tell, passed down to them from their parents and extended family, about the unusual and challenging environment into which they were born.

In the meantime, however, Andrea and Bob can plan for something in the next few weeks that is unexpected, unplanned and wonderful: the hatching of new ducklings.

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Joel Hurowitz

By Daniel Dunaief

February 18th marked an end and a beginning.

On that day, the Mars Perseverance rover descended through the atmosphere with considerable fanfare back on Earth. Using some of the 23 cameras on Perseverance, engineers took pictures and videos of the landing.

The National Aeronautics and Space Administration not only shared the video of the rover descending into the Jezero crater which held water and, perhaps, life three billion years ago, but also offered a view of the elated engineers who had spent years planning this mission.

 

In a calm, but excited voice, a female narrator counted down the height and speed of the rover, which weighs about a ton on Earth and closer to 800 pounds in the lower gravity of Mars. The NASA video showed staff jumping out of their seats, cheering for the achievement.

Launched from Cape Canaveral, the rover took 233 days to reach Mars, which is about the gestation period for a chimpanzee.

Some of the engineers “who got us there have reached the end of their marathon,” said Joel Hurowitz, Associate Professor in the Department of Geosciences at Stony Brook University and Deputy Principal Investigator for one of the seven scientific instruments aboard the Perseverance. 

With ongoing support from other engineers who helped design and build the rover, the scientists “get the keys to the vehicle and we get to start using these things.”

Indeed, Hurowitz and Scott McLennan, Distinguished Professor in the Department of Geosciences at Stony Brook University are part of teams of scientists who will gather information to answer basic questions about Mars, from whether life existed, to searching for evidence of ancient habitable environments, to seeking evidence about the changing environment.

Both Stony Brook scientists were riveted by the recordings of the landing.

Scott McLennan

Hurowitz marveled at the cloud of dust that formed as the rover approached the surface.“You could see these chunks of rock flying back up at the sky crane cameras,” he said. “I was amazed at the amount of debris that was kicked up in the landing process.”

Hurowitz had seen pieces of rock on top of the Curiosity rover after it landed, but he felt he understood more about the process from the new video. “To see it happening, I realized how violent that final stage of the landing is,” he said.

McLennan said this has been his sixth Mars mission and he “never tires of it. It’s always exciting, especially when there is a landing involved.”

Like Hurowitz, who earned his PhD in McLennan’s lab at Stony Brook, McLennan was impressed by the dust cloud. “I understood that a lot of dust and surface debris was displaced, but it was quite remarkable to see the rover disappear into the dust for a short while,” he wrote in an email.

While previous missions and orbiting satellites have provided plenty of information about Mars, the Perseverance has the potential to beam pictures and detailed analysis of the elements inside rocks.

Hurowitz, who helped build the Planetary Instrument for X-ray Lithochemistry, or PIXL, said the team, led by Abigail Allwood at the Jet Propulsion Laboratory, has conducted its first successful instrument check, which involves turning everything on and making sure it works. Around April, the PIXL team will start collecting its first scientific data.

In addition to searching for evidence of previous life on Mars, Hurowitz will test a model for climate variation.

The SuperCam on the Perseverance Rover. Photo by Gregory M. Waigand

From measurements of the chemistry and mineralogy of sedimentary rock, the scientists can deduce whether the rocks formed in an environment that was oxygen-rich or oxygen-poor. Additionally, they can make inferences about temperature conditions based on their chemical compositions.

Looking at variations in each layer, they can see whether Mars cycled back and forth between cold and warm climates.

Warmer periods could have lasted for hundreds, thousands or even tens of thousands of years, depending on how much greenhouse gas was injected at any time, Hurowitz explained. “Whether this is long enough to enable biological development is probably one of the great questions in the field of pre-biotic chemistry,” he said.

The Martian atmosphere could have had dramatic swings between warm and oxygen-poor conditions and cold and oxygen-rich conditions. “This has not really been predicted before and provides a hypothesis we can test with the rover payload for how climate might have varied on Mars,” he added.

Tempering the expectation of confirming the existence of life, Hurowitz said he would be “shocked if we woke one morning and a picture in the rover image downlink [included] a fossil,” he said. “It’s going to take time for us to build up our understanding of the geology of the site well enough.” The process could take months or even years.

Using information from orbiters, scientists have seen minerals in the Jezero crater that are only found when water and rock interact.

With the 11-minute time lag between when a signal from Earth reaches Perseverance, Hurowitz said scientific teams send daily codes up to the rover and its instrument. Hurowitz will be involved in uploading the signals for PIXL.

A Martian day is 40 minutes longer than the Earth day, which is why the Matt Damon movie “The Martian” used the word “sol,” which represents the time between sunrises on Mars.

McLennan, who works on three teams, said PIXL and the SuperCam provide complementary skill sets. With its laser, the SuperCam can measure the chemical composition of rocks at under seven meters away. Up close, PIXL can measure sub millimeter spot sizes for chemistry.

SuperCam will then find areas of interest, enabling PIXL to focus on a postage-stamp sized area.

As a member of the Returned Sample Science Working Group, McLennan, who is a specialist in studying the chemical composition of sedimentary rocks, helps choose which rocks to collect and set aside to bring back to Earth. The rocks could return on a mission some time in the 2030s.

The scientists will collect up to 43 samples, including some that are completely empty. The empty tubes will monitor the history of contamination that the other rock samples experienced. 

For McLennan, the involvement of his former student is especially rewarding. Hurowitz “didn’t just help build the instrument, he’s one of the leaders,” McLennan said. “That’s really fabulous.”

For Hurowitz, any data that supports or refutes the idea about the potential presence of life on Mars is encouraging.

He is “cautiously optimistic” about finding evidence of past life on Mars. “We’ve done everything we can as a scientific community to maximize the chance that we’ve landed some place that might preserve signs of life.”

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Photo from Pixabay

By Daniel Dunaief

Daniel Dunaief

This month, we completed our first pandemic year. As we prepare for a hopeful future, please find below the words that reflected the realities of our past year.

— “We were behind the eight ball on testing for a while now,” Suffolk County Executive Steve Bellone (D) on a conference call with members of the National Association of Counties and the press, March 18, 2020.

– “These are not helpful hints. These are legal provisions. They will be enforced.” Governor Andrew Cuomo (D) on a conference call with reporters, describing his decision to shut down businesses not considered essential, March 20, 2020.

– “A lot of us are thinking about staff on the hospital side who are really being tested in an unprecedented way.” Cathrine Duffy, director of HealthierU, an employee wellness program at Stony Brook University, March 25, 2020.

— “I’ve never seen anything like it.” Joan Dickinson, community relations director at Stony Brook University, in response to the over 100 emails she received each night from people eager to donate to the university, March 27, 2020

— “For the N95 masks to come in without a charge helps all those local entities laying out a lot of cash at the moment.” Rep. Lee Zeldin (R-NY1) in response to the announcement that President Donald Trump (R) would ship 200,000 masks to Suffolk County, April 6, 2020.

— “I never imagined being in the position of reporting the numbers on a daily basis of people who have died in our county from anything like this.” Bellone on his daily conference call with reporters, April 12, 2020.

— “We feel that science will solve this problem, and hopefully soon.” John Hill, director of the National Synchrotron Light Source II, who was part of a team coordinating Brookhaven National Laboratory’s COVID-19 research across all the Department of Energy labs, April 19, 2020.

— “We have a hard winter ahead of us.” Bettina Fries, chief of the Division of Infectious Diseases at Stony Brook Renaissance School of Medicine, regarding projected increases in viral cases, April 23, 2020.

— “I always felt an urgency about cancer, but this has an urgency on steroids.” Mikala Egeblad, associate professor at Cold Spring Harbor Laboratory, in describing her efforts to apply her scientific expertise to COVID, April 26, 2020.

— “Coming to the hospital is still safer than going to the supermarket.” Todd Griffin, the president of Medical Staff and chair of the Department of Obstetrics, Gynecology and Reproductive Medicine at Stony Brook Renaissance School of Medicine, April 30, 2020.

— “We love you, but you can’t come anywhere near us.” Malcolm Bowman, distinguished service professor at Stony Brook University’s School of Marine and Atmospheric Sciences, recalls his extended family in New Zealand telling him and his wife Waveney as they left an old car with food at the airport so the couple could live in a camper in New Zealand , May 1, 2020.

— “At a certain point, it’s not just about the patient. It’s about the whole support system. You’re pulling not just for them, but for their whole family.” Amanda Groveman, Stony Brook quality management practitioner, describing the My Story effort to personalize patient stays at the hospital, May 7, 2020.

— “I always knew you were smart, but now I know you are brilliant.” Marna said to her daughter Tamara Rosen, who  defended her graduate thesis at Stony Brook University through a Zoom call, May 24, 2020.

— The death of Minnesota resident George Floyd at the hands of police officers was “an outrage” and was “unacceptable.” Suffolk County Police Commissioner Geraldine Hart in a statement on a media call, May 30, 2020.

— Army veteran Gary Degrijze has “truly made a remarkable recovery.” Jerry Rubano, a doctor in Trauma/ Acute Care/ Surgical Critical Care in the Department of Surgery at Stony Brook Medicine, said after he spent seven weeks on a ventilator and twice lost his pulse , June 9, 2020.

— “You couldn’t have found a happier group of people.” Dr. Frank Darras, clinical professor of Urology and Clinical / Medical Director of the Renal Transplantation Program at Stony Brook Renaissance School of Medicine, about a transplant at 3:30 a.m. on a Saturday morning, June 12, 2020.

— “My whole career has brought me to be who I am in this moment.” Risco Mention-Lewis, deputy police commissioner, in the wake of protests over policing, July 3, 2020.

— “When you have untreated mental health and substance abuse disorders, the county will pay for that one way or the other.” Children’s Association Chief Executive Officer Jeffrey Reynolds amid an increase in demand for mental health during the pandemic, July 31, 2020.

— “People sent really moving and emotional notes. We saw a lot of good in people” [during a difficult time.] Colby Rowe, Trauma Center Education & Prehospital outreach coordinator who helped coordinate donations to Stony Brook, Aug. 7, 2020.

— “Long Islanders deserve better.” Thomas Falcone, CEO of LIPA, in response to a letter from Senator James Gaughran (D-Northport) questioning LIPA’s oversight of PSEG after extensive power outages and communication failures following Tropical Storm Isaias, Aug. 28, 2020.

— “I tell my patients, I take their hands, I say, ‘Listen, I was in there, too. I know what you’re feeling. I know you’re scared. I know you’re feeling you can die.” Feliciano Lucuix, a patient care assistant at St. Catherine of Siena Medical Center, describing her hospitalization with COVID and then her return to her work in the same hospital, Dec. 14, 2020.

— “As hard and as difficult and sad and heart wrenching [as it was], so many other parts, you just saw such humanity. It was amazing.” Patricia Coffey, nurse manager at the Critical Care Unit at Huntington Hospital reflecting on the challenges and responses of the health care field amid the pandemic, Dec. 31, 2020.

— “When we reach our number, we make an announcement inside.” Michael Connell, who runs the M.A. Connell Funeral Home in Huntington Station, said about alerting people about crowds awaiting a chance to visit with family during a funeral service, Feb. 26, 2021.

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U.S. Department of Energy Secretary Jennifer Granholm joined scientists from DOE national laboratories for a round table conversation on COVID-19 on March 4. Photo from the Department of Energy.

By Daniel Dunaief

Jennifer Granholm, the new secretary of the Department of Energy, is pleased with the role the 17 national laboratories has played in responding to the COVID-19 pandemic over the last year and is hopeful research from these facilities will aid in the response to any future potential pandemics.

There are “70,000 people who are spread out across America solving problems,” Granholm said in a recent press conference that highlighted the effort and achievement of labs that redirected their resources to tackle the public health threat. 

The DOE is “the solutions department” and has “some of the greatest problem solvers.”

“It is super exciting to talk about this particular issue, the issue of the day, the COVID, and what the lab has been doing about it,” she added.

Granholm, who was confirmed by a Senate vote of 64-35 and was sworn in as secretary on February 25th, had previously been the Attorney General in Michigan and was the first female governor of Michigan, serving two terms from 2003 to 2011.

The press conference included three research leaders from national labs across the country, including Kerstin Kleese van Dam, Director of the Computational Science Initiative at Brookhaven National Laboratory in Upton.

Kleese van Dam was the BNL lead for one of the five DOE teams that tackled some of the scientific challenges caused by the virus. She led the effort to inform therapeutics related to COVID-19.

The other four teams involved manufacturing issues, testing, virus fate and transport, which includes airflow monitoring, and epidemiology.

The public discussion was intended to give people a look at some of the “amazing work that you all are doing,” Granholm said.

The Department of Energy formed the National Virtual Biotechnology Laboratory, or NVBL, to benefit from DOE user facilities, such as the light and neutron sources, nanoscience centers, sequencing, and high-performance computer facilities to respond to the threat posed by COVID-19.

Funding for NVBL enabled BNL scientists to pivot from what they were doing to address the challenge created by the pandemic, John Hill, Director of the National Synchrotron Light Source II, explained in an email.

BNL had been constructing a new facility, called the Laboratory for Biomolecular Structures, prior to the pandemic. The public health threat created by the virus, however, accelerated the time table by two months for the completion of the structure. 

The lab has new cryo-electron microscopes that allow scientists to study complex proteins and the architecture of cells and tissues. The cryo-EM facility contributed to work on the “envelope” protein for the SARS-CoV2 virus, which causes COVID-19.

“We at BNL built a new facility which gives further capabilities to look at the virus during the pandemic,” Kleese van Dam said during the press conference. The lab prepared the facility “as quickly as possible so we could help in the effort.”

Kleese van Dam said the three light sources around the country, including the National Synchrotron Light Source II at BNL, have been working throughout the crisis with the pharmaceutical industry, helping them “refine and improve their medications.”

Indeed, Pfizer scientists used the NSLS-II facility to research certain structural properties of their vaccine. At the same time, researchers have worked on a number of promising antivirals, none of which has yet made it into clinical use.

The national laboratories, including BNL, immediately tackled some of the basic and most important questions about the virus soon after the shutdown last spring.

“There was a period last year, in the depths of the first lockdown in New York, when [the National Synchrotron Lightsource-II] was only open to COVID research,” Hill wrote in an email. “That was done both by BNL scientists and others working with our facility remotely. All other research was on hold.”

The facility reopened to other experiments in May for remote experiments, Hill continued.

Kleese van Dan explained that other projects also had delays.

“These [delays] were up front discussed with collaborators and funders and all whole heartedly supported our shift in research,” said Kleese van Dam. “Many of them joined us in this work.”

Hill said the NSLS-II continues to work on COVID-19 and that much of the work the lab has conducted will be useful in future pandemics. “We are also exploring ways to maintain preparedness going forward,” he continued.

BNL is collaborating with other groups, including private companies, to enable a robust and rapid response to future threats.

“BNL is part of a multi-lab consortium  — ATOM (Accelerating Therapeutics for Opportunities in Medicine) — that aims to pursue the therapeutics work in collaboration with other agencies, foundations and industry,” Kleese van Dam wrote in an email.

In response to a question from Granholm about the safety of schools and the study of airflow, Kleese van Dam explained that national labs like BNL regularly study the way aerosols move in various spaces.

“As a national lab, we study pollution and smoke and things like that,” Kleese van Dam said during the press conference.

The lab tested the virus in the same way, exploring how particles move to understand infections.

“When we think about this, we think about how air moves through small and confined spaces,” Kleese van Dam said. “What I breathe out will be all around you. If we were outside, the air I’m breathing out is mixed with clean and healthy air. The load of the virus particles that arrive are much smaller.”

Using that knowledge, BNL and other national laboratories did quite a few studies, including exploring the effect of using masks on the viral load.

People at numerous labs used computer simulations and practical tests to get a clearer picture of how to reduce the virus load in the air.

Granholm pledged to help share information about minimizing the spread of the virus.

“We’re going to continue to focus on getting the word out,” Granholm said. The labs are doing “great work” and the administration hopes to “make the best use of it.”

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Photo by Pexels

By Daniel Dunaief

Daniel Dunaief

I would like to cancel some things from my past and my own life. Here are some things I’d put on my cancel list:

Self doubt: Movies (remember when we used to go out to movies, pay way too much money for popcorn, candy and enjoy previews for upcoming films that looked better than the one we were about to watch?) often encourage us to overcome self doubt. What if we never had those doubts in the first place? We might become arrogant and insufferable, but we also might truly become our own versions of “The Little Engine that Could.” Wait, that hasn’t been canceled, has it? Well, if it has, I’m going to ignore the latest cultural eraser.

Self stuffing: When self doubt crept into our minds, how often did we reach for the kind of comfort food that just didn’t do us any favors? Sure, those cupcakes, cookies and sugar cereal might have tasted good in the moment, but was the momentary satisfaction really worth it? Did the eight vitamins and four minerals do us any good? Let’s cancel that urge and impulse, making it impossible to continue unfortunate patterns.

Self loathing: I admit that the self loathing that has crept in at times in my life has helped me get off the couch and do some sit-ups and push-ups, has driven me to be more productive and has put me on more of the “right track,” to borrow from that Little Engine. Still, maybe all that energy would have been more effective if I used it earlier.

The 2004 Red Sox: Yeah, I know you can’t cancel a team or sports history, but that would be one of the first teams I’d erase from my memory. The Yankees were winning 3-0 in the series and no team had ever come back from such a deficit, plus we had the curse of the Bambino. None of that mattered, as the Sawx not only took the next four games, but then went on to win the World Series. Blech! Now I know how all those New Englanders felt about Bucky Dent, which probably stings a lot less. Bucky Dent is like trying to tease your younger brother with something that makes him smile even more broadly than you do.

Mirrors: We should cancel mirrors. After all, they keep showing how much older and more exhausted we’re getting. Sometimes, like when we conquer the self stuffing and the self doubt, we see the version of ourselves we’d like to be. Other times, though, the mirror tells us, albeit in a backwards way, that we aren’t who we’d like to be and that we need to climb back onto that train car to get to our desired destination.

Report cards: Students, parents and teachers can’t win. If a teacher gives everyone A’s, the teacher will be popular, but the students probably wouldn’t learn as much as they could or should. The teacher who has more of a bell-shaped distribution of grades may reflect the reality of the class as a whole, but he or she may put someone who belongs on the right side of the curve on the left and vice versa. Let’s cancel report cards and let the students prove what they know in some other way. The great thing about this version of cancel culture is that it doesn’t require me to replace it with something that works. 

Bad parenting: We’ve had moments when we have the right intention, but the wrong result. Let’s cancel those unfortunate parenting errors. If kids can get a do-over on the playground, we should get to cancel one or two of our mistakes.

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A rendering of Beelzebufo, a mammoth-sized ancient frog discovered in 2008 by David Krause of Stony Brook University, by Luci Betti-Nash
Luci Betti-Nash drawing warblers
A rendering of Rahonavis, a bird-like feathered dinosaur discovered in Madagascar
Trans Saharan Seaway
Vintana sertichi reconstruction

By Daniel Dunaief

It started over four decades ago, with a “help wanted” advertisement.

Luci Betti-Nash needed money for art supplies. She answered an ad from the Stony Brook University Department of Anatomical Sciences that sought artists who could draw bones. She found the work interesting and realized that she could “do it fairly easily. I could not have imagined a more fulfilling career.”

Betti-Nash spent 41 years responding to requests to provide illustrations for a wide range of scientific papers, contributing images that became a part of charts and graphs and drawing everything from single-celled organisms to dinosaurs. She retired last April.

Her coworkers at Stony Brook, many of whom collaborated with her for decades, appreciated her contributions and her passion and precision for her job.

Maureen O’Leary, Professor in the Department of Anatomical Sciences, said Betti-Nash’s work enhanced her professional efforts. “I couldn’t have had the same career without her,” O’Leary wrote in an email. “Artists are true partners.”

O’Leary appreciated how Betti-Nash noticed parts of the work that scientists miss. 

“I think the most important thing is figuring out together what to put in and what to leave out of a figure,” O’Leary explained. “A photograph shows everything and it can be a blizzard of detail, really too much, and it will not focus the eye. The artist-scientist collaboration is about simplifying the detail to show what is important and how to show it clearly.”

One of O’Leary’s favorite illustrations from Betti-Nash was a pull-out, color figure that envisioned the ancient Trans-Saharan Seaway from about 75 million years ago. The shallow sea, which was described in the movie “Aquaman,” supported numerous species that are currently extinct. Betti-Nash created a figure that showed these creatures in the sea and how water drained from nearby mountains, all superimposed over the geology.

“It told the story of how ancient life turned into rocks and fossils,” O’Leary explained.

Betti-Nash, who continues to sketch from her home office and plans to be selective about taking on future assignments, has numerous stories to tell about her work.

For starters, the world of science is rife with jargon. When she was starting out, she didn’t always stop researchers who tossed around the terms that populate their life as if they were a part of everyone’s vocabulary.

“Some [scientists] would come in and assume you knew exactly what they were talking about,” Betti-Nash said. “It was something they were studying for years. They would assume you knew all the terminology.”

Each discipline, from cell biology to gross anatomy to dinosaur taxonomy had its own terminology, some of which “was way over my head,” she said. 

Early in her career, Betti-Nash felt she didn’t know details she thought she should.

“The older I got, the bolder I got about asking” scientists to explain what they meant in terms she could understand, she said, adding that she felt fortunate to have scientists who were “more than willing and eager to answer my questions when I was bold enough to ask. That was one of the many life lessons I learned … don’t be afraid to ask questions.”

Betti-Nash sometimes had to work under intense time pressure. Collaborating with David Krause, who was at Stony Brook and is now Senior Curator of Vertebrate Paleontology in the Department of Earth Sciences at the Denver Museum of Science, Betti-Nash illustrated the largest frog ever discovered, which lived in Madagascar over 65 million years ago. Called the Beelzebufo, this frog weighed in at a hefty 10 pounds and was 16 inches. Ribbit!

A short time before going to press, the scientific team decided they needed a common object as a frame of reference to compare the size of this ancient amphibian and the largest living frog in Madagascar.

“We scrambled,” Betti-Nash recalled. “We decided on a pencil.” 

She didn’t have time to draw the pencil, so she put it on her scanner, did some quick painting in Photoshop, put a shadow in, added it to the scan of the painting, saved it in the format required for the journal and sent it off.

“Adding the pencil was one of those typical strokes of genius that [Betti-Nash] routinely added to artwork,” explained Krause in an email. “Everyone knows the size of a number 2 pencil.”

Even though she hadn’t sculpted in 32 years, she had to create a sculpture of the frog that students could touch. The sculpture had to be non-toxic, dry and ready within three days.

Betti-Nash turned to the Guild of Natural Science Illustrators, asking for help with ideas for the materials. She also asked Joseph Groenke from Krause’s lab to contribute his fossil preparing experience. She used an epoxy clay that she massaged into shape, and then colored it with acrylic, non-toxic paints.

That sculpture was featured as a part of a display at Stony Brook Hospital for years and has since traveled with Krause to Denver where “kids especially love it, in part because it is touchable,” Krause wrote.

Krause was grateful for a partnership with Betti-Nash that spanned almost 40 years.

“There is no doubt in my mind that [Betti-Nash] made me a better scientist and there is also no doubt that my science is better” because of her, he explained. Krause described her stipple drawings as “incredibly painstaking to execute.” His favorite is of a large fossil crocodile found in Madagascar from the Late Cretaceous called Mahajangasuchus. 

Betti-Nash urges artists considering entering the field of scientific illustrating to attend graduate school or even to take undergraduate courses, which would provide time to learn skills and terminology before working in the field.

She also suggests artists remain “interested in what you’re drawing at that moment, no matter what it is,” she said, adding that drawing skills provide a solid foundation for a career in science illustrating. Computer skills, which help with animation and videos, are good tools to learn as well.

Growing up in Eastchester, Betti-Nash often found herself doodling patterns in her notebooks. When she worked on graph paper, she colored in the squares. She also received artistic guidance from her father, the late John Betti.

A graphic designer, Betti worked for a company in Westchester, where he designed the town seal for Tuckahoe as well as the small airplane wings children used to get when they flew on planes.

During World War II, Betti, who grew up in Corona, Queens, used his artistic skills to create three-dimensional models from aerial photographs. Stationed close to the residence of his extended family in Italy during part of the war, Betti also created watercolor paintings of the Italian landscape.

When she was growing up, Betti-Nash had the “best model-making teacher in my dad,” who taught her to create paper maché.

Married to fellow illustrator Stephen Nash, Betti-Nash plans to remain active as an artist, doing her own illustrations involving nature and the relationship between birds and the environment. 

She currently leads Second Saturday Bird Walks at Avalon Nature Preserve in Stony Brook and Frank Melville Memorial Park in Setauket through the Four Harbors Audubon Society (4HAS.org)

Betti-Nash is pleased with a career that all started with a response to an ad in the paper. “I feel very privileged to have had the opportunity to work as a scientific illustrator,” she said. “I hope I was able to help communicate the science behind the discoveries that the amazing scientists at Stony Brook made during my time there.”

All photos courtesy of Luci Betti-Nash

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Photo courtesy of Pexels

By Daniel Dunaief

Daniel Dunaief

In my daily conversations with a range of people over the last week, I have heard stories I thought I’d share, as a reflection of the reality of our lives.

The first involved a discussion with Joe about his vaccination. Joe had been trying to sign up for a COVID vaccination for weeks. He thought he’d landed a coveted vaccination appointment at Jones Beach. Driving out there for a 6 p.m. appointment, he drove in circles.

The site had the wrong address, he said. In addition, even the correct address, which had a phone on-site that wasn’t working, naturally, was closed that day because the winds were too high.

“Who would put tents up on Jones Beach?” Joe asked, his voice barely rising but his frustration evident from the time wasted trying to get a vaccination that would allow him to do a job that required interacting with the public. “If you want to build a tent, put it somewhere that’s not as windy. It wasn’t even snowing.”

Fortunately, Joe, who spent more time the next day sharing his experience with a vaccination operator, was able to schedule a make-up appointment much closer to home.

The next day, I spoke with Matthew, who is worrying about his son Jim, who is a sophomore in college. Jim, you see, has already received a COVID warning. A second warning or infraction could send his son home, which would, as Matthew put it, “not be good for anybody.”

As it turns out, Jim has a girlfriend, Sarah. Normally, that wouldn’t be such a cause for concern for his parents or for the university. Still, with his girlfriend living in a different penitentiary, I mean, dormitory, Jim is not allowed to visit with Sarah.

The problem is that Sarah, who is an excellent and committed student, not only works hard at school, but also inspires Jim to expend considerable additional academic effort.

If Jim stops seeing Sarah, which he may do to comply with school rules designed to protect the campus from spreading the dangerous virus, he will miss time with his close friend, while he will also likely not study as hard.

My friend Matthew advised Jim to be careful and comply with the rules, although I could tell that he felt his own return on the investment he spends for college will likely be higher if Jim spends more time with his studious friend.

Finally, I spoke with Paul, a friend who regularly attended conferences before COVID shut all those events down. Paul traveled at least four times a year to meetings all over the world, visiting interesting places but, more importantly, speaking with people in his field.

One day in 2019, Paul was sitting in one such conference and was taking notes. As the conference ended, he and the man sitting next to him, whom he’d never met, struck up a conversation. The man suggested a follow-up effort to the work that might help the industry. Realizing he had the ability to do exactly what the stranger suggested, Paul asked if the man would mind if he used the idea. The stranger was delighted and a friendship, and an idea, was born.

I asked Paul how much he missed conferences and if he planned to attend them when the world reopened.

He said he would not only jump at the chance, but might even attend conferences he wouldn’t have previously considered, just to benefit from such random and potentially beneficial interactions. His only hesitation is that he hasn’t gotten his vaccination yet. He wondered what I thought about driving out to Jones Beach.

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