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Daniel Dunaief

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By Daniel Dunaief

Daniel Dunaief

Disclaimer: The following column is intended to provide a lighthearted response to the ongoing pandemic. In no way does it diminish or ignore the suffering or the unimaginable horror for people who have lost loved ones or who are on the front lines of the crisis. I continue to be grateful for all the help, support, and work everyone is doing to keep us safe, fed, and cared for (see last week’s column). This latest column, however, is designed to offer comic relief.

I was thinking about how life has changed in small, and largely insignificant ways. Please find below some “before coronavirus” and “after coronavirus” trivial differences for those of us fortunate enough to be inconvenienced and not irreparably harmed by the virus and when we’re not focused on the anxiety of shuttered businesses and lost income.

Where should we eat?

BC: Do you want to go to the Italian restaurant with the cool music and the frescoes on the wall, or the Chinese restaurant, with the incredible dumplings and the endless supply of hot tea?

AC: Should we go back to the kitchen, the dining room or the bedroom, where there are so many leftover crumbs that we could eat those for dinner without going to the refrigerator?

What should we wear?

BC: We could take the newly pressed suit that’s back from the dry cleaner, the slightly wrinkled suit that we wore a few days earlier, or the jeans and casual shirt that works on a casual Friday.

AC: We could take yesterday’s sweatpants, the ripped jeans that don’t smell too bad, or stay in the pajamas we wore to bed.

What should we do when we see people we know on the sidewalk?

BC: We slow our walk, smile, shake hands or hug and ask how they are doing.

AC: We run across the street, yell in their general direction and wave as we make the same joke we made the day before about the need for social distancing.

How do we start emails?

BC: We might dive right in, ask an important question or ease into it, hoping all is well.

AC: We often start emails by hoping the person we’re writing to and their family are safe.

How should we check on our college-age children?

BC: We can call them or FaceTime to see how they are doing and listen attentively as they share the excitement about school.

AC: We can call or FaceTime them from behind their locked door in our house and ask them how they are doing.

What do we do about the polarizing president?

BC: If we love him, we can find others who admire him. If we hate him, we can blame him for climate change, relaxing regulations, and changing the tone of discourse in Washington.

AC: If we love him, we can thank our lucky stars that he’s leading us and the economy out of this pandemic. If we hate him, we can blame him for our slow reaction and hold him to account for everything he and his administration haves said or didn’t say in connection with the COVIDcovid-19 response.

What do we do if someone sneezes?

BC: We offer a polite “God bless you” or, if we’re fans of “Seinfeld,” we say, “You are so good looking.”

AC: We drop anything we’re carrying and race across the room. When we’re a safe distance, we turn around scornfully, particularly if the person didn’t sneeze into anhis or her  elbow.

What do we think is funny?

BC: We follow our own sense of humor, reserving the right to laugh only when we feel compelled.

AC: We look at a picture of Winnie-the- Pooh and Piglet. We see Winnie telling Piglet to “Back the f$#@$ off,” and we laugh and send it to everyone who won’t get in trouble for receiving an email in which someone curses, after we ask if they and their family are safe.

SBU team member Steve Forrest scales the rock face as chinstrap penguins look on. Photo by Christian Åslund

By Daniel Dunaief

The canary in the Arctic coal mines, chinstrap penguins need more ice. These multitudinous flightless birds also depend on the survival and abundance of the krill that feed on the plankton that live under the ice.

With global warming causing the volume of ice in the Antarctic to decline precipitously, the krill that form the majority of the diet of the chinstrap penguin have either declined or shifted their distribution further south, which has put pressure on the chinstrap penguins.

Indeed, at the end of December, a team of three graduate students (PhD students in Ecology and Evolution Alex Borowicz and Michael Wethington and MS student in Marine Science Noah Strycker) from the lab of Heather Lynch, who recently was promoted to the inaugural IACS Endowed Chair of Ecology & Evolution at Stony Brook University, joined Greenpeace on a five week mission to the Antarctic to catalog, for the first time in about 50 years, the reduction in the number of this specific penguin species.

The team boarded Greenpeace’s ship, the Esperanza, for a five week mission. Photo by Christian Åslund

The group, which included  private contractor Steve Forrest and two graduate students from Northeastern University, “saw a shocking 55 percent decline in the chinstrap on Elephant Island,” Lynch said. That drop is “commensurate with declines elsewhere on the peninsula.”

Elephant Island and Low Island were the targets for this expedition. The scientific team surveyed about 99 percent of Elephant Island, which was last visited by the Joint Services Expedition in 1970-1971.

The decline on Elephant Island is surprising given that the conditions in the area are close to the ideal conditions for chinstraps.

In some colonies in the Antarctic, the declines were as much as 80 percent to 90 percent, with several small chinstrap colonies disappearing entirely.

“We had hoped that Elephant Island would be spared,” Lynch said. “In fact, that’s not at all the case.”

While many indications suggest that global warming is affecting krill, the amount of fishing in the area could also have some impact. It’s difficult to determine how much fishing contributes to this reduction, Lynch said, because the scientists don’t have enough information to understand the magnitude of that contribution.

The chinstrap is a picky eater. The only place the bird breeds is the Antarctic peninsula, Elephant Island and places associated with the peninsula. The concern is that it has few alternatives if krill declines or shifts further south.

“Chinstraps have been under-studied in the last few decades, in part because so much attention has been focused on the other species and in part because they nest in such remote and challenging places,” Lynch explained in an email. “I hope our findings raise awareness of the chinstraps as being in serious trouble, and that will encourage everyone to help keep an eye on them.”

While these declines over 50 years is enormous, they don’t immediately put the flightless waterfowl that tends to mate with the same partner each year on the list of endangered species because millions of the sea birds that feel warm and soft to the touch are still waddling around the Antarctic.

Researchers believe that the biggest declines may have occurred in the 1980s and early 1990s, in part because areas with more regular monitoring showed reductions during those times.

Still, where there are more recent counts to use as a standard of comparison, the declines “show no signs of abating,” Lynch explained.

The evidence of warming in the Antarctic has been abundant this year. On Valentine’s Day, the Antarctic had its hottest day on record, reaching 69.35 degrees Fahrenheit. The high in Stony Brook that day was a much cooler 56 degrees.

“What’s more concerning is the long term trends in air temperature, which have been inching up steadily on the Antarctic Peninsula since at the least the 1940’s,” Lynch wrote in an email.

At the same time, other penguin species may be preparing to expand their range. King penguins started moving into the area several years ago, which represents a major range expansion. “It’s almost inevitable that they will eventually be able to raise chicks in this region,” Lynch suggested.

The northern part of the Antarctic is becoming much more like the sub Antarctic, which encourages other species to extend their range.

Among many other environmental and conservation organizations, Greenpeace is calling on the United Nation to protect 30 percent of the world’s oceans by 2030. The Antarctic was the last stop on a pole to pole cruise to raise awareness, Lynch said.

One of the many advantages of traveling with Greenpeace was that the ship was prepared to remove trash.

“We pulled up containers labeled poison,” Lynch said. Debris of all kinds had washed up on the hard-to-reach islands.

“People are not polluting the ocean in Antarctica, but pollution finds its way down there on a regular basis,” she added. “If people knew more about [the garbage and pollution that goes in the ocean], they’d be horrified. It is spoiling otherwise pristine places.”

Lynch appreciated that Greenpeace provided the opportunity to conduct scientific research without steering the results in any way or affecting her interpretation of the data.

“We were able to do our science unimpeded,” she said.

Counting penguins on the rocky islands required a combination of counting birds and nests in the more accessible areas and deploying drones in the areas that were harder to reach. One of Lynch’s partners Hanumant Singh, a Professor Mechanical and Industrial Engineering at Northeastern University, flew the drones over distant chinstrap colonies. The researchers launched the drones from land and from the small zodiac boats.

The next step in this research is to figure out where the penguins are going when they are not in the colony. “Using satellite tags to track penguins at sea is something I’d like to get into over the next few years, as it will answer some big questions for us about where penguins, including chinstraps, are trying to find food,” Lynch said.

METRO photo

By Daniel Dunaief

Daniel Dunaief

You know those glasses you wear at the eye doctor when you have to identify images that stand out on the card in your hand? These days, I feel as if I’m wearing them everywhere I go.

Take, for example, my trip to the supermarket. Before coronavirus, I often nodded to the people who stock shelves and chatted with the cashiers, acknowledging them but perhaps not appreciating them sufficiently. Nowadays, the entire food services crew stands out.

The people who worked on the farms that grew the products, the ones who went to the factory that refined it, the drivers who transported it to the stores and, eventually, the residents of our community who placed it on the shelves are making it possible for us to feed our families.

Each time I shop, I would walk around giving the local supermarket workers a hug, but that would violate social distancing, and would be pretty awkward.

Then, there are the pharmacists, who stand in their white lab coats mixing our medicines. We need them, now more than ever, to ensure we get the right amount of the right drugs.

Of course, even when I’m not seeing the doctors, nurses, police, and other first responders, I’m well aware of the front line in the battle against the pandemic. Each one of these people is putting their lives on the line when they interact with people who may carry an infection for which their bodies have no resistance, no matter how much coffee they drink or how much they hope they are invincible. With coronavirus glasses, I see them perform their heroic jobs each day, despite the concerns they may have about bringing the disease home to their families or limiting their contact with their relatives.

Fortunately, we are not so isolated that most of us can’t see important people in our lives through FaceTime. Many people contributed to the development of the phones that have become an extension of our bodies. The ones who made the futuristic Jetsons’ notion, in the animated sitcom, of seeing people as we talked to them have made it possible for us to connect from any distance, even if the ones we wish to hug are waiting out the storm in their living room next door.

Scientists throughout the world are working tirelessly to figure out the best ways to treat people lined up in hospitals or to create a vaccine that will protect us in the future. I am privileged to talk to scientists every day, although I haven’t spoken to any of the ones working on a treatment or vaccine. These researchers come from everywhere, are indifferent to national borders, and often are driven to make new discoveries, help humanity and make a difference in the world. Those of us who receive treatments or a vaccine for which they made a contribution can assure them that what they do matters.

The entire team involved in heating, cooling and lighting my home also stand out, as do the ones who created magnificent and inspiring films, books, and home entertainment.

Each day, people like Governor Andrew Cuomo (D) and County Executive Steve Bellone (D) work tirelessly and visibly on our behalf. On Bellone’s daily media calls, he has remained level-headed, determined, and focused during the difficult balancing act of trying to protect our health while working to revive the economy, once the crisis clears.

I’m sure I’ve left many people off the list who deserve appreciation. In fact, if you, the reader, would like to share a few of the people whose work and dedication you appreciate, please write in and share your thoughts to news@tbrnewsmedia.com.

Above, from left, Kenneth Kaushansky, Dean of the Renaissance School of Medicine; Anissa Abi-Dargham; Henry Tannous; Ute Moll; and Michael Bernstein, Interim President of SBU.

By Daniel Dunaief

A heart and lung doctor, a researcher who works on imaging for schizophrenia and a scientist working with a mutation that affects cancer last month received endowed inaugural chair positions at Stony Brook University.

Ute Moll is the Renaissance Endowed Professor in Cancer Biology, Anissa Abi-Dargham is the Lourie Endowed Chair in Psychiatry and Henry Tannous is the General Ting Feng Cheng Endowed Chair in Cardiothoracic Surgery.

In addition to adding the prestigious titles and winning support from local benefactors and philanthropists, the three researchers will each receive annual financial support from their positions that will sustain their research and education efforts. TBR News Media is highlighting the research from each of these standout scientists.

Ute Moll

Ute Moll

A native of Germany, Ute Moll, who is studying the six most common mutated forms of the highly researched p53 gene, is grateful for the donors, the funds and the recognition. “It’s pretty prestigious to have an endowed chair or professorship attached to your name or title,” she said 

Moll described the p53 mutations as the “most common mutation in cancer.” She has been working with a mouse model. The p53 R248 hotspot is the single most common variant in all p53 altered tumor types, which occurs in about 66,000 newly diagnosed cancer patients in the United States each year.

If these mice also have a gene called Myc, they get either liver or colon cancer. By receiving an estrogen derivative drug called Tamoxifen, which is used in breast cancer, the active, mutated version of the p53 gene is turned off when another gene called Cre recombinase is activated. By removing the p53 gene, the mice live two to three times longer than they would have.

In a typical mouse, cancer can cause over 100 tumor nodules, leaving almost no normal liver. When Moll and her colleagues turned off the mutant gene, the size of the cancer is much more limited, with only a few remaining nodules.

One particular mouse lived for more than two months, eventually dying of an unrelated lymphoma. The liver, however, which had an infection across the entire organ, didn’t show a single trace of a tumor. It was completely normal, despite the ubiquitous tumor nodules before treatment.

Thus far, targeting this mutated p53 is a concept Moll and her colleagues have developed in pre-clinical mouse models of lymphoma, colon and liver cancer, but it doesn’t yet have a clinical application. 

Liver cancer used to be relatively rare in the population, driven largely by infection from hepatitis B and hepatitis C, as well as through alcoholism. Amid an epidemic of obesity, people are developing a chronically inflammatory liver condition, which increases the incidence of liver cancer.

Anissa Abi-Dargham

Anissa Abi-Dargham

A specialist in Positron Emission Tomography (or PET) imaging for schizophrenia, Anissa Abi-Dargham is pleased with the opportunity to deploy the funds for her work at her discretion.

“The beauty of these funds is that they are totally flexible,” she explained, adding that she plans to use the funds to pursue new research ideas that might not otherwise get funding until she can use data to prove a concept or principal. 

“This is really a great honor because it means that the institution believes in you and wants to invest and retain you,” she said.

In her work, Abi-Dargham has been using imaging to see what is causing dopamine dis-regulation, either with too much or too little of the neurotransmitter. 

She is looking at two systems that may explain the imbalance: the cholinergic system and the kappa opioid system.

Abi-Dargham had been at Columbia University for 20 years before joining Stony Brook over three years ago. She appreciates the school investing in a state-of-the-art imaging center. “The people in charge of this imaging center are very much investing in promoting imaging for neuroscience and psychiatry,” she said.

Based on her findings in schizophrenia, other investigators in the United Kingdom have documented dopamine levels before schizophrenia symptoms begin.

She hopes her research discovers biomarkers that can be used to predict who is going to convert to having schizophrenia.

Patients do better when the onset of symptoms is later in their lives because their more mature brain has fostered better organized life, skill sets, and relationships.

She is also testing whether other markers, such as a neuromelanin, which is a metabolite of dopamine and binds iron-like materials, will show up on a Magnetic Resonance Imaging scan before the disease.

Henry Tannous

Henry Tannous

Henry Tannous joined Stony Brook University in 2016 and is excited to be a part of the current team and to help shape the future of clinical practice and research.

Tannous called the endowed chair position an “absolute honor.” It will not only allow him to continue with his current work, but it’s also going to enable him to expand his research. He will also use some of the funds to provide continuing education for his staff.

The financial support will allow him to hire research assistants and access national databases. Tannous and his research team of cardiothoracic and lung scientists use registries from the New York State Department of Health registry and the Society of Thoracic Surgeons, each of which provides the data for a price.

With his lung work, Tannous focuses on state 1 lung cancer. Traditionally, he said, people have received a diagnosis late in the development of the disease. Over the past few years, doctors have diagnosed patients at an earlier point.

Earlier diagnoses became more prevalent after Medicare approved lung cancer screening in 2015, which picked up more cases while patients were still in the earlier stages, when the cancer might otherwise be asymptomatic.

“We would like to know more about how the disease affects [patients] and their quality of life,” Tannous said. His lab has a collaboration with Mount Sinai Hospital to learn more about the effect of the disease on the lives of the patients.

With his heart research, he’s focusing on aortic disease and is testing the limits of the Trans Catheter Aortic Valve Replacement.

Photos courtesy of SBU

By Daniel Dunaief

Two researchers from Brookhaven National Laboratory were stuck on a ship trapped in ice near the North Pole — and they couldn’t have been happier.

In fact, one of them, Matt Boyer, an Atmospheric Scientist at BNL, is returning to the German ship Polarstern for six of the next seven months. The Polarstern is part of a 20-nation effort that will gather information about the Arctic to understand climate change. The scientific collaboration, called MOSAiC (Multidisciplinary Drifting Observatory for the Study of Arctic Climate), started in September and will involve collecting data for a full year.

The scientists are measuring aerosols, cloud particles, and other data through conditions that are among the most challenging on the planet. Researchers aboard the Polarstern regularly endure cold temperatures, fierce winds, minimal to no sunlight and the threat of polar bears unafraid of humans.

Janek Uin, an Associate Atmospheric Scientist at BNL, is working with instruments that measure properties of atmospheric aerosol particles such as their size, the concentration of particles per unit volume of air, how the particles are affected by water vapor and how much light the particles scatter, which affects the sunlight that reaches the Earth’s surface.

Arthur Sedlacek, an atmospheric chemist with the Environmental & Climate Sciences Department at BNL, is one of a host of scientists collecting data from the Polarstern. Indeed, Sedlacek traveled to Tromsø Norway when the ship departed, where he prepared to measure the accumulation of black carbon in the Arctic. 

Caused by burning fossil fuels, emissions from distant wildfires, among other things, black carbon can cause polar ice to melt. When there is sun, the black carbon prevents the reflection of the light, which further darkens the white surface, either through exposure of the underlying ground or previously deposited black carbon.

Sedlacek, who did not travel aboard the Polarstern, said scientists around the world are “itching to see the data” from this ambitious mission. The data collection is “so unique and so important that it will not only help us better understand the current (pristine) state of the cryosphere, but it will also [allow scientists] to better understand (and quantify) how the Arctic is responding to climate change.”

Uin, who is an instrument mentor for about 30 instruments worldwide, recalled how he went out for a fire drill. Following his designated path and waiting for the signal to return, Uin decided to snap some pictures of a frozen and uneven landscape that appeared blue during much of the day, when the faint rays of the sun barely made it over the horizon. Unable to maneuver the camera to his satisfaction, Uin took off his gloves. His exposed fingers became numb in the wind. After he put his gloves back on, it took about 10 minutes for the feeling to return to his hands.

Boyer, meanwhile, who spent more of his time working outside than Uin, helped set up the meteorological site about 1 kilometer away from the ship and is monitoring the size and concentration of organic and inorganic aerosol particles.

The size and concentration of the particles determines how they behave in atmospheric processes, Boyer explained. The size of the particle influences its light scattering ability, how long it stays in the atmosphere, the human health impact and its ability to form clouds, among other properties.

The process of working near the North Pole requires a high level of patience. A task that might take two hours in a lab, for example, might require as long as four days to complete in Arctic conditions.

Boyer described how the moisture from his own breath sometimes froze in his face. “I prefer not to wear goggles” because they fog up, he explained. When he exhaled, the water vapor in his breath caused his eyelids to freeze shut. “You have to constantly close your eyes and pull the ice off your eyelids.”

Boyer had to hold onto a piece of metal when it was well below 0 degrees Fahrenheit and windy. Placing the bolts, nuts and screws into a hole with a glove on is “almost impossible,” Boyer said, although once those items are in place, holding a wrench with gloves on is manageable

Each time people work outside, polar bear guards constantly watch the horizon to make sure the carnivorous creatures don’t approach scientists. While the ship is not a cruise vessel, it offers pleasant amenities, including a small pool, a sauna, an exercise room and nourishment Uin and Boyer, who were roommates aboard the Polarstern, appreciated.

“The food was excellent,” Uin said. “Working long hours in extreme conditions in close quarters, the food has to be good. If it’s bad, morale plummets.” The scientist has been on three ice breakers and the food has always been high quality. 

Uin appreciated the opportunity to take the journey and to conduct the scientific research. “I am reminded how lucky I am that people trust me to do this,” he said.

Uin enjoys the opportunity to look at the ice, which appears blue because of the low light. “People think it’s all white,” he said. “There’s a constant twilight and an all-encompassing blue.” He is excited to look at the information the instruments collect and is “certain that the data will help to bring new insights into the very complex processes governing Earth’s climate and help better predict future trends.”

Boyer, who plans to leave BNL this month to pursue his PhD at the University of Helsinki, said he appreciated the opportunity to be a part of a multi-national team. “I’m one of the luckier people on the planet,” Boyer said. “Not many people will see the Arctic and the Antarctic and I’ve seen both,” adding that there is a satisfaction at being involved with something that is “much larger than myself. I’m a part of a community that works together towards a common goal. It’s nice to be a part of an international team working with people from places and countries who put aside their differences.”

All photos from Janek Uin

Photo from METRO

By Daniel Dunaief

Daniel Dunaief

Welcome to the home office. I have been working from home for years and would like to offer a few tips.

For starters, pets are generally awesome. They can reduce the stress from deadlines and from abrasive calls. Much more often than not, they seem absolutely delighted to see us and to give and receive positive attention.

The wag, wag, wag of a dog’s tail is almost as wonderful as the squeal of a happy toddler when he sees the ice cream on his plate or learns about a trip to the store — ah good times, remember when stores were open? — or to a visit with a favorite relative.

But then there’s the dark side. My big dog offers quiet companionship most of the time. He does, however, have an uncanny knack of barking at what appears to be absolutely nothing outside when I’m on the phone with someone who is coming to the point of a long and deeply moving anecdote.

Nothing takes the professional veneer off an interview with a Nobel Prize winning scientist, the chairman of a department or the head of a medical school faster than the unwelcome sound of a dog barking.

Well, that’s not entirely true. I have exacerbated that dilemma. You see, I thought I hit the mute button on my phone and shouted unpleasant words at my wonderful four-legged companion, only to discover that, in my haste, I missed the button, giving my professional contact an earful of seemingly out-of-my-mind comments. 

So, there are two lessons: Keep your barking dogs far from the phone when possible, and make absolutely sure you push the mute button before breaking character and insisting that your beloved buddy stops barking at the squirrel that tortures him — and you — during important calls.

OK, so the next tip is fairly obvious, but bears repeating. The refrigerator is not calling you. While you’re home, you will undoubtedly have competing impulses that you might not have indulged in at the office with a trip to the kitchen. One of them is to fill the momentary lull between calls, or the period when you might otherwise chat at the watercooler about the latest sports games — ah, remember when we used to watch sports in real time? The kitchen is fine and doesn’t need a visit, especially given the dwindling supply of basic items that might be harder to get the next time you go to the supermarket — ah, remember the good times. OK, you get the idea.

Create signals with the rest of the family, who are home with you or back in the nest to alert them to the most important work-related tasks of your day. If you are on a conference call with people who are signing up for off-site responsibilities for the next few weeks, the last thing you want to do is have someone come to your work space and ask if you’ve seen the blue sock to match the one he’s holding with an exasperated look at your door.

Finally, remember that the kind of things you might say in the context of gossip or jokes don’t always translate through texts and emails. No matter how some emojis might indicate that you’re joking — a winking circular blob, perhaps or a shrugging face — the person on the receiving end of your witticisms might not get it and might not find your brilliance so charming, especially if she’s still upset at the words she screamed at her barking dog earlier in the day.

Photo from YouTube

By Daniel Dunaief

Daniel Dunaief

We take so much of our life for granted. In some ways, it’s natural and necessary. After all, if we got up and stared out our window and marveled at the combination of sun and shade on the branches rocking in the wind, bent down to admire the dew clinging to the grass and breathed deeply of the newly blossoming trees every morning, we might never get our kids to school and ourselves to work.

And yet, all the news about the spread of this new virus and the ensuing reaction to protect the population — from closing schools to avoiding subways to staying away from large crowds — gives us an opportunity to appreciate the things, people and sensory experiences we take for granted.

No one will miss the scent of urine wafting up through the subways during a hot summer day when switching problems make everyone stand four, five and six deep on the platform, waiting for the next overcrowded and overheated subway car to arrive.

Still, we may miss so many other sensory, social and everyday experiences if and when we have to lock ourselves in our homes, waiting for the “all clear” sign.

So, what are some of those experiences? It depends on whom you ask and what time of year the question arises.

I appreciate the joy of people watching. After living in Manhattan for decades, I’ve learned to swing my eyes across the street inconspicuously, while I seemed lost in thought or even pretended to be on an invisible phone. Times Square, with its superabundant tourists speaking uncountable languages, wearing unrecognizable colognes and walking in all manner of shoes, is a great place to start.

But then, the line for the Statue of Liberty and Ellis Island offers a similar variety of people from all over the world. Instead of billboards of half-naked and incredibly tone and muscular bodies advertising Broadway shows and underwear, the backdrop for the people watching at the ferry lines includes the unpredictable waves of the Hudson River, which has its own personality, ranging from near stillness to foaming white caps.

Closer to home and nearer to summer, West Meadow Beach blends the natural with the call of the seagulls across the enormous intertidal zone and the salty, wind-carried scent; and the anthropogenic with the plaintive cry of babies overheated by the hot sun, the sound of music vibrating from sound systems and the sight of happy teenagers taking their first lick of their soft-serve ice cream cones.

I enjoy watching the end of a hard-fought tennis match, when two or four people come to the net and exchange pleasant handshakes and share thoughts about a good match or a good game.

The crowds at sporting events, many of whom we might not choose from a potential lineup of friends, become a part of memorable games and evenings, as we exchange high fives with inebriated strangers, share insights about what we would do if we were the manager of the team, or congratulate the parent of one of the players on our daughter’s team for the improvement in her game.

Despite the fact that I tend to avoid a crowded elevator car, an overstuffed subway or even an escalator with too many tired bodies waiting for a machine to bring them to the top, I will miss the chance to share some of these experiences with the random strangers who might become friends, the fellow sports fans who might offer a game-within-a-game entertainment, or the chance encounter with a long-lost friend whose winsome smile is the same as it was decades ago in an eighth-grade math class.

Maureen O’Leary. Photo courtesy of SBU

By Daniel Dunaief

Like the great white shark that needs to keep swimming to stay alive, scientific databases that provide resources to researchers from all over the world can’t stay still or they risk losing their usefulness and reliability.

The directors of these resources need to find funds that will ensure that the data remains accessible and that users, who range from high school students conducting work for a class to the chairman of research departments at colleges, can benefit from the availability of information.

Maureen O’Leary. Photo from SBU

Maureen O’Leary, a Professor and Graduate Program Director at the Department of Anatomical Sciences at the Renaissance School of Medicine at Stony Brook University, is looking to ensure that Morphobank, a web application and database that allows scientists around the world to share raw data on the structure of various organisms to help determine their evolutionary links, receives funds that sustain its mission.

O’Leary helped start MorphoBank in 2000 to encourage researchers to share data and propel science forward and is currently the director. By making observations of the structures of organisms available in one place online, she hoped to help advance the field of phylogenetics — the relationships among organisms in a family tree — while cutting down on the need to reproduce data from the same fossils at museums or other sites.

Up to this point, O’Leary has found financial support for the effort through grants from the National Science Foundation, the American Museum of Natural History and the National Oceanographic and Atmospheric Administration.

Looking to the future, however, O’Leary wanted to create a financial plan that would ensure ongoing funding for a database that has not only helped researchers explore data, but has also enabled collaborators to share information privately in a non-public area of MorphoBank.

O’Leary has been working with Phoenix Bioinformatics, a nonprofit group based in Fremont, California that has developed funding models for databases. Phoenix started its operations in 2013 after the staff of TAIR, a curated database for plant genome information, lost its grant funding.

The business is in the early stages of helping O’Leary with Morphobank, said Eva Huala, the Executive Director of Phoenix and a founding member of TAIR.

Phoenix has helped construct a financial model that is similar to the way university libraries and scientists pay for subscriptions to journals. The prices vary depending on the database the library subscribes to and the amount of usage of that database from the university. 

Huala said Phoenix is providing software that helps recruit members. The company is also enabling users to see whether their institution is supporting MorphoBank. So far, the Executive Director is “encouraged by the response. We know that this often takes several months or longer for libraries to decide” to lend financial support, she said.

The cost of running MorphoBank is connected to the time people spend curating as well as fixing bugs or managing computer-related challenges. Without software patches and fixes, the databases can run into problems.

Universities often require their researchers to make sure the data they collect is available to the scientific community, Huala explained, adding that MorphoBank can give scientists a way to “demonstrate the impact of their research” by offering download and viewing statistics for their data.

Mike D’Emic, an Assistant Professor in Biology at Adelphi University and a member of the Executive Committee of MorphoBank, has used the database for over seven years.

D’Emic suggested that MorphoBank “saves people from reinventing the wheel in doing science” by providing free, raw data. Scientists don’t have to travel to museums or other sites to gather the same information.

An early career researcher or student might have a small grant to visit three or four museums. These scientists can “supplement that data set with information from MorphoBank that’s multiple times the value of a grant they would have gotten,” D’Emic noted.

Scientists can freely use data from MorphoBank that would have taken tens of thousands of dollars to acquire. This includes photographs of a dinosaur skull from distant countries or CT scans that can be expensive to produce.

D’Emic, who helped convince the Adelphi library to provide financial support for the database, said MorphoBank addresses bug reports quickly, fixing problems with a few days.

Prior to O’Leary’s effort to start MorphoBank, a researcher might need to search through the appendices or the published reports from other scientists in their field to access raw data for tree building, sometimes retyping by hand large spreadsheets of numerical scores.

MorphoBank has been “invaluable and transformative in terms of the way people access and replicate science,” D’Emic said.

Some journals have started urging authors to publish their data online. The Journal of Vertebrate Paleontology strongly recommends uploading dataset, character descriptions and images to an online repository.

“For not too much money, MorphoBank has a huge impact on science,” D’Emic said, who said it was a cost effective boost to evolutionary biology and related fields

Scientists have changed significantly in their approach to sharing information. Around 30 years ago, some researchers wouldn’t always share their raw data. Other scientists would then have to spend thousands of dollars to travel to places like Thailand, Australian and Madagascar.

“People have come around” and are more comfortable exchanging data, sometimes as they produce it, D’Emic said. “MorphoBank has been an integral venue for convincing people you should share.”

O’Leary believes researchers have evolved in the way they think about the information they collect as a part of their studies.“We have reached a social transition where scientists get used to not only writing a paper and walking away, but making sure the data content is in a digitally reusable format,” she said.

O’Leary feels fortunate to have received funding for over two decades for MorphoBank. She plans to remain the director when MorphoBank moves to Phoenix. It’s an “important and dynamic tool” and she feels a “responsibility to allow its continuity.”

 

Stock photo

By Daniel Dunaief

Daniel Dunaief

I just celebrated an incredible birthday, thanks to the thoughtfulness of friends and family who took the time to talk with me and shop for greatly appreciated gifts.

Each year, these birthdays have the potential to be challenging, especially given that mine often comes some time around school midterms. Even though I’m no longer watching the calendar to see how many days I have left before I have to take a big test, I still ride that roller coaster vicariously with my children. This year, however, enormous and difficult tests didn’t hang over us, like the academic sword of Damocles.

For starters, before my birthday celebration kicked in, my sister-in-law and brother-in-law sent me AirPods. I knew I was supposed to open the gift on my birthday, but I’m not exactly the most patient person when it comes to opening presents. Gee, I wonder where my kids get that trait?

Anyway, the reaction from my son was almost as enjoyable as the present itself. When he saw me wearing them, he said, “How did you get those?” as if the question were an accusation. “My friends all have them.”

My daughter did a test run with me, chatting with me on FaceTime while she stared at my ears instead of at my uneven sideburns or the hairy bridge connecting my eyebrows. It’s increasingly rare these days for anything I do, say or wear to be considered “up to date,” so this wonderful gift hit the mark.

I’m enjoying using the AirPods at the gym, where I don’t have to worry about the wire bouncing around when I’m running or after I’ve exercised, when I’m panting as I lean over the water fountain.

The best part, though, is that they allow me to talk with someone while I’m walking my dog and picking up his droppings. I don’t have to worry about the wire coming lose when he suddenly pulls hard on the leash to chase a rabbit or to run away from the sudden noise a desiccated leaf makes when it blows in the wind behind us. Yes, despite his 90-pound body, he finds the unexpected noise from leaves threatening.

While I insisted to my wife that she didn’t need to buy anything for me, she purchased several items of clothing, like shorts and shirts that fit, look good and are incredibly comfortable. She also got this terrific jacket that repels the white dog hair that has rendered the rest of my outerwear ridiculous when interacting with members of the general public.

This birthday we ventured to the Big Easy, where the ubiquitous music still resonates. We took a paddleboat ride and heard about the Mississippi River and the site of the Battle of New Orleans. The oak trees lining the bank are about 250 to 300 years old, which means that the same trees stood in the same spot during the battle. 

My teenage son, who isn’t always the picture of patience with his demanding dad, played with me and allowed me to hug him in public during the weekend. That was better than any gift he could have purchased. My daughter, meanwhile, celebrated vicariously from college. A few of her friends wandered into the screen and wished me the best.

Finally, I connected by phone with college roommates, nephews, brothers and my mom, who was a critical part of that day so many years ago. Birthdays have, at times, made me feel older and displaced. This one, with the meaningful conversations, the laughter with my wife and children and the chats with friends and relatives, as well as the “cool” gifts, made me feel so young.

Members of the team at Brookhaven Lab’s Accelerator Test Facility from left, Mark Palmer, Dejan Trbojevic, Stephen Brooks, George Mahler, Steven Trabocchi, Thomas Roser, and Mikhail Fedurin. Photo from BNL

By Daniel Dunaief

Scientists at Brookhaven National Laboratory and Cornell University have tested and developed a new “green” accelerator. Capturing and reusing the energy from electrons that are decelerating, the newly designed model, called CBETA, will have uses in everything from computer chip manufacture to medicine to missile defense to basic science.

Employing permanent magnets, which require no energy to operate, and superconducting material, these researchers brought to fruition an idea first formulated in 1965 by Maury Tigner, professor emeritus at Cornell University.

“It was talked about for many years,” said Thomas Roser, who just completed his 10th year as chairman of the Collider-Accelerator Department at Brookhaven National Laboratory. “To put everything together in an energy efficient way could have a significant impact for the future.”

Indeed, the new design could lower the energy needs of a future facility like the Electron Ion Collider, which BNL plans to complete in 2030.

“We all have a responsibility to contribute to the well-being” of the planet, including in efforts to reduce the energy consumption of devices used to unlock the mysteries of the universe and produce future technology, said Roser.

Schematic of the Cornell-BNL
ERL Test Accelerator.
Image courtesy of Cornell University

One of the many advantages of the new accelerator design, which was tested in the early morning hours of Dec. 24 at Cornell, is that it captures and reuses the energy in a multi-turn particle accelerator. The idea of the accelerator was to enable beams of different energy to travel through the same magnets on slightly different paths in an oblong structure. 

The design is akin to a relay race on a running track. Each lane has runners that move at their own speeds. When it is time for one of the runners to slow down and leave the track, she shares the energy from her sprint with an intermediary, which drives the next runner forward at a rapid pace, while she decelerates in a nearby loop.

In the case of the accelerator, the intermediary is a superconducting radio frequency cavity.

A key design feature is that multiple beams recirculate in these cavities four times. This cuts down on future construction costs and reduces the size of an accelerator from about a football field to a single experimental hall, according to information from Cornell.

A fresh electron beam allows researchers to get a better quality beam than in the traditional way of operating an accelerator, in a ring that would circulate continuously. 

“The beam is always refreshed, and what gets recirculated is the energy,” Roser said.

The high quality, bright beam creates bright lasers that companies may be able to use to manufacture new chips for computer or phone technology. These accelerators could also make infrared lasers that could melt objects. This type of application could help with defense department efforts to thwart an incoming missile. While BNL is taking steps to work on applications in other areas, the Department of Energy laboratory is not involved in such missile defense applications.

In the medical arena, this kind of accelerator could enable the construction of smaller, simpler and lighter devices for proton therapy to treat cancer. The multi-energy beam transport of CBETA would allow the building of more compact and less expensive gantries that deliver beams to the patient.

Using different energies at the same time, doctors could “treat cancers at different depths inside the body,” Roser said. “That’s an application for this unique transport.” Proton therapy could become cheaper and available in more hospitals with this approach, he asserted.

For Dejan Trbojevic, the principal investigator on the CBETA project and a senior physicist from BNL, the successful test of the concept was a validation of over 20 years of work.

“You can do a lot of simulations assuming realistic errors,” but the actual experiment demonstrating the concept “makes a big difference,” he explained in an email.

The BNL scientist was at Cornell in late December, where he and his colleagues celebrated the results with champagne.

Trbojevic, who had developed the concept of using a single beamline instead of multiple beamlines, hopes to use the new design to create a less expensive design to proton therapy treatment for cancer

“I’m trying to make this cheaper so more hospitals can have it,” Trbojevic said. He has already made contact with companies and a professor in Europe who hopes to use the design concept. He has also requested funding from the Department of Energy.

Beyond the excitement of the recent collaboration with Cornell on the new accelerator design, Roser reflected on his first decade as chairman of the Collider-Accelerator Department.

The BNL department is leading the world in many accelerator technologies and is collaborating closely with CERN, which was founded in Europe seven years after BNL.

Indeed, this year marks numerous celebrations for the department. The Relativistic Heavy Ion Collider, or RHIC, has been operating for 20 years and will become a part of the new Electron Ion Collider. At the same time, the Alternating Gradient Synchrotron, where research for three Nobel Prizes was conducted, marks its 60th year of generating scientific results.

And, to top off the historical trifecta, Ernest Courant, a former BNL Scientist who teamed up with Stanley Livingston and Hartland Snyder to create the strong focusing principle, turns 100 in March. Courant, who worked with Trbojevic on a paper describing the single beamline concept in 1999, helped provide a critical step for modern particle accelerators.

As it did 10 years ago, the department is rolling these three celebrations into one in June.

Courant can’t attend the event because he lives in a retirement home in Ann Arbor, Michigan near his son. BNL will likely show photos and video from Ernest’s birthday at the celebration.

As for the recently completed collaboration with Cornell, Roser believes the work is an important step.

“It’s a new concept and a new type” of accelerator, Roser said. “That doesn’t come around very often. There are cyclotrons and there are linear accelerators. This is a combination of a circular and linear accelerator put together in a new way.”