Josh Joseph is a senior journalism student at Stony Brook University with a passion for technology and art. He serves as executive editor and creative director for the Stony Brook Press, SBU’s campus magazine, where he creates graphics and layouts and contributes writing.
Computer science and bioinformatics researchers at Stony Brook University are trying to expand doctors’ understanding of COVID-19 with a little help from artificial intelligence.
Prateek Prasanna, an assistant professor in the biomedical informatics department, is one of many researchers across the globe who are focused on putting machine-learning algorithms to work in the fight against the coronavirus. He is a doctor of biomedical engineering who came to Stony Brook in January 2020, and has previously used AI to study and analyze lung cancers. Prasanna arrived on the cusp of the coronavirus outbreak, and just four months later, he and his team were selected to receive seed grants from the university’s COVID-19 research program, a fund created to accelerate projects that study the virus.
They have spent the months since shaping computer brains to recognize and label certain features on COVID-positive lungs from X-ray images. Once these brains are properly trained, they will be able to detect COVID-19, and even offer a prognosis for the potential severity of each case.
“We saw that there might be these subtle differences in imaging signatures between, let’s say, a patient who is COVID-positive and does not required mechanical ventilation and another COVID-positive patient who needs mechanical ventilation,” Prasanna said on a Zoom call, his face superimposed on an image of Stony Brook University Hospital.
He spoke with a careful, measured cadence, but his excitement resonated as he discussed his findings. “So we hypothesize that there might still be imaging differences between these cases, and using machine learning and AI techniques, we would be able to tease out what these differences are.”
Prasanna’s team includes two researchers from Stony Brook, four from Newark Beth Israel Medical Center in New Jersey and one from the Indian Institute of Technology in Bombay, India. Their expertise also varies, from bioinformatics — the analysis of biomedical data — to electrical engineering and radiology. They began their study with 514 chest X-ray images gathered from Stony Brook and Newark Beth Israel Hospitals. Some showed the lungs of COVID-positive patients and some showed those of COVID-negative patients.
Each image included demographic data about its subject: age, the severity of the disease and underlying medical conditions, among other data points. That data, collected by medical institutions and prepped by the researchers, became what is known in the world of AI as the “ground truth” on which an artificially intelligent computer formed its own understanding of each set of lungs. After processing a number of human-sorted positive and negative cases, the algorithm was able to begin classifying them by itself, generating the probability of sickness for each image.
Machine learning, the basis for Prasanna’s study and thousands of others like it, relies on a computer processor’s ability to observe patterns and by recognizing them, to refine itself — in other words, to learn. In this case, minute features in COVID-positive X-rays — one is called “ground-glass opacity” or GGO — began to emerge as distinct characteristics that the trained algorithm, when tested blind, can use to predict the presence and severity of COVID.
The flexibility of the resulting algorithms allows the team’s research goals to shift with ease. For example, they began to examine the experimental practice known as “proning,” or having certain COVID patients lie on their stomachs instead of their backs during hospital care. Their existing machine-learning model reviewed X-ray scans from patients who were placed in prone positions and those who were not, demonstrating the benefits of the practice.
In May 2020, their research was recognized among 17 research studies to receive seed grant funding from the university’s Office of Research. “In very short order, I think in just a matter of a week, we redirected some funds that we would have used for other seed funding, and we created a seed funding program,” said Richard Reeder, Stony Brook’s senior vice president for research. “We got the funding to them right away … and the idea was that they would carry out research [and] position themselves to be able to put together a proposal for federal funding.”
Prasanna’s team has been using that time and funding to develop algorithms and submit papers to national organizations. So far, their work has been accepted by the 2021 Society of Photo-optical Instrumentation Engineers (SPIE) Medical Imaging Conference, the Journal of Clinical Medicine, the 2021 Medical Imaging with Deep Learning Conference (MIDL) and the Medical Image Computing and Computer Assisted Intervention Society (MICCAI). An additional manuscript is still in revision. “The initial results are quite promising,” Prasanna said. “Still, there’s still a lot of research to be done … before we can even start thinking about, let’s say using some of these studies as a triage mechanism to decide … which patients we need to pay more attention to.”
That research is expected to come as national institutes such as the American College of Radiology and the Radiological Society of North America release larger sets of images and data. These will allow researchers like Prasanna to further sharpen their algorithms, delineating positive diagnoses from negative ones and severe COVID cases from minor ones.
“God forbid, if there’s another sort of wave where you might not have enough testing… can we use imaging to diagnose and predict the trajectory of COVID?”
– Prateek Prasanna, assistant professor in Stony Brook’s Bioinformatics department
Of the first 514 chest X-rays Prasanna’s team used, 463 came from Stony Brook University Hospital’s own COVID-19 database. Known as the Data Commons and Analytic Environment, it was created to enable fast research that could result in medical use.
Dr. Kenneth Kaushansky, the former dean of Stony Brook’s Renaissance School of Medicine and senior vice president of Health Sciences, explained the need for such a database.
“Early on in the pandemic, I felt like we ought to have a single site with highly reliable scrubbed data on every patient we see. I think it took something like 40 people in the Department of Biomedical Informatics — graduate students, volunteers, students, medical students, staff and faculty — to set this up. And now people in radiology or image analysis or computer sciences can get into that database and extract the images, and all the other clinical history that goes with that particular image, and now use deep learning algorithms, AI as well, to sort out ways to better diagnose and prognosticate from images.”
It will likely be months before Prasanna’s algorithm is put to work in a medical setting. Although Prasanna sees his study going in many directions for practical use, one easy application he foresees is as a supplement for existing clinical testing.
“God forbid, if there’s another sort of wave where you might not have enough testing … can we use imaging to diagnose and predict the trajectory of COVID?” Prasanna said. “That, I think, is ripe for transition to clinic.”
In the meantime, Prasanna and his team continue to receive images from Stony Brook as well as medical centers in Newark, India and other areas, feeding the data through their algorithm — and honing its accuracy as it keeps learning.
The hand truck rumbled on the pavement, shaking and shifting nine neatly stacked cardboard boxes. It was a brisk November night, and we wore winter coats and face masks. Tumbling over a curb, we made it to the rear entrance of the Student Activities Center. The building was silent except for a few CulinArt workers shuffling in and out. Lights shone through the windows against the dimming sky, but no human shadows interrupted them. We wedged our way through the double doors and wheeled our payload into the carpeted freight elevator.
On the third floor, I held my ID to the door until an affirmative beep let us into the empty office. One by one, we transferred the boxes onto an empty black folding table. I found a pair of scissors and ripped into the nearest one, revealing two stacks of freshly printed magazines – the December 2020 issue of The Stony Brook Press. The front cover featured telephone poles stretching upwards on a red and blue background, a graphic I had made before any of us knew the coronavirus would irrevocably change our lives.
The stories inside spanned months spent in quarantine, some previously published online, and some left incomplete until now. The issue was finished a month before, when there was still hope it would arrive in time for students to read it — but complications with the printer and the accounting office pushed delivery past the Thanksgiving break. Now, it exists in limbo, boxed up in the office as would-be readers scattered across the country.
Flipping through the pages, I felt the same rush I’ve felt seven times before, the one that comes with seeing something I’ve labored over for weeks finally set in print. It was dulled by the absence of readers. No amount of social media buzz could replace eyes and hands examining our work in person. Aside from the few we picked off, nearly 500 magazines sit idly in the SAC, waiting for Stony Brook to come back to life.
In 2013, the Stony Brook Foundation — the nonprofit arm of the university that receives and manages private donations — established the Discovery Prize, a contest to fund original research with private money at a time when federal support was receding. Each year the prize has been awarded — 2013, 2017 and 2019 — four finalists were selected, and one winner received a $200,000 grant to continue and expand their research team’s work. Previous winners pioneered new methods of cancer research, electron analysis and mapping the unconscious brain. “Our goal is to encourage our faculty to ask the big questions and pursue the unknown,” actor and Stony Brook University donor Alan Alda said in a 2020 promotional film.
This was an unusual year to give a Discovery Prize. In March of 2020, all but the most essential in-person research at Stony Brook paused as COVID-19 began moving across the United States. At the time, all four finalists and their research groups left their labs, preparing for a break that became a year of social distancing and mask wearing. Some were able to transition to a virtual approach, and others lost whole months of research. All of them were affected by the pandemic, as the very nature of life was reshaped by the coronavirus, and none of their labs have yet to return to business as usual.
And yet all four made immense strides in their respective fields, pushing the boundaries of their disciplines and by extension, the horizons of human knowledge.
One was awarded the $200,000 prize. And even though the winner has already been officially announced and the congratulations and accolades are no doubt still pouring in, it’s worth taking a look at the final four and the work they continue to do.
Greg Henkes – Rock Star
In his office on the third floor of the Earth and Space Sciences building, Professor Greg Henkes caught a brief break from the social distancing and mask wearing that his research mandates. He sat at his desk, but behind him signs of his work in progress were visible — a binder filled with creased, typed pages, and an expansive whiteboard marked with calculations and figures.
As a geoscientist, Henkes’ work involves vaporizing rocks into atom-sized particles, searching for clues to the climate conditions on planet Earth millenia in the past. The project made him a finalist for the Discovery Prize.
“This idea of reconstructing — or reanimating — environments in the past is kind of interesting, all over the surface of the Earth if you can find the right rocks,” he said. The metal zipper of his red puffer vest dangled as he gestured enthusiastically.
Last March, as COVID-19 began to spread across the country, Henkes was informed that his lab would have to shut down, pausing his research immediately with no return date in sight. He would return once a week to monitor the lab’s state-of-the-art mass spectrometers — the rock vaporizers.
“These mass spectrometers are, you know, some of them are as expensive as a Ferrari,” he said. “You don’t just sort of pull your Ferrari over to the side of the road, get out of it and walk away, right? You got to go find a garage, and … maybe you put a sheet over the car, so that when you walk away from the car for, you know, two months, you come back to it, and there’s not a ton of dust.”
That maintenance involved regularly checking the machines, monitoring the health of sensitive chemical mixtures known as reagents, and performing updates to the lab’s electronic systems.
Returning from the initial closure was a gradual, meticulous process, governed by Stony Brook’s administration in accordance with multiple levels of regulations. In June, as the first wave of the pandemic began to die down, the Office of Research began a staged return-to-work plan as part of the university’s “Coming Back Safe and Strong” initiative.
“We brought research, faculty, students and staff back, so as to gradually increase the density in labs,” Richard Reeder, Stony Brook’s vice president for research, said. “And we did that with appropriate safeguards too” — all provided by an alphabet soup of agencies: the Centers for Disease Control and Prevention (CDC), the State University of New York (SUNY) and the New York State Department of Health (NYSDOH), among others.
The university administration required researchers like Henkes to develop their own plans for return following those guidelines. His plan involved slowly bringing back his fellow researchers. It also involved a lot of red tape. And other colors as well.
“We would only have no more than two people in our 1,400-square-foot lab space at a time,” Henkes said. “This was, in hindsight, probably unnecessary, but I did run into the lab when it was just me here, and started taping off six-foot … markers with lab tape.” Soon the floor was a rainbow of social-distancing strips.
“We’re making do, but if it weren’t for COVID, a student might be sorting through a cord shed in Alberta, Canada right now. Or if it weren’t for COVID, you know, we might have been just getting back from the field in Kenya.”
– Greg Henkes, Stony Brook Geology professor and Discovery Prize finalist
Henkes works with a team of eight undergraduate, graduate and doctoral students, all of whom focus on their own projects — and the mass spectrometer is an integral part of everyone’s research. Although some of them were deemed essential workers and allowed to re-enter the lab over the course of the break, all of their lab procedures were stalled as they focused on maintaining the machinery for future use.
One such student, Ella Holme, uses the machines in Henkes’ lab to compare rocks from the surfaces of Earth and Mars. Her work analyzing rocks similar to those found on Mars was incorporated into geochemistry equipment onboard NASA’s Perseverance rover, which landed on the surface of the Red Planet last February. When the lab shuttered, plans to continue her research were dashed.
“I was not doing research in person” — for example, running samples on the mass spectrometer — “from about this time last year until mid-June, and it was a big setback,” she said.
As a fifth-year doctoral student in geochemistry, Holme, who lives in Smithtown, had to defend her dissertation over Zoom while maintaining her research, which was largely incomplete.
“I did a lot of writing, or trying to, but my research at the point that quarantine hit was really at a pivotal point where I needed more data before I could really write,” she said. “So I did as much as I could, but it was fairly limited.”
Other members of Henkes’ team were more fortunate. Yang Gao and David Burtt, second- and fourth-year Ph.D. students respectively, were able to work from data they collected before the shutdown. Still, their experiences were shaped by the isolation of working virtually.
“There are definitely pros to being able to write alone in your own house,” Burtt, who analyzes rocks from ancient meteorite impacts, said in the spring. “But you also miss out on easy access to other people for conversations, for editing … just those random conversations where you’re like, ‘You know what, I was thinking about this interpretation of our results. What do you think of that? Am I just blowing smoke right now, or have I actually jumped on something?’”
When the lab was back in operation, some students resumed their two-week sessions on the mass spectrometers, persevering through the layers of lab tape on the floor. Others worked from existing data. Still, a question hangs in the air — what could have been if the pandemic hadn’t hit?
“I could name half a dozen specific cases where like, we’re making do but if it weren’t for COVID, a student might be sorting through a cord shed in Alberta, Canada right now. Or if it weren’t for COVID, you know, we might have been just getting back from the field in Kenya,” Henkes said. “If it weren’t for COVID, we might have more students working on one of the mass spectrometers.”
Mae Saslaw is one of those students, part of a team studying the conditions that may have brought about the evolutionary split between apes and chimpanzees 15 million years ago in East Africa. She hoped to return to Kenya to collect samples over the summer, but the continuation of the pandemic has made her plan tentative.
“That uncertainty is a bit of an issue,” she said in March. “If I don’t go this summer, I will be in a pretty bad situation data-wise — like, I kind of won’t really have anything to work on… I can start writing my dissertation around the data that I don’t have… but at that point, I would be looking at probably extending my timeline overall” — pushing her graduation past 2024.
Saslaw was eventually able to travel with a small group of vaccinated researchers, and anticipates a return to the field in summer 2022.
Scattered on and off campus, the Henkes Lab team, as it’s known, is still recovering from their months in the dark — but their rock-busting Ferrari is roaring back to life.
Kevin Reed – Hurricanes in the Age of Climate Change
When Climatology Professor Kevin Reed joined a Zoom meeting on Feb. 19, 2021, he quickly switched from a view of his darkened kitchen to an almost blindingly saturated virtual background. He superimposed himself at the intersection of Nicholls Road and Shirley Kenny Drive — a sunny view of the sign at Stony Brook’s main entrance, the same image he’d used three months prior when he was featured on PBS NewsHour to describe his team’s research.
Through mathematical climate models, Reed and his team have developed a kind of alternate universe of weather forecasts, showing how much more devastating hurricanes have become due to climate change.
“We change the question that the public and journalists are asking, which isn’t, ‘Was Hurricane Laura due to climate change?’ but, ‘How has Laura changed because of climate change?’” Reed said. “How [have] the different characteristics of that storm … changed over the last 150 years due to human-induced warming?”
On NewsHour, he presented a view of Laura without any of the effects of climate change — still a swirling mass on the map, but smaller and less dangerous.
When the Stony Brook campus was locked down in mid-March 2020, Reed’s sunny Zoom background became his permanent virtual residence. His tight-knit team of graduate students transitioned quickly to online meetings, running their simulations remotely through supercomputers at the National Center for Atmospheric Research, stationed in Tennessee and California.
“I still think that we all struggle individually with, you know, the human interaction — even if you’re a numerical modeler, that human interaction of discussing results, right? Over a coffee, or randomly in the hall, when we see each other or in our one-on-one meetings, you know, that’s gone away.”
– Kevin Reed, Stony Brook Climatology professor and Discovery Prize finalist
Alyssa Stansfield, one member of Reed’s team, is a fourth-year doctoral student. Her research into the impact of climate change on rainfall during extreme weather events easily transitioned to a new virtual setting.
“I was able to continue with my work pretty much unimpeded,” she said. “I consider myself very lucky. I know a lot of people in our department who do use actual labs more — they’re more on the marine science side — but they have definitely been impacted by the pause in research work. Even now, I honestly don’t go onto campus much, because I just don’t have to, and I felt like, you know, if I don’t have to risk being on campus, why add another person?”
Still, Reed said they faced some inevitable difficulties.
“I still think that we all struggle individually with, you know, the human interaction — even if you’re a numerical modeler, that human interaction of discussing results, right?” he said. “Over a coffee, or randomly in the hall, when we see each other or in our one-on-one meetings, you know, that’s gone away.”
Stansfield particularly regretted the loss of community at the tight-knit School of Atmospheric and Marine Sciences, which is composed of 500 students and 90 faculty members, often involved in highly focused in-person research at off-site locations.
“I’ve never even met the new student in our group in person,” she said. “We used to have in-person seminars every week where we would have lunch afterwards together, and now those are virtual. And we used to have some fun events throughout the year within our department, which obviously have not been able to happen. … I’m like, really looking forward to the fall semester where we can hopefully get the in-person stuff going back again.”
Reed’s group proves that, even when research means manipulating code and examining maps, the pandemic can destabilize the process and deeply affect each person involved. As Stansfield and her fellow team members await a return to the pre-pandemic norm, Reed visits the lab a few times a week, maintaining his presence amid his scattered surroundings.
Eszter Boros – Turning on a Radioactive Light Switch to Find Cancer
In her video for the Discovery Prize finalists’ webpage, Chemistry Professor Eszter Boros wore lab goggles and a white lab coat. Behind her, clear tubes and funnels wove a structure of flowing chemicals.
Her work involves the development of what she calls a “radioactive light switch” — certain metal ions that, when injected into the body, can emit a flash of blue light upon contact with a cancerous tumor. Those compounds then work in conjunction with a novel light-activated form of therapeutic drugs, allowing for hyper-targeted cancer treatments — “a sort of more broadly applicable, more clinically relevant chemotherapy,” as Boros put it.
Before implementing their treatments on a broader scale, Boros and her team test on mice to ensure efficacy and safety. That process had to stop entirely when the shutdown occurred.
“We had this mouse population that we purchased, looking forward to doing a lot of experiments, maybe in March and April,” Boros said. “And then of course, we couldn’t do any of it because everybody was at home. It was good for the mice, because they were just hanging out at the animal facility, getting old and chubby, basically eating and having a good time. But we weren’t able to do our experiments.”
In the meantime, the Division of Laboratory Animal Resources, staffed by essential lab workers, cared for the mice at Boros’ expense.
“It came at a financial cost, but at the end of the day, it kept people safe in my lab,” she said. “I wasn’t raging in my living room that we couldn’t do these animal experiments, because in the grand scheme of things, it was much more important that we were able to keep our trainees safe, our lab members safe and ourselves safe.”
For Boros’ research team — two postdoctoral researchers, seven graduate students and one undergraduate student — the pause was a time to reflect, and even to learn new skills. Angus Koller, a graduate researcher in his second year, delved into computational chemistry at home, bringing a new field into the scope of the lab’s study.
“In my case, I kind of had a unique opportunity,” Koller said. “For a long time, Eszter wanted someone in the lab group to do things involving computational chemistry, like chemical modeling and things like that. So that was one kind of project I had, was teaching myself how to do that through the quarantine since it was something I didn’t need to be in the lab to do.”
“We’re expected to keep working as if, you know, we just got sent home, we’re in detention or something, but everything else should keep going — but we tend to forget that we are in a global pandemic.”
– Eszter Boros, Stony Brook Chemistry professor and Discovery Prize finalist
Additionally, the transition to virtual research was complicated by a personal matter — Boros was nearly four months pregnant when the shutdown began, and her son was born in the middle of the pandemic. She split her time between the lab and caring for her newborn, allowing her team to work more independently.
Like the other groups spread far and wide by the shutdown, Boros’ team faced difficulties supporting each other and communicating their ideas. To better assist their efforts at home, Boros transformed the team’s once weekly in-person meetings into a series of Zoom sessions over the course of each week. On Mondays, the group would share findings from literature, on Wednesdays, they held a midweek check-in, and on Fridays, Boros met individually with each team member, ensuring any problems with their progress were addressed. She said that the meetings also helped ease personal stressors.
“Trying to just keep morale up somehow, I tried to get them to talk about what kind of movies they’re watching on Netflix and things like that, and who’s watching Tiger King and whatnot,” she said. “As an advisor, you’re trying to just kind of make up on the fly what helps keep the lab afloat the best way you can.”
“We were having Wednesday check-ins to be able to communicate with everyone,” Kirsten Martin, a third-year graduate researcher, said. “It was also just like an update on, ‘What am I having issues with? What do I need some help with?’ So that was really helpful for facilitating that communication.”
Although Zoom calls limited some of the in-person connection that made the lab flow, it also enabled an entirely different form of collaboration, knocking down borders of distance and time. Guest speakers and colleagues from universities across the country shared insights and information with Boros and her team virtually.
“Normally, when you do things like departmental seminars, it would always be an in-person thing — you’d have to fly somebody from wherever, bring them to the department, and then have them give their presentation,” Koller said. “But with the quarantine, it normalized the whole Zoom thing a lot more. So we’ve had seminar speakers who live in different countries even, or different states, and things like that. So it’s kind of nice in that regard. You can kind of get to know some people that you would basically never get to interact with, because of time barrier issues and things like that.”
For Boros and her team, one of the most valuable lessons learned from the pandemic involved managing expectations.
“We’re expected to keep working as if, you know, we just got sent home, we’re in detention or something, but everything else should keep going — but we tend to forget that we are in a global pandemic,” she said. “And this is, for our generation especially, it’s completely unprecedented. … Now we’re experiencing this constant baseline stress and baseline anxiety that we need to take into consideration and maybe not be so hard on ourselves occasionally.”
Eric Brouzes – Plumbing the Depths of a Single Cell
Biomedical Engineering Professor Eric Brouzes and his team are self-described plumbers, but not the kind who unclog toilets or fix broken pipes. They work at a scale smaller than a human hair, using tiny microfluidic tubes to analyze and sequence living tissues on the single-cell level. Unlike other methods of single-cell genomics, which require that tissues be broken down into isolated cells, the project Brouzes proposed for the Discovery Prize allows for sequencing within unbroken tissue.
“Cells don’t live by themselves,” Brouzes said. “They are in the ecosystem, and it’s really important to understand how they communicate, how they coordinate their action. So that’s the question we’re addressing with the Discovery Prize.”
When research at Stony Brook shut down, most of the work at Brouzes’ lab on the second floor of the Bioengineering building ground to a halt. He proposed one possible use of microfluidics as a diagnostic tool for COVID-19, which allowed him a limited presence through the shutdown period. But he was the only one in the lab for that two-month span. He used the time to monitor the team’s instruments and chemical reagents.
“We had a very limited presence, but still a presence during that time,” Brouzes said. “So that mitigated the risks of something going bad.”
Beyond basic maintenance, Brouzes and his team, made up of three graduate students and one undergraduate student, suffered from the lack of physical presence. All the research work that went into their Discovery Prize proposal was created “at the bench” — in-person in his lab. Forced to scatter for two months, their progress languished.
“For us, it was about time,” Brouzes said. “Dynamics in the lab can be complicated and can be fragile. So when you’ve got, for instance, a project that starts working out … you want to basically keep it rolling. And then you have to couple that with the funding of the lab as well. So we are at a point where we needed dynamics to go quickly, to get those data, and then request more funding and so on.”
Evan Lammertse, a fourth-year doctoral student, worked as an independent paid researcher in Brouzes’ lab. His time off campus was complicated by a herniated disc that went untreated through the early months of the pandemic, leaving him in chronic pain as he tried to complete what work he could with the data he had collected before the shutdown.
“I had only completed maybe 40 percent of my experiments that I had scheduled when the university shut down,” he said. “The direct result … was me not being able to collect that extra 60 percent, but the impact on my work was a lot broader than that, because it was kind of intertwined with that physical injury that I had. … I couldn’t even leave the house to walk around the neighborhood and get some fresh air. I was stuck inside for months. … The overbearing sense of powerlessness … certainly had an effect on my mental health.”
“COVID has kind of forced us to institutionalize things that previously were just informally done in lab, talking amongst people, you know, without having to create the structure for it.”
Even after returning to the lab last fall, working on microfluidic instruments proved to be more difficult. Maria Alvarez Amador, a first-year doctoral student, found herself struggling with procedures that she could have resolved had others been in the lab to help her.
“The paper instructions of how to do something don’t tell the whole story of the minutiae of what works and what doesn’t, especially in microfluidics, because you’re working on a small scale — any difference in temperature and the pressure you apply could mean your device has been successfully fabricated or not,” she said. “Once you’re in a roadblock, you really need other people to bounce off from in order to get over those roadblocks and make progress.”
Additionally, as with other research groups, Brouzes’ team began to lose the knowledge they would have gleaned from outside sources like conferences and literature and shared through discussions. When Brouzes set guidelines for his researchers’ outside work, he was met with some pushback.
“He kind of laid out expectations that he had of us as grad students, and a lot of those were more like experiential learning and like reading papers in your field and attending more seminars, and just being more extracurricularly engaged,” Lammertse said. “And my response to that was like, okay, that’s well and good, but it’s really hard to do those kinds of things without a social structure in which to do them. It’s a lot harder to stay engaged and in a dialogue with your colleagues, and learn from your colleagues, when you’re not physically present with them in the lab.”
The team said that the weight of the pandemic has had a significant impact on their ability to work. Small annoyances and adjustments accumulated over the course of the year, infringing on their ability to focus.
“There’s a lot of small things in your everyday that have changed that add up to all the stresses,” Alvarez Amador said. “Not just not seeing people, not just wearing a mask all day, not just being stuck at home, but like, where you can eat actually … tiny things that add up and affect your psyche.”
Additionally, the potential for the lab to close for two weeks after a COVID-19 exposure, in accordance with university protocol at the time, loomed over the researchers’ heads, as Alvarez Amador explained. “Every time you get a sore throat, you’re like, ‘Oh, if I test positive, I am halting my work for two weeks, I’m halting everybody’s work for two weeks,’” she said. “So there was that mental component of always being stressed out — if you hear somebody had COVID, you’re like, ‘Oh, do I have it? Do we have to get shut down for two weeks and [will I] be the reason that nobody’s making progress on the lab?’”
In order to manage these additional stressors, the team began meeting over Zoom on Wednesday mornings last January. They also maintained a journal club, which meets on Thursdays, in which one group member picks a piece of literature for the entire group to discuss.
“COVID has kind of forced us to institutionalize things that previously were just informally done in lab, talking amongst people, you know, without having to create the structure for it,” Lammertse said. “But when you don’t have everyone in the lab every day, you kind of need to do the work to create the spaces for these discussions to happen.”
The Brouzes lab anticipates a return to greater normalcy in the fall, but until then, they continue to deal with the underlying stresses of the pandemic world as they plumb the depths of single-cell genomics.
And the Winner Is . . .
“I’m very much humbled and incredibly grateful,” Boros said as she accepted the award at a virtual event on April 28 that included the finalists, judges and President Maurie McInnis. “This enables really exciting science for my research group and my students, who are super excited.”
With the $200,000 prize, Boros and her team will further develop their light-activated cancer treatments, seeking publication in medical journals and hopefully a contribution to clinical implementation down the line.
“Although much has changed over the last year of the pandemic, the passionate, committed pursuit of knowledge, research and discovery at Stony Brook University has not,” McInnis said.
Through their perseverance and adaptability, Boros, Brouzes, Henkes, Reed and their teams proved her right.