Authors Posts by Daniel Dunaief

Daniel Dunaief

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Stony Brook University. File photo

Stony Brook University has been at the center of the COVID-19 pandemic, as hospital staff has treated and comforted residents stricken with the virus and researchers have worked tirelessly on a range of projects, including manufacturing personal protective equipment. Amid a host of challenges, administrators at Stony Brook have had to do more with less under budgetary pressure. In a two-part series, Interim Provost Fotis Sotiropoulos and President Maurie McInnis share their approaches and solutions, while offering their appreciation for their staff.

Part I: Like many other administrators at universities across the country and world, Fotis Sotiropoulos, Dean of the College of Engineering and Applied Sciences and Interim Provost of Stony Brook University, has been juggling numerous challenges.

Named interim provost in September, Sotiropoulos, who is also a SUNY Distinguished Professor of Civil Engineering, has focused on ways to help President Maurie McInnis keep the campus community safe, keep the university running amid financial stress and strain, and think creatively about ways to enhance the university’s educational programs.

Stony Brook University which is one of two State University of New York programs to earn an Association of American Universities distinction, is in the process of developing new degree programs aimed at combining expertise across at least two colleges.

“We have charged all the deans to work together to come up with this future-of-work initiative,” Sotiropoulos said. “It has to satisfy a number of criteria,” which include involving at least two colleges or schools and it has to be unique. Such programs will “allow us to market the value of a Stony Brook education.”

Sotiropoulos said Stony Brook hoped that the first ideas about new degrees will emerge by the middle of January.

Fotis Sotiropoulos. File photo from SBU

Under financial pressure caused by the pandemic, the university has “undertaken this unprecedented initiative to think of the university as one,” Sotiropoulos said. Looking at the East and West campus together, the university plans to reduce costs and improve efficiency in an organization that is “complex with multiple silos,” he said. At times, Stony Brook has paid double or triple for the same product or service. The university is taking a step back to understand and optimize its expenses, he added.

On the other side of the ledger, Stony Brook is seeking ways to increase its revenue, by creating these new degrees and attracting more students, particularly from outside the state.

Out-of-state students pay more in tuition, which provides financial support for the school and for in-state students as well.

“We have some room to increase out-of-state students,” Sotiropoulos said. “There is some flexibility” as the university attempts to balance between the lower tuition in-state students pay, which benefits socioeconomically challenged students, and the higher tuition from out-of-state students.

While the university has been eager to bring in talented international students as well in what Sotiropoulos described as a “globally-connected world,” the interim provost recognized that this effort has been “extremely challenging right now,” in part because of political tension with China and in part because Chinese universities are also growing.

Stony Brook “recognizes that it needs to diversify right now. The university is considering strategies for trying to really expand in other countries. We need to do a lot more to engage students from African countries,” he said.

Sotiropoulos described Africa as an important part of the future, in part because of the projected quadrupling of the population in coming decades. “We are trying to preserve our Asian base of students,” he said, but, at the same time, “we are thinking of other opportunities to be prepared for the future.”

While the administration at the university continues to focus on cutting costs, generating revenue and attracting students to new programs, officials recognize the need to evaluate the effectiveness of these efforts for students. “Assessment is an integral part,” Sotiropoulos said. The school will explore the jobs students are able to find. “It’s all about the success of our students,” he added. The school plans to assess constantly, while making adjustments to its efforts.

Pandemic Response

Stony Brook University has been at the forefront of reacting to the pandemic on a number of fronts. The hospital treated patients during the heavy first wave of illnesses last spring, while the engineering school developed ways to produce personal protective equipment, hand sanitizer, and even MacGyver-style ventilators. The university has also participated in multi-site studies about the SARS-CoV-2 virus that causes COVID-19.

Stony Brook has been involved in more than 200 dedicated research projects across all disciplines, which span 45 academic departments and eight colleges and schools within the university.

Sotiropoulos, whose expertise is in computational fluid mechanics, joined a group of researchers at SBU to conduct experiments on the effectiveness of masks in stopping the way aerosolized viral particles remain in the air, long after patients cough, sneeze, and even leave the room.

“Some of these droplets could stay suspended for many minutes and could take up to half an hour” to dissipate in a room, especially if there’s no ventilation, Sotiropoulos said, and added he was pleased and proud of the scientific community for working together to understand the problem and to find solutions.

“The commitment of scientists at Stony Brook and other universities was quite inspirational,” he said.

According to Sotiropoulos, the biggest danger to combatting the virus comes from the “mistrust” of science, He hopes the effectiveness of the vaccine in turning around the number of people infected and stricken with a variety of difficult and painful symptoms can convince people of the value of the research.

Sotiropoulos said the rules the National Institutes of Health have put in place have also ensured that the vaccine is safe and effective. People who question the validity of the research “don’t understand how strict this process is and how many hurdles you have to go through.” 

Part 2 will appear in next week’s issue.

Illustration depicting Falcatakely amid nonavian dinosaurs and other creatures during the Late Cretaceous in Madagascar. (Credit: Mark Witton)

By Daniel Dunaief

Dromomeron and Falcatakely lived nowhere near each other. They also lived millions of years apart, offering the kind of evolutionary pieces to different puzzles that thrill paleontologists.

Left, Alan Turner holds a model of the maxilla of Falcatakely, with a CT reconstruction on his computer screen.

These two creatures, the first a three-foot long dinosaur precursor discovered in Ghost Ranch, New Mexico, and the second a crow-sized bird fossil discovered in Madagascar, have taken center stage in recent scientific circles.

What they have in common is Alan Turner, Associate Professor in the Department of Anatomical Sciences at the Renaissance School of Medicine at Stony Brook University.

The discoveries, which were made over a decade ago, were recently parts of publications in consecutive issues of the prestigious journal Nature. “It’s really exciting,” Turner said. “I definitely feel fortunate” to contribute to these two publications.

Turner, who is not the lead author in either study, emphasized that these papers were only possible through teamwork. “These large, collaborative efforts are one of the ways these really significant discoveries can happen,” he said.

The work that includes Dromomeron, in particular, is one that “any one of our groups couldn’t have done [alone]. It hinged on a series of discoveries across multiple continents.”

Each paper helps fill out different parts of the evolutionary story. The Dromomeron discovery helps offer an understanding of a major evolutionary transition from the Triassic Period, while the Falcatakely find offers a look at the diversification of birds during the Cretaceous Period.

Dromomeron

Starting with the paper in which Dromomeron appears, researchers used a collection of dinosaur precursor fossils to study a smaller group of animals called lagerpetids, whose name means “rabbit lizard” or “rabbit reptile.”

These creatures lived during the age of the earliest relatives of lizards, turtles and crocodylians.

Above, a reconstruction of a pterosaur, a lagerpetid from the Triassic Period/Rodolfo Nogueria

Pterosaurs, which have a characteristic elongated fourth finger that forms a large portion of their wing, lived 160 million years ago, which means that the earlier, flightless lagerpetids roamed the Earth about 50 million years before pterosaurs.

Turner discovered Dromomeron in Ghost Ranch, New Mexico 14 years ago. Since then, other scientists have unearthed new bones from this prehistoric rabbit lizard group in North America, Brazil, Argentina and Madagascar.

Scientists involved in this paper used micro-CT scans and 3D scanning to compare lagerpetid and pterosaur skeletal fossils to demonstrate overlaps in their anatomy. The shape and size of the brain and inner ear of these lagerpetid fossils share similarities with pterosaurs.

The inner ear, Turner explained, is particularly important for animals like the pterosaur, which likely used it the way modern birds do when they are in flight to help determine their location in space and to keep their balance.

Lagerpetids, however, didn’t fly, so paleontologists aren’t sure how these ancient rabbit lizards used their inner ear.

Turner said the Dromomeron discovery was initially more of a curiosity. In fact, when researchers found it, “we had a blackboard in this collection space where we were working,” Turner recalled. “It was unceremoniously referred to as ‘Reptile A.’ There weren’t a lot of things to compare it to. At that point we knew we had a thing but we didn’t know what it was.”

A colleague of Turners, Randall Irmis, Chief Curator and Curator of Paleontology, Associate Professor of Geology and Geophysics at the University of Utah, traveled to Argentina, where he noticed a creature that was similar to the find in New Mexico.

Irmis’s trip “allowed our team to confirm our comparison [between Dromomeron and Lagerpeton] first-hand. From there, we were able to build out the larger evolutionary context,” Turner explained in an email.

Falcatakely

Meanwhile, Turner and Patrick O’Connor, Professor of Anatomy and Neuroscience at Ohio University and lead author on the study, shared their discovery of a bird they located in Madagascar that they called Falcatakely.

The bird’s name is a combination of Latin and Malagasy, the language of the island nation of Madagascar, which means “small scythe” and describes the beak shape.

Right, an artist reconstruction of the Late Cretaceous enantiornithine bird Falcatakely forsterae with its unique beak/Sketch by Mark Witton

The scientists found a partial skull in a quarry in Madagascar. The fossil was embedded in rocks. Turner and O’Connor analyzed it through CT scanning and through careful physical and digital preparation by their colleague Joe Groenke, laboratory coordinator for the O’Connor lab.

The discovery of grooves on the side of the face for a beak took the researchers by surprise.

“As the face began to emerge from the rock, we immediately knew that it was something very special, if not entirely unique,” O’Connor said in a press release. 

“Mesozoic birds with such high, long faces are completely unknown, with Falcatakely providing a great opportunity to reconsider ideas around head and beak evolution in the lineage leading to modern birds.”

As with the Dromomeron find, the discovery of Falcatakely didn’t provide a eureka moment when the scientists found it 10 years ago.

“We didn’t know [what we had] when we collected this material,” Turner said. “It wasn’t until we CT scanned the block in an effort to begin the preparation that we said, ‘Wait a second. There’s something really weird in this block. The flat part turned out to be the side of the face.”

Turner originally thought it could have been the breast bone of a larger dinosaur. During the pandemic, he has come back to projects that have been sitting around for several years. Some have “probably danced on the periphery that have now come to the dance,” in terms of his focus.

In looking back on the ingredients that made these two Nature papers possible, Turner added another element. These publications underline “the importance of investing in long term field work expeditions,” he said.

Photo from Pixabay

By Daniel Dunaief

Daniel Dunaief

For my family and me, the pandemic-triggered life change started almost exactly 10 months ago, on March 13. How different is the life we lead now from the one we led way back in March? Comparing answers to the same questions then and now can offer a perspective on the time that’s passed and our current position.

Question: What do we do?

March 2020: Shut businesses down, encourage people to stay home and track everything. Talk about where we are “on the curve” and hope that we can “flatten the curve” and reach the other side, allowing us to return to the lives and habits we used to know.

January 2021: Try to keep infection rates down and take measured chances in public places, while hoping officials allow schools, restaurants and other businesses to remain open.

Question: What do we eat?

March 2020: Pick up take out food whenever we can. Go to the grocery store and cook. Baking rapidly became a release and relief for parents and children, who enjoyed the sweet smell of the house and the familiar, reassuring and restorative taste of cookies and cakes.

January 2021: In some places, we can eat indoors. Many people still order take out or cook their own food.

Question: What do we do with our children?

March 2020: Overburdened parents, who are conducting zoom calls, conference calls and staring for hours at computer screens, face the reality of needing to educate their children in subjects they either forgot or never learned.

January 2021: Many students continue to go to school, even as the threat of closing, particularly in hot spots, continues.

Question: What do we do for exercise?

March 2020: People take to the streets, order exercise equipment or circle the inside or outside of their house countless times, hoping to break free from their blinking, beeping and demanding electronic devices.

January 2021: Gyms have reopened, with some people heading to fitness centers and others continuing their own version of counting the number of times they’ve circled the neighborhood, with and without their dogs.

Question: What can we do about work?

March 2020: Many businesses close, asking employees to work from home.

January 2021: Many businesses are trying to stay open, even as others have continued to ask their employees to work from home, where they can talk on computer screens in mismatched outfits, with nice blouses and shirts on top and gym shorts or pajamas.

Question: What can we plan for?

March 2020: We cancel weddings, parties, family gatherings and all manner of events that involve crowds.

January 2021: We have learned not to make plans that are set in stone, because the calendar has become stone intolerant. We make plans and contingency plans.

Question: What do we do for entertainment?

March 2020: We secretly binge watch TV shows, although we don’t share our indulgences.

January 2021: After we ask how everyone is doing, we regularly interject questions about the latest TV shows or movies.

Question: What do we notice in the supermarkets?

March 2020: Toilet paper and paper towels are hard to find.

January 2021: Toilet paper and paper towels are generally available, but we may only be allowed to buy two packages. The cost of paper goods and other items seems to have risen.

Question: Do we let our children play sports?

March 2020: Almost every league in every sport shut down, following the lead of professional teams.

January 2021: Youth leagues have restarted.

Question: What’s a cause for optimism?

March 2020: We believe in flattening the curve.

January 2021: The vaccine offers hope for a return to a life we used to know.

St. Catherine Chief Nursing Officer Mary Jane Finnegan gives a flu shot during a free mobile clinic at the end of September. Photo from St. Catherine hospital

They lost patients, sleep and time with their families and yet, through some of the most difficult conditions in over a century, they persevered, brought together by the shared goal of saving lives threatened by the pandemic.

The Times Beacon Record Newspapers is pleased to honor the health care workers who put themselves in harm’s way to offer comfort, cures and solutions for COVID-19.

State Sen. Jim Gaughran (D-Northport) described health care workers as “heroes beyond belief.” He added, “There are folks who have gotten sick and died, simply because they were just doing their jobs.”

Unusual Requests

Indeed, in some cases, these health care workers took on tasks that aren’t typically a part of their job description or training.

Tricia Coffey on the phone at Huntington Hospital. Photo from Coffey

Take Kristen Thomas, a registered nurse at Mather Hospital in Port Jefferson. A priest came up to her in the halls of the hospital to ask for an unusual favor. A person had died and the family, who couldn’t be by his side, asked for last rites. The priest knew he couldn’t enter the room.

He asked, “Would you mind taking holy water and anointing the patient?”

She approached the patient, made the sign of the cross and prayed, as the priest stood outside the door.

“A moment like that, you never really plan to do that,” Thomas said. “We tried to give the family a little bit of closure. They didn’t get to attend the normal [rituals].”

For the community and health care workers, normal took on new meaning, especially in the first few months of the pandemic, when Suffolk County became an epicenter of the virus.

With family unable to sit by the bedside, nurses often stepped up, holding up iPad and phones so the family could spend time together virtually.

Marilin Dilone, Emergency Department nurse at Stony Brook University Hospital, called the young family of one of her patients.

Marilin Dilone, emergency department nurse at SBUH decked in full PPE gear. Photo from SBUH

His wife “put the baby on the phone — the baby looked like he was maybe 10 months old. The baby was making noises. I swear [the patient] opened his eyes. The wife is crying. Such a moment, we take for granted. He could hear her say, ‘I love you.’ To be able to provide that was very humbling for me.”

Like Dilone and so many other nurses, Robert Collins, a nurse at Mather Hospital ,shared how he held an iPad up to patients whose conditions were deteriorating so they could say goodbye to their families.

He had to stay in the room because some of the patients couldn’t hold the iPad.

“You do that once or twice, it kind of sticks with you,” Collins said.

Deep Connections

The connections the medical staff made to the families of patients extended well beyond the typical interactions.

“We had patients for an extended period of time,” said Patricia Coffey, nurse manager of the Critical Care Unit at Huntington Hospital.

Coffey, who spent 11 weeks actively caring for patients as her managerial duties “went to the wayside,” said the staff talked to families for extended periods of time. She spoke with some families daily, spending as much as two-and-a-half hours each day on the phone.

The nurses felt like members of the family because the normal support system couldn’t provide bedside support.

“You were channeling the family to the patient,” Coffey said. The nurses were “rooting so hard” for the patients.

When one of those patients who was in the hospital died after a long battle, she said it was “unbelievably heartbreaking — you felt like one of your own family members had died.”

She still keeps in touch with family members.

Mather Nurse Robert Collins. Photo from Mather

Coffey said one of her neighbors was admitted to the hospital with COVID and was on her floor. Coffey’s children and her neighbor’s children grew up together and their daughters were friends.

She not only spoke with his wife every day during her 60-hour weeks, but she also called her coworkers over the weekend to ask how he was doing.

The conversations with the neighbor’s wife were “a little hard. I wanted to be honest with her. He was very critical. At the same time, I was trying to be hopeful. It was a hard balance.”

Coffey said he was “one of the lucky ones who survived.”

Dilone of SBUH described how the work was more physically demanding.

She would “try not to ask for people” as she didn’t want to expose others if it wasn’t necessary. “You are taking care of patients more by yourself, turning them and doing chest PT [physiotherapy] — it was physically more demanding,” Dilone said.

Dark Moments

Watching patients who died took its toll, even on people who have been in the medical profession for decades.

MaryJane Finnegan, chief nursing officer at St. Catherine of Siena Medical Center in Smithtown, described the unusually high number of people dying from the virus. The hospital was running out of space for the dead. The morgue was filled and an additional refrigeration truck outside also filled quickly.

Mather Nurse Kristen Thomas. Photo from Mather

“One day, eight people died — usually in a week, you can have eight people die, but not eight in a day,” Finnegan said.

Nikki Fiore-Lopez, chief nursing officer at St. Charles Hospital in Port Jefferson said a nurse was present for the death of her mentor. Watching her die was “one of the darkest moments” for the nurse, Fiore-Lopez said.

Many medical professionals encouraged their patients to fight through the worst of the virus.

Stony Brook’s Dilone stayed with a patient whose blood oxygen level kept dropping. She wouldn’t let him fall asleep because she was worried he’d get intubated. She reminded him of his family and that he needed to help himself.

“I felt like Nurse Ratched,” Dilone said, referring to the dreaded nurse from the movie “One Flew Over the Cuckoo’s Nest.”

Dilone spent hours with this patient. Later, a doctor told her keeping the man awake prevented him from getting intubated.

Unexpected Challenges

With a virus no one had battled before, health care workers had to be flexible, learning about everything from new protocols for admitting patients to the latest and best treatments.

Chief Nursing Officer at St. Charles hospital Nikki Fiore-Lopez delivers flowers to patients at Christmas with Foundation Board Chair member Doug Casimir in 2019. Photo from St. Charles

The staff had to confront the “speed with which everything changed,” said Dr. Eric Morley, associate professor and clinical director in the Department of Emergency Medicine at Stony Brook University’s Renaissance School of Medicine. “Every day, there were new protocols, new ways to deal with things.”

Hospitals had to create a forward triage system to deal with the flood of COVID patients amid all the other potential emergencies hospitals routinely have.

These efforts required hundreds of employees to “get on the same people to sort people out,” Morley said. Training staff to manage the flow of patients required constant communication.

Even some of the smaller elements of managing the crisis took Morley’s time, such as getting new traffic signs to direct people to an alternate site.

Hospital managers were continually confronted with numerous unexpected challenges.

Ken Roberts, president of Mather Hospital, said the hospital had to ensure the PPE was hospital grade and not counterfeit.

“There were a lot of suspicious and unscrupulous suppliers when supply and demand was unbalanced, and everyone was in crisis,” he explained in an email.

Health care workers tapped into their personal skills to connect with patients.

Angel Figueroa, a registered respiratory therapist at SBUH who grew up in New York City and learned Spanish thanks to his Puerto Rican heritage, walked into some rooms and spoke Spanish to patients.

When he greeted patients in Spanish, “I would see their eyes open up [and think], ‘Somebody understands me.’”

They would ask him numerous questions, particularly because the medical information came at them so quickly. 

Mather’s Collins described how the routine changed so dramatically the moment he arrived at work.

Mather President Ken Roberts holds a sign thanking health care workers. Photo from Mather

“Rapid response bells were going off as soon as you walked in,” he said. “You didn’t take your coat off” before patients needed attention. “People were not doing well. That was happening more frequently than before. That was an adjustment.”

On the other side of the struggle, health care workers felt a tremendous sense of relief when patients continued their recoveries at home.

“When people were discharged, the staff was thrilled,” St. Catherine’s Finnegan said. “We’d play the [Beatles] song, ‘Here Comes the Sun.’ A lot of hospitals did that. People would gather as many as possible to wish the person well as they were wheeled out.”

Teamwork

Through the difficulties, though, Morley appreciated the support from the community and the families, along with the teamwork and camaraderie from so many departments and staff that all pulled together.

Roberts expressed similar sentiments.

“I was extremely pleased at the teamwork displayed by all hospital staff during the height of the pandemic,” he said.

The Mather president was also grateful for the letters, cards, donated meals, handmade masks and donated PPE.

“The local communities we serve gave us and continue to give us tremendous support and encouragement,” Roberts said. “That has meant so much to the staff to know that the community was supporting them and recognizing their efforts.”

Stony Brook Respiratory Therapist Angel Figueroa wearing mask and shield. Photo from SBUH

Coffey, from Huntington Hospital, was impressed with how, even amid such extraordinary and challenging times, numerous groups collaborated.

“In many ways there were positive things — the community, the team, everyone working together,” she said. “Parts of it were so uplifting. 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.” 

Lasting Thoughts

Finnegan said the staff was incredibly appreciative of all the food local restaurants donated.

In fact, some of them joke that they gained the “COVID-19,” referring to the weight they put on while they were working numerous shifts and benefiting from all the donated food.

Morley “rediscovered” Twinkies during COVID in the break room. He has since been able to lose the weight the snack cakes added.

While gyms were closed, Collins relieved stress by buying a 400-pound tractor-trailer tire that he flipped up and down along his driveway. He also took a sledgehammer and “beat on it.”

The exertion would make him tired enough that the stress would dissipate for the day.

Dr. Eric Morley from SBU participates in COVID testing. Photo from SBU

Ultimately, what made an ever-expanding job — that affected so many aspects of health care workers’ personal and professional lives — manageable was the shared sense of purpose and the inspiration people drew from each other.

“The fact that the staff was out there doing it” helped give her energy, St. Charles’ Fiore-Lopez said. “We had patients to care for, we had shifts. We had days and weeks and months to get through. They put one foot in front of the other and I needed to do the same.”

Morley appreciated the way the Stony Brook staff pulled together during an intense and challenging time.

“Although it was grueling, it was a special thing to go through with that group of people,” he said.

Michael Schatz and Aspyn Palatnick. Photo by Lauryl Palatnick

By Daniel Dunaief

Michael Schatz, Adjunct Associate Professor at Cold Spring Harbor Laboratory, saw some similarities to his own life when he met the then 14-year old Aspyn Palatnick.

Palatnick, who was a student at Cold Spring Harbor High School, had been developing games for the iPhone. When he was that age, Schatz, who is also a Bloomberg Distinguished Associate Professor of Computer Science and Biology at Johns Hopkins University, stayed up late into the evening programming his home computer and building new software systems.

Meeting Palatnick eight years ago was a “really special happenstance,” Schatz said. He was “super impressed” with his would-be young apprentice.

When he first met Schatz, Palatnick explained in an email that he “realized early on that he would be an invaluable mentor across research, computer science, and innovation.”

Palatnick was looking for the opportunity to apply some of the skills he had developed in making about 10 iPhone games, including a turtle racing game, to real-world problems.

Knowing that Palatnick had no formal training in computer science or genetics, Schatz spent the first several years at the white board, teaching him core ideas and algorithms.

“I was teaching him out of graduate student lecture notes,” Schatz said.

Schatz and Palatnick, who graduated with a bachelors and master’s from the University of Pennsylvania and works at Facebook, have produced a device which they liken to a “tricorder” from Star Trek. Using a smart phone or other portable technology, the free app they created called iGenomics is a mobile genome sequence analyzer.

The iPhone app complements sequencing devices Oxford Nanopore manufactures. A mobile genetic sequencer not only could help ecologists in the field who are studying the genetic codes for a wide range of organisms, but it could also be used in areas like public health to study the specific gene sequences of viruses like SARS-CoV-2, which causes COVID-19.

In a paper published in GigaScience, Schatz and Palatnick describe how to use iGenomics to study flu genomes extracted from patients. They also have a tutorial on how to use iGenomics for COVID-19 research.

While developing the mobile sequencing device wasn’t the primary focus of Schatz’s work, he said he and others across numerous departments at Johns Hopkins University spent considerable time on it this summer, as an increasing number of people around the world contracted the virus.

“It very rapidly became how I was spending the majority of my time,” said Schatz.

Palatnick is pleased with the finished product.

“We’ve made DNA sequence analysis portable for the first time,” he explained in an email.

Palatnick said the app had to use the same algorithms as traditional genomics software running on supercomputers to ensure that iGenomics was accurate and practical. Building algorithms capable of rendering DNA alignments and mutations as users tapped, scrolled and pinched the views presented a technical hurdle, Palatnick wrote.

While Schatz is optimistic about the vaccinations that health care workers are now receiving, he said a mass vaccination program introduces new pressure on the virus.

“We and everyone else are watching with great interest to see if [the vaccinations] cause the virus to mutate,” Schatz said. “That’s the big fear.”

Working with the sequences from Nanopore technology, iGenomics can compare the entire genome to known problematic sequences quickly. Users need to get the data off the Oxford Nanopore device and onto the app. They can do that using email, from Dropbox or the web. 

In prior viral outbreaks, epidemiologists traveled with heavier equipment to places like West Africa to monitor the genome of Ebola or to South and Central America to study the Zika virus genome.

“There’s clearly a strong need to have this capability,” Schatz said.

Another iGenomics feature is that it allows users to airdrop any information to people, even when they don’t have internet access.

Schatz urged users to ensure that they use a cloud-based system with strong privacy policies before considering such approaches, particularly with proprietary data or information for which privacy is critical.

As for COVID-19, people with the disease have shown enough viral mutations that researchers can say whether the strain originated in Europe or China.

“It’s kind of like spelling mistakes,” Schatz said. “There are enough spelling mistakes where [researchers] could know where it came from.”

Palatnick described iGenomics as an “impactful” tool because the app has increased the population of people who can explore the genome from institutional researchers to anyone with an iPhone or iPad.

In the bigger picture, Schatz is broadly interested in learning how the genome creates differences.

“It’s important to understand these messages for the foods we eat, the fuels we use, the medicines we take,” Schatz said. “The next frontier is all about interpretation. One of the most powerful techniques is comparing one genome to another.”

Schatz seeks out collaborators in a range of fields and at numerous institutions, including Cold Spring Harbor Laboratory.

Schatz and W. Richard McCombie, Professor at CSHL, are studying the genomes of living fossils. These are species that haven’t evolved much over millions of years. They are focusing on ancient trees in Australia that have, more or less, the same genetic make up they did 100 million years ago.

As for Palatnick, Schatz described his former intern and tricorder creating partner as a “superstar in every way.” Schatz said it takes considerable fortitude in science, in part because it takes years to go from an initial idea on a napkin to something real.

Down the road, Schatz wouldn’t be surprised if Palatnick took what he learned and developed and contributed to the founding of the next Twitter or Facebook.

“He has that kind of personality,” Schatz said.

Photo from Pixabay
Daniel Dunaief

I have brought three fictional characters in to discuss their thoughts for 2021. Please welcome Yoda from the “Star Wars” series, Jack Ryan from Tom Clancy books, and Jane Craig from the film “Broadcast News.” I will call you all by your first names. Well, except for you, Yoda.

TBR: After such a tumultuous 2020, I wanted to ask you what you all thought would likely happen next year.

Yoda: Tough to say, the future is. If the answers you don’t like, the questions you must change.

Jack: Look, I’m not sure what we’re doing here, but I think the vaccine offers real hope for change. Your world, such as it is, should be able to move in the right direction.

Jane: The trends at this point are horrific. You have enormous numbers of positive tests each day, hospitalizations are up and the number of dead continues to rise.

TBR: Yoda, you’re kind of off point and sound like a backwards fortune cookie. Jack, I appreciate the optimism and Jane, I think you’re focusing on the negatives.

Jane: We can’t preclude the possibility that the positive infections will continue to climb for months. While it’d be swell to have a big party to celebrate the vaccine and the return to whatever version of normal each of us has, it’s important that we protect ourselves and our families.

Jack: She’s right. Everyone doesn’t have the vaccine and everyone hasn’t taken it, which means we won’t reach herd immunity for a while. While this is killing the entertainment industry, among so many others, it’s necessary for us to sit tight for a while. At the same time, we need to consider the possibility that other governments will become opportunistic about this messy transition at the White House. We need to protect ourselves and remain vigilant. This is a dangerous time, in so many ways, and we need to analyze all kinds of traffic.

Yoda: Know something about vigilance, do I. Messy, this world has become. Goodness, hope and optimism, there remains. Effort to get there will it take.

TBR: Jane, this question, in particular, seems right up your alley. What do you think about the news business in 2021?

Jane: I’m not going to lie to you, it’s been a tough year for everyone, particularly in the news business. We are not the enemy. When we do our jobs well, people get to hear the truth. They can make informed decisions that affect their lives. Are there problems? Of course, but that doesn’t make the entire industry corrupt, any more than it would in any other business.

Yoda: Inside each of us, the enemy resides. Confront it, we must.

Jack: I’ve dealt with journalists all the time. They are a competitive group, I’ll give them that, but they are necessary to shine light, at the right time, on everything from the fight against the virus to the battle against corrupt governments.

TBR: Do you think we’ve learned any lessons from 2020?

Jack: It’s been a brutal year and so many people have lost so much. The numbers don’t tell the entire story. We can only live with what we know: we can protect ourselves and our family through policies that have nothing to do with politics. Careful analysis and science brought us the vaccines. We need to make informed decisions about using them.

Jane: Exactly my point, Jack. We can and should make informed decisions, which the media, at its best, can support.

Yoda: Mistakes, everyone makes. Opportunities to learn, we have. Family and those fortunate enough to share life with us, we must cherish.

Carlos Simmerling

By Daniel Dunaief

They know what happens. They’re just not sure how it happens.

Carlos Simmerling, Marsha Laufer Endowed Professor of Physical and Quantitative Biology and Professor of Chemistry at Stony Brook University, has spent over 22 years trying to answer the question of how processes at a molecular level occur.

Using chemistry, physics and computer programs he helped create, Simmerling determines the intermediate structural changes that occur with biomolecules such as nucleic acids and proteins, which would be extremely difficult to impossible to do at a bench or in a laboratory.

In March, as the United States was in the beginning of various school and office lockdowns in response to the spread of the pandemic, Simmerling endured the same discomfort and loss of control.

Researchers at Brookhaven National Laboratory, including Kerstin Kleese van Dam, Director of the Computational Science Initiative, reached out to Simmerling to see if his lab might use their experience and tools to understand the spike protein on the coronavirus that causes COVID-19.

Except for two people who were on the cusp of finishing their PhD’s, everyone else in the lab “shifted to work on this instead. We put everything else on hold and it’s been nonstop since March.”

Simmerling said he and his lab group decided at a special lab meeting on March 13th that it was important to contribute whatever they could to this unprecedented crisis.

Without the same kind of restrictions or limitations that lab groups that depend on working at a bench or conducting in-person experiments might have, the Simmerling group could work every day, forging ahead to understand the way the protein operates and to look for critical steps or weaknesses that might assist doctors down the road.

Recently, Simmerling and his lab group exchanged emails over Thanksgiving, during which the group felt this commitment to COVID research gave them a “shared purpose” and helped them feel as if they were “doing something.”

While the Simmerling lab appreciated the opportunity to contribute to efforts to combat COVID-19, they also recently received a national award in high-performance computing. Called the Gordon Bell Special Prize, the award recognizes “outstanding research achievement towards the understanding of the COVID-19 pandemic through the use of high-performance computing.”

The award, which was announced at the virtual SuperComputing 2020 Conference and recognizes the work of the Simmerling lab and some collaborators they worked with since early in the pandemic, includes a $10,000 prize.

The kind of research Simmerling and his team conducted may help either with this specific virus or with any others that might threaten human health again.

“We were not well prepared in science and humanity in general,” Simmerling said. “We have to come up with better tools.”

While he is pleased that pharmaceutical companies are getting closer to introducing vaccines for COVID-19, Simmerling said any such solutions would apply to this specific virus and not to any subsequent forms of coronavirus or other potential threats to human health.

People who contracted SARS or MERS, which are coronavirus cousins, didn’t develop an immunity to COVID-19.

“Even if we all get vaccinated, that won’t help us for the next one, and we’ll likely have other ones,” Simmerling explained. “Science needs to do a better job getting deeper into how these work.”

At this point, the models Simmerling and his staff have created are working and are providing the kind of clues that could contribute to providing suggestions for future experiments. The lab is “now at the stage where we are seeing new things not seen in the experiments and suggesting new experiments to test our hypotheses,” said Simmerling.

His lab has focused on the dynamics of proteins and other biomolecules to see how they move around in time. He simulates the shape changes when molecules interact, including in the 2000s when he worked on proteins in the human immunodeficiency virus.

Simmerling likens the study to the process of shaking other people’s hands. When two people come together, their hands adapt to each other when they interact, changing shape as they move up and down.

With the spike protein in COVID-19, scientists have seen what it looks like before it interacts. The structure after it unlocks the cell is fuzzier and scientists aren’t sure if they are relevant to the actual virus or something vaguely similar to it.

“We only get snapshots at the beginning and the end,” he said. “What we need to do is figure out how it works.”

He uses software his lab has developed with a few other labs in the country. Scientists around the world use this Amber system. They take steps in time and calculate the forces on the atom, which requires millions of iterations.

Simmerling said other people sometimes think he and his team download the structure, plug it into a computer, run it and then publish a paper. That’s far from the case, as the computer does the number crunching, but people like Simmerling spend considerable time trying to understand a molecule like the spike protein well enough to develop ideas about how it might move and change.

Simmerling took a circuitous route to the world of using chemistry and physics on a computer. When he entered college at the University of Illinois at Chicago, he wanted to be a chemist. The only problem was that he didn’t enjoy working in the lab with all the chemicals.

Half way through his college education, he left school and started working at a computer company. Eight years later, he decided to return to college, where he planned to earn his chemistry degree.

“When I went back to school, I told my [teaching assistant] that I wish I could do [chemistry] on computers rather than experiments,” Simmerling said. “He introduced me to the professor [Ron Elber] who became my PhD advisor. That brought together things I was interested in.”

He knew programming and how to use computers.

“Sometimes, you’re the sum of your choices,” Simmerling said.

He and his wife Maria Nagan, who also does computer modeling at Stony Brook University, live in Port Jefferson. In non-pandemic times, Simmerling enjoys sailing throughout the year.

As for the prize, Simmerling said the “recognition is nice” and he would like his lab to contribute to “models to change how we combat infectious disease.”

Pixabay photo

By Daniel Dunaief

Daniel Dunaief

What if James Bond had to wear a mask? What would it look like and would it become a fashion accessory and a multi-functional gadget at the same time?

It could be all black to match his dapper tuxedo. If he ever wore a bow tie that was a different color, he could coordinate the two items to keep the visual integrity of the ensemble.

Then again, maybe it’d be pink with a small ribbon, to show that he’s finally caught up to the times and, after all those years of leading ladies who fall in love with him at their own peril, he sees an opportunity to show his appreciation for women and the fight against breast cancer.

Maybe the mask would have a bright light built into it. He could use the light to interrogate someone, to shine it in someone’s eyes who was about to shoot him or to distract a vicious dog or lion that was about to eat him, but who followed the light around the room instead. He could also use the light in dark tunnels or underneath pyramids.

A problem with masks, even the ones we change each day, is that they don’t change what our faces do beneath them. It’s hard to sense the difference between a hidden smile and a smirk.

Remember those mood rings, which changed color depending on how we were feeling? A modern Bond could have a mood mask.

A James Bond mask wouldn’t simply be colorful. It would also be a communicator, akin to Maxwell Smart’s shoe in “Get Smart.” By tilting his head once to the right, Bond could speak with M or Q or any other one-letter person or, perhaps, another 00 like him, who would be able to speak with him through their mask. Tilting his head twice to the right would hang up the phone. He could dial by touching his tongue to a keypad in his mask.

By tilting his head to the left once, Bond could order a vodka martini, shaken not stirred, from the nearest bar.

In fact, keeping up with modern times, maybe Bond wouldn’t need to speak at all, but the mask could pick the ideas in his head, like, “hey, that woman over there looks intelligent. I can’t wait to speak with her about her hopes and aspirations. After we get to know each other well, we can establish a trusting relationship and then blow stuff up, kill some bad people, save the world and then spend some time undercover, if you know what I mean.”

A James Bond mask would also be the modern version of his all-purpose watch. Contoured to his face, he could whistle, causing the mask to break glass by releasing a supersonic sound. It could also shoot out a lifesaving dart or even provide oxygen for him if he were trapped underwater by a bad guy who didn’t realize that you can’t drown Bond while he’s wearing his mask.

Given the physical demands of the job, the mask would also come with a built-in coolant. Instead of sweating into the mask, the mask would be made of a dry-fit material while, on cue, it would release a comfortable and sweet-smelling coolant that would also cover up his bad breath.

Maybe he’d have a mask that played the theme song from his movies. Each time he bit down, he could sway and swagger to the familiar and engaging theme, annoying the evildoers with a song that almost always signals a Bond victory.

Snow blanketed the ground as a winter storm hit the North Shore Dec. 16 into 17. Photo by Kyle Barr

*Update: This version of the story includes the number of homes who are still without power as of 4 p.m.

The Nor’easter that hit the east coast cut out power to thousands of homes on Long Island. By 4 p.m. on Thursday, the number of homes without power declined to 348. Earlier in the day, 3,444 homes were without electricity. PSEG Long Island said it had restored power to more than 98% of the homes affected by the storm.

PSEG LI expected to restore power to all homes by the end of the day.

“We expect to restore power to all remaining customers today,” PSEG LI said in a statement.

PSEG added personnel, including tree and line crews, to repair damage and restore outages. The utility had more than 1,300 line workers, tree trimmers, surveyors and other personnel on site to restore power.

“This storm brought down trees and wires throughout our service area,” John O’Connell, Vice President, Transmission & Distribution, PSEG Long Island, said in a statement. “We know that being without power for any length of time is a hardship and we thank our customers for their patience as we work through the damage and difficult conditions to restore their power [as] safely and quickly as possible.”

In an update on the storm, County Executive Steve Bellone (D) described the number of power outages as “good news,” as outages were a “big concern here because of the nature of the storm.” Bellone spoke with reporters at the Department of Public Works in Commack.

“We did not see a significant number of power outages in this storm,” Bellone added.

Bellone suggested that outages may have been lower because some of the limbs and trees that could have come down had already fallen or been removed.

Suffolk County Police Department Chief Stuart Cameron, meanwhile, thanked the Department of Public Works and the police department for working through the night.

As of 8 a.m., Chief Cameron said the county had 171 accidents since 4 p.m. the night before. Police were working on two active crashes, which is lower than they would normally have.

Chief Cameron also wanted to thank many residents of Suffolk County for heeding the advisory and staying off the roads.

Some of the ramps for the Long Island Expressway still had plenty of snow and slush on them. Chief Cameron advised drivers to consider taking the next ramp, if their exit appeared challenging from the conditions.

Chief Cameron also urged residents to give themselves plenty of time to clear their car of snow and ice before they need to leave their homes.

“My car was heavily iced,” Chief Cameron said. “It took me a long time to clean” it off.

Looking at the forecast for Friday, Bellone said the colder temperatures could create conditions for black ice. He urged people to be “careful throughout [Thursday] and into tomorrow as well.”

A look at Port Jefferson Harbor from the Village Center during Winter Storm Grayson as blizzard-force winds and more than a foot of snow pound the coast in January, 2018. File photo

As the nor’easter bears down on the mid-Atlantic states, the forecast for Long Island continues to include considerable snow, although the forecast varies by area.

The estimated snowfall ranges from 6 inches to 13 inches.

“We know the storm will be hitting us harder on the west end of Suffolk County, rather than the east end, where we’ll see lower amounts,” County Executive Steve Bellone (D) said during a weather update at the Commack Department of Public Works.

The storm will also hit harder in the north, rather than the south shore.

“This is going to be a heavy, wet snow, which is, of course, something that creates its own set of challenges,” Bellone said.

Bellone urged residents to return to their homes as early as possible tonight. The storm is expected to increase in intensity this evening through the overnight hours. During that time, snow could accumulate at the rate of one to two inches per hour.

“You should be off the roads by the latest, at 9 p.m. tonight.

While the east end will get lower snow totals, the area will have higher winds, with gusts of up to 57 miles per hour.

The county is opening its emergency operations center today and expects to have it open through tomorrow at 4 p.m..

The Department of Public Works has 200 vehicles ready, with about 19 tons of salt at their disposal to help clear the snow and ice from the roads.

Bellone urged residents to try to work from home on Thursday, if they can.

“Tomorrow is a day, if you can, to stay home,” Bellone urged.

Suffolk County Police Department Chief Stuart Cameron said this type of heavy snow can clog the chute of a snow blower.

“You should never, ever stick your hand” in the chute, Cameron cautioned, even if the device is turned off, because a blade can rotate and severely injure someone’s hand.

Cameron also advised against bringing a barbecue or generator inside the house because they release carbon monoxide, which can be dangerous to homeowners.

At this point, Bellone said there were no changes to the bus schedule. He urged residents to check for any modifications, particularly tomorrow after the snowstorm passes.

To report and receive status updates on an outage Text OUT to PSEGLI (773454) or to report an outage online visit www.psegliny.com

To register, have your account number available and text REG to PSEGLI (773454)

Downed wires should always be considered “live.” Do not approach or drive over a downed line and do not touch anything contacting the wire. To report a downed wire, call PSEG Long Island’s 24-hour Electric Service number: 1-800-490-0075