Science & Technology

Klaus Mueller (third from left) with Akai Kaeru co-founder Eric Papenhausen (right) and interns Shenghui Cheng (second from left), on whose PhD thesis the software was based and Darius Coelho, who earned his PhD in Mueller’s lab. Photo courtesy of Akai Kaeru

By Daniel Dunaief

About 40 percent of the counties in the United States are at high risk for COVID-19 and related death rates, according to a new computer program created by Stony Brook University Computer Science Professor Klaus Mueller.

Putting together data from the over 3,000 counties throughout the United States, Mueller used a computer program he created with a start up company he co-founded, called Akai Kaeru LLC, to search for counties that present factors that would put them at greater risk for an increase in COVID-19 deaths.

Analyzing data from 500 factors, the scientists found that death rates increased in communities with a combination of traits that are catalytic for the spread and fatality rate of the virus. These include sparsely populated counties with a poor and aging population; counties with sleep-deprived, low-educated, low-insured residents; and wealthy counties with high home ownership and increasing housing debt, among other factors.

Many of the counties are in the southern United States. In June, Mississippi, Louisiana and Georgia had the highest density of high-risk counties at a coverage of 80 to 90 percent.

Mueller said he considered this approach in late April. When the data from the Centers for Disease Control and Prevention came online, the group did its first test run on May 10th, which ended on June 10th.

When he looked at the June 10th mortality rates throughout the country, he was amazed at how effectively the patterns based on the conditions from the computer algorithm predicted increases.

To be sure, not all of the counties that fit one or more of these sets of conditions had high death rates in May, but others that were similar had. The preconditions existed, but the spark to cause those deaths hadn’t occurred, Mueller said.

“In June, some of these so far untouched counties caught the virus and they flared up like a tinderbox,” Mueller explained in an email. “This phenomenon continued in July for other counties that had escaped it so far but had the critical condition sets.”

In June, some of the counties that had characteristics that made them vulnerable caught the virus, Mueller explained.

Mueller anticipates a rapid increase in August in counties in Florida and Texas, in which the virus has spread and the conditions for increased mortality are prevalent.

“There are counties in these states that from the socio-economic perspective look a lot like those that already experienced great tragedy,” he wrote.

Mueller explained that people in many counties think they’re not at risk even if their neighbors are. The danger, however, comes from a spark, such as a visit by someone carrying the virus, that increases the infection, hospital and mortality rates.

Indeed, in wealthy counties where residents are stretched thin by the costs needed to maintain their homes, the incidence of illness and death is also higher. In part, that reflects how some of the people in these communities cut corners in terms of health insurance.

Mueller said Akai Kaeru, which means “red frog” in Japanese, is working on a dashboard that will be accessible from a web browser where users can click on a map of counties and see the risk and the patterns that define it. The staff at Akai Kaeru, which includes three principals and four interns, have virtual team meetings each weekday at 11 am. The dashboard they create can help residents see the other counties that share similar characteristics. Users can also compare the death rate in these counties to the average death rate in the United States.

While the observations of trends linking characteristics of a county with COVID-related health challenges could be useful for county and state planners, Mueller acknowledged that these observations are “just a start. Now, you know where to look, which is way better than before.”

The data could be useful for policy and law makers as well as for actuaries at life insurance companies.

Mueller believes this artificial intelligence tool acts like a magnet that pulls out the proverbial needle from the data haystack.  Local leaders can use the dashboard to see the critical conditions for their counties. They can try to find solutions to remove those conditions.

Demonstrating how the health care system in similar areas became overwhelmed can increase compliance with social distancing and mask-wearing guidelines.

Mueller added that the predictions from the model are only as good as the data he used to analyze trends across the country. He and his team aren’t making these observations or collecting this information themselves.

He said some counties have a lower likelihood than the average of developing a wider contagion. While the entire state doesn’t have the same lower probability of the disease spreading, areas like Montana and Indiana have fewer of the variables that typically combine to create conditions that favor the spread of the virus.

Mueller suggests that the risks from COVID-19 are tied to compliance with policies that reduce the spread of the disease and to the development of a vaccine.

Despite the high infection rate through April and May and the deaths during those unprecedented months, Suffolk County isn’t at the same level of risk as some regions in the south. “Suffolk is much better than those counties in the South and even Westchester, Rockland and adjacent counties in Connecticut and New Jersey,” Mueller said. “But it is not without risk.”

Prior to developing a program to analyze epidemiological trends with COVID, Mueller worked with medical visualization, which included the three-dimensional data of human parts that were generated through computed tomography, or CT.

In his work, the Computer Science professor seeks to find ways to communicate high-dimensional data to the lay population. He has routinely worked on clustering and has partnered with Pacific Northwest, Brookhaven National Laboratory, and health care companies.

Mueller has been at Stony Brook University since 1999. He earned his PhD from Ohio State University. Originally from Germany, he has done considerable work online, including teaching.

He and his wife Akiko, who works on marketing for his company, have an eight-year-old daughter named Nico.

Readers interested in learning more about his research with COVID can find information at the following link: https://akaikaeru.com/covid-19-1.

John Inglis. Photo courtesy of CSHL

By Daniel Dunaief

In the post COVID-19 world, the pace of science and, in particular, scientific publishing has changed, giving researchers a sense of urgency to share information that might lead to preventions, treatments and cures.

Cold Spring Harbor Laboratory has produced two preprint research services, bioRxiv and MedRxiv, that complement the longer peer-reviewed path to publication.

After numerous scientists restructured their labs to contribute to the growing body of knowledge and information about COVID-19, these researchers turned to preprint services to share the results of their work and the evolution of their thoughts on how to defeat the virus.

“It’s absolutely unprecedented for scientists to drop what they are doing and switch their focus to something completely new to aid society and mankind in general,” said John Inglis, the co-founder of bioRxiv and one of the members of joint management group for medRxiv.

MedRxiv, which started in June of 2019, helped provide the scientific community with an outlet for their health science research, with the caveat that the results haven’t received a thorough peer review, as they might in the New England Journal of Medicine, Cell, or other periodicals.

The number of preprint research papers has climbed dramatically this year, as scientists race to get their results from the bench to the server. The number of papers in bioRxiv increased to 88,268 in June from 71,458 in January. The increase at the newer medRxiv is much more dramatic, climbing from 953 in January to 7,541 in June.

The number of pandemic related papers on medRxiv and bioRxiv in total is 6,458, with 5,133 on medRxiv and 1,325 on bioRxiv.

Pandemic-related papers account for close to 70 percent of the new research published on medRxiv since January 1st, while the percentage of virus-related papers on bioRxiv is 6.2%, in large part because bioRxiv includes numerous other subject areas, including ecology, bioinformatics, plant biology and zoology.

The world has taken notice of all these papers, with page views peaking in April for medRxiv to almost 11 million for the month.

While the papers aren’t peer reviewed, the managers of these sites urge readers to remain cautious in their interpretation and use of these findings, while the scientific community continues to duplicate any encouraging or compelling results.

“We remind people all the time that these are preprints,” Inglis said, as the site has numerous reminders about the early nature of the findings. “They are preliminary reports and should not guide clinical practice or be reported as established information. That’s a battle we’re still fighting.”

The peer review process has also picked up some speed, as journals, inundated with potential game-changing material, have been accelerating the process of reading and reviewing papers. The median time between posting an article on bioRxiv and publication in a journal before the pandemic was nine months. Some papers in medRxiv have been published in journal in as few as 35 days.

For medRxiv, the screening process requires an ethics statement, a funding statement, and any potential conflicts of interest. These requirements are “all far more familiar in medical publishing than in scientific publishing,” said Inglis.

At bioRxiv, which recently introduced a competing interest statement as well for authors, freelancers and a group of Principal Investigators look at everything before it posts, to make sure it’s science and that it’s not dangerous. The screeners turn the manuscripts back to the team if they have any concerns.

“We felt, early in the pandemic, that it was necessary to make sure we have people with expertise in outbreak science,” Inglis explained. “We brought on volunteers.”

According to Inglis, the percentage of manuscripts that scientists submit, but that bioRxiv doesn’t publish, is between 5 and 10 percent, while that figure is closer to 20 to 25 percent for medRxiv.

Inglis said numerous scientists have done some modeling based on public data, but that the preprints don’t accept those papers unless they contain additional research.

The preprint management team was “worried about the indiscriminate use of these models to guide public policy,” he said.

Additionally, the team excluded manuscripts that might be dangerous to human health or human-health related behavior. They didn’t want people to rush out and take something that, theoretically, might help, but that hasn’t received sufficient testing. A treatment might block a receptor, but also have significant side effects.

Inglis said the team of people who work at the preprints, which includes five full-time preprint-platform dedicated staff members and seven other CSHL staff with other responsibilities, including the founders, tech developers and production staff, worked seven days a week, with long working days to meet the increased need and demand.

People working on this effort “are not doing it because they are getting rich or handsomely acknowledged.” An arduous job with thousands of papers, the staff are working out of a “sense of purpose and mission,” Inglis explained.

The Chan Zuckerberg Initiative and CSHL provide financial support for these preprints. The research community has shared their appreciation for these preprints and CSHL generously acknowledges the work of the staff.

Inglis and Richard Sever co-founded bioRxiv. MedRxiv is managed by Sever and Inglis in collaboration with Professors Harlan Krumholz and Joe Ross from Yale and Dr. Theo Bloom and Claire Rawlinson from BMJ, which was originally called the British Medical Journal.

Inglis said numerous papers have become game-changers in the battle against the virus, including a study from two weeks ago in the United Kingdom on dexamethasone, a steroid that was proven effective in severe cases of COVID-19. Indeed, just recently, a Bethesda hospital became the first in the nation to use the steroid to combat the virus.

The team working in preprints at CSHL appreciates the opportunity to contribute to the public health crisis.

Inglis is pleased with how the community trusted the preprints with their work, while numerous members of the community helped screen manuscripts and provide advice about how to react to the needs of the pandemic.

Stock photo

By Elof Axel Carlson

Elof Axel Carlson

In the life sciences, progress works incrementally.

The cell theory, for example, began in the 1600s with the observation of a cellular composition of cork bark with one the first microscopes. There was no cell theory (all the organisms we see are composed of cells) until 1838. The cell doctrine (cells arise from preexisting cells) came a generation later in the 1850s. A decade later, stain technology was introduced. In the 1930s electron microscopes were introduced. Molecular biology wasn’t introduced until the 1950s.

With each incremental advance, new tools, new data and new experiments are carried out. This can result in new insights on how life works, and it can be applied to disease in humans and other living things.

We manipulate life when we treat it because nature has no doctors or living things are at the whim of luck for their survival and evolution allows the healthiest, the most adapted, to survive and pass on their lucky genes. But today’s scientists can use a great deal of that incremental knowledge and apply it to our benefit.

One lead I find very exciting to read about and I am confident the next generation of science students will be excited by the advances taking place — It is now possible to begin a field of molecular neurology. The physiology of nerve cells is well worked, and we know how nerve impulses are transmitted and how reflexes form, and many other experimental approaches have provided an understanding of normal and diseased functioning of the nervous system. But the genes involved have been elusive.

Two fields have been added to the arsenal of approaches for exploring this. One is the field of stem cell research. The other is the use of fruit flies as model organisms to study the molecular genetics of fruit fly brains. Flies have the advantage of a limited number of activities that can be explored. They have courtship rituals, they have innate responses to gravity or to light, and they have vision, hearing, and taste as well as response to pain.

Some of the biochemical pathways in fruit flies are also found in humans and there is a surge of interest in using two approaches. One is finding chemicals  that shift slumbering stem cells into active nerve cells. This would allow treatments in coming years for neuromuscular disorders like multiple sclerosis. It could also slow down the aging process in which our stem cells lose the capacity to replace aged and dying neurons in the brain causing senility and other neurological disorders like Parkinson disease.

I am also a realist and historian of science. I know that such imagined future worlds can take decades or generations to achieve. We do not live in a totally known universe, and we only know a fraction of the way life has evolved over 3 billion years on earth. But by studying gene mutations involved with neuron formation and function, of stem cell activation, and of how humans can devise interventions for our health, we can feel confident that a lot more useful knowledge will emerge.

My realist side also tells me that all knowledge can be abused and we have learned to enact legislation to regulate most of our scientific and technological and malevolent intentions or warped values so that some do not exploit new technologies and shut down the progress needed to enlighten us and benefit us in an always troubled world.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

Eric Yee. Photo by Felicia Allard

By Daniel Dunaief

In the second of a two-part series, Times Beacon Record News Media will feature the work of Eric Yee, who, like his wife Felicia Allard who was featured last week, is joining the Pathology Department at Stony Brook University.

Eric Yee

Eric Yee, who started as an Associate Professor and Director of Surgical Pathology at Stony Brook Renaissance School of Medicine on July 1, described the focus of his scientific research as translational.

He consults with and helps science researchers put together ideas for experiments, while he and his wife Felicia Allard focus on bringing that work into the clinical setting.

“We provide expertise mainly in clinical gastrointestinal and hepatobiliary pathology,” Yee explained in an email. “We also give insights and perspectives as practicing pathologists to help [with the] analysis of data and how that data in the lab or in animal models may be relevant to clinical medicine.”

Yee completed a gastrointestinal pathology fellowship, working on collaborative research projects and publishing manuscripts with investigators.

As one of the newest members of the staff at Stony Brook, he has worked on some studies looking at certain kinds of inflammatory diseases in the liver. He collaborated with senior investigator Zhenghui Gordon Jiang of Beth Israel Deaconess Medical Center to look at mediators of inflammation in the disease steatohepatitis. He has also worked on different cancer research projects, which is part of the appeal of Stony Brook.

Stony Brook has “important pancreatic research,” Yee said, adding that. Pathology Department Chair Ken Shroyer is a “renowned investigator whose research team has done great work that has led to important insights into pancreatic cancer biology.”

Pancreatic cancer is of particular interest to Yee in his clinical work and he hopes to explore the variety of research expertise at Stony Brook, to support ongoing efforts and to develop projects of his own.

Relocating to Stony Brook from the College of Medicine at the University of Arkansas for Medical Sciences, where Allard and Yee both worked in the Pathology Department, took some convincing for both of the scientists.

“We were very happy in Little Rock and purchased a home in Arkansas two years prior and were just starting to set down roots,” Yee described in an email. “We made lifelong friendships and very much enjoyed the camaraderie among our peers and other departments.”

Yee and Allard had no plans to leave as they approached their third year and were hesitant to move.

In his first visit, Yee said he was impressed with the amount of research in the Stony Brook department, which, he said, has more researchers compared to other institutions of similar size.

On the other side, however, Yee said he and Allard had to reconcile the higher cost of living in New York. They also weren’t eager to make too many moves in their career, especially when they were happy in Arkansas.

Even after the first visit, Yee said he was hesitant to make a move, which would require time to settle in, build relationships, find a home, learn a new system, and find new opportunities, among other challenges..

Shroyer was “very understanding of my hesitation,” Yee explained. “He’s been one of my mentors since medical school and knew exactly where I was coming from.

Clinically, the couple also believed in the potential for career growth.

“There’s a lot of energy in the department,” Yee said. He also appreciated the opportunity to be the Director of Surgical Pathology, where he could shape the operations that support the clinical mission. He would like to optimize the department by specialization, creating a sub-specialty model.

“This is something I want to do to increase the efficiency in the department,” Yee explained. “I’m hoping as we sub-specialize that we make our clinical work flow more efficient” which will create more consistency. “Part of what I’d like to do is to help [Shroyer] create a department where it’ll allow the clinical faculty to thrive.”

Yee thinks any work efficiencies will provide researchers with more time to build on their teaching efforts, and to develop new lectures and teaching models.

Yee will measure his success through a comprehensive report that includes an analysis of the efficiency of the response to clinical needs. He hopes to create a system that will enable the success of the entire anatomic pathology division. He will also become actively engaged in the academic mission, which is measured in the number of publications as well as in staff appointments to editorial boards or major national societies.

“The more people we can get into the national arena the better it is for the institution,” Yee said. These contributions bring good public relations and expertise to the institution.

Yee and Allard will also contribute to Stony Brook through their efforts in education.

Yee believes the school has an advantage in telepathology and distance learning. He believes the Department of Bioinformatics led by Dr. Joel Saltz facilitates telepathology and distance learning.

With the uncertainty caused by COVID-19, Yee believes maintaining social distancing and finding innovative ways for communication and education will provide valuable alternatives to communicate and collaborate.  Radiology has had digital methods in place to send MRIs and CAT scans for a longer period of time than pathologists, who still produce glass slides.

“There will always be some challenges and limitations that are unique to pathology,” Yee suggested.

A native of San Francisco, where he and his older brother, who now works in Boston, grew up, Yee was interested in medicine during the middle of his college career.

Yee and Allard met in medical school and, among numerous other parts of their lives they have in common, discovered they were both fans of the Star Wars films. Early on when they were dating, the pathology couple saw Star Wars: Episode III – Revenge of the Sith together.

Yee enjoys tennis, table tennis, riding road bikes and hiking. He has also developed an appreciation for bird watching, which has allowed him to practice amateur photography.

The couple also shares an interest in music, as Yee grew up playing the piano, while Allard played the trumpet.

When he was in medical school, Yee published his first  paper with Shroyer. He has remained in touch with the pathology chair over the years and appreciates the advice Shroyer has offered.

Yee described Shroyer as an “inspirational leader” and appreciates his energy, selflessness and passion, among other qualities.

Seven students took top honors and 15 others received honorable mentions in the first-ever virtual version of the annual elementary school science fair sponsored by the U.S. Department of Energy’s Brookhaven National Laboratory in Upton. Girls and boys in kindergarten to grade 6 entered 129 science and engineering projects for the competition. They represented 38 elementary schools across Suffolk County.

The seven students to receive top honors as well as medals and ribbons are kindergartener Jude Roseto of Cutchogue East Elementary School, Mattituck-Cutchogue Union Free School District, “Friction with Bubbles”; first grader Emerson Spooner of Raynor Country Day School, “Save the Earth: One Plastic Straw at a Time”; second grader Sara Jain of Tamarac Elementary School, Sachem Central School District, “Shrink It Up”; and third grader Mia Trani of Fort Salonga Elementary School, Kings Park Central School District, “Housing the Homeless.”

Top honors also went to fourth grader Rebecca Bartha of Raynor Country Day School, “Dynamic Duckweed: A Solution to Pollution in Local Water”; fifth grader Reilly Riviello of Cherry Avenue Elementary School, Sayville Public Schools, “What Material is the best to protect your property from Flash Flooding” and sixth grader Emma Tjersland of Hauppauge Middle School, Hauppauge School District, “Drug Facts: Impacts of Medicine Exposure on Daphnia Magna Heart Rate.”

“Thinking like scientists and engineers is so important for students — asking questions, testing assumptions, drawing conclusions, and thinking about future research,” said Amanda Horn, a Brookhaven Lab educator who coordinated both the virtual science fair and a new Science Share program. “The Lab has hosted science fairs for years to encourage students and we didn’t want COVID-19 to stop us in 2020.”

Science fairs at Brookhaven Lab were typically held in person at the Lab site and students, their families, teachers, and school administrators were invited to attend. With schools closed and Brookhaven Lab’s site mostly inaccessible to limit the spread of COVID-19, Horn, Scott Bronson and their colleagues in Brookhaven’s Office of Educational Programs (OEP) quickly adjusted plans to hold the 2020 science competition virtually.

As in years past, students first qualified for the Lab’s fair by winning their schools’ “local” science fairs, some of which were also held virtually. Projects completed by individual students and groups were accepted — one project per grade per school.

Instead of bringing projects to Brookhaven Lab for an all-day on-site event, parents and teachers submitted photos of students’ projects. OEP staff then distributed the photographs and a rubric among 23 judges, comprising Brookhaven Lab scientists, engineers, and technical staff as well as teachers from local elementary schools. To maintain objectivity and limit potential biases, information such as students’ names, schools, and districts was not shared.

The 15 students who received Honorable Mentions were kindergarteners Taran Sathish Kumar of Bretton Woods Elementary School, Hauppauge School District, “Strength of Spaghetti” and Evelyn Van Winckel of Fort Salonga Elementary School, Kings Park Central School District, “Are Your Hands Clean?”; first-graders Mason Rothstein of Lincoln Avenue Elementary School, Sayville Public Schools, “3,2,1…Let It Rip” and John Henry of Frank J. Carasiti Elementary School, Rocky Point Union Free School District, “Lego Rubber Band Cars”; and second-graders Agnes Van Winckel of Fort Salonga Elementary School, Kings Park Central School District, “The Flight of a Football” and Cassie Danseraeu and Katelynn Hausmann of West Middle Island Elementary School, Longwood Central School District, “Can Aloe Vera Juice Save Strawberries from Mold?”

Honorable mentions were also given to third-graders Mihir Sathish Kumar of Bretton Woods Elementary School, Hauppauge School District, “Strength of Electromagnets” and Matthew Mercorella of Sunrise Drive Elementary School, Sayville Public Schools, “Think Twice Before Melting the Ice”; fourth-graders Samuel Canino of R.J.O. Intermediate School, Kings Park Central School District, “Riddled With Puck Shot,” Jack Gomez of R.J.O. Intermediate School, Kings Park Central School District, “Infinipower” and Madelyn Kalinowski of Laurel Hill School, “Wash Away Germs”; fifth-graders Alexandra Barry of Remsenburg-Speonk Elementary School, Remsenburg-Speonk Union Free School District, “Mutiny on the Bounty” and Gavin Pickford of R.J.O. Intermediate School, Kings Park Central School District, “Is This The Last Straw”; and six-graders Karly Coonan of Raynor Country Day School, “The Last Straw” and Pranav Vijayababu, Hauppauge Middle School, Hauppauge School District, “Save Our Seas.”

“Suffolk County, New York State, the country, and the world need scientists and engineers now and in the future. The students in this science fair are young, but they aren’t too young to have fun with investigative science and engineering processes,” said Scott Bronson, Brookhaven Lab’s manager for K–12 programs.

“Once again, the students who participated were exceptional. Their projects showed it. Congratulations to each of them. And, ‘Thank you,’ to every parent, teacher, mentor, and volunteer who helped them — and will continue to help them along the way.”

For more information, visit https://www.energy.gov/science/.

Photos courtesy of BNL

Felicia Allard

By Daniel Dunaief

Stony Brook University recently added a wife and husband team to its Pathology Department. Felicia Allard and Eric Yee are joining SBU from the University of Arkansas.

Allard and Yee will “replace an individual who had moved to a leadership position at another institution and to meet increased caseloads in surgical pathology and cytopathology,” Ken Shroyer, the chairman of the Pathology Department, explained in an email.

Times Beacon Record News Media will profile Allard and Yee over the next two weeks.

Felicia Allard

Eric Yee and Felicia Allard. Photo by Joshua Valencia

A self-described “mountain girl” from Colorado, where she attended medical school and met her husband Eric Yee, Felicia Allard had only been to Long Island three times before accepting a job at Stony Brook.

She came once when she was interviewing for a residency and twice during the interview process.

Allard and Yee accepted the jobs in the middle of February and weren’t able to look at potential homes during the height of the lockdown caused by COVID-19.

For now, the couple have moved into temporary housing in Port Jefferson Station, as they look for longer term living options.

Allard, who will be an Associate Professor at SBU, said the move started with Pathology Department Chair Ken Shroyer, who was looking to fill two positions and reached out to Yee.

Shroyer was involved in a type of cancer work that interested her.

“The active pancreatic cancer research group was a big draw for me as I am hoping to expand my research career,” Allard explained in an email.

Allard said she was particularly interested in pancreatic cancer, in large part because of its intractability and the poor prognosis for most patients.

“It was clear to me that this is one of the areas where we had a lot of work to do in terms of being able to offer any type of meaningful treatment to patients,” she said.

Allard said she, like so many others in the medical community, entered the field because she wanted to make a difference. She searched for areas where the “greatest good could be done, and pancreatic cancer is still one of those.”

In her initial research, she studied the pancreatic neoplasm, exploring how cells went from pre-invasive to invasive to metastatic conditions. She is interested in how the tumor interacts with the patient’s immune system.

While Allard will continue to provide clinical services, she plans to collaborate with Shroyer in his lab. “I’m hoping naturally to be integrating into Dr. Shroyer’s group,” Allard said.

Shroyer welcomed Allard to the department and to his research team.

Allard is “a highly-qualified surgical pathologist with subspecialty expertise in GI tract pathology,” Shroyer wrote in an email. “She has a specific interest in pancreatic cancer, which will also complement our translational research program,” he said.

Shroyer expects that Allard will be integrated into several cancer research programs and he is “looking forward to having her join my team that is focused on the validation of prognostic and predictive biomarkers for pancreatic cancer.”

Shroyer’s lab, which includes Luisa Escobar-Hoyos, who is an Assistant Professor in the Department of Pathology, will work with Allard to advance the translational aspects of keratin 17 research, building on earlier work to understand the mechanisms through which K17 causes tumor aggression, he explained.

As for her clinical work, Allard said she analyzes biopsies and resections from the esophagus, stomach, intestines, liver, and pancreas. She has also used cytopathology to look at pap smears and to analyze salivary tumor aspirations.

The time to consider any of these slides varies broadly. Sometimes, she receives a slide and the diagnosis is unequivocal within 30 seconds. Other times, a biopsy from a six-month old patient with diarrhea, for example, can have an extensive list of differentials. In that case, the diagnosis can take considerably longer, as a baby could be sick because of an autoimmune disorder, inflammatory bowel disease or an infection.

She said she can “perseverate for hours or even days” over the subtle clues that may help with a diagnosis.

Allard likened the diagnostic process to reading a detective novel, in which the reader might figure out the perpetrator on page three, while other times, the culprit isn’t discovered until page 300.

Allard said she and her husband have a similar clinical background.

Yee is “more of a tech geek than I am,” she said. “He understands artificial intelligence, computer science and bioinformatics more than I do. He is also interested in administrative and leadership to a greater degree.”

Allard said she and Yee may have professional overlaps, but they have unique interests, backgrounds and perspectives that they bring to work that give them each different strengths.

Allard said she knew she wanted to go into medicine in her junior year of high school. When Doctors Without Borders won the Nobel Peace Prize in 1999, she recalls being impressed with that distinction.

In medical school, she said the field of pathology appealed to her because she appreciated the marriage of clinical care and basic science in the field.

She and Yee started dating just before medical school started for her. Yee was two years ahead in school. They continued their relationship from a distance while he did his residency at Beth Israel Deaconess Medical Center at Harvard Medical School. While she was a resident, Allard said Yee had the “distinct pleasure of trying to train me.”

She likes to explore the boundaries of diagnosis to understand the nuances and all the data that factor into interpretations, to tease the art from the science.

Outside of her work, Allard enjoys reading and calls her Kindle one of her favorite possessions. She hopes to learn how to sail while a resident of Long Island.

Allard is excited to start working at Stony Brook. Shroyer was “very persistent and once he got us up to New York to interview, he was persuasive with respect to the type of career growth we could both potentially have,” she said.

Marci Lobel. Photo from SBU

By Daniel Dunaief

Pregnant women with access to the outdoors are less stressed during the pandemic.

In fact, according to an unpublished finding that isn’t yet peer reviewed, pregnant women who had outdoor access were 67 percent less likely to worry about contracting the virus and 63 percent less likely to feel stress about being unprepared for the birth.

Lobel with a recent doctoral student, Jennifer Nicolo-SantaBarbara.

Stony Brook University recently awarded a project led by Dr. Heidi Preis in the Department of Psychology, with co-Principal Investigators Dr. Marci Lobel in the Department of Psychology and Dr. Brittain Mahaffey in the Department of Psychiatry and Behavioral Health that explored the link between stress and pregnancy. The researchers are hoping to identify what helps pregnant women and what may make them more vulnerable to the impacts of stress.

Stony Brook provided a total of $398,200 in seed funding to 17 research projects in response to the pandemic. Researchers at Stony Brook had put together 63 submissions, using a peer review process to choose the projects to fund, including the COVID-19 Pregnancy Experiences (or COPE) Study. The funding, which is for one year, is designed to provide the kind of seed funding that will lead to further research and that other funding agencies will support.

The COPE study tapped into a global network of collaborators that Lobel, who is the Director of the Stress and Reproduction Lab at SBU, established over the past 30 years to compare the different factors that mitigate or exacerbate stress for pregnant women in Spain, Israel, Italy, Germany Poland and Switzerland.

“The biological impact of COVID-19 is getting the lion’s share of attention, as it should,” said Lobel. “We don’t yet know enough about how the psychological impact will affect vulnerable groups, like pregnant women.”

Indeed, Lobel has spent three decades studying the effect of stress and related psychological factors on pregnancy. In other studies, major stressors, such as earthquakes, ice storms, and periods of warfare, confirm the toxic impact of prenatal stress, particularly for preterm births and low birth weight, she said.

Lobel and her colleagues created a self-report instrument called the Pandemic-Related Pregnancy Stress Scale, or PREPS, in which women report their specific concerns or anxieties caused by COVID-19.

Throughout the United States, the team sought responses from about 4,500 women recruited through social media at the end of April and the beginning of May.

Marci Lobel with her family at Yosemite in 2016. The photo credit is: Photo courtesy of Marci Lobel.

Among the women in the study, just over half of them were pregnant with their first child. In many studies that predated the current work, including some from her own research group, Lobel said women pregnant with their first child had higher levels of stress.

In some preliminary findings, 21.7 percent of pregnant women in the study reported severe levels of anxiety. “I think that is higher than what we typically would find in a population study of pregnant women,” Lobel said.

Women with a history of interpersonal violence also reported higher levels of stress and those whose prenatal appointments were canceled or altered were 1.78 times more likely to experience high stress related to a lack of preparedness and 1.49 times more likely to experience high stress related to worries about perinatal infection.

Some women in the study have found ways to reduce the accumulating stress about the health care crisis. The techniques that work for some women, Lobel said, may not work for others, suggesting that stress relief is specific to the individual and is usually determined by the situation itself.

“I don’t recommend any particular way of coping,” Lobel said. “What works for one may not work for another. It’s good to have a tool kit with lots of ways of coping.”

Indeed, some of the techniques pregnant women have found helpful include meditation, prayer, and faith-based practices. Pregnant women have also benefited from social support, which is particularly important during the pandemic when some women may feel “literally and figuratively isolated from others,” Lobel said.

Of all the research Lobel has done, the one that has received the most attention and landed her in the bible for pregnant women, “What to Expect When You’re Expecting,” was a study on optimism. She found that women who were more optimistic had better birth outcomes due in part to the better are they took of their health during pregnancy.

Coping with stress by avoidance predicts increases in emotional distress, Lobel explained. This corroborates much research which shows that avoidance is usually an ineffective way to cope with stress, except in limited cases such as when a stressful situation is brief and uncontrollable.

When people avoid the things that bother them, they can do it cognitively or through alcohol, which is especially dangerous for pregnant women and their developing fetuses. Avoidance can also involve excessive sleeping, as pregnant women may decide they don’t want to deal with life and stay in bed all day.

The scientists plan to collect a second set of data from these women, who were recruited through social media and who represent a diverse socioeconomic background, race and ethnicity, sexual orientation, and other factors, on July 15th.

Lobel said she already has some preliminary, unpublished findings from Poland, which are showing the same kinds of stressors and distress among pregnant women. Polish women have expressed stress related to worries about lack of preparation for birth during the pandemic and stress related to worries about infection.

Lobel said the researchers hope to explore a host of questions as they collect more information. They hope to look at obsessions and compulsions and would like to measure anger. They also will measure levels of depression and anxiety and will compare that to the norms for non-pregnant women.

On the other side of the stress meter, the group will study how being pregnant during the pandemic may help some women appreciate their pregnancy more. For some women, the pregnancy may give them strength to deal with the pandemic, as they focus on having a baby.

The researchers will also explore the level of control women feel over the outcome of their pregnancy and the health of their baby. Feeling in control can create a positive response associated with lower distress.

While Lobel and her colleagues won’t answer all these questions in a year, they hope their initial studies will lead to more funding and research. “Hopefully, we’ll get a [National Institutes of Health] grant to follow up these women for a couple of years to study them and their children to see if there are any developmental or mental or physical health effects” of the pandemic.

Kevin Reed. Photo from SBU

By Daniel Dunaief

At the beginning of this month, the North Atlantic started its annual hurricane season that will extend through the end of November.

Each year, the National Oceanic and Atmospheric Administration offers a forecast in May for the coming season. This year, NOAA’s Climate Prediction Center anticipates a 60 percent chance of an above-normal season. The Center anticipates 13 to 19 storms, although that number doesn’t indicate how many storms will make landfall.

These predictions have become the crystal ball through which forecasters and city planners prepare for a season that involves tracking disturbances that typically begin off the West coast of Africa and pick up energy and size as they travel west across the Atlantic towards Central America. While some storms travel back out to sea, others threaten landfall by moving up the Gulf Coast or along Atlantic Seaboard of the United States.

Kevin Reed, an Associate Professor at Stony Brook University’s School of Marine and Atmospheric Sciences, and Alyssa Stansfield, a graduate student in his lab, recently predicted the likely amount of rainfall from tropical cyclones.

Alyssa Stansfield at the 33rd Conference on Hurricanes and Tropical Meteorology in 2018. Photo by Arianna Varuolo-Clarke

 

Using climate change projection simulations, Reed and Stansfield came up with a good-news, bad-news scenario for the years 2070 through 2100. The good news in research they published in Geophysical Research Letters is they anticipate fewer hurricanes.

The bad news? The storms will likely have higher amounts of rain, with increased rain per hour.

“If you focus on storms that make landfall over the Eastern United States, they are more impactful from a rainfall standpoint,” Reed said. “The amount of rainfall per hour and the rainfall impact per year is expected to increase significantly in the future.”

In total, the amount of rainfall will be less because of the lower number of storms, although the intensity and overall precipitation will be sufficient to cause damaging rains and flooding.

Warmer oceans and the air above them will drive the increased rainfall, as these storms pass over higher sea surface temperatures where they can gain energy. Warmer, moist air gives the hurricanes more moisture to work with and therefore more potential rainfall.

“As the air gets warmer, it can hold more water in it,” Stansfield said. “There’s more potential rain in the air for the hurricanes before they make landfall.”

Stansfield said the predictions are consistent with what climatologists would expect, reflecting how the models line up with the theory behind them. She explored how climate change affects the size of storms in this paper, but she wants to do more research looking at hurricane size in the future.

“If hurricanes are larger, they will drop rainfall over a larger area,” which could increase the range of area over which policy makers might need to prepare for potential damage from flooding and high winds, Stansfield said.

While her models suggest that storms will be larger, she cautioned that the field hasn’t reached a consensus about the size of future storms. As for areas where there is greater consensus, such as the increased rainfall their models predict for storms at the end of the century, Stansfield suggested that the confidence in the community about their forecasts, which use different climate models, is becoming “more apparent as more modeling groups reach the same conclusion.”

Alyssa Stansfield at Sequoia National Park in 2018. Photo by Jess Stansfield

In explaining the expectations for higher rainfall in future storms, Reed said that even storms that had the same intensity as current hurricanes would have an increase in precipitation because of the availability of more moisture at the surface.

While storms in recent years, such as Hurricanes Harvey, Florence and Dorian dumped considerable rain in their path because they moved more slowly, effectively dumping rain over a longer period of time in any one area, it’s “unclear” whether future storms would move more slowly or stall over land.

Several factors might contribute to a decrease in the number of storms. For starters, an increase in wind sheer could disrupt the formation of some storms. Vertical wind sheer is caused when wind speed and direction changes with increasing altitude. Pre-hurricane conditions may also change due to internal variability and the randomness of the atmosphere, according to Reed.

Reed said the team chose to use climate models to make predictions for the end of the century because it is common in climate science for comparison to the recent historical record. They also used a 30 year period to limit some of the uncertainty due to internal variability of weather systems.

Stansfield, who is in her third year of graduate school and anticipates spending another two years at Stony Brook University before defending her graduate thesis, said she became interested in studying hurricanes in part because of the effects of Superstorm Sandy in 2012.

Alyssa Stansfield at Yosemite in 2019. Photo by Kathy Stansfield

When she was younger, she and her father Greg used to go to the beach when a hurricane passed hundreds of miles off the coast, where she would see the impact of the storm in larger waves. At some point, she would like to fly in a hurricane hunter plane, traveling directly into a storm to track its speed and direction.

Stansfield said one of the more common misconceptions about hurricanes is that the category somehow determines their destructive power. Indeed, Superstorm Sandy was a Category 1 hurricane when it hit New York and yet it caused $65 billion in damage, making it the 4th costliest hurricane in the United States, according to the NOAA.

After Stansfield earns her PhD, she said she wants to continue studying hurricanes. One question that she’d like to address at some point is why there are between 80 to 90 hurricanes around the world each year. This has been the case for about 50 years, since satellite records began.

“That’s consistent every year,” she said. “We don’t know why that’s the number. There’s no theory behind it.” She suggested that was a “central question” that is unanswered in her field. 

Understanding what controls the number of hurricanes will inform predictions about how that number will change in response to climate change.

Photo from SBU

Pierce Gardner, MD, Professor Emeritus at the Renaissance School of Medicine at Stony Brook University, is the recipient of the 2020 Dr. Charles Mérieux Award for Achievement in Vaccinology and Immunology from the National Foundation for Infectious Diseases (NFID). The award honors individuals whose outstanding lifetime contributions and achievements in the fight against vaccine-preventable diseases have led to significant improvement in public health.

Dr. Gardner’s career has centered on global health policy and training the next generation of public health providers to tackle health issues in low-resource countries. The Setauket resident has done extensive international work and has been a consultant for the World Health Organization, the Centers for Disease Control, and the Armed Forces Epidemiological Board (now the Defense Health Board). He served in many educational roles while at the Renaissance School of Medicine and remains instrumental in fostering students’ global health interests related to their career paths.

Previous recipients of this national award include luminaries in infectious diseases such as D.A. Henderson (who wiped out smallpox), Arnold Monto (a pioneer in influenza vaccine), and Kristin Nichol (a pioneer in pneumococcal vaccination).

Saket Navlakha. Photo from CSHL

By Daniel Dunaief

When people walk into their own home, they immediately ignore sensory cues around them. They may not notice the picture of their children on the wall, the lush leaves of the ficus plant, or the constant smell of soup that greets them when they return from work.

Similarly, animals and even flies become accustomed to cues in their environment, habituating to them so they can focus on more important signals, like the smell of nearby food or the appearance of a fly swatter.

Cold Spring Harbor Laboratory Associate Professor Saket Navlakha and his post doctoral researcher Yang Shen recently studied the way flies subtract smells from the environment, giving them the opportunity to focus instead on odors that might be more important to their lives.

In a paper last month in the Proceedings of the National Academy of Sciences, Navlakha and Shen converted the way flies use a signal filtering process to create a computer algorithm.

Navlakha explained that the tandem were using computer science to understand better a basic biological phenomenon of habituation and how it happens. “We’ve been studying background subtraction,” he said in a recent interview.

One of the applications for their work is in electronic noses. Hotels and even military departments may in the not too distant future use these systems to process odors to determine what’s in the environment.

These electronic noses detect faint signals within noisy backgrounds. Habituation enables them to remove from consideration those scents that would otherwise distract from the goal of scanning the environment for new information.

Navlakha suggested that humans, who are often a visually dominant species, are not always the best species at using a sense of smell to perceive the environment.

Saket Navlaka with his wife Sejal Morjaria, during a run in Port Washington in mid-May. Photo by Lawrence Lau

“Many other species rely on their noses as much as we rely on vision,” he said. “We don’t always have an intuitive sense of what is possible in the olfactory space. Sometimes, that limits our imagination.”

While Navlakha is not crafting sensors that can detect compounds, he is working on the computer science analogs to odor recognition and discrimination. He is exploring the kind of data analysis that would have applications in a range of fields. 

In one example, he said a sensor in an airport might be surrounded by a symphony of smells, including new pungent or even subtle toppings on pizza or even a new cologne from someone working in a watch repair store. 

The sensor might need to sift through all that data to find someone who is transferring a toxic chemical through an airport, the scent of which might be faint and almost insignificant compared with the other odors spreading through the terminal.

In a more everyday example, a sensor in the refrigerator might detect the subtle changes in odors emitted by foods that are starting to become inedible, such as an onion or cream cheese.

“You want to detect” when food is starting to turn so you can “eat it and use it” before it becomes inedible, Navlakha said. “These are the kind of problems we are exploring on the data analysis side.”

Navlakha specifically looked at the activity of Kenyon cells, which are special odor neurons. When a fly receives a new scent, about five percent of these cells turn on, developing a unique activity tag.

Once the fly becomes habituated to a smell that isn’t relevant for its survival — either to indicate the presence of food or to announce the arrival of a predator — Navlakha believes the number of Kenyon cells that make up the tag for the odor declines. While this is his theory, he said more work needs to be done to confirm these predictions.

A new odor repeats the process, bringing the fly’s attention to a new smell. The fly brain in principal can reverse the subtraction process for habituated odors if the odor becomes more rare or important for the fly’s survival. Researchers need to conduct more work to confirm this as well.

Navlakha hopes to frame the fluid process of recognizing, habituating and bolstering the signal for odors to understand how the brain is functioning.

He said the fly brain responds to smells based on two mechanisms. In the first, the fly has an innate, evolutionary behavior. In the second, the fly learns through experience. Navlakha studied the learned behaviors.

The next steps involve pushing more on the experimental front, determining the limits of odor discrimination and looking at the role of habituation.

He hopes to extend an experiment that others have done with people. Experimenters took three odors that were all relatively similar that come from three flowers. Most people could not discriminate between two out of the three odors. In an experimental group, they allowed people to habituate to one of three smells and then they had to discriminate between the other two. By subtracting out the common part of all three smells, they were more successful at decoding the difference between the others.

“We want to see if we can do this in fruit flies” while recording from a region of the fly brain called the mushroom body.

Navlakha also bought an electronic nose. Using this artificial system, he wants to test odor discrimination algorithms.

“One thing this would allow us to do is to test and validate these algorithms to see how well they perform,” he explained. “There are all kinds of tests to see what kind of power these sensors have.”

In the PNAS paper, Navlakha mostly used the literature for their biological inspiration. They discussed numerous parts of the paper with biological collaborators and including biological experiments. They did not introduce any new biological data.

He came across this literature about 18 months ago.

“We thought it was interesting because we could understand the whole series of transformations when a fly smells,” he said. He worked on how to understand the process from input to output.

During the COVID-19 lockdown, he has been spending considerably more time doing theoretical work and modeling. He and his wife Sejal Morjaria have also gotten out of the house to do some running.

As for his work, Navlakha is hoping to build on what he’s done so far and expects he will, if you’ll pardon the pun, follow his nose as the research progresses.