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Power of 3

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Attendees at a conference at CSHL, an in-person tradition started in 1933. These conferences were suspended from 1943 to 1945 during WWII and were virtual during the pandemic in 2020 and for most of 2021. Photo by Miriam Chuai/CSHL

By Daniel Dunaief

For scientists, meetings and conferences aren’t just a chance to catch up on the latest research, gossip and see old friends: they can also provide an intellectual spark that enhances their careers and leads to new collaborations.

Amid the pandemic, almost all of those in-person conferences stopped, including the annual courses and meetings that Cold Spring Harbor Laboratory hosts. The internationally renowned lab has run meetings since 1933, with a few years off between 1943 and 1945 during World War II.

CSHL’s David Stewart. Photo by Gina Motisi/CSHL

While scientists made progress on everything from basic to translational research, including in laboratories that pivoted towards work on the SARS-CoV-2 virus, which causes COVID-19, they missed out on the kinds of opportunities that come from in-person interactions.

Assuming COVID infection rates are low enough this fall, CSHL is hoping to restart in-person conferences and courses, with the first conference that will address fifty years of the enzyme reverse transcriptase scheduled for Oct. 20th through the 23rd. That event was originally scheduled for October of 2020.

One of the planned guest speakers for that conference, David Baltimore, who discovered the enzyme that enables RNA to transfer information to DNA and is involved in retroviruses like HIV, won the Nobel Prize.

“I am hoping that there will be significant participation by many eminent scientists, so that is in itself somewhat [of] a ceremonial start,” wrote David Stewart, Executive Director of meetings and courses at Cold Spring Harbor Laboratory.

To attend any of the seven in-person meetings on the calendar before the end of the year, participants need to have vaccinations from either Pfizer, Moderna, Johnson & Johnson or AstraZeneca.

Attendees will have to complete an online form and bring a vaccination card or certificate. Scientists who don’t provide that information “will not be admitted and will not get a key to their room or be able to attend the event,” Stewart said.

CSHL also plans to maintain the thorough and deep cleaning procedures the lab developed. 

Stewart hopes that 75 to 80 percent or more of the talks presented will be live, with a virtual audience that could be larger than the in-person attendance.

“It is important to have a critical mass of presenters and audience in-person, but there’s no real limit on how large the virtual audience could be,” he explained.

Typically, the courses attract participants from over 50 countries. Even this year, especially with travel restrictions for some countries still in place, Stewart expects that the majority of participants will travel from locations within the United States.

The Executive Director explained that CSHL was planning to introduce a carbon offset program for all travel to conferences and courses that the facility reimburses starting in 2020. After evaluating several options, they plan to purchase carbon offsets from Cool Effect and will encourage participants paying their own way to do the same or through a similar program.

The courses, meanwhile, will begin on October 4th, with macromolecular crystallography and programming for biology. CSHL hopes to run six of these courses before the end of the year, including a scientific writing retreat.

“We are looking to 100 percent enrollment for our courses, so likely this year that will largely be domestic,” Stewart explained.

The courses, which normally have 16 participants, may have 12 students, as the lab tries to run these training opportunities safely without masks or social distancing.

From March of 2020 through the end of last year, the lab had planned 25 meetings and 25 courses. As the pandemic spread, the lab pivoted to virtual meetings. “I felt like a car salesman trying to sell virtual conferences,” Stewart recalled. For the most part, the lab was able to keep to its original schedule of conferences, albeit through a virtual format.

In addition to the scheduled meetings, CSHL decided to add meetings to discuss the latest scientific information related to COVID research. 

Stewart approached Hung Fan, a retired virologist at the University of California at Irvine, to help put together these COVID exchanges. Those meetings occurred in June, July, August, October, and January. The sixth one recently concluded.

The meetings addressed “everything around the science of the virus,” Stewart said, which included the biology, the origin, the genomics, the immune response, vaccines, therapeutics and diagnostics, among other scientific issues.

“There was a lot of excellent work being done around SARS-CoV-2,” Stewart said. “We were trying to identify that early on. It was helpful to have people who knew the field well.”

Fan said he combed through preprints like the CSHL-based bioRxiv and related medRxiv every day for important updates on the disease.

Fan described the scientific focus and effort of the research community as being akin to the Manhattan Project which built the atomic bomb during World War II, where “everybody said, ‘We have a common enemy and we want to apply all our capabilities to combating that.”

While Fan is pleased with the productive and valuable exchanges that occurred amid the virtual conferences, he recognized the benefit of sharing a room and a drink with scientific colleagues.

“A lot of the productive interactions at meetings take place in a social setting, at the bar, over dinner” and in other unstructured gatherings, he said. “People are relaxed and can share their scientific thoughts.”

After presentations, Fan described how researchers discuss the work presented and compare that to their own efforts. It’s easier to talk with people in person “as opposed to making a formalized approach through letters and emails.”

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A group of gelada monkeys in Ethiopia. Photo from Jacob Feder

By Daniel Dunaief

Timing can mean the difference between life and death for young geladas (an Old World monkey species). Geladas whose fathers remain leaders of a social group for as much as a year or more have a better chance of survival than those whose fathers are displaced by new males under a year after they’re born. 

New males who enter a social group can, and often do, kill the young of other males, giving the new male leaders a chance to impregnate the female members of their social group who might otherwise be unable to conceive.

Jacob Feder

 

The odds of a new male leader killing a young gelada are about 60 percent at birth, compared to closer to 15 percent at around a year of age, according to researchers at Stony Brook University (SBU).

Additionally, pregnant gelada monkeys often spontaneously abort their unborn fetuses once a new male enters the group, as the mother’s hormones cause a miscarriage that enables them to dedicate their resources to the future progeny of the next dominant male.

At the same time, the survival of females depends on becoming a part of a group that is just the right size.

Jacob Feder, a graduate student at SBU, and Amy Lu, Assistant Professor in the Department of Anthropology in the College of Arts and Sciences at Stony Brook, recently published a paper in Proceedings of the Royal Society B that explores the ideal group size that optimizes the longevity of females and the number of their offspring.

The researchers discovered a Goldilocks effect. By studying the behavioral and group data for over 200 wild geladas over the course of 14 years, they determined that a mid-size group with five to seven females has the greatest benefit for their own fitness and for the survival of their offspring.

“There tends to be a trade off” in the dynamics that affect female geladas in different groups, Feder said. Females in the biggest groups face a higher risk of takeovers and takeover-related infanticide, since males are more likely to try to dominate a part of larger social groups where they have greater reproductive opportunities.

By contrast, individuals in the smaller groups may live on the periphery of a multi-group dynamic. These females are less protected against predators.

In their native Ethiopia, geladas are vulnerable to leopards, hyenas, and jackals, among others.

For the females, the survival of their offspring depends on the ability of males to remain in the group long enough.

“The male turnover is one of the major drivers of their reproductive success,” explained Feder.

Researchers have seen new males enter a group and kill infants born from another father. The infants, for their part, don’t often recognize the need to avoid new males, Lu said.

When males enter big groups, females often have to reset their reproduction.

Groups with about nine to 11 females often split into units of four to seven, Feder said. A new male might become the leader for half of the females, leaving the remaining male with the other half. Alternatively, new males may take over each group.

The pregnant females who are part of a group with a new male will spontaneously abort their offspring about 80 percent of the time, as females “cut their losses,” Feder said

About 38 percent of females live in a mid-sized group that is close to optimum size.

Gelada charm

According to Feder and Wu, geladas are a compelling species to research, Feder and Wu said.

Feder found his visits to the East African nation rewarding, especially when he had the opportunity to watch a small female named Crimson.

An important part of daily life for these primates involves grooming, where primates comb through each other’s hair, remove insects and, in many cases, eat them.

Crimson, who was a younger member of the group when Feder started observing geladas, didn’t have much grooming experience with this activity. Instead of running her hands over the body of her grooming partner, she focused on her mouth. Her partner’s wide eyes reflected surprise at the unusual grooming choice.

One of the favorites for Lu was a monkey who has since passed away named Vampire. A part of the V group, Vampire was taller and bigger than most adult females. She displaced male geladas, some of whom were larger than she, almost as often as they displaced her.

“If you go out in the field enough, you know the individuals pretty well,” Lu said. “They all have their own personalities. Some of them walk in a different way and react to situations differently.”

A resident of Centereach, Feder grew up in northern Connecticut, attending Wesleyan University as an undergraduate, where he majored in music and biology. A bass guitar player, Feder said he “dabbles in anything with strings.”

In fourth grade, Feder read a biography of Dian Fossey, which sparked his interest in biology.

While he has yet to combine his musical and science interests with geladas, Feder said these monkeys have a large vocabulary that is almost as big as chimpanzees.

Lu, meanwhile, started studying geladas as a postdoctoral researcher. They’re a great study species that allow scientists to ask compelling questions about reproductive strategies. “At any point, you can follow 20 social groups,” Lu said.

Lu, whose two children are four years old and 16 months old, said she has observed the similarities between human and non-human primate young.

“Babies throw tantrums, whether it is my child or a gelada infant protesting being put on the ground,” she described in an email. Gelada infants use a sad “cooing” sound. Sometimes, the sad cooing sound is real and sometimes “they just get what they want.”

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Rebecca Smith at the Sólheimajökull glacier in Iceland, where the scientist did field work during the 2015 Astrobiology Summer School. Photo from Rebecca Smith

By Daniel Dunaief

Rocks may not speak, move or eat, but they can and do tell stories.

Recognizing the value and importance of the ancient narrative rocks on Earth and on other planets provide, NASA sent vehicles to Mars, including the rover Perseverance, which landed on February 18 of this year.

Perseverance brought seven instruments, most of them identified by the acronym-loving teams at NASA, that carry out various investigations, such as searching for clues about a water-rich environment that may have sustained life about 3.5 billion years ago.

Several instrument teams developed and monitor these pieces of equipment, including Joel Hurowitz, Associate Professor in the Department of Geosciences at Stony Brook University and Deputy Principal Investigator on the Planetary Instrument for X-ray Lithochemistry, or PiXL.

In addition to the instrument leads, NASA chose participating scientists who can contribute to several teams, providing scientific support for a host of questions that might arise as the rover explores the terrain of the Red Planet 128 million miles from Earth.

Rebecca Smith, a post-doctoral researcher at Stony Brook in Geosciences Professor Scott McLennan’s lab, is one such participating scientist.

“I get to move around between all these different groups, which is fun,” said Smith, whose appointment will last for three years. While the Mars2020 program takes up about 20 percent of Smith’s time, the remainder is focused on the Mars Science Laboratory mission. Smith is likely to spend almost all of her time on Mars2020 starting this September.

Smith has helped make the science plans for the rover. The scientist and other researchers help select targets for the instruments that will help answer specific science questions. For this work, they collaborate with different science teams. Smith plans to get more involved with specific instrument teams soon, including SuperCam, PiXL and Sherloc.

For Smith’s own research, the scientist has a suite of rock samples that include lacustrine carbonates and hydrothermally altered volcanic rocks. The volcanic rocks formed under conditions that might be analogous to those once present in Jezero crater, where the rover landed and is currently maneuvering. The crater is just north of the Martian equator and has a delta that once long ago contained water and, potentially, life.

On Earth, Smith is using versions of the SuperCam, PiXL, and Sherloc to understand how these rocks would look to different instruments and determine what baseline measurements they need to tell the different types of rocks apart using the instruments aboard the rover.

Smith has studied rocks on Earth located in Hawaii, Iceland and the glaciers in the Three Sisters Volcanic Complex in Oregon.

Many planetary geologists use Earth as an analog to understand geologic processes on other planets. It is still uncertain if the climate of early Mars was warn and wet or cold and icy and wet, Smith explained in an email, adding, “It is possible the minerals we see with the rovers and from orbit can help us answer this question.” 

Most of the work the scientist been involved with is trying to understand how Mars-like volcanic rocks chemically weather under different climates.

Through previous research on Mars, scientists discovered that large regions had poorly crystalline materials. The poorly crystalline nature of the materials makes them difficult to identify using rover-based or orbiter-based instruments.

“The fact that they could have formed in the presence of water makes them important to understand,” Smith explained.

Part of the work Smith is doing is to understand if poorly crystalline material formed by water have specific properties that relate to the environment or climate in which they formed.

Smith said the bigger picture question of the work the teams are doing is, “was there life on Mars? If not, why not? We think that Mars, for the first billion years or so, was pretty similar to Earth around the same time and Earth developed life.”

Indeed, Earth had liquid water on its surface, which provided a habitat for microbial life about 3.5 billion years ago.

The ancient rock record on Mars provides a better-preserved history because the Red Planet doesn’t have plate tectonics.

“Based on what we know about Earth, if life ever developed on early Mars, it would likely have been microbial,” Smith wrote.

Other goals of Mars2020 include characterizing the climate and the geology. Both goals focus on looking for evidence of ancient habitable environments and characterizing those to understand a host of details, such as the pH of the water, the temperature and details about how long the water was on the surface.

Part of the reason NASA put out a call for participating scientists is to “bridge instrument data” from different pieces of equipment, Smith explained.

“I love the collaborative nature of working on a team like this,” Smith offered. “Everybody is interested in getting the most important information and doing the best job that we can.”

Smith enjoys the opportunity to study potentially conflicting signals in rocks to determine what they indicate about the past.“Geology is just so complex. It’s a big puzzle. Forces have been acting over a very long period of time and forces change over time. We are trying to tease apart what happened and when.”

While Smith works at Stony Brook, the post-doctoral scientist returned to California during the pandemic to live closer to her family. After finishing the current research program, Smith plans to remain open to various options, including teaching.

Smith appreciates the opportunity to work on the Mars 2020 mission, adding, “I’m really grateful for that during this past year in particular.”

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Pixabay photo

By Daniel Dunaief

Rain can put a damper on life, as the two children at the beginning of Dr. Seuss’s The Cat in the Hat shared and as the itsy bitsy spider that went up the water spout only to get washed out again discovered.

As it turns out, rain, clouds, wind and foul weather can reduce the trading decisions of people who buy and sell large sums of money in stocks, as they grapple with their own reactions to clouds that they’d like to go away and come again some other day.

Danling Jiang

Danling Jiang, associate dean of research and faculty development in Stony Brook University’s College of Business; Lin Sun, Assistant Professor at George Mason University; and Dylan Norris, Assistant Professor at Troy University recently published a study in which they explored the effect of cloudy or inclement weather in the two weeks before an earnings surprise on investor reactions.

Every three months, public companies provide a detailed disclosure of their profits and losses, giving investors a chance to look over the equivalent of a quarterly report card.

Like helicopter parents who monitor every line, sentence and word in a report card, institutional investors tend to have a stronger reaction, either positively or negatively, if those numbers are considerably different than they expected. An “A” in advanced calculus might be like profits that exceed estimates by 10 percent, while a “C” might be the equivalent of an unexpected loss in a business that had been doing well.

As it turns out, institutional investors are less likely to react as strongly, at least initially, to an earnings surprise if the skies in the two weeks before they review the earnings announcements are cloudy or unpleasant.

“We find strong supporting evidence in our empirical tests which reveal increases in the pre-announcement unpleasant weather of institutional investors results in muted immediate market responses to earnings news and amplified port-earnings-announcement drifts,” Jiang explained in an email.

Over the course of two to three months, the stock price reflects a more typical pattern that aligns with the direction of the earnings surprise.

The researchers published their work in the Journal of Corporate Finance.

These results, which came from an analysis of reactions to earnings surprises from 1990 to 2016, validate and extend previous efforts to understand how weather affects investor decisions.

Earlier studies revealed the effects of weather on individuals’ psychological and physiological states, according to Jiang.

“These effects have also been shown to influence financial decisions and security prices, even through the actions of sophisticated market participants such as market makers and security analysts,” she said.

The three academics started working together when Lin and Jiang were faculty and Norris was a PhD student at Florida State University.

“We were fascinated by the idea present in prior research that weather seems a perfect exogenous shock to investor psychology and physiology,” said Jiang. “This exogenous feature allows us to draw some causality of psychology on market pricing in a new setting with institutional investors and earnings announcements.”

The researchers chose the years 1990 to 2016 because they had the data in their possession.

“We tried to ensure that our sample period was long enough to confirm the weather effect was a persistent force throughout time and not merely a phenomenon of a small segment in time,” said Jiang who added that solving the weather-related muted effect by adding brighter lights to a trading floor could backfire, as excessive bright lights can have negative effects.

“Overillumination can cause fatigue, stress and anxiety,” she explained. “It is also likely that most traders are subject to the weather at some point during the day” through arriving at work, leaving for lunch or glancing out the window. That means the weather still likely influences them even when they may be in a brightly-lit indoor setting.

The researchers used two measures of weather conditions. One integrated wind, cloud and rain, and the other used cloud cover only. Both measures produced similar findings.

Using earlier studies and their own research, it appears accounting for the combined effect of simultaneous weather parameters or focusing on cloud cover better captures any physiological or psychological effects as opposed to using wind or rain alone, said Jiang.

Public companies are unlikely to trigger a more muted response to earnings surprises by recruiting investors from areas with greater cloud cover, as prior research demonstrated that seasonal climate norms don’t appear to affect the behavior of investors once they acclimate, so to speak, to the weather.

In addition to the 14-day window to create the weather measures, the researchers generated a seven-day measure that showed similar results.

Announcement day weather may also affect market reactions to earnings news and “we do not discredit its importance,” Jiang said. Indeed, other research has shown that the weather in New York City at the time of an earnings announcement impacts market reactions.

The explanation for the muted reaction to earnings is based on psychological and physiological reactions of institutional investors to weather, including anxiety and sadness as well as fatigue and decreased activity.

“In addition to causing delayed information processing, weather could cause a reduction in energy amongst some traders,” said Jiang

That means institutional investors may struggle with the same factors that made the boy and Sally from The Cat in the Hat struggle while it was “too wet to go out and too cold to play ball. So we sat in the house, we did nothing at all,” Dr. Seuss wrote.

While institutional investors don’t do nothing at all, they are less active, at least according to the recent research, than they are when the sun shines brightly, reliably and more consistently.

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Photo courtesy of CSHL

By Daniel Dunaief

Cold Spring Harbor Laboratory’s DNA Learning Center and the Red Cloud Indian School recently launched a program called Students Talk Science in which high school students could ask questions from several senior scientists about the vaccine for COVID-19 and healthcare disparities in minority communities.

Dr. Eliseo Pérez-Stable

 

The talks are a component of a program called STARS, for Science, Technology & Research Scholars, an effort the group started in 2019 to build interest and experience in STEM for minority students. The Students Talk Science program engaged the STARS participants and students from the Red Cloud Indian School on the Pine Ridge Indian Reservation.

Jason Williams, Assistant Director of Inclusion and Research Readiness at the DNA Learning at CSHL; Brittany Johnson, an educator at the DNA Learning Center; Katie Montez, a teacher at the Red Cloud Indian School ;and Carol Carter, Professor in the Department of Microbiology and Immunology at the Renaissance School of Medicine at Stony Brook University, wanted to connect minority students with practicing physicians and scientists in leadership positions at the National Institutes of Health to allow them to ask questions of concern regarding the vaccines.

Dr. Monica Webb-Hooper

“We did this to empower them to function as trusted resources for their families, friends and network,” Carter, who participated as an individual rather than as a formal representative of Stony Brook University, explained in an email.

The conversations included interactions with Dr. Eliseo Pérez-Stable, Director of the National Institute on Minority Health and Health Disparities, or NIMHD at the National Institutes of Health; Dr. Monica Webb Hooper, Deputy Director of the NIMHD; Dr. Gary Gibbons, Director of the National Heat, Lung and Blood Institute; and Dr. Eugenia South, Assistant Professor in Emergency Medicine at the Hospital of the University of Pennsylvania and the Presbyterian Medical Center of Philadelphia.

The high school students prepared informed questions.

Dr. Gary Gibbons

“The students were encouraged to do their own research” on the interview subjects, Williams explained. “We asked students not to look just at [each] interviewee’s science work, but also any personal background/ biography they could find. Students had multiple opportunities for follow up and were largely independent on their choices of questions.”

Samantha Gonzalez, a student at Walter G. O’Connell Copiague High School, asked South about her initial skepticism for the vaccine.

South acknowledged that she had no interest in taking the vaccine when she first learned she was eligible. “I almost surprised myself with the fierceness with which I said, ‘No,’” South said. “I had to step back and say, ‘Why did I have this reaction?’”

Some of the reasons had to do with mistrust, which includes her own experiences and the experiences of her patients, whom she said have had to confront racism in health care. In addition, she was unsure of the speed at which the vaccine was developed. She had never heard of the mRNA technology that made the vaccines from Moderna and Pfizer/ BioNTech possible.

“I had to do my own research to understand that this wasn’t a new technology,” she said.

Dr. Eugenia South

South went through a learning process, in which she read information and talked to experts. After she received answers to her questions and with the urging of her mother, she decided to get the vaccine.

“I’m so thankful that I was able to do that,” South said.

The team behind Students Talk Science not only wanted to empower students to make informed decisions, but also wanted to give them the opportunity to interact with scientists who might serve as personal and professional role models, providing a pathway of information and access that developed amid an extraordinary period.

“We wanted to engage high school students in something unique going on in their lifetime,” Carter said.

To be sure, Carter and Williams said the scientific interactions weren’t designed to convince students to take the vaccine or to urge their parents or families to get a shot. Rather, they wanted to provide an opportunity for students to ask questions and gather information.

“We purposely did not participate in the discussions because our goal was not to convince or ‘preach,’ but to enable students and their networks to make informed decisions,” Carter said.

Parents had to read and sign off on the process for students to participate. The organizers didn’t want a situation where they were doing something that conflicts with a parents’ decisions or views.

Williams added that the purpose of the conversations was never to say, “you must get the vaccine. Our purpose is to talk about information.”

The objective of these interactions is to help minority students find a track for a productive career in ten years.

In addition to questions about hesitancy, Williams said some of the high school students expressed concerns about access to vaccines. He is pleased with the result of this effort to connect students with scientists and doctors.

The group was “able to get some of the most important scientists in the country to sit with high school students,” he said. “It was very powerful to give students access to these role models.”

The goal is to stay with these students, mentor them and stay in touch with them until they graduate from college and, perhaps, return as research scientists.

Even for students who do not return, this type of interaction could provide an “impactful experience that prepares them for other opportunities,” Williams explained, adding that the STARS program would incorporate the Students Talk Science Series into the program more formally in the future, with new students and topics most likely during the school year.

The interviews are available at the following website: https://dnalc.cshl.edu/resources/students-talk-science/.

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Above, microscopic image showing brown, antibody-based staining of keratin 17 (K17) in bladder cancer. Image from Shroyer Lab, Stony Brook University

By Daniel Dunaief

Detectives often look for the smallest clue that links a culprit to a crime. A fingerprint on the frame of a stolen Picasso painting, a shoe print from a outside a window of a house that was robbed or a blood sample can provide the kind of forensic evidence that helps police and, eventually, district attorneys track and convict criminals.

Kenneth Shroyer MD, PhD                  Photo from SBU

The same process holds true in the world of disease detection. Researchers hope to use small and, ideally, noninvasive clues that will provide a diagnosis, enabling scientists and doctors to link symptoms to the molecular markers of a disease and, ultimately, to an effective remedy for these culprits that rob families of precious time with their relatives.

For years, Ken Shroyer, the Marvin Kuschner Professor and Chair of Pathology at the Renaissance School of Medicine at Stony Brook University, has been working with a protein called keratin 17.

A part of embryological development, keratin 17 was, at first, like a witness who appeared at the scene of one crime after another. The presence of this specific protein, which is unusual in adults, appeared to be something of a fluke.

Until it wasn’t.

Shroyer and a former member of his lab, Luisa Escobar-Hoyos, who is now an Assistant Professor at Yale, recently published two papers that build on their previous work with this protein. One paper, which was published in Cancer Cytopathology, links the protein to pancreatic cancer. The other, published in the American Journal of Clinical Pathology, provides a potentially easier way to diagnose bladder cancer, or urothelial carcinoma.

Each paper suggests that, like an abundance of suspicious fingerprints at the crime scene, the presence of keratin 17 can, and likely does, have diagnostic relevance.

Pancreatic cancer

A particularly nettlesome disease, pancreatic cancer, which researchers at Stony Brook and Cold Spring Harbor Laboratory, including CSHL Cancer Center Director David Tuveson, have been studying for years, has a poor prognosis upon diagnosis.

During a process called surgical resection, doctors have been able to determine the virulence of pancreatic cancer by looking at a larger number of cells.

Shroyer and Escobar Hoyos, however, used a needle biopsy, in which they took considerably fewer cells, to see whether they could develop a k17 score that would correlate with the most aggressive subtype of the cancer.

“We took cases that had been evaluated by needle biopsy and then had a subsequent surgical resection to compare the two results,” Shroyer said. They were able to show that the “needle biopsy specimens gave results that were as useful as working with the whole tumor in predicting the survival of the patient.”

A needle biopsy, with a k17 score that reflects the virulence of cancer, could be especially helpful with those cancers for which a patient is not a candidate for a surgical resection.“That makes this type of analysis available to any patient with a diagnosis of pancreatic cancer, rather than limiting it to the small subset of cases that are able to undergo surgery,” Shroyer said. 

Ultimately, however, a k17 score is not the goal for the chairman of the pathology department.

Indeed, Shroyer would like to use that score as a biomarker that could differentiate patient subtypes, enabling doctors to determine a therapy that would prove most reliable for different groups of people battling pancreatic cancer.

The recently published report establishes the foundation of whether it’s possible to detect and get meaningful conclusions from a needle biopsy in terms of treatment options.

At this point, Shroyer isn’t sure whether these results increase the potential clinical benefit of a needle biopsy.

“Although this paper supports that hypothesis, we are not prepared yet to use k17 to guide clinical decision making,” Shroyer said.

Bladder cancer

Each year, doctors and hospitals diagnose about 81,000 cases of bladder cancer in the United States. The detection of this cancer can be difficult and expensive and often includes an invasive procedure.

Shroyer, however, developed a k17 protein test that is designed to provide a reliable diagnostic marker that labs can get from a urine sample, which is often part of an annual physical exam.

The problem with bladder cancer cytopathology is that the sensitivity and specificity aren’t high enough. Cells sometimes appear suggestive or indeterminate when the patient doesn’t have cancer.

“There has been interest in finding biomarkers to improve diagnostic accuracy,” Shroyer said. 

Shroyer applied for patent protection for a k17 assay he developed through the Stony Brook Technology Transfer office and is working with KDx Diagnostics. The work builds on “previous observations that k17 detects bladder cancer in biopsies,” Shroyer said. He reported a “high level of sensitivity and specificity” that went beyond that with other biomarkers.

Indeed, in urine tests of 36 cases confirmed by biopsy, 35 showed elevated levels of the protein.

KDx, a start up biotechnology company that has a license with The Research Foundation for The State University of New York, is developing the test commercially.

The Food and Drug Administration gave KDx a breakthrough device designation for its assay test for k17.

Additionally, such a test could reveal whether bladder cancer that appears to be in remission may have recurred.

This type of test could help doctors with the initial diagnosis and with follow up efforts, Shroyer said.“Do patients have bladder cancer, yes or no?” he asked. “The tools are not entirely accurate. We want to be able to give a more accurate answer to that pretty simple question.”

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Matt Damon in a scene from ‘The Martian’

By Daniel Dunaief

One of the seminal, and realistic, scenes from the movie “The Martian” involves astronaut Mark Watney, played by Matt Damon, clearing the dust from a solar panel.

The cleaning process not only made it possible for the space station on Mars to continue to generate solar energy, but it also alerted the National Aeronautics and Space Administration staff on Earth to the fact that Watney somehow survived a storm and was alive and stranded on the Red Planet.

Alexander Orlov Photo from SBU

Back in 1967, engineers from NASA proposed a system to remove dust from solar panels, which can deprive space stations of energy and can cause rovers and other distant remotely operated vehicles to stop functioning. Washing these solar cells on dried out planets with water is not an option.

That’s where Alexander Orlov, a Professor of Materials Science and Chemical Engineering in the College of Engineering and Applied Science, his graduate student Shrish Patel, Victor Veerasamy, Research Professor of Materials Science and Chemical Engineering at Stony Brook University, and Jim Smith, Chief Technology Officer at Bison Technologies and a board member at the Clean Energy Business Incubator Program at SBU, come in.

Working at a company Orlov founded called SuperClean Glass, Orlov, Patel and other colleagues tried to make an original effort started by NASA feasible. The particles have an electric charge. An electric field they created on the solar glass lifts the particles and then throws them away.

The process recently became a finalist in the Department of Energy’s American-Made Solar Prize for 2021. The 10 companies who are finalists get a $100,000 prize and $75,000 in vouchers from the Department of Energy to test their technology.

The DOE will announce two winners in September of 2021, who will each get an additional half a million dollars and $75,000 in vouchers to develop and test their prototypes.

Orlov, who was delighted that this effort received the recognition and the funds, said the company would use the money to develop prototypes and verify that ‘this technology works at the National Renewable Energy Lab.”

SuperClean Glass is creating prototypes of larger scale to show that turning on a power supply will cause dust to levitate and be removed within seconds.

At this point, Orlov estimates that companies can recoup the additional cost of using this technology within four to five years. The average lifespan of a solar panel is about 25 years, which means that companies could increase their energy efficiency for the 20 years after the initial investment in the technology.

Orlov said the current state of the art for cleaning solar panels typically involves using either water, getting people to dust off the surface, or deploying robots.

This device used for experiments is a highly transparent electrodynamic shield deposited on glass to repel dust from solar panels. Image courtesy of SuperClean Glass Inc

In Egypt, where labor costs are lower, companies can pay people to remove dust with brushes. While robots reduce the cost of labor, they are not always efficient and can break down.

Some companies put a coating on the panels that allows rainwater to wash the dust away more easily. That, however, relies on rain, which is scarce in desert conditions.

Orlov originally became involved in trying to develop an alternative to these methods when Sam Aronson, the former director of Brookhaven National Laboratory, contacted him following a visit to the Turkana Basin Institute in Kenya.

When he visited the archeological site in Kenya, Aronson saw that dust frequently reduced the efficiency and effectiveness of the solar panels. The dust problem is not specific to Kenya or the United States, as many of the most attractive sites for solar panels are in regions with considerable sun and little rainfall. The benefit of minimal precipitation is that it provides access to critical sunlight, which generates energy.

The downside of these sites, however, is that the dry, sunny climates often produce dust.

Orlov researched the NASA technology, where he discovered that it wasn’t efficient and couldn’t be scaled up.

Using $150,000 he received from the New York State energy Research and Development Authority, or NYSERDA, Orlov and Patel started reaching out to solar panel manufacturers to determine the price point at which such a dust cleaning removal service might be viable.

“We conducted interviews with 180 people who use solar panels to find out the particular price point where this technology becomes attractive,” Orlov said. That was the steep curve, to do economic analysis, financial projections and to understand what the market wants. All that is not present in [typical] academic research.”

They reduced the power consumption for electrodes by a factor of five. They also explored commercial methods for scaling up their manufacturing approach.

Dust isn’t the same throughout the world, as it is a different color in various areas and has different mineral contents.

“In the future, depending on where this might be deployed, there needs to be some tweaking of this technology,” Orlov said.

As a part of the technology roadmap for the work they are proposing, the SuperClean effort includes a self-monitoring system that would activate the electrodes on the shield if needed to repel an accumulation of dust.

Orlov described the market for such a self-cleaning and efficient process as “very significant.” He is hoping to provide a field demonstration of this approach later this year. If the process continues to produce commercially viable results, they could license the technology within two to three years.

In the near term, Orlov is focused on producing results that could enhance their positioning for the DOE’s grand prize.

“There are a lot of steps before September to be eligible” to win the $500,000, he said. The biggest hurdle at this point is to get positive results from the National Renewable Energy Lab and demonstrate that the technology is effective and also durable.

“Our expectation is that it should last for 25 years, but the lab, which is going to do the testing, is the gold standard to verify that claim,” he said.

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From left, John Inglis and Richard Sever. Photo from CSHL

By Daniel Dunaief

Scientists rarely have people standing at their lab door, waiting eagerly for the results of their studies the way the public awaits high-profile verdicts.

That, however, changed over the last 16 months, as researchers, public health officials, school administrators and a host of others struggled to understand every aspect of the basic and translational science involved in the Sars-Cov2 virus, which caused the COVID-19 pandemic.

With people becoming infected, hospitalized and dying at an alarming rate, businesses closing and travel, entertainment and sporting events grinding to a halt, society looked to scientists for quick answers. One challenge, particularly in the world of scientific publishing, is that quick and answers don’t often mesh well in the deliberate, careful and complicated world of scientific publishing.

The scientific method involves considerable checking, rechecking and careful statistically relevant analysis, which is not typically designed for the sharing of information until other researchers have reviewed it and questioned the approach, methodology and interpretation.

The pandemic changed that last year, increasing the importance of preprint servers like bioRxiv and medRxiv at Cold Spring Harbor Laboratory, which provide a way for researchers to share unfiltered and unchecked information quicker than a scientific review and publishing process that can take months or even years.

The pandemic increased the importance of these preprint servers, enabling scientists from all over the world to exchange updated research with each other, in the hopes of leading to better basic understanding, diagnosis, treatment and prevention of the spread of the deadly virus.

The importance of these servers left those running them in a bind, as they wanted to balance between honoring their mission of sharing information quickly and remaining responsible about the kinds of information, speculation or data that might prove dangerous to the public.

Richard Sever and John Inglis, Assistant Director and Executive Director of Cold Spring Harbor Laboratory Press, created pandemic-specific criteria for work reporting potential Covid-19 therapies.

“Manuscripts making computational predictions of COVID-19 therapies are accepted only if they also include in vitro [studies in test tubes or with live cells] or in vivo [studies in live subjects] work,” the preprint directors wrote in a recent blog. “This restriction does not apply to non-covid-19 work.”

Inglis and Sever continue to decline research papers that might cause people to behave in ways that compromise public health.

“We are simply doing our best to tread carefully in the early days of clinical preprints, as we gain experience and bias our actions toward doing no harm” the authors wrote in their blog.

In the first few months after the pandemic hit the United States, the pace at which scientists, many of whom pivoted from their primary work to direct their expertise to the public health threat, was the highest bioRxiv, which was founded in November of 2013, and medRxiv, which was started in June of 2019, had ever experienced.

These preprint servers published papers that wound up leading to standards of care for COVID-19, including a June research report that appeared on June 22nd in medRxiv on the use of the steroid dexamethasone, which was one of the treatments former President Donald Trump received when he contracted the virus.

The rush to publish information related to the virus has slowed, although researchers have still posted over 16,000 papers related to the virus through the two pre-print servers. MedRxiv published 12,400 pandemic-related papers since January of 2020, while bioRxiv published over 3,600.

At its peak in late March of 2020, medRxiv’s abstract views reached 10.9 million, while downloads of the articles were close to five million.

Currently, bioRxiv is publishing about 3,500 papers a month, while medRxiv put up about 1,300 during a month. Close to 60 percent of the medRxiv papers continue to cover medical issues related to the pandemic.

The numbers of page views are “not anywhere near the frenzy of last year,” Inglis said in an interview. 

With the volume of papers still high, people can receive alerts from the preprint servers using parameters like their field of interest or word searches.

“The real question is how to sort out the gold from the dross,” Inglis said. While some people have suggested a star system akin to the one shopping services use, Inglis remained skeptical about the benefit of a scientific popularity contest.

“Have you looked at the stuff [with four or five stars] on Amazon? It’s one thing if you’re buying a widget, but it’s different if you’re trying to figure out what’s worthwhile science,” he said.

Other organizations have reviewed preprints, including the Bloomberg School of Public Health at Johns Hopkins.

“By sheer diligence, the [Johns Hopkins team] go into medRxiv mostly and simply pick out things they think are striking,” Inglis said. 

At the same time, a team of researchers led by Nicolas Vabret, Robert Samstein, Nicolas Fernandez, and Miriam Merad created the Sinai Immunology Review Project, which provides critical reviews of articles from the Cold Spring Harbor Laboratory preprint sites. The effort ranks COVID-related preprints according to their immunological relevance. Fernandez created a dedicated website to host and integrate the reviews. The group also worked with Nature Reviews Immunology to publish short weekly summaries of preprints, according to a comment piece in that journal.

BioRxiv and medRxiv were founded on the belief that early sharing of results as preprints would speed progress in biomedical research, better equipping scientists to build on each other’s work.

“My team is proud to have contributed to the response to this worldwide human tragedy,” Inglis said. “We’re also glad we made the decision to set up a separate server for health science, in which the screening requirements are different and more stringent.”

Inglis explained that the pre-print servers have “learned a lot in the past year” about providing information during a crisis like the pandemic. “If another pandemic arose, we’d apply these learnings and respond immediately in the same way.”

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Xiaoning Wu at her recent PhD graduation with Kevin Reed. Photo by Gordon Taylor

By Daniel Dunaief

If they build it, they will understand the hurricanes that will come.

That’s the theory behind the climate model Kevin Reed, Associate Professor at the School of Marine and Atmospheric Sciences at Stony Brook University, and his graduate student Xiaoning Wu, recently created.

Working with Associate Professor Christopher Wolfe at Stony Brook and National Center for Atmospheric Research scientists, Reed and Wu developed an idealized computer model of the interaction between the oceans and the atmosphere that they hope will, before long, allow them to study weather events such as tropical cyclones, also known as hurricanes.

In his idealized program, Reed is trying to reduce the complexity of models to create a system that doesn’t require as much bandwidth and that can offer directional cues about coming climate change.

“When you’re trying to build a climate model that can accurately project the future, you’re trying to include every process you know is important in the Earth’s system,” Reed said. These programs “can’t be run” with university computers and have to tap into some of the biggest supercomputers in the world.

Reed’s work is designed to “peel back some of these advances that have happened in the field” which will allow him to focus on understanding the connections and processes, particularly between the ocean and the atmosphere. He uses fewer components in his model, reducing the number of equations he uses to represent variables like clouds.

“We see if we can understand the processes, as opposed to understanding the most accurate” representations possible, he said. In the last ten years or so, he took a million lines of code in a climate model and reduced it to 200 lines.

Another way to develop a simpler model is to reduce the complexity of the climate system itself. One way to reduce that is to scale back on the land in the model, making the world look much more like something out of the 1995 Kevin Costner film “Waterworld.”

About 30 percent of the world is covered by land, which has a variety of properties.

In one of the simulations, Reed reduced the complexity of the system by getting rid of the land completely, creating a covered aqua planet, explaining that they are trying to develop a tool that looks somewhat like the Earth.

“If we could understand and quantify that [idealized system], we could develop other ways to look at the real world,” he said.

The amount of energy from the sun remains the same, as do the processes of representing oceans, atmospheres and clouds.

In another version of the model, Reed and Wu represented continents as a single, north-south ribbon strip of land, which is enough to change the ocean flow and to create currents like the Gulf Stream.

The expectation and preliminary research shows that “we should have tropical cyclones popping up in these idealized models,” Reed said. By studying the hurricanes in this model, these Stony Brook scientists can understand how these storms affect the movement of heat from around the equator towards the poles.

The weather patterns in regions further from the poles, like Long Island, come from the flow of heat that starts at the equator and moves to colder regions.

Atlantic hurricanes, which pick up their energy from the warmer waters near Africa and the southern North Atlantic, transfer some of that heat. Over the course of decades, the cycling of that energy, which also reduces the temperature of the warmer oceans, affects models for future storm systems, according to previous studies.

Reed said the scientific community has a wide range of estimates for the effect of hurricanes on energy transport, with some researchers estimating that it’s negligible, while others believing it’s close to 50 percent, which would mean that hurricanes could “play an active role in defining” the climate.

Reed’s hypothesis is that a more rapid warming of the poles will create less of an energy imbalance, which will mean fewer hurricanes. This might differ in various ocean basins. He has been studying the factors that control the number of tropical cyclones.

Reed and Wu’s research was published in the Journal of Advances in Modeling Earth Systems in April.

Wu, who is completing her PhD this summer after five years at Stony Brook, described the model as a major part of her thesis work. She is pleased with the work, which addresses the changing ocean as the “elephant in the room.”

Oftentimes, she said, models focus on the atmosphere without including uncertainties that come from oceans, which provide feedback through hurricanes and larger scale climate events.

Wu started working on the model in the summer of 2019, which involved considerable coding work. She hopes the model will “be used more widely” by the scientific community, as other researchers explore a range of questions about the interaction among various systems.

Wu doesn’t see the model as a crystal ball so much as a magnifying glass that can help clarify what is happening and also might occur in the future.

“We can focus on particular players in the system,” she said.

A native of central China, Wu said the flooding of the Yangtze River in 1998 likely affected her interest in science and weather, as the factors that led to this phenomenon occurred thousands of miles away.

As for her future, Wu is intrigued by the potential to connect models like the one she helped develop with applications for decision making in risk management.

The range of work she has done has enabled her to look at the atmosphere and physical oceanography and computational and science communication, all of which have been “useful for developing my career.”

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From left, Shawn Serbin, Scott Giangrande and Chongai Kuang. Photo from Brookhaven National Laboratory

By Daniel Dunaief

Chongai Kuang is doing considerably more than standing in the middle of various fields throughout the southeast, looking up into the sky, sticking his finger in the air and taking notes on the potential appeal of the area.

Entrusted with finding the right spot for the third ARM Mobile Facility, or AMF3, Kuang, who is an Atmospheric Scientist in the Environmental & Climate Sciences Department at Brookhaven National Laboratory, is gathering considerable amounts of information about different areas in the southeast.

In March of 2023, the ARM3 mobile facility, which has been operating in Oliktok Point, Alaska, will have a new home, where it can gather information about atmospheric convection, land-atmosphere interactions and aerosol processes.

In addition to finding the right location for this facility, Kuang will coordinate with the larger science community to make recommendations to ARM for observations, measurements, instruments and sampling strategies. Observations from these fixed and mobile facilities will improve and inform earth system models.

Kuang would like to find a strategic place for the AMF3 that is “climactically relevant to provide important observations on clouds, aerosols, and land atmosphere interactions that are needed to answer science drivers” important in the southeastern United States, Kuang said. These facilities will help researchers understand how all these atmospheric phenomena interact with solar radiation and the Earth’s surface.

The AMF3 should provide information that informs climate, regional and weather models.

In 2018, the Department of Energy, which funds BNL and 16 other national laboratories, held a mobile facility workshop to determine where to move the AMF3. The group chose the Southeastern United States because it has atmospheric convection, high vegetative-driven emissions and strong coupling of the land surface with the atmosphere. This area also experiences severe weather including tornadoes and hurricanes, which have significant human and socioeconomic impacts, said Kuang.

The most violent weather in the area often “tests the existing infrastructure,” Kuang said. “This deployment can provide critical observations and data sets,” in conjunction with regional operational observational networks.

Atmospheric phenomena as a whole in the southeastern United States includes processes and interactions that span spatial scales ranging from nanometers to hundreds of kilometers and time scales spanning seconds to days.

Kuang’s primary research interests over the past decade has focused on aerosol processes at nanometer scales, as he has studied the kinds of miniature aerosol particles that form the nuclei for cloud formation. These aerosols affect cloud lifetime and spatial distribution.

“Our research is challenged by disparate scales relevant to phenomena we’re trying to characterize, from nanometers to the length scale of convective systems, which are tens of kilometers or even larger,” Kuang said. These scales also present opportunities to study coupled science with convection, aerosol and land-atmosphere interactions.

The ARM observatories around the world provide atmospheric observations of aerosols, clouds, precipitation and radiation to inform and improve Earth system models.

“We are going to leverage as much as we can of the existing networks,” Kuang said. The ARM has a fixed site in Oklahoma, which provides data for the Southern Great Plains Site, or SGP. The Southeastern site, wherever it winds up, will provide a context for large-scale atmospheric phenomena.

The way aerosols, clouds and weather systems form and change presents a challenge and an opportunity for research stations like AMF3, which will seek to connect phenomenon at spatial and time scales that affect where Kuang and his team hope to locate the site.

Kuang is also staying abreast of the latest technology and is also contributing to the development of these capabilities. The technology the AMF3 may use could be developed between now and when the site starts gathering data.

“We have the opportunity now to start thinking about what the next generation measurement capabilities and emerging technologies are that could be operational in 2023,” he said. “We are in conversations with the broader community and with different vendors and with a number of different investigators who are developing new technologies.”

Researchers hope to understand the coupling between the land surface and atmospheric phenomenon. “That will have feedback on radiation and precipitation and the impact on land-surface interactions,” Kuang explained. The current plan is for the new facility to operate for about five years.

While Kuang is focused on the scientific drivers for the site selection, he has also been exploring the dynamic with potential research partners, including universities, seeking ways to add educational partners.

“We have hopes and plans for this kind of deliberate, targeted outreach within the region,” Kuang said. “We want to organize activities like summer school, to provide young scientists with primers and an introduction about how observations are made within their backyard.”

The work he’s trying to do now is “setting the table and preparing the soil for the eventual siting” of the station.

Kuang will measure his success if the new site improves poorly represented model processes.

Once the DOE chooses a site, Kuang plans to develop and execute an initial science plan that uses AMF3 observations. As an ARM instrument mentor, he will also be responsible for a set of instruments that measure aerosol size and concentration.

A resident of Wading River, Kuang started working at BNL in 2009 as a postdoctoral researcher. When he’s not working, he describes cooking as “therapeutic,” as he and his wife, Anyi Hsueh, who is a psychiatric nurse practitioner, have explored Southeastern Asian and Middle Eastern cuisines.

Kuang is working with Associate Ecologist Shawn Serbin and Meteorologist Scott Giangrande, in site selection. The work presents an “important responsibility and our site science team envisions the AMF3 southeastern united States [site] to enable transformational science,” he said.

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