CLOSE
Authors Posts by Daniel Dunaief

Daniel Dunaief

1461 POSTS 0 COMMENTS

by -
0 1251
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.”

by -
0 60
A scene from Broadway's 'Dear Evan Hanson'

By Daniel Dunaief

Daniel Dunaief

With my fingers crossed, I am excited about the return of shows on Broadway, which is scheduled to reopen in September.

Something magical happens when a curtain rises, taking an excited audience on a musical journey to other places and other times.

Decades ago, I attended a production of “The King and I.” While the famous Yule Brenner played the title role, I found the experience utterly meaningless.

I remember asking my mother what those small people were doing so far away from me, as we watched that production in the third balcony.

“Next time,” my mother said through gritted teeth to my father, “I’m getting the tickets.”

Sure enough, my parents took my brothers and me to “A Chorus Line.” The experience was as different as standing across the street, looking through the fog at a candy store and sitting at the counter, reading through a menu and enjoying the smell of warm waffles and ice cream and the sight of tantalizing delicacies akin to what I imagined Turkish delights from the Narnia series would taste like.

The live performance so completely captivated me that I left the auditorium humming some of the songs and hoping everything would work out for characters who came from broken homes and broken dreams. Each of the actors was taking his or her shot, hoping for approval, and a job, doing what he or she loved.

I have found numerous shows that have been as moving and as thrilling, including more modern performances, like “Dear Evan Hansen.”

The combination of sights and sounds, the emotional range from humor to tragedy and the riveting live voices that cause seats to vibrate and artwork to come alive provide a completely immersive artistic experience.

I don’t always love every moment in a show, and I don’t always understand what a director or actor is conveying, but that doesn’t stop me from trying or from appreciating the effort.

When I was in high school, I joined the pit orchestra of the musicals “The Wizard of Oz” and “West Side Story.” I far preferred the latter, with its more complicated and intricate music, although participating in each performance provided artistic highlights for my high school career.

On one of my first dates with my wife, we attended “A Funny Thing Happened on the Way to the Forum,” starring Nathan Lane. The show, which I had seen once or twice before, was a familiar pleasure, while Lane’s periodic breaking of character and hamming up the role tickled the audience, sharing the equivalent of a modern-day wink with an appreciative crowd.

After the show, I was thrilled to find that my wife shared my love and appreciation for the Great White Way. We repeated lines that amused us, commented on the sets, and appreciated the spectacular stage presence of an acting legend who, somehow, show after show, seemed to be completely in the moment.

As we continue to emerge from a pandemic in which we discussed books we’d read and Netflix shows we’d seen, I am eagerly looking forward to returning to the cushioned seats, the brightly-colored programs, the friendly ushers, and the hard-working cast members who inspire and elevate my life with their dedication, talent and hard work.

Who knows? This year, I might even go back to dressing up for the occasion, tying a tie, finding matching dark socks, and wearing dress shoes as the lights return to live performances, the orchestra holds up its instruments, and the actors take deep breaths, preparing to serenade those lucky enough to score tickets to a transformative ride.

by -
0 1717
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.

by -
0 69
Photo from Pixabay

By Daniel Dunaief

Daniel Dunaief

Aliens are all the rage these days.

People are excited about the declassified documents that seem to suggest a technology that exceeds American understanding and know-how.

Of course, one possible explanation is that other people built them. With billions of intelligent humans scattered around the planet, it’s possible that we have fallen a few steps behind the most advanced surveillance technology of the world, making these sudden flying objects that disappear an enormous mystery, even as our fellow humans elsewhere are snickering.

While that only feeds into the advanced state of American paranoia, it doesn’t preclude the possibility that these technological mysteries are human-generated. Then again, maybe someone has built a time machine and is tooling around in a craft from future humans. If that’s the case, why didn’t our descendants do more to fix historical tragedies, global warming or other human errors?

Another tantalizing option exists: what if they are, indeed, alien? What if advanced creatures from another planet, galaxy, solar system, or celestial neighborhood, have come into our airspace to spy on us, learn our secrets and decide whether to stick their appendages out at us so we can meet them and become acquaintances or allies?

I was thinking about what I might say to an alien scout gathering information to decide whether to bring all manner of other creatures to our planet to share a drink, catch a baseball game, and argue the merits of communism versus capitalism.

I imagine a conversation might go something like this:

Alien: So, tell me about yourself?

Me: Well, uh, I’m human.

Alien: What does that mean?

Me: I guess it means I can talk to you and that, unlike other animals on this planet, I have imagined what this conversation might be like for much of my life.

Alien: How do you know other creatures didn’t imagine it?

Me: Maybe they did, but they seem kind of busy trying to avoid getting eaten.

Alien: That doesn’t mean they couldn’t imagine it.

Me: I suppose. So, where are you from?

Alien: Somewhere else.

Me: Wow, helpful. Can you tell me about yourself?

Alien: Yes, but I made a long trip and I’d like to hear about you, first. Do you mind?

Me: Now that you put it that way, I wouldn’t want to be considered intergalactically rude. So, what else can I tell you?

Alien: What’s the best and worst part of humanity?

Me: It’s hard to come up with one of each. Our ability to help each other is near the top of the list. Oh, as is our ability to imagine something, like traveling to the moon or Mars, and then making it happen. Music and art are also pretty amazing.

Alien: What about the worst?

Me: Destruction? Hatred? Violence? Excluding people? Preying on people’s weaknesses? Using our trauma to traumatize other people?

Alien: You sound complicated. Can we trust you?

Me: We don’t trust each other, so, going by that, I’d say, caveat emptor.

Alien: What does that mean?

Me: It means, “let the buyer beware.”

Alien: Hmm. So, who is this near your leg?

Me: That’s the family dog.

Alien barks at the dog. The dog barks back. The alien nods.

Alien: We’ve decided to go in a different direction.

Me: Wait, where are you taking my dog?

Alien: He’s not yours, and he’s chosen to join us.

Me: Can I come?

Alien laughs and flies off, buzzing close by a jet, the sound of the family pet laugh-barking in the skies.

by -
0 965
Photo from Deposit Photos

One of the larger centers for the Novavax vaccine trials, Stony Brook University Hospital recruited 376 patients for a potential fourth vaccine against COVID-19 .

Benjamin Luft

The Gaithersburg, Maryland-based company announced earlier this week that its vaccine was effective in 90.4% of the participants in its phase 3 trials, which is typically the last clinical hurdle before approval from the Food and Drug Administration. The trials occurred in the United States and Mexico.

With 30,000 people participating in the clinical study, the Stony Brook participants accounted for about 1.25% of the total study group.

“The quality of our data is among the highest,” said Benjamin Luft, chief investigator of the Novavax trial and director and principal investigator of the Stony Brook WTC Wellness Program.

At its peak, the Novavax trials, which began on Dec. 28, involved 10 to 12 full-time staff at Stony Brook to prepare and administer the vaccines.

“The staff worked extremely hard,” Luft said. “I think everybody takes a great deal of satisfaction in being a small part of this great machine that ultimately produced these vaccines that we all benefit from.”

Novavax reportedly plans to produce as many as 100 million doses of the vaccine per month starting in the third quarter and as many as 150 million per month in the fourth quarter.

The Novavax vaccine, which received $1.6 billion from Operation Warp Speed in 2020, differs from the other three approved vaccines. Pfizer/BioNtech and Moderna use messenger RNA and the Johnson & Johnson vaccine uses a combination of the gene for the spike protein with an altered adenovirus, which causes the common cold.

Novavax, by contrast, uses a piece of the spike protein from COVID-19 to train the immune system to recognize the foreign invader.

Vaccine providers can store the Novavax vaccine, which requires two doses, at typical refrigerator temperatures, unlike the mRNA vaccines, which require ultra cold storage. The Novavax vaccines are usable for up to three months after they are stored.

Luft said the vaccine might have a real benefit in places that don’t have these cold storage facilities.

Earlier one morning this week, Luft received several emails from colleagues in South America who had heard about the trial and knew he was involved.

“They are so excited for their countries that they could get access to such a vaccine,” Luft said.

The clinical trials for Novavax occurred at a time when the original Wuhan strain, which formed the basis for the vaccine, wasn’t the only COVID-19 threat.

“The variants that were in the community were different” during the Novavax trial, Luft said. The vaccine was not retooled for the new variant, which is what made the results so encouraging.

Like the other vaccines, the Novavax vaccine had some side effects, which included fever, head aches and soreness at the site of the injection that went away over the course of a day or two.

At this point, Novavax plans to submit its data for potential approval to the Food and Drug Administration by the end of the third quarter.

Luft expressed his appreciation for the opportunity Stony Brook and the residents in the area who participated in the study had to contribute to this effort.

“I was just so delighted” with the results, Luft added. “It was just so gratifying to be a part of the cog in the great wheel” for a process that proved effective.

by -
0 234
Adrian Popp

Adrian Popp, chair of Infection Control at Huntington Hospital/Northwell Health and associate professor of medicine at Hofstra School of Medicine, spoke with TBR Newspapers to discuss the current state of vaccinations in Suffolk County, the return to school in the fall, workplace issues, and tic-borne challenges for residents. Please find below an abridged version of the interview below. If you’d like to listen to the entire interview, view the video above.

COVID-19

TBR: How close are we to the 70% threshold for herd immunity to COVID-19?

Popp: We were hoping vaccination would start rolling out pretty fast and actually that happened. Over the last several months, more and more people got vaccinated. Right now, it’s open more or less like just show up and you can get a vaccine. You don’t even need an appointment anymore. The number of people vaccinated in Suffolk County is, percentage-wise, around 55% of eligible persons.

TBR: What about the rates at which people are seeking the vaccines? Has that slowed?

Popp: The number getting vaccinated has somewhat plateaued. The most eager people who wanted to get vaccinated did. Now, we’re seeing people who are actually still willing to get vaccinated and doing it and also some of people who are on the fence getting more information and speaking with other people who actually received the vaccine. More and more people are getting confident that the vaccine is safe, efficacious, and I hope this trend will continue.

TBR: What about schools in the fall? Will students return without masks and at full capacity?

Popp: At this point, the rate of coronavirus in Suffolk County is very low and has been decreasing since March steadily and is at almost a minimum even compared to last year. The question is, what will happen down the road? What will happen in the fall? We know that coronavirus has a propensity to be more active in cold environment. It’s hard to predict, because of these variants coming from different parts of the world. We should be hopeful that the fall will look good as long as more and more people get vaccinated. Hopefully, by September, we’ll reach about 70%, then going back to school will be easier.

TBR: As offices reopen and people return to work, how should companies handle rules, especially if some people aren’t vaccinated?

Popp: Offices vary in size, the number of people, how many are sitting in one room, close to one another. One has to make a decision on a case-by-case basis. Ideally, everyone working in one office should be vaccinated. It’s a difficult situation, mandating people to get vaccinated. It’s a fine line between your personal liberties and public policies.

TBR: When might a booster be necessary?

Popp: The need for the booster is being debated [as] the efficacy of the vaccine, the immunogenicity of the vaccine is probably higher than what I expected to see. From the early stages of December, we do find that they hold their antibodies quite well. The expectation is that this could last maybe two years or so. We don’t know that yet. One has to give it time and really find out.

TBR: What about weddings?

Popp: The wedding situation is quite a big situation. A lot of people have postponed the wedding in the hopes of having a real thing later on. The approach people have taken varied from A to Z. There is no cookie-cutter way to say this is the right thing to do and that’s the wrong thing to do. A friend of mine getting married is asking every person to be vaccinated. If you’re not vaccinated, you’re not allowed in the wedding. This is the decision of the groom and bride. Other venues are obviously more open, and they invite everybody and so forth. In the end, you have to be comfortable with the decision you make and you’re going there to have fun, you can’t have fun and celebrate if you’re truly nervous.

Tick-borne diseases

TBR: What about tick-borne diseases? Is there messaging people should keep in mind?

Popp: In the last three years, I have seen more tick-related diseases than before. We’re not talking only Lyme disease, could be also babesiosis, ehrlichiosis, and Rocky Mountain Spotted fever. Rocky Mountain Spotted fever used to be very unusual on Long Island. Now, we do see cases. I have already seen cases this year. When you go somewhere walking or hiking in some woods or meadows that may have ticks that may be around there, what you do at the end of the day when you come home, you get your shower, do a body check. Have someone else look at areas you can’t see well on your back, back of your legs.

by -
0 910
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.”

by -
0 64
Pixabay photo

By Daniel Dunaief

Daniel Dunaief

You don’t have to look hard to see them alongside the road. They aren’t even always on the sharpest curves or the steepest hills.

There, along the median or over there, by the right side of the road, are the homemade crucifixes, the flowers, the stuffed animals and the personal effects of people who never made it wherever they were going, their lives ending on or near asphalt as other vehicles collided with theirs.

My family recently took a road trip, where we easily could have become another statistic, and our family or friends could have just as easily been visiting the spot where it ended for one, two, three or all four of us.

I was driving during a recent weekend, excited by the open road and eager to remove the family from the neighborhood patterns that have defined our lives for well over a year.

My wife navigated, checked her email, exchanged texts with friends, and regularly asked if I wanted her to drive, if I needed a drink, or if I was hungry.

Our son was napping behind me, his head tilted back and to the left. Our daughter was immersed in virtual interactions with her friends, head down, a Mona Lisa smile plastered on her face.

With my peripheral vision, I traced the flow of the taller and shorter trees that passed by, the familiarity of the Texas, Indiana, Ohio and California license plates on nearby cars and trucks, and the click, click, click of the road that churned beneath our wheels.

Up ahead, the driver of one of the thousands of SUVs that dot the American landscape hit his brakes. My wife instantly saw it and closed her eyes. Unlike me, she typically hits her brakes as soon as she sees the red lights at the back of the car in front of her.

I immediately take my foot off the accelerator, where it hovers over the brake. As we rapidly approached the car in front of us, I applied the brake with some force, coming to an almost complete stop just feet before reaching the bumper.

I exhaled in relief, while immediately hitting the hazards. I wanted the cars behind me to know I wasn’t merely touching my brakes, but that I, and all the other cars around me, were stopping.

For a moment, I chatted with my wife. I have no idea what she or I was saying, when I noticed a truck coming towards at an incredible rate of speed.

“Hold on! This isn’t good!” I shouted, waking my son and drawing my daughter away from her phone.

I reflexively tapped my accelerator and drove my car directly towards the nearly stopped SUV on my right side. The truck, meanwhile, dove into the thin shoulder.

As it flew by, the truck somehow missed us completely. The car next to me honked in frustration, as the driver, who must have moved to her right, glared. I wanted to tell her that a truck might have crushed our family if the driver and I hadn’t each made last second adjustments.

Her lane kept moving, and she likely didn’t give my sudden maneuver another thought. With my hands in a vice grip on the wheel and my breathing rapid, I stared at the truck in front of me. I wasn’t sure whether I would have liked to punch or hug the driver, who didn’t notice me slowing down, see my hazard lights or leave himself enough room to stop. At the same time, though, he — and it could have been a woman, because I never saw the driver — turned onto the small shoulder, finding just enough space to squeeze past me without destroying my car, my family or my life.

For the next several minutes, I struggled to drive, as the image of the speeding truck with nowhere to go in my rear view mirror replayed itself in my head.

“Are you okay? Do you need me to drive?” my wife asked anxiously.

My family and I were okay. We weren’t a part of a sad story that ended on an American highway. Skid marks left on the road weren’t a marker for the final seconds of our lives.

We are grateful for the combination of factors that turned a close call into a near miss. Perhaps this happened for a reason beyond giving us more opportunities to extend the journeys of our lives. Perhaps one of the purposes is to provide a warning to everyone else to remain vigilant, to brake early and to stay sharp and focused on the roads.

by -
0 1392
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.”

by -
0 40
Pixabay photo

By Daniel Dunaief

Daniel Dunaief

I’m not much of a planner. I put together professional plans, creating a schedule for stories I’d like to research and write, and I coordinate calls and meetings all week, but I don’t tend to go through the calendar to figure out when to visit socially with friends and family or to attend cultural events.

This summer, however, I’m incredibly grateful for the opportunity to look at the calendar and consider a wide range of activities that would have been difficult or impossible a year ago.

I’m delighted to plan to visit with my extended family. I haven’t seen my brothers in over 19 months. I have visited with them on the phone and zoom, but that’s not nearly the same thing as seeing them in person, throwing a ball with them, flying a kite off the beach or just sitting on the couch and having a free-flowing conversation.

I am also delighted to consider planning a trip to museums. On one of our first dates, my wife and I went to the Metropolitan Museum, where we wandered slowly through the exhibits, continuing to build on our relationship even as we studied the artifacts left behind by the generations that fell in love and married hundreds of years earlier. I recall wandering through those wide hallways close to a quarter of a century ago, listening to my wife’s stories and delighting in laughter that, even now, provides validation and meaning to each moment.

I am hoping to travel to Washington, D.C., this summer, to see the air and space museum. Each of the planes hovers overhead, and the space capsules from the early days of the NASA program are inspirational, giving me a chance to picture the world from a different vantage point, seeing the shimmering blue waters that cover the Earth.

I have watched planes fly overhead throughout the pandemic, but I haven’t ventured to the airport or onto a plane. I’m looking forward to the opportunity that flight provides to turn trips that would take over 10 hours into one- or two-hour flights.

Visiting family, friends and strangers in different areas, eating foods that are different and unfamiliar and experiencing life outside of the small circles in which we’ve restricted ourselves opens up the possibilities for the summer and beyond.

My son can prepare for the start of college and my daughter for a return to college with the hope that they can enjoy more of the academic, social, extracurricular and community service experiences that they imagined when they envisioned these years of growth, development and, hopefully, independence.

I spoke with a scientist recently who told me that the inspiration for a work he’d just completed came from a conversation he had during a conference a few years ago. He had been sitting in an auditorium, listening to a speech, when he and a stranger exchanged thoughts about the implications of the work. From that interaction, he started a new project that became a productive and central focus of his research efforts. As soon as conferences are back on the calendar, he hopes to return to the road, where such unexpected and unplanned conversations can trigger inspiration.

To be sure, I recognize that the realities of travel and planning don’t always dovetail with the hopes and expectations. I recently visited with our extended community at a social gathering, where I stood downwind of someone who wore so much cologne that I couldn’t taste the food I was eating.

I’m sure there’ll also be lines, traffic jams and literal and figurative turbulence as I leave our home cocoon. 

Still, this summer, I’ll be grateful for the opportunity to do so much, including and especially, the chance to plan.

Prev1...434445...147Next Page 44 of 147
TBR News Media is your local news and entertainment website.
We provide you with the latest breaking news and information for your community.
Contact us: [email protected]

Most Viewed

©