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Authors Posts by Daniel Dunaief

Daniel Dunaief

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What keeps us young? Well, certainly eating healthy foods, exercising and sleeping are all on that list.

But there’s something else that works, too. If you can, try hanging out with a group of younger people at a party, even if the music is loud and incomprehensible.

At a recent party, I wasn’t sure what my daughter was saying, as I watched her sing every word with her eyes wide open and her hands fluttering at her sides like a butterfly’s wings.

It’s as if both of my children have sped up the needle so fast on their speech that I suspect that what’s coming out of their mouths probably started out as distinct words at some point. I’m hoping that the message they are repeating isn’t something offensive or objectionable, like, “Environmental regulation is bad, so let’s put the fox in charge of the hens at the Environmental Protection Agency. Go fox, Go fox, Go fox.” No, wait, this isn’t about politics.

A room full of children at the party, held by a family friend, made me think a bright scientist may one day figure out how to harness that energy, store it and release it at just the right time, either when someone needed to warm a house or a heart.

The next generation seems to follow a simple formula: Why walk when you can run, skip or flip, why talk when you can shout and why stay on the ground when you can challenge gravity to hold you down?

I recognize that loud parties filled with perplexing music may not be everyone’s cup of tea. The decibel level may damage hearing aids, destabilize pacemakers, or rattle fillings or dentures.

You don’t need to attend a kids party, especially if you weren’t invited to one, to share the exuberance of youth. Have you stopped your car on the way back along familiar routes to watch a T-ball baseball game, to listen to a chorus singing music you might know, or to watch a marching band trying to master John Philip Sousa while figuring out what yard line they’re supposed to be on when they reach the high notes?

All that energy begets energy. I’ve heard people talk about how their children keep them young. Imagine multiplying that, even for a day or a few hours, by however many kids are celebrating the moment in a way that doesn’t get bogged down in blinking Blackberries, a pending deadline or a need to disappear into the immobile ether of the television.

And if you’re fortunate enough, you can engage with some of the next generation in questions they raise about the world. Many of us think we are pretty knowledgeable. That may be the case, until a child asks us a question we can’t answer. Of course, we could rush to the internet to find an answer we might soon forget, or we could try to inch our way to an answer or even revisit a question we hadn’t pondered in years.

I’m sure teachers feel the same kinds of highs and lows that appear in so many other jobs. They have to discuss the Magna Carta year after year, or explain how the change in Y over the change in X represents the slope of a line.

But, then, every once in a while, a student may ask a new question that brings the material to life and gives the teacher an opportunity to learn from the student. The best answers inevitably lead to the next best questions.

Energy, insight, curiosity and joy don’t exist solely in the world of youth, but they are often easier to spot among a group of children whose joie de vivre lifts off at a party.

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Patricia Wright speaks at the Earth Optimism Summit in April. Photo by Ronda Ann Gregorio

By Daniel Dunaief

Determined to share success stories instead of doom and gloom, Nancy Knowlton, the Sant Chair of Marine Science at the Smithsonian Institution’s National Museum of Natural History, decided to change the tone of the conservation dialog.

Knowlton organized the first Earth Optimism Summit around the most recent Earth Day this April. She searched for speakers who could share their progress and blueprints for success. That included Patricia Wright, a Stony Brook University distinguished professor who has developed an impressive legacy during her 25 years in Madagascar.

Nancy Knowlton, organizer of the first Earth Optimism Summit in April. Photo by Ronda Ann Gregorio

In Madagascar, the 10th poorest country on Earth, optimism has been growing, perhaps even more rapidly than the 1,000 endemic trees that have been making a comeback in the island nation off the southeast coast of Africa. The growth of those trees has encouraged the return of animals that had retreated from an area thinned out by selective logging.

“This year, the rare and furtive bird, the scaly ground roller, came back and nested,” Wright reported. The “black and white ruffed lemur gave the area the thumbs up and reestablished territories and reproduced.”

The critically endangered golden bamboo lemur also doubled the size of its population. “The forest took 25 years to recover, but it can recover,” Wright said in her speech. Dedicated to the study of lemurs, Wright in 1991 helped create Ranomafana National Park, which is the third largest park in Madagascar. She served as a plenary speaker for a gathering that drew over 1,400 people to Washington. Scientists and policymakers held sister summits in nine other countries at the same time.

“You can’t possibly make progress in conservation if you only talk about the problems,” said Knowlton, a co-host of the summit. Knowlton knew Wright from serving on the Committee for Research and Exploration, where the two interacted six times a year. When she was putting together the list of speakers, Knowlton approached the 2014 winner of the Indianapolis Zoo Prize to see if she could share a positive message in conservation.

When Wright accepted, Knowlton was “thrilled, not only because she’s a good storyteller, but because she’s also done incredibly important work in Madagascar.” Indeed, Wright said national parks have greatly expanded from only two in the 1980s. “Now with the work of many dedicated environmentalists, including the enlightened policy of the U.S. government through USAID, we have 18 National Parks and a National Park Service to manage and protect them,” she told the session.

Restoring trees to the area also offers economic opportunity, Wright said. Under the endemic trees, farmers can grow crops like vanilla, chocolate, cinnamon and wild pepper, she said. “All these products can be marketed for high prices. We will take back that land and make it productive again, doubling or tripling its value,” Wright continued.

A scientist featured in the 2014 film “Island of Lemurs: Madagascar,” Wright has engaged in a wide range of efforts on behalf of the Malagasy. Last year, she negotiated with a mayor on the island to pick up trash in exchange for the purchase of several wheelbarrows. She also helped encourage the renovation of 35 schools in communities around Ranomafana, where students learn critical thinking and molecular biology. This, Wright said, is occurring in a country where three out of five students don’t remain in school past fifth grade. “More children in this region are graduating from high school and over a handful have received university degrees,” she explained.

A health team also walks to 50 nearby villages, carrying medicines and basic health lessons. SBU brought drones last year, which can fly medicines as far as 40 miles away. Drones could monitor the outbreak of any unknown and potentially dangerous disease and can offer health care for people who live in ares that are inaccessible by road.

The financial support of the National Science Foundation helped create Centre ValBio, a field station and campus in the middle of the rainforest. The research station has modern facilities and equipment to conduct genetics and disease analyses. “We provide tools and training and even fiber-optic cable internet, the fastest in the region,” Wright said. They are expanding the research facilities this year.

Through research efforts, Wright and other scientists have also discovered two new species of lemurs and found two others that were considered extinct. Restoring the national forest not only brought back animals that had retreated into the inner part of the forest, but it also encouraged the growth of ecotourism.

In 1991, there was only one tourist hotel and now there are 32 hotels, providing facilities for the 30,000 tourists. “That can start to change an economy,” Wright suggested. “Cottage industries have developed like the woman’s weaving group and the basket weavers and blacksmiths who all make a good living from selling to tourists and researchers.”

Wright attributes these positive steps to a dedication to working with residents in the area. “We have been successful by training local residents and university students, by listening to what the communities want, rather than what we think is best,” she said.

Knowlton suggested that “you can’t helicopter conservation into a particular place. It’s got to be built from the ground up. She’s done it in Madagascar.” While these are positive steps, Wright declared this is just the beginning. “There are endless possibilities of scientific knowledge and research,” she said. “They all matter and impact our daily lives.”

As for the Earth Optimism Summit, Knowlton said this is just the beginning as well, originally thinking of organizing a second summit in 2020, but may hold the next one sooner. “We’re identifying what’s working and putting a spotlight on it,” Knowlton said. “The feedback has been extraordinarily, unbelievably positive. We’ve come to realize that people are demanding” another conference.

She appreciated Wright’s contribution to April’s conference.“By sharing her successes, Pat Wright brings home the message that if she can do it, so can we all,” Knowlton said. “The summit succeeded because Wright and over 240 other speakers made it obvious, through the successes that they shared, that solving the environmental problems we face is not out of reach.”

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There’s a part of us that wants to shed the limitations of civilization. What difference do all those arbitrary lines in society make anyway?

Say, for example, we’re standing in a grocery store and the line isn’t moving quickly enough. Then again, what line could possibly move at a speed we’d find acceptable? We look at our phones to distract us. We can watch movies we’ve seen a hundred times, check our voicemail, email, messaging service and telepathic connections, if we’ve got the right app.

The phone doesn’t offer much relief, as our boss has sent us an instant message that reads, “If you don’t bring those cupcakes back within three minutes, you will be on cupcake duty for the next six months.”

It’s our fault. We saw that lane six was probably longer than lane seven, but we picked six because we saw a headline in a magazine about Julia Roberts and we wanted to read the other headlines in a magazine that was out of stock in lane seven.

Lane six is at a complete stop as the cashier waits for the override.

“Come on!” we want to scream. “We gotta deliver these cupcakes before we lose our job!”

But we don’t scream any curse words, despite an impulse that is working its way up our spinal column. Another urge hits us. We want to jump on the conveyor belt and dance to “Cotton Eye Joe,” while kicking away the other groceries. But we don’t do that, either.

We hold back because everyone has a camera, and we don’t want to be the supermarket dancer on YouTube forever.

We consider convincing ourselves that our venting might become a way to contribute to society. Maybe other people waiting in line somewhere can laugh at us, as we act out their frustration fantasies.

But, no, we’d have a hard time going to PTA meetings or running for office if our opponent could show we didn’t have the temperament to be a leader.

We keep our composure. It’s just cupcakes, right? Then again, we still have to do our work and this means we’ll be home later than we wanted and we won’t get a parking spot near the gym tonight, which means we might have to walk an extra quarter of a mile before we run 6 miles. It’s so unfair!

Curses are echoing around our brain. We grind our teeth, tap our feet, shake our head slowly and blow our bangs off our overheated and thickly lined forehead.

We hear the words, “Come on, come on, come on,” in our head, but no one else seems to care about our agony. Oh, great, now we have to go to the bathroom, which will be difficult because as soon as we get back to the office we are serving the cupcakes at the party.

Don’t think about the need for the toilet. Oh, right, sure, that’s worked so well in the past. Why hadn’t we thought about that around, say, tax season? Sure, if you don’t think about it, taxes will just go away.

Then the curse words slipped out. We shouted them. We look around, wondering if we’ve damaged our reputation. This can be the smallest town on the planet. No one is holding a cellphone in our direction. No one seems to be waiting for us to do it again. Everyone does, however, take a step back from us.

We breathe a sigh of relief until it hits us: Two rows away is an overheated mother with three children holding onto her shopping cart. One of them — he looks like he’s about 6 years old — is staring at us without blinking. Maybe crossing that line was a mistake, as shame has replaced anger.

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Escobar-Hoyos, center, holds her recent award, with Kenneth Shroyer, the chairman of the Department of Pathology at Stony Brook on the left and Steven Leach, the director of the David M. Rubenstein Center for Pancreatic Cancer Research on the right. Photo by Cindy Leiton

By Daniel Dunaief

While winter storm Niko in February closed schools and businesses and brought considerable precipitation to the region, it also coincided with great news for Luisa Escobar-Hoyos, who earned her doctorate from Stony Brook University.

Escobar-Hoyos, who is a part-time research assistant professor in the Department of Pathology at Stony Brook University and a postdoctoral fellow at Memorial Sloan Kettering Cancer Center, received word that she was the sole researcher selected in the country to receive the prestigious $600,000 Pancreatic Cancer Action Network–American Association for Cancer Research Pathway to Leadership Award.

When she heard the news, Escobar-Hoyos said she was “filled with excitement.” After she spoke with her husband Nicolas Hernandez and her current mentor at MSKCC, Steven Leach, the director of the David M. Rubenstein Center for Pancreatic Cancer Research, she called her parents in her native Colombia.

Her mother, Luz Hoyos, understood her excitement not only as a parent but as a cancer researcher herself. “My interest in cancer research started because of my mom,” Escobar-Hoyos said. Observing her example and “the excitement and the impact she has on her students and young scientists working with her, I could see myself” following in her footsteps.

The researcher said her joy at winning the award has blended with “a sense of responsibility” to the growing community of patients and their families who have developed a deadly disease that is projected to become the second leading cause of cancer-related death by 2020, according to the Pancreatic Cancer Action Network, moving past colorectal cancer.

The Pancreatic Cancer Action Network has awarded $35 million in funding to 142 scientists across the country from 2003 to 2016, many of whom have continued to improve an understanding of this insidious form of cancer.

David Tuveson, the current director of the Cancer Center at Cold Spring Harbor Laboratory, received funds from PanCan to develop the first genetically engineered mouse model that mimics human disease. Jiyoung Ahn, the associate director of the NYU Cancer Institute, used the funds to discover that two species of oral bacteria are associated with an over 50 percent increased risk of pancreatic cancer.

Over the first decade since PanCan started awarding these grants, the recipients have been able to convert each dollar granted into $8.28 in further pancreatic cancer research funding.

In her research, Escobar-Hoyos suggests that alternative splicing, or splitting up messenger RNA at different locations to create different versions of the same protein, plays an important part in the start and progress of pancreatic cancer. “Her preliminary data suggest that alternative splicing could be associated with poorer survival and resistance to treatment,” Lynn Matrisian, the chief science officer at PanCan, explained in an email. “The completion of her project will enhance our understanding of this molecular modification and how it impacts pancreatic cancer cell growth, survival and the progression to more advanced stages of this disease.”

Escobar-Hoyos explained that she will evaluate how mutations in transcriptional regulators and mRNA splicing factors influence gene expression and alternative splicing of mRNAs to promote the disease and aggression of the most common form of pancreatic cancer. Later, she will evaluate how splicing regulators and alternatively spliced genes enriched in pancreatic ductal adenocarcinoma contribute to tumor maintenance and resistance to therapy.

Escobar-Hoyos will receive $75,000 in each of the first two years of the award to pay for a salary or a technician, during a mentored phase of the award. After those two years, she will receive $150,000 for three years, when PanCan expects her to be in an independent research position.

Escobar-Hoyos said her graduate research at Stony Brook focused on ways to understand the biological differences between patients diagnosed with the same cancer type. She helped discover the way a keratin protein called K17 entered the nucleus and brought another protein into the cytoplasm, making one type of tumor more aggressive.

While Escobar-Hoyos works full time at Memorial Sloan Kettering, she continues to play an active role in Kenneth Shroyer’s lab, where she conducted experiments for her doctorate. She is the co-director of the Pathology Translational Research Laboratory, leading studies that are focused on pancreatic cancer biomarkers. The chair in the Department of Pathology, Shroyer extended an offer for her to continue to address the research questions her work addressed after she started her postdoctoral fellowship.

“When you do research projects and you develop them from the beginning, they are like babies and you really want to see how they evolve,” Escobar-Hoyos said. Numerous projects are devoted to different aspects of K17, she said.

Shroyer said Escobar-Hoyos had already been the first author on two landmark studies related to the discovery and validation of K17 even before her work with pancreatic cancer. “She has also conducted highly significant new research” that she is currently developing “that I believe will transform the field of pancreatic cancer research,” Shroyer wrote in an email.

Shroyer hopes to recruit Escobar-Hoyos to return to Stony Brook when she completes her fellowship to a full-time position as a tenure track assistant professor. “Based on her achievements in basic research and her passion to translate her findings to improve the care of patients with pancreatic cancer, I have no doubt she is one of the most promising young pancreatic cancer research scientists of her generation,” he continued.

Yusuf Hannun, the director of the Stony Brook Cancer Center, said Escobar-Hoyos’s work provided a new and important angle with considerable promise in understanding pancreatic cancer. “She is a tremendous example of success for junior investigators,” Hannun wrote in an email.

Escobar-Hoyos said she is hoping, a year or two from now, to transition to becoming an independent scientist and principal investigator, ideally at an academic institution. “Because of my strong ties with Stony Brook and all the effort the institution is investing in pancreatic research” SBU is currently her first choice.

Escobar-Hoyos is pleased that she was able to give back to the Pancreatic Cancer Action Network when she and a team of other friends and family helped raise about $4,000 as a part of a PurpleStride 5K walk in Prospect Park earlier this month.“I was paying forward what this foundation has done for me in my career,” she said.

Matrisian said dedicated scientists offer hope to patients and their families. “Researchers like Escobar-Hoyos spark scientific breakthroughs that may create treatments and ultimately, improve the lives of patients,” she suggested.

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Have you seen it? In the pace at which we live our lives, it’s possible you missed it. I was at the drugstore recently and I saw it on the side of a box. It took a moment to process. How often does a product surprise you?

It had the potential to be a “you got your chocolate in my peanut butter” moment. When I was younger, my older brother, or No. 1 son as he’s been described on these pages for decades, used to mix all kinds of foods. Perhaps it was a prelude to him becoming a scientist. He’d combine foods that would defy even the current cooking shows. To his credit, he’d choke down even the ones that were spectacular failures because he didn’t want to waste food, and because who knew at what point a displeasing food might become an acquired taste? After all, how many people remember their first sip of beer? Did it tickle their taste buds or did they want to find water or a soda to wash it down?

So, back at the drugstore, I scratched my unshaven chin — I was buying razors to remedy that problem — when the image on the side of a box diverted my attention from important thoughts: How much longer would this take? Would I meet my deadlines? Was I supposed to wash some mission-critical clothing last night for some must-win game today?

As I looked at that image, I could imagine the moment Igor came up with the idea. There he was at a barbecue. With his acquired-taste beer a few inches from his left hip, he surveyed the food on his overloaded plate. He had a thick cheeseburger on a sesame seed bun, half sour pickles, an enormous mound of sauteed onions and mushrooms, coleslaw, and several Pringles sitting next to his burger. Igor works for Pringles and he won’t attend any picnic without bringing his favorite curved chip. The burger was on its way to his mouth when he realized he was missing something. He stood up to kiss his sister-in-law, maneuvered around his nephew who was bouncing a pink ball against the steps, and he and his burger arrived safely at the condiment table. On Igor’s way back to his beer, the pink ball rolled underfoot, causing him to turn his ankle and mix up the contents of the plate.

He hobbled to his spot and surveyed the damage to his food. His ankle could wait. Igor, like my brother, pressed on. He sighed at his precious Pringles. They were broken into tiny pieces, which was no fault of the distinctive packaging, and they looked like they’d been through a battle. They were covered in ketchup. Did he dare throw out the Pringles, he wondered, as he sipped his acquired-taste beer?

No, his loyalty to a product that paid for his mortgage and his three Jeeps ran too deep to toss even a single chip. Igor found the small part of a chip not smothered in ketchup and brought it to his mouth. Aware that every eye was on him, he nodded slowly, as if the taste was something extraordinary.

“Well,” his brother said, trying to be helpful, “why not, right? We put ketchup on French fries, which are also made from potatoes, right?”

Was it a weakness or a strength on Igor’s part that made him insist this was an inevitable combination that would become a must-have item for July Fourth barbecues? I suppose it’s up to us to decide whether ketchup-flavored potato chips are the next peanut butter cup.

If they are, maybe Pringles can edit a Seinfeld clip where George Costanza double-dips his chip into a bowl of ketchup?

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Ride For Life presents CSHL with $300,000 for ALS research: from left, CSHL Director of Annual Giving and Donor Relations Karen Orzel, CSHL Assistant Professor Molly Hammell, Ride for Life Founder Chris Pendergast, Stony Brook Associate Professor Josh Dubnau and Ride for Life board member Frank Verdone. Photo by Jessa Giordano, Cold Spring Harbor Laboratory

By Daniel Dunaief

The past can come back to haunt us, even in the world of genetics. Over the course of millions of years, plants and animals have battled against viruses, some of which inserted their genes into the host. Through those genetic struggles, explained Molly Hammell, an assistant professor at Cold Spring Harbor Laboratory, cells develop “elaborate ways to fight back,” even as they continue to make copies of these pieces of DNA.

Sometimes, when our defenses break down, these retrotransposons, or jumping genes, can become active again. Indeed, that appears to be the case in a fly model of amyotrophic lateral sclerosis, also known as ALS or Lou Gehrig’s disease.

Working on a fruit fly model of ALS, Joshua Dubnau, an associate professor at Stony Brook University, Lisa Krug, who earned her doctorate at Cold Spring Harbor Laboratory and is now working at Kallyope in New York, and Hammell showed that these ancient genetic invaders play an important role in the disease amid activation by a protein often linked to ALS called TDP-43.

A recent study, published in PLOS Genetics, “really proves that retroviral reactivation (as a consequence of TDP-activity) is … central to either causing or accelerating neuronal cell death when TDP-43 inclusions are present,” explained Hammell in an email. If TDP-43 plays the same role for humans, this would suggest that targeting this protein or the jumping genes, it activates could lead to potential treatment for ALS.

These collaborators showed that an aggregation of this protein turned on jumping genes. These genes can make copies of themselves and insert themselves in other parts of the genetic code. In this case, TDP-43 expression disrupts the normal immune-like system that silences retrotransposons such as gypsy, which is a particular type of jumping gene in the fruit fly.

When gypsy was activated, the fruit fly exhibited many of the features of ALS, including protein pathology, problems with movement, shortened life span and cell death or glia and neurons in the brain. The scientists were also able to turn gypsy off, which improved the health and extended the life span of the fly.

Mimicking this protein results in broad activation of several retrotransposons. If this also occurs in people, the disease may activate a retrotransposon that is the human analog to gypsy, called HERV-K, as well as other retrotransposons. The study also suggests that DNA damage caused by retrotransposons may active a cell suicide mechanism. Finally, this effort showed a means by which the protein disrupts the normal immune surveillance that keeps retrotransposons quiet.

To be sure, Dubnau cautioned that animal models of a disease may not translate when returning to people. Researchers need to look at more patients at all the retrotransposons in the human genome to monitor its prevalence, Dubnau suggested. If the link between retrotransposon activation and the development of ALS is as evident in humans as it is in the fruit fly, scientists may take an approach similar to that which they took to battle the human immuno-deficiency virus, or HIV. Retrotransposons have an RNA genome that needs to be copied to DNA. This, Dubnau explained, is the step in the process where researchers attacked the virus.

In a small subset of HIV patients who have motor neuron symptoms that are similar to ALS, Avi Nath, a senior investigator at the National Institutes of Health discovered that treating patients with the typical HIV medication cocktail helped relieve their ALS symptoms as well.

“What is not known is whether, for some reason, this subset of patients had an ALS syndrome caused by HIV or they were curing them” by treating HIV, Dubnau said. Nath is currently involved in one of two clinical trials to see if HIV medications help ALS patients. The next step for Dubnau and Hammell is to screen the tissue of numerous ALS patients after their death to see if their retrotransposons were elevated.

In addition to NIH funding, the scientists received financial support from Ride for Life, which is a not-for-profit organization started in 1997 that raises funds for research to find a cure for ALS, supports patients and their families through patient services and raises awareness of ALS. Every May, Ride for Life conducts a 12-day, 100-mile patient wheelchair ride across Long Island. Dubnau and Hammell, who received a $300,000 grant from Ride for Life in 2015, said they have been inspired by Ride for Life founder Chris Pendergast.

Meeting Pendergast “has had a big impact,” Dubnau said. “He’s a force of nature. He’s an incredibly strong and intelligent person.” Receiving funds from Ride for Life created a sense of personal obligation to Pendergast and many other people who “had raised that money through sweat and effort.”

Without funding from the Ride for Life Foundation, “We would not have the resources to obtain these samples and do the sequencing experiments necessary to prove that this is a clinically relevant phenomenon in a large number of ALS patients,” Hammell said.

Through an email, Pendergast explained that Ride for Life chose to fund the work by Dubnau and Hammell because the research met several criteria, including that it might lead to new strategies to treat ALS and the research was on Long Island, which is a “powerful affirmation for our generous donors.”

Pendergast emphasized the importance of funding basic ALS research. “We need to know why it develops, how it progresses [and] how it can be diagnosed and monitored,” he urged.

A resident of Huntington, Dubnau and his wife Nicole Maher, who works at the Nature Conservancy as a climate scientist, have a nine-year-old daughter, Caitlin. Reflecting both of her parents’ professional interests, Caitlin is going to a statewide science fair, where she is presenting her work on how temperature affects the life span of insects.

As for his research, Dubnau hopes a further exploration of TDP-43 might reveal an important step in the progression of ALS. He hopes this discovery may suggest a strategy researchers and clinicians can take that might “stop the cascade of events” in ALS.

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Percy Zahl. Photo courtesy of BNL

By Daniel Dunaief

When he was in high school in Negenborn, Germany, Percy Zahl built his own computer, with some help from one of his father’s friends. Nowadays, Zahl spends considerable time improving the computer capability of an open-source community drive software project that helps researchers see structures and interactions at a subatomic level.

Recently, Zahl, who is an associate scientist in the Proximal Probe Microscopy facility at the Center for Functional Nanomaterials at Brookhaven National Laboratory, completed an extensive upgrade to software called Gnome X Scanning Microscopy, or GXSM, that adds a whole suite of new features. Zahl re-coded about half of the original 300,000 lines of code during this project.

The software, which is used to operate any kind of scanning probe microscopy system which includes atomic force microscopy and scanning tunneling microscopy, has a wide range of applications, from understanding catalysts that facilitate chemical reactions, to capturing gases, to biomedical sensors.

Oliver Monti, a professor of chemistry and biochemistry and a professor of physics at the University of Arizona, has been working with Zahl for over four years and has been using this system to explore atomic and molecular-scale processes that determine efficiency in plastic solar cells and other next-generation low-energy-use technologies. He said he uses the GXSM for data analysis.

Zahl “often introduces modifications and upgrades as instantaneous response to some scientific need,” which has “helped us solve specific problems efficiently,” Monti explained in an email. A former student of Monti’s needed to analyze molecule-to-molecule interactions. The two came up with an algorithm to study that and, unprompted, Zahl “introduced a version of this algorithm to his software.”

Percy Zahl (front of line) during a Tour of Somerville race in 2011. Photo by Anthony Skorochod.

Monti said he is “very much aware of the most recent release,” which he considers a “major upgrade” and he is in the process of installing it. The new software allows the export of images in formats such as PDF and SVG, which are editable and resolution independent, Zahl explained. A PDF output of a graph has publication quality, while the images with high-resolution displays are enhanced and sharper than the previous bitmap PNG files.

The upgrade also includes making a remote control process for automating scanning and manipulation tasks “easy to use,” which is a “big plus for less experienced users,” Zahl explained. It can help automate complex or tedious repetitive jobs. As an example, Zahl said the need to scan an image that takes 10 minutes each for 20 different settings creates a laborious task. “I can either sit there and enter manually a new number every 10 minutes” or he can program a script that he made to use a list of bias voltages and hit execute in the new remote console, he explained, leaving him time to work on other projects for the next two hours and 20 minutes.

Recently, Zahl ran a spectra covering the area of a molecule, which is a task he can do reliably without worrying about user typos or errors. An additional noncontact atomic force microscopy simulation plug-in module provides researchers with a more efficient way to generate data. The new approach measures the force between atoms and molecules of the surface of a sample and a probe smaller than the diameter of an atom. Zahl has calculated and simulated forces between atoms, taking into account all atoms of a molecule and the probe atom and finds the equilibrium position of his probe. Using that three-dimensional force field, he can extract an image that he compares to the model.

Zahl spends about three quarters of his time working with users like Monti, while he dedicates the remaining time to his own projects. He appreciates the opportunity to work with many different systems and with people in a wide range of scientific disciplines.

“It’s really as diverse as it can get in this particular field of fundamental surface science — a specialty of solid state physics,” Zahl explained in an email. He has the experience to work with many different sample types while still continuing to learn “all the tricks on how to get the best images possible.”

Monti appreciates Zahl’s dedication to his work. “Data processing and analysis can be challenging,” he explained. His students often compare a trip to BNL to drinking from a firehose.

Zahl has been “essential in helping us figure out how to sift through the data and quickly focus on the most important observations,” Monti added. That appreciation extends well beyond Monti’s lab. “Whenever I meet colleagues across the world who had the pleasure to interact with [Zahl], they lavish praise on his scientific and technical expertise,” Monti said.

Bruce Koel, a professor in the Department of Chemical and Biological Engineering at Princeton University, appreciated Zahl’s contribution to his research on chemical reactions at surfaces. Zahl has “enabled us to do very high impact research,” Koel explained in an email. This work would “not have been possible without [Zahl’s] technical support and guidance about what experiments could be done.”

A resident of Rocky Point, Zahl rides the 20 miles to work as often as he can on one of several of his bicycles. An avid cyclist, Zahl has a high-end racing bike, a commuter bike and a mountain bike from those “beloved times” riding mountain trails in Switzerland.

In Chile, he reached a top speed of around 56 miles per hour descending the Osorno Volcano. In a YouTube video of his ride, he can be seen passing a car in a clearing along the windy road.

As for his work, Zahl remains committed to continuing to improve the software scientists use to enhance their visual understanding of the small surfaces of the substances they study. “I am pretty much always working on some new details or fixing this and that tiny issue,” he said. “No software is ever done. It’s evolving.”

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When I was in college, I wrote an essay in a seminar. In such a small class, we read everyone else’s writings each week and needed to be prepared to share our observations or else face the ignominy of our teacher either excusing us from the room or glaring at us until we cracked.

One of the other writers had written this spectacular story about four people at a dinner party. She had moved the reader through the thoughts of each of the characters, until she got to the fourth person, whose social anxiety receded when he started choking. His inability to control noises that interrupted her stories irritated his wife, who glared at him until he read her vexed expression and retreated to the kitchen. Separated from the group, he choked to death. The ending was so powerful that I was sure my prose was inferior.

When my turn came, I waited through the usual polite beginning, as my classmates shared what they thought worked. Great, I thought, it won’t take long before we transition to the unnerving category of “what could he have done better.”

It took some time before people starting quibbling with my choice of words. Certainly, I could maneuver through the minor discomfort of a new word here or a different turn of phrase there.

Professor Brilliance sat in his green corduroy pants, with his oversized left foot rising and falling diagonally above his right knee to his rhythm, tilting his head to the side, awaiting a worthy insight.

“Well,” he said, scanning the room slowly, “has anyone spotted clichés?”

Oh no! Clichés? Clichés! I thought I had scrubbed out the clichés. I quickly scanned words that floated unevenly above the page, hoping to find any and expose them before anyone else did.

His foot stopped, and so did my breathing.

“No,” he nodded slowly, “I didn’t see any, either.”

This had to be only a temporary respite before the scissors started slicing.

“Now, let’s go over the introduction to this fine piece,” he said.

Was that sarcasm? Did he mean that it was fine, or was he acknowledging its shortcomings?

As we went line by line through the piece, my writing held up to the scrutiny. Some of my classmates even defended a few phrases, suggesting that they found them perfectly fine just as they were.

The professor saved his lone arrow for his final remark.

“This is a solid piece of writing,” he said, before adding, “for someone your age.”

And there it was, ladies and gentlemen. The backhanded compliment that sent me back to the children’s table, wondering what the adults might be discussing.

Now that I’m older than Professor Brilliance was when he shared that line, I have considered whether he had a point and the answer is, yes and no.

My experiences have changed my perspective. I recognize the value of history, even if I despised memorizing dates and names for a test. I also understand the Chinese devotion to their elders, not because I’m older, but because I have an increasing appreciation for all the decisions my parents and their generation made.

At the same time, when I hear the ideas my children share, I don’t minimize them in the context of their shorter lives. Instead, I recognize the wisdom that comes from their experiences in a handheld techno world they maneuver through more deftly than I.

All these years later, I guess I’d have a comeback to my professor’s observation. “Maybe you’re right,” I’d say, “or, maybe, I’m young enough to know better.”

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At the first meeting of the HiTOP consortium. Kotov is in the center. Photo from HiTOP consortium.

By Daniel Dunaief

Instead of lamenting the shortcomings of a system they felt didn’t work as well as it should, Roman Kotov and a growing group of collaborators whose numbers now exceed 50 decided to do something about it. An associate professor of psychiatry at Stony Brook University, Kotov and his collaborators are building their own mental health tool, which, they hope, will offer specific diagnoses for everything from anxiety to schizophrenia.

Roman Kotov. Photo from SBU School of Medicine

The current resource psychologists and psychiatrists use is called the “Diagnostic and Statistical Manual of Mental Disorders 5,” which came out in 2013. The latest version of the DSM, as the manual that offers psychologists and psychiatrists a way to link a collection of symptoms to a diagnosis is called, “felt far too limited,” Kotov said. “Once we started discussing [an alternative], almost everyone was interested in the scientific community. They thought it was a good and necessary idea.”

Called the Hierarchical Taxonomy of Psychopathology, or HiTOP, the developing classification system uses scientific evidence, illness symptoms and impaired functioning in its diagnoses. Another HiTOP co-creator, David Watson, the Andrew J. McKenna Family professor of psychology at the University of Notre Dame, recognized Kotov’s important early work on the project.

Kotov “deserves sole credit for the idea of putting all of our data together to provide the basis for an alternative model,” Watson explained in an email. “He did some preliminary work along these lines, which convinced us that this was a great idea that was worth pursuing.” Watson, who served as Kotov’s graduate adviser at the University of Iowa, said that his former student leads meetings and conference calls for the HiTOP group.

The HiTOP system, which was recently described in the Journal of Abnormal Psychology, views mental disorders along a spectra, while also using empirical evidence to understand overlap among disorders and classify different symptoms within a given diagnosis. As an example, Kotov said that depression in the DSM is “treated as one thing. We know that depression is heterogeneous.”

Indeed, some people with depression may have lost their appetite and have trouble sleeping, while others may be eating and sleeping considerably more than they would if they weren’t depressed. “In some ways, these are opposite presentations, yet they get the same diagnosis” in the DSM, Kotov said.

HiTOP unpacks this variability into seven dimensions, which describe symptom types. That is helpful not only for a diagnosis but also for a treatment. HiTOP also goes beyond the binary description of the presence or absence of a particular symptom, offering clinicians a way of indicating the severity of a problem. At this point, HiTOP is a developing prototype and not a completed diagnostic tool. The scientists developing this tool have made inroads in four primary areas: anxiety and depression, substance use problems, personality problems and psychotic disorders.

“The HiTOP system currently is incomplete, as it primarily focuses on more common and widely studied forms of psychopathology,” Watson suggested, “but mental health professionals certainly could use it to assess/ diagnose a broad range of conditions.” Mental health professionals can view this new resource at the website https://medicine.stonybrookmedicine.edu/HITOP.

Kotov hopes this new paradigm will “focus on science and do everything we can to keep unpolitical, nonscientific considerations out of it,” he said. “We hope that it provides the most up-to-date alternative” to the DSM. The HiTOP approach, Kotov said, relies more heavily on scientific evidence, which can include genetic vulnerabilities, environmental risk factors and neurobiological abnormalities.

Kotov, who is working on several projects, said HiTOP takes about a quarter of his time. He is also involved with a long-term study of schizophrenia and bipolar disorders, which was started in the early 1990s, before he arrived at Stony Brook in 2006.

Kotov is following up on this cohort, looking at outcomes for treatment and analyzing risk factors and processes that determine the course of an illness. He is also leading a study on first responders to the 9-11 attack on the World Trade Center, which is exploring the physical and emotional consequences of participating in the response to the unprecedented attack.

Kotov and his collaborators are investigating the health of responders in their daily life using mobile technology. They are also studying how personalities affect their health, which may soon help guide personalized treatment.

Another project involves the study of children who are 14 to 17 years old and explores the emotional growth and personality development. This study includes reports, surveys and interviews. During those years, “much happens as far as personality development,” Kotov said.

Colleagues at Stony Brook praised Kotov’s scientific contributions. Kotov is a “rising star” and is “perhaps best known for his work on the role of personality in psychopathology and, increasingly, for work on classification of psychiatric disorders,” Daniel Klein, a distinguished professor in the Department of Psychology at Stony Brook, wrote in an email.

A resident of Port Jefferson, Kotov lives with his wife Tatiana, who is a controller for a small company in Manhattan. The couple has two young daughters. Kotov grew up in Russia in a small town near Moscow. He was always interested in science and developed a particular curiosity about psychology when a high school psychology teacher sparked his interest when he was 15.

As for the HiTOP effort, Kotov is convinced this endeavor will offer the mental health community a valuable tool. “We believe that describing patients more accurately, precisely and reliably will help provide better and more personalized care,” he said.

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He’s cold and he wants to go home.

He has to go to the bathroom and he can’t stand here another minute.

He’s way too hot under all that equipment and he wants to go swim somewhere.

Yes, these are just some of the sinister motives often attributed to umpires, referees or officials at games, as coaches and parents try to explain a call that they clearly saw the other way.

Yet if you ask most of the parents on the other team, including those who seem like eminently reasonable people, they would tell you that they thought the umpire made the right call.

Here we are again, with Little League baseball underway and with championship T-shirts, sweatshirts and trophies at stake.

Standing between the starting point for all those teams and the ultimate glory are the other teams, the weather which forces endless makeup games, huge parties that take half the team from a scheduled game and, of course, the umpires.

I have tremendous sympathy for those umpires because I was one decades ago. No, I didn’t call Derek Jeter out or ring up Alex Rodriguez. My brother and I signed up to umpire Little League games.

In several games, batter after batter would get into a full count. Invariably the hitter would take a pitch that was somewhere between the outside corner and just outside. With every eye on the field staring at me, I had to make a difficult choice.

Yes, of course, there is a strike zone, and in the strike zone is a strike and outside the zone is a ball, but what if the ball is squeezing along the edge of the plate, near the bottom of the strike zone?

I aimed for consistency, but I also became involved in “make good” calls. I’d call a borderline strike a ball on the first batter, disappointing the pitcher and catcher, and then I’d call the next borderline strike a strike, deflating the hitter and his teammates.

Numerous pitches were so close that I knew the groans would come even before my arm signaled for the hitter to go to first or return to the bench.

Once, before a game, a coach came up to me and told me that he was a bit of a hothead and that I should feel free to eject him from the game. Too bad I didn’t have the foresight then to ask him what he was doing coaching 8-year-olds in the first place if he felt the need to argue calls.

Sure enough, in the second inning, he screamed at me for a called strike. After I ejected him, he winked at me as if we had each played our defined roles. His players tried not to snicker as they watched him leave the field for what I understand was one of many such dismissals.

Nowadays, people complain about officiating in professional sports constantly, especially with endless video replays from angles no individual referee could possibly have at the same time, much less an umpire on a hot, dry baseball field.

I recognize that we live in a society where we have a right to express ourselves, but we also have a responsibility to accept the rule of law. Like it or not, the umpires on the field establish and enforce those rules.

Maybe, as we push our lawn chairs into the cars on our way to another game, we should remember that the umpire isn’t out to get anyone. The official is just trying to do his or her best to make sure both teams have an equal opportunity to succeed.

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