Authors Posts by Daniel Dunaief

Daniel Dunaief

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When they work as they should, they become a part of a process that helps us remember the Amendments to the Constitution, the Pythagorean Theorem, or the words to a love poem by Elizabeth Barrett Browning. When they don’t work correctly, we can run into all kinds of problems, some of which can get worse over time.

The N-methyl-D-aspartate receptor, also known as the NMDA receptor, which has parts that are bound in the membrane of brain cells, or neurons, is at the center of learning and memory.

Up until last year, only parts of the NMDA receptors sticking out of the membrane were known. A lack of a three-dimensional understanding made it difficult to see how this receptor works. Hiro Furukawa, an associate professor at Cold Spring Harbor Laboratory, and his postdoctoral researcher, Erkan Karakas, provided considerably more structural details of this receptor.

“The structures of the full-length NMDA receptor that [Furukawa’s] lab generated last year are seminal,” said Lonnie Wollmuth, a professor in the Department of Neurobiology and Behavior at Stony Brook University and a collaborator with Furukawa on other work. “They are fundamental to understanding how the NMDA receptor operates and how it can be modified in the clinic.”

Wollmuth suggested Furukawa has an “outstanding” reputation and said the structure of the receptor will “drive the field in new directions.”

Furukawa cautioned that scientists are still missing a structural understanding of a piece of the receptor that protrudes into the cell. Seeing the structure of this receptor will “provide clues for developing new compounds and for redesigning existing compounds to minimize side effects associated with nonspecific targeting,” Furukawa explained.

When NMDA receptors open, sodium and calcium ions flow into the cells. Too much calcium in the cells can cause toxicity that results in the neurodegeneration observed in Alzheimer’s disease and injuries related to strokes. Changes in the concentration of these ions can excite the neuron and cause symptoms such as epilepsy.

Seeing the structure of this receptor can provide a road map to find places on it that can become too active or inactive. Researchers typically look for binding sites, where they can send in a drug that can affect the function of the receptor. The more binding pockets scientists like Furukawa find, the greater the opportunity to regulate the NMDA receptor function.

Furukawa’s lab includes two graduate students, four postdocs and a technician. He is collaborating with scientists at Emory University to design and synthesize novel compounds based on the protein structures. As he gets more research funding, Furukawa would like to add more expertise in bioinformatics, which involves using computer science and statistics to understand and interpret large collections of data.

Experts in this field can go through a database of compounds quickly, enabling scientists to conduct the equivalent of thousands of virtual experiments and screen out candidates that, for one reason or another, wouldn’t likely work.

Furukawa is also studying autoimmune disorders in which immune cells attack these important receptors. One of these diseases is called anti-NMDA receptor encephalitis. Susannah Cahalan wrote an autobiographical account of her struggle with the disease in a New York Times Best Selling Book called “Brain on Fire: My Month of Madness” in 2012.

Furukawa is collaborating with a group at the University of Pennsylvania to find a way to detect the autoimmune antibodies that causes encephalitis. He is working to find a way to quench autoimmune antibodies for an anti-NMDA receptor.

Furukawa lives in Cold Spring Harbor with his wife, Megumi, who used to be an elementary school teacher but is now taking care of their sons Ryoma, 7, and Rin, 4.

Furukawa, who moved from Japan to Boston in fifth grade, then back to Japan for junior high school and finished high school in Missouri, is enjoying an opportunity to grow his own vegetables on Long Island.

As an undergraduate at Tufts, Furukawa was more interested in international politics and economics than in science. When he took chemistry and physics classes, he said the work “clicked comfortably” and he wound up majoring in chemistry. As an eight-year-old, he recalled watching the stars at night through a telescope. When he saw a ring of Saturn for the first time, he was so excited that he couldn’t sleep.

Furukawa’s colleagues appreciate his dedication to his work.

“He is certainly driven,” said Wollmuth. “He is in an extremely competitive field, so he must work efficiently and hard.”

‘CinemAbility’ film director Jenni Gold with actress Jane Seymour. Photo courtesy of ‘CinemAbility'

St. Charles Hospital in Port Jefferson invites the public to a free week of movies filled with inspiration, perspiration and determination. In honor of the 25th anniversary of the Americans with Disabilities Act, St. Charles will host a moviethon from Sept. 28 through Oct. 2. Each night, starting at 6 p.m. at the Wisdom Conference Center, the hospital will host films that share stories of people with different abilities.

The movies include “Wampler’s Ascent,” which chronicles Stephen Wampler’s remarkable climb to the top of El Capitan at Yosemite National Park. Confined to a wheelchair because of cerebral palsy, Wampler nevertheless did the equivalent of 20,000 pull-ups over the course of five nights and six days to make what is often a landmark rock climb.

“This is a story about a gentleman who is very visibly disabled,” said Jennifer Semel, medical director of Physical Medicine and Rehabilitation at St. Charles and one of the organizers of the event. “He is in constant motion. He has to lean on his limbs to quiet them down. It shows what perseverance can do.”

Semel said her work at the hospital centers around making patients as functionally independent as possible, which, she said, “goes hand in hand with the ADA.”

Semel’s goal is to take people who have spinal injuries or strokes and return them as much as possible to their quality of life. Her staff also works with children born with cerebral palsy or other conditions. Semel finds her work “very rewarding” because she and her staff can help people with various challenges gain independence.

The movies may help members of the community understand the world of people with disabilities better and may inspire them to become involved and contribute where they can, she said. “Exposing individuals who don’t have physical or developmental challenges to the world that does gets them to see the world through those people’s eyes,” Semel said.

All of the films “expose us to different sides of disabilities,” she said. “Some of the challenges and successes re-instill in all of us the importance of equal rights for people with disabilities.”

While the movies will provide a window into the lives of people with different abilities, they aren’t as effective as a day of real life experience, Semel said. When she was training as a physician, she had to spend a day in a wheelchair.

“You never know what that’s like until you’ve done it,” she said. “Not having a curb on a Manhattan sidewalk can be the end of an outing. The challenges in our world that we don’t recognize as people without physical disabilities are hard to capture” completely in the movies.

Semel is encouraged by the progress she sees in the community. “There have been tremendous strides in terms of making places, restaurants and public places accessible to individuals,” Semel said. “There’s no question that there’s a long way to go.”

Semel coordinated the moviethon with Mike Apostoli, the care coordinator in the Community Re-Entry Program at St. Charles. Apostoli facilitates the Patient and Family Advisory Council, which is a group of patients and caregivers who have been through the rehabilitation program. The group meets monthly and was pleased to provide feedback on the movie choices.

“We tried to stick to movies that were consistent with what it is that we do here,” Apostoli said. “It reflects the patients we see with similar challenges, limitations and assets.”

Apostoli said stroke, spinal cord and brain injuries are often like a tsunami for people’s lives, transporting them to another world. “If we can give people who have not gone through that a glimpse into what that’s like, we will have met a very large challenge to begin to formulate better attitudes,” which includes getting services approved through insurance.

The movies profile compelling people who have sometimes achieved something extraordinary. Apostoli suggested the public can become aware that the average person with a disability may not achieve something as remarkable, but they can overcome obstacles to have a meaningful day. “They may not be climbing mountains, but that doesn’t mean what they are doing isn’t just as difficult,” he said.

Each night, a senior member of the staff will introduce the movie. Semel said she hopes to invite individuals with disabilities and the community to join the celebration. She is also hopeful that this may become an annual event.

Semel said the group screened 27 films and narrowed the list down to five. Along with “Wampler’s Ascent,” which will be screened on Sept. 29, the screenings will include “CinemAbility.” Narrated by Jane Seymour, the film takes a look at the evolution of disability in entertainment by interviewing filmmakers, studio executives and celebrities, including Jamie Foxx, Helen Hunt, Marlee Matlin, Ben Affleck, Gary Sinese and Geena Davis, on Sept. 28.

“Endless Abilities,” a movie about four best friends who have physical disabilities who drive across the country seeking adaptive sports for people like them will be screened on Sept. 30. The movie includes footage of these athletes water skiing, snow skiing and surfing.

“The Intouchables,” the French subtitled film based on a true story about a friendship between a handicapped millionaire and his ex-con caretaker who refuses to take pity on him, will be screened on Oct. 1 followed by “A Whole Lott More” on Oct. 2, which examines the impact of Lott Industries’ struggles and examines the world of employment options for people with disabilities while focusing on three people who each have a different attitude toward work. The film was the winner of the Cincinnati Film Festival for Best Documentary in 2013.

St. Charles Hospital is located at 200 Belle Terre Road, Port Jefferson. The moviethon is free but advance reservations are required for each film by calling 631-474-6797.

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To reply all, or not to reply all, that is the question. But, seriously, when is replying to everyone by email necessary? I know we live in a world where we share every thought that occurs to us because we can. Distributing our thoughts electronically to as many people as possible gives new meaning to the words “publish
or perish.”

Still, something about replying all is the equivalent of spraying graffiti, with your initials on it, in my email box. I already get more than enough emails from all the stores that send me hundreds of discounts a day. With all these discounts, I feel like an idiot for paying the listed price for anything. But I digress.

I know there are times when replying all is helpful. You see that the conference room is unavailable. Sharing the news will allow everyone to be more productive through the day.

There might be a time when you need everyone on a list to know something, like not to park on a side street where the permit-parking-only signs might be hard to see.

But do all 100 of us on a long email distribution list really need to know that you, specifically, received the email? Not only do people tell us they got the message we all received, but some of them feel the need to embarrass themselves in the process.

A teacher asks all the parents in her six classes to confirm that they received her message. A reply-all message that says: “The Smiths received the email and couldn’t be more excited about the start of a new school year. Every morning, Johnny can’t wait to sit in your class,” is a surefire way to sabotage Johnny as he navigates through the middle school minefield.

Then there are the simple emails that don’t require any reply, such as an email with the address of a field or a meeting.

“Got it, Dan. We’ve been there so many times before.”

Of course you know where it is — everyone knows where it is. The directions and the address for the GPS make it possible for everyone to get there.

Seasonal greetings are not, repeat not, an opportunity to hit reply all, especially when the group includes people you’ve never met.

An email that “wishes everyone a healthy and a happy start to the new school year” is not an opportunity to echo the same, exact thoughts to strangers.

“So do we” is not an appropriate reply-all response, nor is “Ditto for us” or “Same to everyone else” or “The Dunaiefs feel the same way.” Adding emojis doesn’t make the email message more personal. It’s like doodling next to your graffiti. Cut it out, people — we’re not all 12.

I’m tempted, when these reply-all messages come through, to write something snarky, but in a distribution list that includes people I don’t know, someone will undoubtedly take it the wrong way because, let’s face it, there’s always someone ready to take offense.

Then there are the reply-all messages that seem to highlight a specialized talent or experience. Someone might, for example, be asking people to bring baked goods to a party, a meeting or a fundraiser. By indicating that you’ll bake miniature tarte tatin, crème brûlée or flourless chocolate soufflé, you seem to be bragging first and contributing to something a distant second.

It reminds me of that old joke about an 80-year-old man who goes to a priest to confess that he spent a magical evening with two 25-year-old women. The priest, in shock, asks the gentleman how long it’s been since last confession.

The man said, “Confession? I’ve never gone to confession. I’m not religious.”

The skeptical priest replied, “So why are you telling me this?”

“Are you kidding?” the man answered. “I’m telling everyone I know.”

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Professor Helen Benveniste. File photo from SBU

Sleeping doesn’t just provide a break from the daily grind, prevent you from chowing down on more Oreo cookies, or keep you out of trouble when it gets dark. It may also serve an important brain-cleaning function, getting rid of tau and beta amyloid proteins.

Merely shutting your eyes and letting the sandman sprinkle dust on your forehead may not be enough. You might actually help your brain, over the long term, with the way you sleep.

Helene Benveniste, a professor of anesthesiology and radiology and vice chair for research in the Department of Anesthesiology at Stony Brook University, recently conducted research on anesthetized rodents, tracking how the glymphatic system worked in various sleep positions. The animals were better at flushing tau and beta amyloid proteins from their brains when they slept laterally, or on their sides, than when they slept on their stomachs. Resting on their backs wasn’t as efficient as sleeping on their sides, although it was better than face down.

These proteins aren’t just a part of everyday maintenance. They likely play a role in the onset of Alzheimer’s disease and other age-related neurological problems, Benveniste said.

Since Benveniste published her study in the Journal of Neuroscience in early August, she has received a flood of emails from around the world, including from Brazil, France and Colombia, with people asking about various sleep positions and neurological disorders.

The Stony Brook professor said it is too soon after this study to come to any conclusions about sleep or preventing cognitive disorders. For starters, she and a research team that included scientists at the University of Rochester, NYU Langone Medical Center and Stony Brook conducted the studies on animal models, rather than on humans.

“In general, the rodent is a pretty good model for core aspects of human brain function,” said Dennis Choi, the chairman of the Neurology Department at Stony Brook. The specifics, however, can differ from one species to another. As a result, Benveniste said, “I don’t think anybody should panic” about the way he or she sleeps.

Scientists know that in the glymphatic pathway, cerebrospinal fluid moves through the brain and exchanges with interstitial fluid to get rid of waste. In the studies with rodents, the face down position seemed to divert the cerebrospinal fluid away from the brain, Benveniste said.

The research could be another step toward understanding how sleep might help with the human glymphatic system.

An anesthesiologist who does clinical work one day a week, Benveniste said she started thinking about conducting this kind of study a few years ago. Benveniste is a “good example of a physician/scientist,” Choi said.

Two years ago, a study by a co-author on the paper, Maiken Nedergaard from the University of Rochester, showed that sleep or general anesthesia enhances the clearance of waste from the brain of rodents.

“Since I am an anesthesiologist, I immediately thought about how body/head positions during anesthesia might affect clearance,” Benveniste said. The data took over a year and a half to collect and analyze.

“The quantitative aspect of this system should not be overlooked. To find out how these [proteins] are moving through the brain is a huge issue,” she said. The collaboration with Jean Logan, senior research scientist in the Department of Radiology at NYU “enabled us to move forward.”

Benveniste used a dynamic contrast MRI method to calculate the exchange rates between the cerebrospinal fluid and the interstitial fluid. The next step in these studies is to move toward the human brain. Benveniste said she is working with colleagues at the National Institutes of Health.

Just from observing wildlife outside the lab, Benveniste said many animals tend to sleep in what she and her team found was the optimum position for clearing waste in rodents: on their sides. “Even elephants lie down in recumbent, lateral positions,” she added.

As for Benveniste, she said she naturally sleeps on her right side. She said she’s well aware of how well she slept during the night. If she wakes up after getting enough rest, she said she thinks, “this was a good night’s sleep. This was good for my brain.”

Benveniste, who lives in Northport with her husband, Peter Huttemeier, is also an advocate of exercise for brain health, although she doesn’t suggest marathon running. “I do think this may be affecting the cerebrospinal fluid flow dynamics,” she said, adding that she wants to take up yoga.

Benveniste is eager to continue to build on this sleep study. “The workings of this system so far has been an amazing exploratory adventure,” she said.

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The night starts off with the top dog standing in front of a packed auditorium, selling all of us on the idea that what our children are about to receive in the form of another year of education at their fine institution is a spectacular blend of academic learning, extracurricular opportunities, social growth and development, and personal inspiration.

Ah, can’t you just hear the academic angels singing?

Somewhere in that magical evening known as Back to School Night, the principal and his or her vice-principal minions suggest how spectacular the teachers are, how magnificent the community is, how incredible the resources are and, most of all, how wonderful the parents are for being involved and coming to this Evening of Champions.

These people who are in these top academic positions are often doctors, although they’re not the kind with stethoscopes and they don’t have a waiting room full of old copies of People magazine.

They assure us that they’re people, too, and that they’ve been where we are. They know what it’s like to have someone they’ve brought into the world treat them as if they’re somewhere between an athlete’s foot fungus and a pimple surfacing on the tip of their nose just before the most incredible moment of their lives.

But, wait, there’s more. Their teachers tell us what they’ll learn, they smile, shake our hands — and assure us how excited they are to be sharing in this experience with our wonderful children.

Wonderful? Seriously? We can only hope that’s the case when they’re in school because the “wonderful” has been squeezed out of them by hormones that turn their voices into violins with broken strings, by their tough-love coaches, and by their would-be girlfriends and boyfriends who have decided that today is perfect to send them a text saying, “Sorry, we can’t date anymore because I’m looking for someone better.”

It’s almost like one of those old-fashioned sing-alongs, where we watch teachers with their Smart Boards at the front of the room, following the bouncing ball as it wows us with one after another of the stops on the journey to enlightenment.

For comic relief, we might get to hear from a teacher who seems about as comfortable speaking in public as I did when I was in seventh grade. He might look down at his feet as he talks, read from a script or take two huge gulps before each sentence. Speaking in front of a group of people, we realize quickly, is not exactly the ideal way to spend his day.

As they talk, they tell us how much they love a subject that, truth be told, might not be their first choice. However, the nearest district hiring biology teachers is an hour away and our school desperately needs a language arts teacher. They implore us to share information about our kids. That’s when we reach into our sales bag and suggest how eager our children are to fill their minds with inspiration and information. We plaster an enthusiastic smile on our faces as we hand in our creative writing assignments.

We emerge from the school, ready to take all that sales energy and turn ourselves into cheerleaders for education and our children.

“Oh, honey, I met your science teacher last night and she seemed so spectacular.”

“That’s interesting, Dad, because my science teacher is a man.”

“Wait, are you joking?”

The children share a devilish smile, pick up their heavy backpacks and trudge off to a place where the sounds in the real world corridors — real and in their own heads — are often nothing like a chorus of those academic angels.

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Paul Friley and James Forward serve meals to the homeless as a part of a group called the Rogue Saints. Photo from Friley

Paul Friley traveled the world when he was young. His family moved from Tokyo to Hong Kong to London to Bartlesville, Oklahoma, changing countries whenever his father, Charles, who worked for Phillips Petroleum and later for North American Coal, got a new assignment.

He absorbed quite a bit about his father’s life and work from listening to discussions about energy at home. “The conversations at Thanksgiving dinners were useful later in life,” Friley said.

Indeed, Friley now works for Brookhaven National Laboratory, where he is the leader of the Energy Policy and Technology Group. He regularly travels to Korea, Taiwan and India. He has also visited Hong Kong, Mexico, Columbia, the Philippines, Sweden, Italy, Japan, South Africa and France.

He shares the analytical work he and his team do with a range of energy projects, from coal sequestration to solar power to wind turbines. The job, he said, is rewarding not only in collecting information but in helping to share it with decision makers.

“We’re over there trying to improve their capacity to do all the analysis,” Friley said. He speaks with people from different ministries, including some in nonprofits and academia, to “figure out where we can make a difference.”

J. Patrick Looney, the chair of the Sustainable Energy Technologies Department at BNL, explained that Friley’s analysis “provides decision makers with insights on the options available” as they explore energy policy decisions.

Friley, who reports to Looney, is “known for his work on the impacts of federal funding on our energy future,” Looney continued.

Friley specifically works on a USAID project called Enhancing Capacity for Low Emission Development Strategies. In this program, USAID, the State Department and other agencies work with partner countries to develop knowledge, tools and analyses to estimate greenhouse gas emissions and identify and put into use ways to grow while minimizing emissions.

Friley spent the last year working with about 100 other energy professionals, including some from five other national laboratories, on the 2015 “Quadrennial Technology Review” (QTR). Due for release this month, the review will be over 500 pages, with a lengthy appendix. It will analyze the state of technology and will suggest areas where the Department of Energy should focus its research and development.

The review “will detail where we are and where we can go,” Friley explained. It will examine technologies ranging from power generation and smart grids to buildings, manufacturing, clean fuels production and transportation.

Looney described the QTR as playing “an important and growing role in setting priorities for federal investments to catalyze the development of advanced, scalable, clean energy technologies.

Looney said the QTR can and does have wide-ranging implications in the world of energy policy and decisions.

“To be a part of something that touches so many and has such importance to U.S. energy policy is really an honor,” Looney said.

Officials in Congress, the Department of Energy and Department of State can “use it as a guide book,” Friley said. “It’s written as a document that any layperson could read and understand” and will be available online. Once the review is published, Friley, who currently works in Washington, D.C., will return as a full-time employee of BNL.

He said his work involves looking at policy and technology impacts relative to a baseline projection. He recognizes the many unknowns in
his work.

“Weather patterns, recessions, booming economic growth, wars, hurricanes and many other factors … are not predictable over a 40- to 50-year time frame,” he explained.

He runs a model in which he sees how much of a reduction in consumer bills people would see if the country can hit its goals at cost and performance, he said.

Friley is married to Kate Miller, an independent life coach. The couple have a six-year-old daughter, Lilly, and a three-year-old daughter, Ivy.

When he’s not analyzing energy alternatives, Friley works with a group called the Rogue Saints, which cooks meals once or twice a month for the homeless. It also is looking to provide meals for veterans every three months.

As for his work, he said he tries to “present an unbiased projection of the potential impacts of potential energy policy or technology improvements.”

Looney said Friley’s work “helps us all understand better our potential energy futures, and the inevitable myriad trade-offs we have to consider.”

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Disney has owned the imagination of children’s minds for decades. When I was a child, I certainly was well aware of Mickey Mouse and all his pals. “Mic” — see you real soon — “key” — why? Because we like you — “Mouse.” The catchy and inviting songs and cartoons helped define my childhood, much the way endless texting, emojis and Taylor Swift songs do for this generation.

Recently, we took our son to the Broadway production of “Aladdin.” While the singing, dancing, staging, choreography, sets and lighting were truly spectacular, something occurred to me. What role do parents play in these Disney stories, which become the foundation of our children’s cultural legends?

Looking at Aladdin himself, the Broadway version suggests he loved his parents and that he thinks they were spectacular people. That’s nice, but they are gone from the picture, which makes them invisible saints, who help by inspiring him to be better or reminding him from a distance that he hasn’t done much with his life besides living as a “street rat” with a heart.

Then, there’s the ridiculous, all-powerful sultan. He has educated his daughter and given her a chance to think for herself. Ultimately, though, he wants her to get married so her husband can rule the kingdom. That’s an inconsistent message from one of the many single parents Disney has brought to life.

How, exactly, can he not notice that his evil adviser manipulates him and is clearly out for his throne? Despite Jasmine’s fury with Jafar, the sultan doesn’t see Jafar for what he is. It seems this well-intentioned wealthy man who lives in a spectacular castle doesn’t listen to his daughter.

In “Beauty and the Beast,” Belle’s father Maurice, who is also a single parent, is an absent-minded genius she has to protect. Peter Pan? He takes kids away from their parents to Never Never Land. In “The Little Mermaid,” Ariel runs away from her father Triton to pursue a life — and a love — he has forbidden. Looking for Ariel’s mother? She’s not under or above the sea.

Speaking of a child without a mother, in “Finding Nemo” poor Nemo grows up under the overprotective fin of his humorless clownfish father Marlin. Sure, Marlin is heroic but he has a long journey, physically and emotionally, to find his son — and in a way, himself.

I don’t recall seeing Cinderella’s father at all, leaving her with the evil stepmother — seems like a bad call on the father’s part there, too — and her horrible stepsisters.

Maybe taking away parents — or turning them into buffoons — creates plot points that these heroes have to overcome. It gives them a chance to learn to trust themselves and their friends and to believe in who they are. I realize the stories aren’t about the parents and maybe, in some backhanded way, these stories encourage kids to find courage when their parents can’t simply hand it to them or purchase it online from Amazon.

I guess there wouldn’t be as much of a heroic role for a child who helped conquer something just by learning or listening to his well-intentioned parents or to grandparents who attend every concert and are eager to hear about school.

Taking parents away, or giving them questionable judgment, creates opportunities for kids to take control of their perilous lives.

Perhaps Disney has bequeathed real-life parents a gift through all these invisible or flawed guardians. It gives the rest of us a chance to say, “I messed up here, honey, but it could be worse: I could be a Disney parent.”

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Hello, ladies,” the gentleman at the front door said. The blushing and grinning reminded me of middle school, where the athletic star walks into a room and the girls swooned.

Except that, in this case, it wasn’t a group of middle school girls, it was their middle-aged mothers.

“Hey, bub,” I wanted to shout, “back here, behind the considerably taller women sits a man.”

Of course, I didn’t say that, because I didn’t want to stand out, or even up, for that matter. I had a good seat and was waiting for a key moment to contribute something or to clear out.

I was at a do-gooders gathering. That’s not the name of it, because people don’t generally come up with such generic sounding names for a collection of people who want to make a change, to help people, to make a difference in the world. But, really, that’s what they were.

Why were they there? Who knows? I didn’t ask them. I suppose it could have been that they all felt a strong calling to contribute. It could have also been that they had friends who would be there that night and they wanted to do their part, alongside their close friends, to effect change. Or maybe it was because they were required to be there, because their daughters played on a sports team and the parents of the team captains had the responsibility to make sure everyone, and they meant everyone, as email after email said, attended and contributed.

After all, for this effort to be successful, they needed 100 percent participation. Lovely, lovely, lovely. But wait; I seem to recall reading this book called The Chocolate War, which kept springing to mind as I was furiously typing details of this meeting to my wife.

For instance, I told her that I’d never smelled such a powerful combination of floral scents. The host of this gathering had gone deep into the well of potpourri for a scent that, I’m guessing, carried over the river and through the woods all the way to grandma’s house. I also told her that I was the only man in the room and that there was a plate of cookies in the center of the island that no one touched.

Anyway, in The Chocolate War, by Robert Cormier, Jerry Renault, on an assignment from a group of unofficial student leaders, is told not to sell chocolates as part of a fundraising campaign. When the assignment ends and he’s supposed to decide to accept the chocolates, he continues to refuse. Ultimately, he suffers serious consequences from rebelling against the school and the Vigils, the student thugs who effectively run the school.

I’m not suggesting that these delightful women, with their floral-scented kitchens and earnest, sincere, and heartfelt grins and plans are anything like the Vigils. They are working toward a great cause and are encouraging complete participation. But, something feels wrong about the compulsory nature of a good act.

Instead of everyone working for one, particular effort, perhaps this group could encourage full participation in a charity, good cause or effort of each player, or a family-choice activity. I get it, of course. The complete effort of the players and all their families could easily be greater than the sum of the parts of small efforts from each person.

Maybe it was because I was the only man in the room, or maybe it was because I am such a fan of The Chocolate War, but I couldn’t help wondering if there was a coercive undercurrent to all this cheerleading.

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Barbara Chapman on the side of a pyramid during her trip to Egypt. Photo from Chapman

If the smartest people in the world gathered in a room, they might struggle to collaborate. An Australian astrophysicist might have a different way of solving problems from the Spanish sociologist. That doesn’t even address language barriers.

Similar principles hold true for the world’s best super computers. While each may have an ability to perform numerous calculations, gather information, and extrapolate from patterns too complicated to discover with a pencil and paper, they can be limited in their ability to work together efficiently.

That’s where a leader in the field of parallel computing comes in. Barbara Chapman, who has been at the University of Houston since 1999, has taught rising stars in the field, written textbooks and enabled the combination of supercomputers to become more than the proverbial sum of their parts.

And, this week, she is bringing her talents to Long Island, where she’s starting the next step in her career as a professor of Applied Math and Statistics, and Computer Science at Stony Brook, as part of the Institute for Advanced Computational Science and as an affiliate at Brookhaven National Laboratory.

Calling Chapman a “pioneer in the world of parallel computing,” Sunita Chandrasekaran, who was a post-doctoral researcher in Chapman’s lab, predicted Chapman would “attract top graduate students from across the globe. Many students would love to do research under Chapman’s supervision.”

Lei Huang, an assistant professor in the computer science department at Prairie View A&M University in Texas, considers Chapman his “mentor,” and said she is “always patient with students,” making her a “valuable asset” to Stony Brook. Huang, who did his Ph.D. and worked as a post doc in Chapman’s lab, added that she proposed and implemented innovative language features to improve performance and productivity of programming on supercomputers.

Chapman, who grew up in New Zealand, said she left the more temperate region of Houston driven, in part, by the intelligence and personality of Robert J. Harrison, Stony Brook’s director for the Institute for Advanced Computational Science. Additionally, Chapman sees opportunities to work with local collaborators.

Chapman works to make it easier for scientists and other users to get computers to solve their problems and gain insights from massive amounts of data. She strives to get high-powered computers to work together efficiently.

Scientists need to give computers a way of telling the cores how to interact and collaborate. Dividing up the work and ensuring that these computers share data are among the challenges of her role.

The new Stony Brook scientist helped develop OpenMP, which can be used to program multicores and is an industry standard used in cell phones, among other things.

President Obama unveiled plans to build an exascale computer, which might be capable of performing a billion billion operations per second. Building this computer will have numerous challenges, including hardware, power, memory, data movement, resilience and programming.

Chandrasekaran, who recently joined the University of Delaware as an assistant professor, said software programming needs to be more intuitive, portable across platforms and adaptable without any compromise in performance. Chapman, she said, is a leader in these fields, bringing together national laboratories, vendors and academia.

As a part of a group of researchers asked to identify opportunities for collaborations between the United States and Egypt, Chapman also journeyed to Egypt. While it was a “wonderful experience,” Chapman said the efforts were put on hold indefinitely after the revolution.

Applications that exploit supercomputers range from astrophysics to the automotive industry to analyzing old texts, to determine if the works of classical scholars were written or translated by the same person, Chapman said.

Chapman and her colleagues work to design features to support the next generation of computers. In the next few years, Chapman expects computers to have more complex memory, while the cores will be more heterogeneous.

At the same time, hardware manufacturers are focused on green computing, enabling the same computing power while using less energy.

Chapman enjoys working in an academic setting, where she can inspire the next generation of computer scientists. She will start teaching at Stony Brook in 2016.

While Chapman’s work centers around helping computers get the most from their collaborations, she also believes the workforce would benefit from attracting, training and supporting people from a broader range of backgrounds, including African-Americans, Hispanics, and women.

“If we had a much more diverse group of people, how would our use of computers change?” she asks. “Would we find other uses of computers?”

Chapman is encouraged that her concern about diversity is a matter numerous people in Washington are discussing. “I chaired a small study on this last year for the Department of Energy,” she said. “There’s a lot of buy-in to the notion that it’s important to change that.”

Chapman said an early experience working with the National Aeronautics and Space Administration ignited her interest in computer science. She worked with people who were exploring what happens when a spacecraft re-enters Earth’s atmosphere. They were designing materials that are better able to withstand the heat and speed of returning to Earth.

“People can use machines for finding out what’s going on in the universe in the big picture,” she said. “That got me hooked.”

This version corrects the title of Sunita Chandrasekaran.

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Professor Allen Tannenbaum. Photo from Stony Brook University

It’s a dangerous enemy that often turns deadly. Worse than its potentially lethal nature, however, cancer has an ability to work around any roadblocks scientists and doctors put in its path, rendering some solutions that bring hope ineffective.

Researchers around the world are eagerly searching for ways to stay one, two or three moves ahead of cancer, anticipating how the many forms of this disease take medicine’s best shot and then go back to the business of jeopardizing human health.

Allen Tannenbaum, a professor of computer science and applied mathematics and statistics at Stony Brook University, has added a field called graph theory to some of the tools he knows well from his work in medical imaging and computer vision.

A normal, healthy cell is like a factory, with genes sending signals through proteins, enzymes and catalysts, moving reactions forward or stopping them, and the genetic machinery indicating when and how hard the parts should work.

Cancer, however, is like a hostile takeover of that factory, producing the factory equivalent of M16s that damage the cell and the individual instead of baby toys, Tannebaum suggested.

By analyzing how proteins or transcription networks interact, Tannenbaum and his colleagues can develop a model for the so-called curvature of interactions.

Looking at the interactions among parts of the genetic factory, Tannenbaum can determine and quantify the parts of the cell that are following cancer commands, rather than doing their original task.

Curvature isn’t so much a bending of a physical space as it is a change in the way the different proteins or transcription factors function in the discrete networks Tannenbaum uses in cancer and biology.

“The parts are not doing their job the same way,” Tannenbaum said. “We can look and see graphically how different things compare.” He and his collaborators recently published their findings in the journal Scientific Reports.

Using mathematical formulas to define a range of interactions, Tannenbaum can determine how quickly a cancer or normal cell can return to its original state after a disturbance. This ability is called its robustness.

The study “brings to light a new way to understand and quantify the ability of cancer cells to adapt and develop resistance,” explained Tryphon T. Georgiou, a professor in the Department of Electrical and Computer Engineering at the University of Minnesota, who has known Tannenbaum for over 30 years and collaborated on this study. “It also provides ways to identify potential targets for
drug development.”

Tannenbaum studied cells from six different tumor types and supplemented the study with networks that contain about 500 cancer-related genes from the Cosmic Cancer Gene Census.

In treatments for cancers, including sarcomas, researchers and doctors sometimes try to pull the plug on cancer’s energy network. This method can slow cancer down, but cancer often resumes its harmful operations.

Using models of cancer on a computer, Tannenbaum and the five graduate students and four postdoctoral fellows can run virtual experiments. He can hand off his results to biologists, who can then run tests. Once those scientists collect data, they can offer information back to Tannenbaum.

“This is a team effort,” said Tannenbaum, who works with scientists at Memorial Sloan Kettering, the University of Texas MD Anderson Cancer Center and Brigham and Women’s Hospital.

Georgiou described Tannenbaum as a “brilliant scholar” and a “mathematician with unparalleled creativity,” who has been a “pioneer in many fields,” including computer vision. Indeed, a computer vision program could assist nurses in the intensive care unit on different shifts assess the level of pain from someone who might not otherwise be able to communicate it.

Georgiou called Tannenbaum’s work on cancer a “mission” and said Tannenbaum is “absolutely determined to use his remarkable skills as a mathematician and as a scientist” to defeat it.

Tannenbaum, who recently took his grandchild to a Mets win at CitiField, said coming to Stony Brook in 2013 was a homecoming, bringing him closer to his native Queens. He cited two famous graduates from Far Rockaway High School: the physicist Richard Feynman, who helped develop the atomic bomb, and Bernie Madoff.

He and his wife Rina, who is a professor in materials science and engineering at Stony Brook, live in Long Island City.

Tannenbaum hopes to continue to build on his work applying math to solving cancer.

“There’s a lot of mathematical play left and then testing the predictions in a biological/medical setting,” he said.