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Daniel Dunaief

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Joel Saltz. Photo from SBU

By Daniel Dunaief

In the battle against cancer, doctors and scientists use targeted drugs to treat the disease. They also employ radiation, starve it of the nutrients it might need to grow, block key metabolic pathways in its development and encourage the immune system to attack these genetically misdirected cells that grow out of control. A developing field in this battle includes the use of computers, artificial intelligence and math.

Joel Saltz, the Cherith Chair of Biomedical Informatics at Stony Brook University, recently teamed up with researchers from Emory University and the University of Arkansas and won an $8 million grant from the National Cancer Institute to coordinate radiology and pathology information in the battle against cancer.

“By gathering more information, researchers can understand better what’s happening, what might happen and how best to treat cancer,” Saltz said. The grant will be divided equally among the three institutions over the course of five years. Saltz will be collaborating with Ashish Sharma at Emory and Fred Prior at the University of Arkansas.

Saltz has been working with Sharma for several years, when the two were at Ohio State and then moved together to Emory. This is Saltz’s first major grant with Prior, although the two have also known each other for years and have been working in the same NCI program.

Prior has considerable expertise in radiology, while Saltz is adding his pathology background to the mix. Radiology has used digital imaging for a long time and, until recently, pathology data was collected on glass slides. Saltz is helping bring digital pathology to this effort.

“We had been on panels for many years with NCI saying we need to do this sort of” collaboration, Saltz added, and now the trio is putting that idea to work.

Yusuf Hannun, the director of the Cancer Center at Stony Brook, sees the potential for this type of collaboration. “This is a very important effort that builds on several areas of outstanding strength” at the Cancer Center, the director explained in an email.

Exploring information from digitized radiology and pathology samples will “allow us to understand individual cancers at a much higher level. It should improve accuracy in diagnosis [and offer an] ability to provide better informed prognosis” and individual therapy, Hannun continued.

Researchers on the current grant, which is part of the Information Technology for Cancer Research, plan to expand resources for integrative imaging studies, build on the capacity to acquire high-quality data collections, dedicate resources to support reproducible research and increase community engagement.

Saltz will use the portion of the Stony Brook funds to develop new software integration tools and curation and work with researchers to analyze and understand their patient data. Over time, he will also hire additional staff to build out this expertise. He has collaborated with Kenneth Shroyer, chair of the Department of Pathology at Stony Brook, on pancreatic and ovarian cancer and on breast cancer with pathology professor Patricia Thompson, who is also director of basic science at the Cancer Center. Shroyer “plays an important role” in all his research, Saltz said.

“Digital pathology will supplement that art of surgical pathology with quantitative data, to improve diagnostic accuracy,” Shroyer wrote in an email, which will “inform decisions on how to optimize therapeutic intervention for the treatment of cancer and many other diseases.”

Shroyer interviewed Saltz before Stony Brook hired its first bioinformatics chair. “Based on his research focus, including his pioneering efforts in digital pathology, he clearly stood out as my top choice.”

Saltz and Shroyer have generated maps of patterns for immune cells in tumors. “We and others have shown that these are related to how patients respond to treatment,” Saltz said. He described his work with these scientists as “basic clinical cancer research,” in which he develops and enhances technology to understand various types of cancer.

This particular grant is “more about technology and curation,” Saltz said. “People are developing new algorithms, in artificial intelligence and machine learning.” By making this information available, scientists from around the world who have insights into the specific types of cancer can use it to predict responses to treatment and develop and refine the algorithms that underlie the computer analysis.

Using specific cancers from radiology and pathology studies is akin to sitting in a football stadium and examining a blade of grass from the bleachers, Saltz suggested, borrowing from a phrase he’d heard at a recent panel discussion with Liron Pantanowitz from the Department of Pathology at the University of Pittsburgh Medical Center.

“What we do is we create catalogs of every blade of grass and every worm and weed,” Saltz added. “It’s a huge database problem” in which he is integrating software development.

Hannun, who has been working to help Stony Brook University earn a National Cancer Institute designation, suggested that this bioinformatics work is “a critical component of our plans” and represents an area of exceptional strength.”

Cancer bioinformatics is “one of the main pillars of our research program and it integrates well with our efforts in imaging, metabolomics, improved diagnostics and improved therapeutics,” Hannun explained.

As for his department, Saltz said Stony Brook will have its first biomedical informatics Ph.D. graduate at the end of 2017. Yanhui Liang joined Stony Brook when Assistant Professor Fusheng Wang came to Long Island from Emory. Xin Chen will graduate in May of 2018.

The doctoral program, which launched last year, has five current students and “we’re hoping to get a bigger class this year,” Saltz said. “Informatics involves making techniques for better health care,” Saltz said. People with medical degrees can do fellowship training in clinical informatics.

A resident of Manhasset, Saltz lives with his wife Mary, who is an assistant clinical professor of radiology at Stony Brook University. Over the course of the next five years, Saltz said he believes this grant will continue to allow him and his collaborators to develop tools that will help provide insights into cancer research and, down the road, into personalized cancer treatment.

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The fictions start when we’re young.

Santa Claus is coming to town. Oh yeah? Well, hopefully he isn’t traveling on the New York area transit system, which seems to be making two types of stops these days: late and later.

Certainly, young children can and should revel in the stories that animate this time of year, when cold and snow usually replace warm and bright weather.

And yet it might be a good time to reflect on the myths of our youth, just to compare them to our realities. Let’s start:

• Everyone gets what they deserve or what’s coming to them. Hmm, does it seem fair or merit based that some of the finest teachers in the country, who serve as an inspiration to children year after year, earn barely enough to afford modest cars that warm up just as they arrive at school? Compare this iniquity with athletes who spit at each other, curse at their coaches, fight on the field and charge people for autographs, yet are earning exorbitant salaries to play children’s games.

• It’s the beauty on the inside that counts. That sounds nice and, in some cases, it actually plays out that way, as people cherish the character, spirit and energy of the person they meet, rather than dwelling on how much they fit the modern ideal for a man or woman. And yet for every magazine cover with a regular-looking bloke or woman, there are 10 or more who look like lithe or buff caricatures of real people.

• Slow and steady wins the race. Yeah, maybe for turtles and rabbits, but everyone is racing to win, win, win at all costs. Sure, patience and gradual steps toward a goal make sense, but a capitalist society is driven by those who are the first movers, who make the unexpected discoveries and who patent their method, idea or product first.

• Winning isn’t everything. Oh, no? It sure does seem like cause for enormous celebrations. The Winter Olympics are coming up in February. Will we revel in the effort the athletes took to get there, will we celebrate the man or woman who finishes fourth, and will we congratulate the athlete who didn’t make it to the medal round? Maybe, but then again aren’t we more likely to remember the names and achievements of those who finished first or, gulp, second?

• Be who you are. That sounds lovely, but doesn’t that depend on what state you’re in? In some states, if who you are involves altering gender expectations, that might be problematic. Yes, we are all urged to celebrate ourselves and our identity, but others don’t necessarily join the party if they feel threatened by those we embrace.

• Truth, justice and the American way. No, I’m not referring to Superman here, although those are the words from the famous comic book hero. Listening to people fight about the direction of the country suggests that the American way isn’t what it used to be. Ask President Trump, who is so fond of deriding what he describes as “fake news.” We as a nation can’t agree on truths anymore, because we have become so adept at fighting the appearance of disagreeable facts.

• Happily ever after. This catchphrase depends on whom you ask, but seems to involve riding off cheerily into some sunset aboard a horse-drawn carriage. Years like 2017 can present bumps in the road, the way acne suddenly appears on the face of a developing teenager. That doesn’t mean life won’t involve a “happily ever after.” Maybe we should revise the homily to suggest that it will likely require work, in which the payoff, down the road, is worth the challenges.

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Here we are, Thanksgiving Day, and I’d like to share some things I’m not thankful for. I recognize, of course, all that I do have to be thankful for, but in this moment and in this year it seems fitting to make a not-so-thankful list.

Nicknames: They’ve become ubiquitous. I never liked the nicknames Joe Girardi had for all the Yankees, usually adding a “y” at the end of their last names. Why? Is Gardner too hard to say?

I’m also not a huge fan of the nicknames the president of the only country not in the Paris climate accord has given to all his adversaries and nemeses.

I ask, in all sincerity, does the man occupying the White House who gets to fly on Air Force One have a positive nickname for anyone? Does he, for example, call anyone “Superstar” or “Force of Nature,” or simply “Champ”? Does he think anyone is a “dynamo,” “real winner” or “miracle”? No, I suspect he doesn’t because that might mean that their superpowers would be comparable or, gasp, stronger than his.

Pundits: Everyone on TV, in the comment section of news articles and on the internet seem to know better than everyone else. Some of these pundits seem to be playing a game of mad libs where they change the names, dates and details about their punditry, but their perspectives and their “shame, shame, shame, he’s a bad Democrat/ Republican” outrage get old incredibly quickly. If you have no new thoughts, then don’t pretend to offer something new.

I’d enjoy it if a newscaster said, “And now we’re going to turn to someone that hates Republicans who, no doubt, will offer an oversized portion of outrage.”

Fake news: It’s a convenient label for those who don’t like what they hear. It’s a way to undermine the messenger. I know there are news organizations who play fast and loose with the facts. There are also members of the media who have made a point of blending editorial and news, decrying the lack of moral — or even logical — leadership in Washington. Still, many reporters are eager to find facts and to give people a chance to make decisions for themselves. Ultimately, many journalists are serving society by shining lights in dark corners and by sharing information that informs the public. Without the news, people would need to rely on official sources to tell them their version of the truth. That doesn’t sound very democratic.

Deliciously evil desserts: Around this time of year, cooks in places like The Good Steer make incredible pumpkin pie. Why does it have to taste so good and why can’t I stop at just one or six pieces? Can’t they add string beans or cauliflower to the pie to make it slightly less palatable?

Misspellings and myselfisms: I know that seems incredibly elitist and English-language snobby of me, but I bristle at emails urging me to do something before it’s too late. I would like to reply that it’s “to” late to correct their emails. As for the “myself” problem, I have heard someone say several times in the last few weeks, “If you have a problem, you should talk to Ted or myself.” Really? My problem is that if you took Ted out of that sentence, you’d be suggesting people talk to myself.

Teenage odors: Yes, I know the teenagers are growing, their hormones are surging and they are some of the most active people on Earth. Still, get a group of them in a room, in a car or in any confined space and you might long for the innocent days of diapers and spit-up.

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Minghua Zhang

By Daniel Dunaief

Minghua Zhang spent a sabbatical year in China trying to improve climate models, which included analyzing errors of current models.

A professor at the School of Marine and Atmospheric Sciences at Stony Brook University, Zhang focused on the Southern Great Plains of the United States. He explored how the current models did not accurately simulate convection, which created a warm and dry bias.

In convection, heat and moisture get carried upward. The models account for summer rainfall but do not calculate the organizational structure of the convective systems, which led them to simulate insufficient precipitation.

By adding in the new information, Zhang predicts in recent research published in the scientific journal, Nature Communications, that the projected warming in the region would be 20 percent less than previously thought. Precipitation, meanwhile, would be about the same as it is today, instead of the drying that was previously anticipated.

“The resolution of the models is not high enough to predict the change of the convection with a high degree of precision,” Zhang explained in an email.

He suggested that using 10 times the specificity of model calculations, he expects a clearer picture of the likely climate by the end of the 21st century. This is like looking through binoculars at a nondescript moving shape in the distance. By adding focal power to the lens, the image can become sharper and clearer.

The climate is a big picture view of trends over the course of many years. That is distinct from weather, which involves day-to-day variations and which meteorologists describe each morning and evening with colorful images of cold and warm fronts on local maps.

“You have many things you can’t see and now you have better binoculars,” he suggested. “This tiny thing in the binoculars can make a bigger impact. What we see is that these [variables] actually matter.”

Zhang suggested that a climate model that better accounts for summer rainfall still includes higher temperatures in this sensitive region. “The warming is going to be there and will be significant,” he said. If carbon dioxide emissions continue at their current rate, the warming will still be about five degrees by the end of the century, he suggested. That, he predicted, will still have a significant impact on agriculture.

Edmund Chang, a professor at the School of Marine and Atmospheric Sciences at Stony Brook who was not involved in this study, said this research addresses “a specific bias of the model that needs to be taken care of.” He added that researchers know that the “models are not perfect” and suggested that the “scientific and climate modeling community is trying to refine and improve” these tools.

Chang agreed that the refinement “doesn’t change the fact that we still project a large increase in the temperatures over the central United States.”

The Southern Great Plains region has some unique elements that make climate predictions challenging. It has considerable organized convection, which increases the occurrence of tornadoes. There’s also a large coupling between the soil moisture and the clouds, which means that whatever happens on the land has feedback for the atmosphere.

Zhang said his research focus is on climate simulation modeling. He knew the models had problems simulating convective events, which is why he started exploring this specific region. “The way the models are constructed, the granules are not small enough,” he said.

Chang expected that this work would “spur more research on trying to understand this mechanism. Model developers will need to try to find out how to improve the physical model.”

Zhang has been working for the last two years with scientists from Tsinghua University in China, which included his time on sabbatical. “When you are on sabbatical, you have more time to really think about problems,” he said.

Chang added that sabbaticals can provide some time to focus on specific scientific questions. During a typical semester that includes administrative responsibilities and teaching, professors “are very busy,” He said. “We really don’t have an extended period of time to focus on one project. The sabbatical gives us a chance to focus.”

Zhang hopes this study “motivates people to think about how to improve their models in describing” other climate systems.

One of the many challenges scientists like Zhang face in developing these climate models is that their computers are still not powerful enough to resolve elements like clouds, which not only dot the landscape and provide shade during the summer but also send the sun’s energy back into space.

The system he’s studying is “chaotic by nature,” which makes accounting for elements that change regularly challenging. He suggested that these studies were akin to the butterfly effect. Scientists have suggested that someone who went back in time and committed a seemingly trivial act, like killing a single butterfly, might return to his familiar time and surroundings to discover profound changes.

While that’s an exaggeration, that’s still the kind of system he said researchers are confronting as they try to account for, and weigh, climate defining factors. That’s why he’s looking for statistical, or probabilistic, predictions that are averaged over time periods.

The United States, China and the European Union are all pursuing more powerful computers for these kinds of applications, Zhang said.

Zhang, who is the editor-in-chief of the Journal of Geophysical Research: Atmospheres, has been involved in an advisory capacity with the United States Department of Energy in developing these models. A

s for this specific effort, Zhang said he was pleased that the paper pointed out a research direction to refine models for climate in this area. “What we see is that these things [including convection] actually matter,” he said. “That’s the main contribution of this paper.”

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We rarely get anything completely right the first time. I’m not just saying that because I’m a second child. I idolize my older brother. In fact, I’m fond of my younger brother, too.

We need practice. When we’re young, we take a few steps and we fall hard. Fortunately, at that age, we’re practically made of plastic, bouncing off the nearby floor as if it were a downy soft trampoline. As we age, the floor gets harder.

With each figurative step through life, we make adjustments, learn on the fly and revise our approach.

We recently visited a few colleges with our daughter. The cheerful school representatives were selling us on the idea that their classes were great, the students they admitted were incredible and the opportunities were extraordinary.

One theme that stuck out, especially after several schools presented it as if unique, was that they made students uncomfortable. They wanted to challenge their undergraduates to reach outside their comfort zone. They wanted eager students to fall down and, in so doing, learn to get back up.

This idea of falling is part of the charm of enjoying the ride. We listen to elementary school music concerts in which someone plays a few notes after the conductors arms have stopped moving, we nod encouragement when the young person on stage says a few of the wrong words in a speech, and we suggest to our kids that they’ll spell “because” correctly the next time.

The country may have forgotten that our strutting president, who has been in the public eye for so long, has never been a politician. He’s definitely outside his comfort zone, acting like a president when he hasn’t even been, to borrow a phrase from him, “elected dog catcher.”

People pounce on every mistake, every breach of protocol and every misstatement, ready to tar and feather him for saying or writing something that probably would play better on a fictionalized reality TV show than it does for him as president of the United States.

He’s so eager to be a part of every story and to expand his brand — something he’s been doing reflexively for years — that he doesn’t appear to take the time to recognize or
acknowledge mistakes.

I know how it is to say, “my bad.” Many people consider admitting a mistake some sign of weakness, instead of a reflection of strength and self awareness. Erring, as the saying goes, is human.

You don’t get many free passes when you’re president. You either learn or you don’t, you either unify or you don’t, and you either say or do the right thing, or you don’t.

Still, it seems to me that he might endear himself to more people, and win higher ratings, if he took a few extra seconds to think about whether he might write or respond to something in a different way. He doesn’t seem burdened by the kind of reflection that allows for his own second thoughts to enter the discussion.

People are eager to rip him apart each day, but let’s remember something his handlers and cohorts seem to embrace regularly: He gets angry when people point out that he’s fallen down. Maybe he can meet us halfway, by learning to take an extra second to edit his thoughts or speech. When he takes a few steps without falling, we can breathe a sigh of relief, the way parents do when they’re no longer bending over to protect their children from bumping their heads on nearby coffee tables.

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Your phone is across the room. You want it to come to you and you put out your hand. Nothing happens. You scrunch your face and flex the muscles in your outstretched fingers, but, still, nothing happens.

Someday the iPhone C (for 100) or iPhone M (1,000) may fly through the air when you reach for it (avoiding people’s heads along the way). And, someday, we may figure out how to use the energy field described in such detail in the Star Wars franchise.

Yes, just as the new iPhone X (a mere 10) arrives at Apple stores, Star Wars is revving its intergalactic engines, bringing an aging Luke Skywalker and his rebel friends back, yet again, to battle with evil.

At the heart of the franchise is the Force, which would be a convenient skill to have when we can’t find the remote control or our phones.

So, what is this Force and do we only acknowledge it in the movies?

Thousands of years ago, long before Darth Vader, when primitive people struggled through a drought and needed rain, they prayed, they did rain dances or they carved images of rain in the walls so that future archeologists and artists could analyze and appreciate them years later.

I’m not minimizing or trivializing religion or a belief in any deity. I am suggesting, however, that the Force and the battle between good and evil and the free-flowing energy that is a part of this mythology come into play in our daily lives.

As we prepare to walk out the door, our shoelace snaps. We don’t have time to take the lace out of the shoe and put another one in. We’re also not completely sure if we have other laces handy.

We demand to know “Why now?” from the lace. We might even get annoyed and say, “No, no, no, come on! I can’t be late.”

To whom are we talking? Are we personifying the shoelaces so we can complain? By expressing our frustration to the shoelace, perhaps we are externalizing our anger.

But, maybe the dark side is challenging us in a moment of weakness, encouraging us to get angry, to take off our shoes, open the door and throw them deep into woods?

We get into our car and turn the key. It doesn’t start. We hold our breath. “Please, please, please, you can do it,” we beg and try again.

From whom are we asking for help? Are we seeking assistance from a deity who might be nearby or everywhere? Are we speaking to the inanimate engine, hoping that Bessie, like Herbie the Love Bug, will come to life, rev her engine and shift back and forth from one tire to the other in a happy car dance? Maybe we promise Bessie a refreshing oil change if we can just get to work today.

Or are we talking to a Force that makes things go our way, the way we hope a Force encourages our loved ones to answer the phone while we’re waiting for them or our favorite team to succeed in the moment?

We may hope many of the objects we talk to, apart from our electronic friends Siri and Alexa, will respond to our needs, the way earlier people hoped that their efforts affected the weather.

Movies may come and go from the big screen, but we live through our own nonintergalactic battles, escaping from the shadows of our fathers, perhaps, or finding our own destinies. As we do, we may turn to some version of the Force, or something like it, for help in a pinch.

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From left, BNL Staff Scientist Lihua Zhang, former postdoctoral researcher Vitor Manfrinato and BNL Senior Scientist Aaron Stein. Photo courtesy of BNL

By Daniel Dunaief

It took a village to build this particular village or, more precisely, a pattern so small it could fit thousands of times over on the head of a pin.

Working at Brookhaven National Laboratory’s Center for Functional Nanomaterials, a team of researchers wanted to exceed the boundaries of creating small patterns with finely honed features. The group included Aaron Stein, a senior scientist at CFN, Charles Black, the head of CFN, Vitor Manfrinato, a former postdoctoral researcher at BNL and several other key members of the BNL team. The team added a pattern generator that allowed them to control a microscope to create a pattern that set a record for drawing at the 1-nanometer scale.

Just for reference, the width of a human hair is about 80,000 to 100,000 nanometers. The size of the pattern is a breakthrough as standard tools and processes generally produce patterns on a scale of 10 nanometers. “We were able to push that by a factor of five or 10 below,” Stein said. “When you get to those small size scales, that’s pretty significant.”

In this case, the novelty that enabled this resolution originated with the idea of employing the scanning transmission electron microscope, which isn’t typically used for patterning to create these images. The scanning transmission electron microscope has an extraordinarily high resolution, while the pattern generator allowed them to control the patterns they drew and other aspects of the exposure.

Researchers at CFN are focusing on this spectacularly small world to manipulate properties such as chemical reactivity, electrical conductivity and light interactions. “This new development is exciting because it will allow other researchers to create nanomaterials at previously impossible size scales,” Kevin Yager, a group leader at CFN explained in an email. “There are numerous predictions about how materials should behave differently at a size scale at 1 to 3 nanometers. With this patterning capability, we can finally test some of those hypotheses,” he said.

Stein and the research team were able to create this pattern on a simple polymer, polymethyl methacrylate, or PMMA for short. “It’s surprising to us that you don’t need fancy materials to create these kinds of features,” said Stein. “PMMA is a common polymer. It’s Plexiglas. It’s kind of exciting to do something that is beyond what people have done” up until now.

One of the many possible next steps, now that the researchers have developed this proof of principle, is to apply this technique to a substance that might have commercial use. Taking the same approach with silicon, for example, could lead to innovations in electronics. “We can make them with a high clarity of patterns and sharp corners, which we can’t do with other techniques,” Stein said.

The BNL research team would “like to apply this to real world research,” which could include electronics and transistors, as well as photonics and plasmonics, he added. This project arose out of a doctoral thesis that Manfrinato was conducting. He is one of the many scientists who came to BNL, which isa Department of Energy funded user facility that provides tools to conduct research for scientists from around the world.

Manfrinato was a doctoral student in Professor Karl Berggren’s group at the Massachusetts Institute of Technology. In an email, Manfrinato explained that he was interested in pushing the resolution limits of e-beam lithography. “BNL has state of the art facilities and expert staff, so our collaboration was a great fit, starting in 2011,” he explained.

Other scientists thought it was worthwhile to continue to pursue this effort, encouraging him to “come here and work on this. It’s a home grown project,” Stein said. Manfrinato worked on his doctorate from 2011 to 2015, at which point he became a postdoctoral researcher at BNL. His efforts involved several groups, all within the Center for Functional Nanomaterials at BNL. Stein, Manfrinato and Black worked on the lithography part of the project, while Lihua Zhang and Eric Stach developed the microscopy. Yager helped the team to understand the processes by which they could pattern PMMA at such small scale lengths.

“No one or two of us could have made this happen,” Stein said. “That’s really the joy of working in a place like this: There are [so many] permutations for collaborating.” Indeed, the other scientists involved in this study were Yager; Zhang, a staff scientist in electron microscopy; Stach, the electron microscopy group leader at CFN; and Chang-Yong Nam, who assisted with the pattern transfer.

Manfrinato, who is now a research and development engineer at a startup company in the San Francisco Bay area, explained that this lithographic technique has numerous possible applications. Other researchers could create prototypes of their devices at a level below the 10-nanometer scale at CFN. Manfrinato interacts with the BNL team a few times a month and he has “exciting results to be further analyzed, explored and published,” he wrote in an email.

Stein said BNL would like to offer this patterning device for other users who come to BNL. Ultimately, researchers use materials at this scale to find properties that may vary when the materials are larger. Sometimes, the properties such as color, chemical reactivity, electrical conductivity and light interactions change enough to create opportunities for new products, innovations or more efficient designs.

A resident of Huntington, Stein and his wife Sasha Abraham, who works in the planning department for the Town of Huntington, have a 15-year-old daughter Lily and a 13-year-old son Henry.

As for his work, Stein said he’s interested in continuing to push the limits of understanding various properties of nanomaterials. “My career has been using the e-beam lithography to make all sorts of structures,” he said. “We’re in a regime where people have not been there before. Finding the bottom is very interesting. Figuring out the limits of this technique is, in and of itself” an incredible opportunity.

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The greater bamboo lemur will struggle to survive amid a shorter rainy season. Photo by Jukka Jernvall

By Daniel Dunaief

An elusive primate is living on a shrinking island within an island. The greater bamboo lemur, which is one of the world’s most endangered primates, now inhabits a small section of Madagascar, where it can find the type of food it needs to survive.

The greater bamboo lemur, which was one of numerous lemurs featured in the 2014 iMax movie, “Island of Lemurs: Madagascar,” is finding that the time when it can eat the most nutritious types of bamboo is narrowing each year amid a longer dry season.

Patricia Wright has dedicated her life to helping lemurs in Madagascar. File photo from SBU

In a publication last week in the journal Current Biology, Patricia Wright, the founder of Centro ValBio research campus, driving force behind the creation of Ranofamana National Park and a distinguished professor of anthropology at Stony Brook University, along with several other researchers, including Jukka Jernvall from the University of Helsinki and Alistair Evans from Monash University, showed that the population of lemurs is threatened by a changing climate. The bamboo that sustains the greater bamboo lemurs depends on water to produce shoots that are higher in nutrition.

Indeed, when the rains come, the new bamboo shoots are “filled with protein,” said Wright. Jernvall, however, predicted that the driest season will get longer by a day each year. By 2070, rains necessary for bamboo growth and greater bamboo lemur survival will be delayed by as much as two months.

This is problematic not only for the current generation of greater bamboo lemurs but also for the more vulnerable younger generations, who need their lactating mothers to eat more nutritious bamboo to help them grow. Bamboo shoots typically come up from the ground about two weeks after the rains begin, in the middle of November. Bamboo lemurs, whose annual clocks are set to the rhythm of an island off the southeast coast of Africa that is the size of California, are born around the time of these bamboo-shoot-producing rains.

“Any village elder will tell you that the rains used to come at about Nov. 15 and continue until March 15,” Wright said. “That’s the way the world was, even in the 1980s and 1990s and probably many years before that. Suddenly, we started to get some evidence of climate changes and periods of a longer dry season.”

Above, a mother greater bamboo lemur holds her infant, which weighs about half a pound at birth. Photo by Jukka Jernvall

Wright is currently in Madagascar, where she says there is a drought right now. “No water for our research station means no electricity since we are near a hydroelectric power plant,” she explained by email. In fact, in some years, the rains start as late as January, which reduces the food offerings for the mother lemur, who weighs about 6.5 pounds, and her offspring, who need considerable nutrition to grow from birth weights Wright estimates are less than half a pound. The lemur mother “has to have nutritious shoots to feed her baby milk,” Wright said. “She can survive on leaves and trashy stuff in the culm, but she can’t raise her babies” on it.

Wright and Jernvall worked together in 2005 on a study of climate and another type of lemur called sifakas, whose name comes from the alarm sound it makes. In their earlier work, Wright and Jernvall found that aging sifakas with worn teeth could still produce offspring, but that their infants typically died if the weather was dry during the lactation season, Jernvall explained in an email.

“This alerted us about the potential impact of climate change,” he continued. “The bamboo lemur were an obvious concern because they are critically endangered and because they eat the very tough bamboo.”

Jernvall said the work on bamboo lemurs combines Wright’s efforts in Madagascar with climate modeling he performed with Jussi Eronen at the University of Helsinki and an analysis of dental features conducted by Evans and Sarah Zohdy, who is currently at Auburn University. Stacey Tecot, who is on sabbatical from the University of Arizona, also contributed to the research.

Wright believes some efforts can help bring these bamboo lemurs, who survive despite consuming large amounts of cyanide in their bamboo diet, back from the brink. Creating a bamboo corridor might improve the outlook.

Growing bamboo would not only benefit the lemurs, who depend on it for their survival, but would also provide raw materials for the Malagasy people, who use it to construct their homes, to build fences and to cover their waterways.

Bamboo corridors could be a “win-win situation,” where scientists and local communities grew and then harvested these hearty grasses, Wright continued. She has started a bamboo pilot study near one of the small populations of lemurs and hopes the lemurs can expand their range.

The greater bamboo lemur will struggle to survive amid a shorter rainy season. Photo by Jukka Jernvall

Like other animals with unusual lifestyles, the greater bamboo lemurs offer a potential window into an unusual adaptation. Through their typical diet, lemurs consume a high concentration of cyanide, which is stored in the bamboo. Understanding the bamboo lemur could provide evidence of how one species manages to remain unaffected by a toxin often associated with spies and murder mysteries.

As a part of her efforts to improve the chances of survival for this lemur, Wright is considering moving some lemurs to a protected area. She needs permission from Madagascar officials before taking any such actions and recently met with Madagascar National Park official to discuss such remediation efforts.

In Madagascar, Wright said observing the bamboo lemur is challenging because it is such a “cryptic animal.” She has sat beneath a tree where a lemur is hiding for seven hours waiting for it to emerge, watching as a lemur brought in its legs and curled up its body to hide from the scientist’s inquisitive eyes. “I’d get really hungry, so they would win and I would leave,” Wright recalled.

She suggests that the data in the Current Biology article demonstrates the urgency to take action to protect these primates. “We are trying our best to help the bamboo lemur not go extinct,” she said. “Bamboo corridors should help, but we may have to irrigate the bamboo during November to January.”

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What would a victory be without a trophy? We faced that awful question this week.

In the championship game, my daughter’s volleyball team battled their opponent and their nerves to win that coveted trophy, to claim the top honors in their division, and to cap off a successful and rewarding season that involved floor burns, mishits, turned ankles and all manner of emotional challenges as they went toe-to-toe with teams in gyms filled with exuberant fans.

Nothing went right in the beginning of the match. They gave away point after point, until the unflappable coach, whose only sign of anxiety was a few extra gulps of water, called timeout and told the team to relax and play their game.

They were down 12-2 in a 25-point game. Maybe, my wife and I thought, they’d make the first game respectable, get their bearings and then win the second and third games. The benefit of a best-of-three-game set is that they didn’t have to win the first game.

And then a funny thing happened on the way to a potential lopsided loss. They pulled themselves together and they made important shots that landed just inside the line. Momentum, which is such an intangible, shifted quickly, forcing the other coach to call a hasty timeout.

Ultimately, they won that first set, 25-23. The second set was closer throughout, but they also won that one, 25-20, leading to a euphoric celebration. They took turns holding a trophy, which had a volleyball figurine and a plaque.

The coach handed the trophy to my daughter, who was the captain. She cradled it like it was an infant, passing it gently to her teammates who posed for their own pictures with the team’s prize. She got to take the trophy home for the weekend. I drove her friend and her to a diner for some celebratory curly fries and raced home to relatives who were eating a wider variety of food.

After the meal, I offered to take Uncle Jordan, who had come out from the city, back to the train. My wife graciously suggested he sit in the front seat. As soon as he sat down, he asked, “Hey, what’s that?”

Yup, he sat on the trophy, wounding our daughter’s “baby.” When I turned on the light in the car, I saw that the figurine was still intact, but the plaque dangled at an angle.

Jordan laughed. Our son was in hysterics. My wife, who was in the back seat, laughed nervously, while I considered going into panic mode, wondering if I should call the factory in Singapore to ask it to ship another trophy overnight.

We thought about gluing the pieces back together, but that would be like bringing a messy art project to school. Maybe we could take it out of the car and run over it 20 times, and then say we lost it. No, destroying it wasn’t the answer.

“Take it to Home Depot,” Jordan suggested.

What if they couldn’t fix it? What would we tell our daughter?

When she got to our house that night, I did everything I could to keep her from asking about, or looking for, the coveted trophy.

The next morning, we raced to Home Depot, where a couple of good-humored men at the tool rental section got to work. Fortunately, they repaired it. When we returned, we shared the story with our daughter who laughed, too, even as she compared the pictures of the trophy from the night before to the rescued object in her hand. Somehow, like her team, the trophy endured.

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Pavel Osten. Photo by Joelle Wiggins

By Daniel Dunaief

Male mice, as it turns out, might also be from Mars, while female mice might be from Venus. Looking at specific cells in the brain of rodents, Cold Spring Harbor Laboratory Associate Professor Pavel Osten has found some noteworthy differences in their brain cells.

In the scientific journal Cell, Osten presented data that showed that in 10 out of 11 subcortical regions of the mouse brain, female mice showed greater flexibility and even more cells. These regions of the brain are responsible for reproduction, and social and parenting behaviors. “There were more cells [in these regions] in the female brain, even though the brains tended to be bigger in the males,” Osten said.

These results are part of a multiyear collaboration called the National Institutes of Health’s Brain Initiative Cell Census Network.

In the recent Cell article, Osten indicated that his analysis offered a surprising result in the number of cells of specific types in various regions of the cortex. “Those areas that have higher cognitive functions have different compositions,” he said. The ratios of cell types “vary according to the level of cognitive function.” In retrospect, Osten indicated that he saw the logic in such a cellular organization. “It makes sense that different cortical areas would have different cell type composition tuned to the specific cortical functions,” he explained.

In an email, Hongkui Zeng, the executive director of structured science at the Allen Institute for Brain Science, in Seattle, Washington, suggested that “people never looked at this issue carefully before. She added that the “sexual dimorphism was somewhat expected, but it is still interesting to see the real data.”

Pavel Osten sailing in St. Barts and St. Martin last summer. Photo from Pavel Osten

Osten used a system called qBrain to see and count inhibitory neurons in the mouse brain. Over the next five years, he and his collaborators will build an online resource database for other researchers that will have distribution maps for numerous cell types throughout the mouse brain.

Osten estimates that there could be hundreds or even a thousand cell types within the brain that are largely uncharacterized in their specialized functions. A cell type is defined by its function in terms of its morphology, including dendritic and axonal branches. These cells are also defined by their physiology, which includes spiking properties, and connectivity, which indicates which cell is talking to other cells.

The anatomy and physiology of the cells will validate these transcriptome single-cell RNAseq studies, which probe for the variability between cells based on their gene expression, which includes differences due to day-to-day variability and differences from distinct cell types.

By analyzing the location and modulatory functions of these cell types, Osten would like to determine ways human brains differ from other animal brains. “In the human, we can mainly analyze the location and distribution which includes the ratios of specific cell types and our hypothesis is that fine-tuning the ratios of neuronal cell types may be a powerful evolutionary mechanism for building more efficient circuits and possibly even for distinguishing between human and other animals,” Osten explained in an email.

Humans, he continued, don’t have the largest brains or the most neurons. At one point, spindle neurons were considered unique to humans, but other researchers have shown that great apes, elephants and cetaceans, which is a group that includes whales and dolphins, also have them.

Osten’s hypothesis is that one of the differences is that the ratios of cells of different types built a computational circuit that’s more powerful than the ones in other species.

When he studies mouse brains, Osten collects information across the entire brain. With humans, he explores one cubic centimeter. The human work is just starting in his lab and represents a collaboration with Zsófia Maglóczky from the Hungarian Academy of Sciences at the Institute of Experimental Medicine in Budapest.

Each mouse brain dataset is between 200 gigabytes and 10 terabytes, depending on the resolution Osten uses to image the brain. He can process 10 terabytes of data in about a week.

Osten uses machine learning algorithms that develop with guidance from human experts. This comes from a long-standing collaboration with Sebastian Seung, a professor of computer science at Princeton University.

He suggested that the research has a translational element as well, offering a way to study cellular and wiring elements characteristic of diseases. “We are looking at several of the models that are well established for autism.” He is also planning to write grants to find funds that supports the analysis of brains from people with schizophrenia and Alzheimer’s disease.

The analysis is a promising avenue of research, other scientists said. “It will be extremely interesting to compare the ratio of different cell types in various diseased brains with normal healthy brains, to see if the diseases may preferentially affect certain cell types and why and how,” Zeng explained in an email. “This could be very helpful for us to devise therapeutic means” to treat diseases.

Zeng has known Osten for about seven years. Last year, she began a collaboration using qBrain to quantify cell types.

A current resident of Williamsburg, where his reverse commute is now about 40 minutes, Osten works with a company he and Seung started called Certerra, which provides a rapid analysis of brain activity at different times. The company, located in Farmingdale, has a growing customer base and has a staff of about five people.

As for the recent work, researchers suggested it would help continue to unlock mysteries of the brain. This research is “a basic but important step toward understanding how the brain works,” Zeng added. “This paper provides a new and efficient approach that will be powerful when combined with genetic tools that can label different cell types.”

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