Stony Brook University

Elaine Gross, Christopher Sellers, Crystal Fleming, Miriam Sarwana and Abena Asare speak about race at ERASE Racism forum. Photo by Kyle Barr

In a politically charged time, race is seen as a third-rail issue, one that if touched leads to political headache in the case of a politician or a rough time around the holiday dinner table for everyday folks.

Which is why Elaine Gross, president of Syosset-based ERASE Racism, which wishes to examine and make meaningful change to race relations in New York, said Long Island was the perfect time and place to start meaningful conversations about race and racism, both in the overt and covert displays of prejudice.

“Even though we are becoming more diverse, that doesn’t mean we have what we want going on in our schools,” Gross said. “Long Island is home to 2.8 million people so we’re not a small place, but tremendously fragmented.”

The nonprofit, which was originally founded in 2001, made its first stop at Hilton Garden Inn, Stony Brook University Nov. 29 during a five-series Long Island-wide tour called How Do We Build a Just Long Island? The mission is to start a dialogue about meaningful change for race relations in both Suffolk and Nassau counties. Four panelists, all professors and graduate students at Stony Brook, spoke to a fully packed room about their own research into the subject and took questions from the audience on how they could affect change in their own communities.

Christopher Sellers, history professor and director of the Center for the Study of Inequalities, Social Justice, and Policy, has studied what he described as “scientific racism,” of people who look at the superiority and inferiority of other races as an objective truth, an idea that was born during the enlightenment and colonial period used to justify conquering nations overseas. It’s a form of understanding identity that lives on in many people, Sellers said.

“It’s as old as western society itself,” he said.

Race is an important issue in a county that is very segregated depending on the town and school district. An image created by the nonprofit and compiled with information from the New York State Department of Education shows a district such as Port Jefferson is made up of 80 percent white students, while in the Brentwood school district 79 percent of students are Latino and 12 percent are black.

Panelists argued that racism exists and is perpetuated through local policy. Abena Asare,
assistant professor of Modern African Affairs and History said that racism currently exists in the segregated schools, in lack of public transportation, zoning laws and other land-use policies created by local governments.

“Many of the policies on our island that insulate and produce structural racism are based on a false narrative on what Long Island was, who it is was for, and the fear of where it is going,” Asare said. “Creating new futures requires that we expose the version of the past that justifies or separates an unequal status quo.”

Crystal Fleming, an associate professor of sociology at Stony Brook, spoke about how historically the idea of white supremacy is ingrained in America’s social consciousness, that lingering ideas of one race’s entitlement to security and citizenship over other races have helped perpetuate racist ideas and policy.

“When we talk about systemic racism, it’s not black supremacy, it’s not Native American supremacy, it’s not Asian supremacy, it’s white supremacy,” Fleming said. “We need to be brave and talk frankly about these matters.”

Miriam Sarwana, a graduate student in psychology at Stony Brook, said after the civil rights movement of the 1960s racism did not simply die, but it became subtle, only used in the safety of the home. This is compounded by the lack of interaction between races on a daily basis.

“These biases are influenced by the social, societal and cultural [elements] in our lives, and can be influenced both directly and indirectly,” Sarwana said. “A white adult has little or no interaction with African-Americans, and then starting childhood this person may be exposed to negative images of African-Americans.”

The panelists said that the extreme segregation in school districts has resulted in an even greater disparity of resources and attention for nonwhite races. The issue, Asare said, after the forum, was that the 125 public school districts on Long Island have remained insular, leading to communities becoming disparate and inclusive. She said the best way to deal with this is to consolidate school districts, even along town lines, which could lead to bigger savings for school districts, more resources to less-served districts and allow for better cross-pollination of races between schools.

“The fact that those types of discussions are not normally occurring here speaks to a larger issue, that segregation works for a lot of people around Long Island,” Asare said.

The final Erase Racism forum in this series will be held Dec. 10 at the Radisson Hotel in Hauppauge at 6 p.m. Visit www.eraseracismny.org for more information or to register for the event.

Weisen Shen in front of a twin-otter airplane in the Antarctic during the 2017-18 season. Photo by Zhengyang Zhou

By Daniel Dunaief

Ever sit alone in a house and hear noises you can’t explain? Was that the wind, the house settling (whatever that means) or the cat swatting at the string hanging from the blinds?

Those sounds, which are sometimes inexplicable and are called ambient noise, are often hard to trace, even if we walk around the house and listen outside every room.

Weisen Shen
Photo by John Griffin

For Weisen Shen, an assistant professor in the Department of Geosciences at Stony Brook University, ambient noises deep below the Antarctic continent and elsewhere can be and often are clues that unlock mysteries hidden miles below the frozen surface.

A geoscientist who uses computer programs in his research, Shen would like to study the temperature well below the surface. He developed an in-house code to understand and interpret seismic data.

The speed at which Earth rumbling passes from one area to another can indicate the relative temperature of an area. Seismic activity moves more slowly through warmer rocks and moves more rapidly through colder crust, which has a higher rigidity. According to Shen, these temperature readings can help provide a clearer understanding of how much heat is traveling through the surface of the solid Earth into the ice sheet.

Shen traveled to the Ross Ice Shelf in the 2015-16 season and ventured to the South Pole in the 2017-18 season. He is currently seeking funding to go back to the Antartica. Earlier this year, he published an article in the journal Geology in which he found evidence that the lithosphere beneath the Transantarctic Mountains is thinner than expected.

Shen pointed out that seismic properties aren’t just related to temperature: They can help determine the density of the material, the composition and the existence of fluid such as water. He looks for surface geology and other types of geophysical data to detect what is the dominant reason for seismic structure anomalies. He also uses properties other than speed, such as seismic attenuation and amplitude ratios, in his analysis.

This kind of information can also provide an idea of the underlying support for mountain ranges, which get built up and collapse through a lithographic cycling.

As for ambient noises, Shen explained that they can come from ocean fluctuations caused by a hurricane, from human activities or, most commonly, from the bottom of the ocean, where the dynamic ocean wave constantly pushes against the bottom of the earth. By processing the noises in a certain way, he can extract information about the materials through which the noise traveled.

Shen published an article in the Journal of Geophysical Research in which he discussed a noise source in Kyushu Island in the Japanese archipelago. “The noise is so subtle that people’s ears will never catch it,” he said. “By deploying these very accurate seismic sensors, we will be able to monitor and study all the sources of those noises, not just the earthquakes.”

Studying these lower volume, less violent noises is especially helpful in places like Antarctica, which is, Shen said, a “quiet continent,” without a lot of strong seismic activity. He also uses the images of earthquakes that occur elsewhere, which travel less violently and dramatically through Antarctica.

Shen decided to study Antarctica after he earned his doctorate at the University of Colorado at Boulder. “I have this ambition to get to all the continents,” he said. In graduate school he told himself, “If you ever want to get that work done, you have to crack this continent.”

During his postdoctoral work, Shen moved to St. Louis, where he worked at Washington University in the laboratory of Doug Wiens, professor of Earth and planetary sciences.

In addition to conducting research in Antarctica, Shen collaborated with Chen Cai, a graduate student in Wiens’ lab. Together with other members of the Washington University team, they used seismic data in the Mariana Trench to show that about three to four times more water than previously estimated traveled beneath the tectonic plates into the Earth’s interior.

That much water rushing further into the Earth, however, is somehow offset by water returning to the oceans, as ocean levels haven’t changed dramatically through this part of the water cycle process.

“People’s estimates for the water coming out is probably out of balance,” Wiens said. “We can’t through millions of years bring lots of water through the interior. The oceans would get lower. There’s no evidence” to support that, which means that “an upward revision of the amount of water coming out of the Earth” is necessary. That water could be coming out through volcanoes or perhaps through the crust or gas funnels beneath the seafloor, he suggested.

Wiens praised all the researchers involved in the study, including Shen, whom he said was “very important” and “wrote a lot of the software we used to produce the final images.”

A resident of Queens, Shen lives with his wife Jiayi Xie, who works as a data scientist at Xaxis, a subcompany of the global media firm GroupM. The couple has an infant son, Luke.

Shen grew up in the southwestern part of China. When he was younger, he was generally interested in science, although his particular passion for geoscience started when he was in college at the University of Science and Technology of China, USTC, in Hefei, Anhui, China.

The assistant professor, who teaches a geophysics class at Stony Brook University, currently has two graduate students in his lab. He said he appreciates the support Stony Brook provides for young faculty.

As for his work, Shen is excited to contribute to the field, where he enjoys the opportunity and camaraderie that comes from exploring parts of Earth that are relatively inaccessible. He feels his detailed studies can help change people’s understanding of the planet.

Erase Racism is holding events across Long Island. Photo from Erase Racism website

A Syosset nonprofit and a Stony Brook University department are teaming up to open up a public dialogue pertaining to one of Long Island and America’s oldest societal problems.

ERASE Racism, a regional organization founded in 2001 that advocates for public policy to promote racial equality in housing, education and more, and SBU’s Center for the Study of Inequalities, Social Justice, and Policy, a department founded in 2017 that provides a forum for the promotion of various forms of student and faculty engagement on the same issues, will co-host the first of a series of forums meant to jump start a community conversation on racial inequality.

The series of forums, entitled How Do We Build a Just Long Island? will kick off at the Hilton Garden Inn on the SBU campus Nov. 29 at 6 p.m.

“This whole thing is premised on the fact that everybody can educate themselves,” ERASE Racism President Elaine Gross said in an interview. “It’s not about anyone calling anyone a racist. It’s not a blame and shame kind of thing. Let’s make sure we have all the facts, let’s make sure we understand the context.”

Gross said so far about 400 people have registered to attend the event. She said from the organization’s inception its goal has been to identify institutional and structural racism and seek to educate the public about the history that has led to places like Long Island being so racially segregated today.

“It is embedded — it doesn’t require that all of the players be racist people, or bad people, it only requires that people go along with the business as usual,” she said.

Christopher Sellers, SBU history professor and director of the center, said part of the thinking behind the forums is to frame the conversation in a way for people not exposed to racial inequality or injustice on a daily basis to see barriers and exclusions they may not have viewed as such. He said the goal is to ultimately expand the discussion from the confines of the campus and into the community. He called Long Island the perfect place to begin this dialogue.

“Demographic change causes people to get more defensive and fall back on these racializing tool kits they may have picked up from their own past,” he said, adding that data suggests Long Island has become more racially diverse during recent decades, specifically seeing an increase in those of Hispanic descent.

Sellers said he feels a sense of urgency to begin a wide discussion on racial intolerance despite the perception from many that in the decades since the civil rights movement society has made sufficient progress in creating a just America for all. In “Hate Crime Statistics, 2017” released Nov. 13, the FBI reported a 17 percent increase in incidents identified as hate crimes from 2016 to 2017, with nearly 60 percent of those incidents being motivated by racial or ethnic bias. From 2015 to 2016 there was a roughly 5 percent increase in these incidents. From 2014 to 2015, hate crimes went up by about 7 percent.

“We need as a university to do something, we as academics can no longer sit on our hands,” Sellers said. “This is maybe a more urgent matter than we’ve considered before.”

Gross said the aim of the events is education.

“We didn’t plan to be doing this at a time when the country is so divided and there’s so much overtly biased comments, racist comments being said at the highest levels,” Gross said. “We planned this because we felt that even though with all of the work that we’ve done, we felt that was really needed was a regional public discussion and understanding of how things are connected.”

To register for the event and to get more information on the remainder of the forums — slated for Riverhead, Hempstead, Melville and Hauppauge — visit www.eraseracismny.org.

Students will now be enrolled in the Renaissance School of Medicine at Stony Brook University. Photo from Stony Brook University

The day before Thanksgiving, Stony Brook University showed its gratefulness for the employees of an East Setauket hedge fund firm.

On Nov. 21, Dr. Samuel L. Stanley Jr., SBU’s president, announced that Stony Brook University School of Medicine has been renamed the Renaissance School of Medicine at Stony Brook University. The programmatic name change honors employees of East Setauket-based hedge fund Renaissance Technologies who have donated to SBU through the decades, according to the university. Jim Simons, former SBU math department chair and co-founder of Renaissance Technologies, and his wife, Marilyn, kicked off the donations more than 35 years ago. Since then, more than $500 million has been donated by 111 Renaissance families, according to a press release from SBU.

“By sharing their talents, their time and their philanthropic giving over the years, 111 current and former employees of Renaissance, almost all of whom did not graduate from Stony Brook University, have committed to Stony Brook’s success and have given generously of their time and treasure to advance the mission of New York’s premier public institution of higher education,” Stanley said in a statement. “It is fitting that we name the academic program that has a tremendous impact on so many in recognition of this generosity and vision as the Renaissance School of Medicine.”

Marilyn Simons commended the Renaissance employees for their generosity in a statement.

“Stony Brook University is an important institution in the Long Island community and it’s certainly had a significant impact on Jim’s and my life,” she said. “Support from Renaissance, particularly for the university’s work in the sciences, medical research and the delivery of health care services, has enhanced the university’s medical services to the Long Island community.”

The name change has faced some opposition in the past few months from residents of the surrounding communities, including members of the North Country Peace Group, a local activist group. Members Myrna Gordon and Bill McNulty attended a Stony Brook Council meeting in December 2017. The council, which serves as an advisory board to the campus and SBU’s president and senior officers, gave Gordon, McNulty and another community member the opportunity to discuss their reasons for opposing the name change, according to Gordon. She said eight months ago, the activist group also submitted a petition with 800 signatures protesting the name change to SUNY trustees and Carl McCall, chairman of the board of trustees.

Gordon said in a phone interview the protesters object to some of the ways Renaissance makes its money, including investing in private prison systems. They also took exception to the financial contributions to the campaign of President Donald Trump (R) and alt-right groups by former co-CEO Robert Mercer, who has since stepped down.

Despite the opposition to the new program name, Gordon said she and other NCPG members are proponents of the university and many of them attend educational, cultural and sporting events at the campus on a regular basis.

Andrew Schwartz. Photo courtesy of Stony Brook University

By Daniel Dunaief

In the era of social media, people reveal a great deal about themselves, from the food they eat, to the people they see on a subway, to the places they’ve visited. Through their own postings, however, people can also share elements of their mental health.

In a recent study published in the journal Proceedings of the National Academy of Sciences, Andrew Schwartz, an assistant professor in the Department of Computer Science at Stony Brook University, teamed up with scientists at the University of Pennsylvania to describe how the words volunteers wrote in Facebook postings helped provide a preclinical indication of depression prior to a documentation of the diagnosis in the medical record.

Using his background in computational linguistics and computational psychology, Schwartz helped analyze the frequency of particular words and the specific word choices to link any potential indicators from these posts with later diagnoses of depression.

Combining an analysis of the small cues could provide some leading indicators for future diagnoses.

“When we put [the cues] all together, we get predictions slightly better than standard screening questionnaires,” Schwartz explained in an email. “We suggest language on Facebook is not only predictive, but predictive at a level that bears clinical consideration as a potential screening tool.”

Specifically, the researchers found that posts that used words like “feelings” and “tears” or the use of more first-person pronounces like “I” and “me,” along with descriptions of hostility and loneliness, served as potential indicators of depression.

By studying posts from consenting adults who shared their Facebook statuses and electronic medical record information, the scientists used machine learning in a secure data environment to identify those with a future diagnosis of depression.

The population involved in this study was restricted to the Philadelphia urban population, which is the location of the World Well-Being Project. When he was at the University of Pennsylvania prior to joining Stony Brook, Schwartz joined a group of other scientists to form the WWBP.

While people of a wide range of mental health status use the words “I” and “me” when posting anecdotes about their lives or sharing personal responses to events, the use of these words has potential clinical value when people use them more than average.

That alone, however, is predictive, but not enough to be meaningful. It suggests the person has a small percentage increase in being depressed but not enough to worry about on its own. Combining all the cues, the likelihood increases for having depression.

Schwartz acknowledged that some of the terms that contribute to these diagnoses are logical. Words like “crying,” for example, are also predictive of being depressed, he said.

The process of tracking the frequency and use of specific words to link to depression through Facebook posts bears some overlap with the guide psychiatrists and psychologists use when they’re assessing their patients.

The “Diagnostic and Statistical Manual of Mental Disorders” typically lays out a list of symptoms associated with conditions such as schizophrenia, bipolar disorder or depression, just to name a few.

“The analogy to the DSM and how it works that way is kind of similar to how these algorithms will work,” Schwartz said. “We look at signals across a wide spectrum of features. The output of the algorithm is a probability that someone is depressed.”

The linguistic analysis is based on quantified evidence rather than subjective judgments. That doesn’t make it better than an evaluation by mental health professional. The algorithm would need more development to reach the accuracy of a trained psychologist to assess symptoms through a structured interview, Schwartz explained.

At this point, using such an algorithm to diagnose mental health better than trained professionals is a “long shot” and not possible with today’s techniques, Schwartz added.

Schwartz considers himself part computer scientist, part computational psychologist. He is focused on the intersection of algorithms that analyze language and apply psychology to that approach.

A person who is in therapy might offer an update through his or her writing on a monthly basis that could then offer a probability score about a depression diagnosis.

Linguistic tools might help determine the best course of treatment for people who have depression as well. In consultation with their clinician, people with depression have choices, including types of medications they can take.

While they don’t have the data for it yet, Schwartz said he hopes an algorithmic assessment of linguistic cues ahead of time may guide decisions about the most effective treatment.

Schwartz, who has been at SBU for over three years, cautions people against making their own mental health judgments based on an impromptu algorithm. “I’ve had some questions about trying to diagnose friends by their posts on social media,” he said. “I wouldn’t advocate that. Even someone like me, who has studied how words relate to mental health, has a hard time” coming up with a valid analysis, he said.

A resident of Sound Beach, Schwartz lives with his wife Becky, who is a music instructor at Laurel Hill Middle School in Setauket, and their pre-school-aged son. A trombone player and past  member of a drum and bugle corps, he met his wife through college band.

Schwartz grew up in Orlando, where he met numerous Long Islanders who had moved to the area after they retired. When he was younger, he used to read magazines that had 50 lines of computer code at the back of them that created computer games.

He started out by tweaking the code on his own, which drove him toward programming and computers.

As for his recent work, Schwartz suggested that the analysis is “often misunderstood when people first hear about these techniques. It’s not just people announcing to the world that they have a condition. It’s a combination of other signals, none of which, by themselves, are predictive.”

Stony Brook University representatives and legislators joined Jim and Marilyn Simons, holding scissors, at a ribbon-cutting ceremony at SBU Nov. 1. Photo from Stony Brook University

Stony Brook University is stepping into the future when it comes to cancer research and patient care.

“Imagine what we will accomplish once this building is filled with the pre-eminent doctors and scientists from across campus, the state and the globe.”

— Dr. Samuel L. Stanley Jr.

A ribbon-cutting ceremony was held Nov. 1 to commemorate the completion of construction of the Medical and Research Translation building, where Stony Brook University Cancer Center will be the primary occupant. The eight-level, 240,000-square-foot facility features expanded state-of-the-art space that will be used by clinicians and researchers to discover new cancer treatments, educate students, create more space for patients and family, and more. The building is slated to be opened to patients in January.

At a presentation after the ceremony, SBU President Dr. Samuel L. Stanley Jr. said the MART is the result of public and private funds and donations. Support from Gov. Andrew Cuomo (D), the State University of New York and Empire State Development led to a $35 million NYSUNY 2020 challenge grant. Also, $50 million from a $150 million gift from Jim Simons, founder of Renaissance Technologies, and his wife Marilyn, and $53 million in funds secured by state Sens. John Flanagan (R-East Northport) and Ken LaValle (R-Port Jefferson) added to donations from supporters.

The university president said the MART will bring together national and international experts in various fields including applied mathematics, imaging, chemistry, biology and computer science.

“Imagine what we will accomplish once this building is filled with the preeminent doctors and scientists from across campus, the state and the globe,” Stanley said.

Dr. Kenneth Kaushansky, senior vice president of health sciences and dean of the school of medicine, said the idea of the facility was conceived eight days after his arrival at Stony Brook nine years ago. He said it was envisioned as a catalyst for highly advanced cancer research and a facility to provide outstanding clinical care to patients.

“Because cancer researchers, educators and clinicians would occupy the same building and wait in the same lines for coffee, juice and food, what I’d like to term productive collisions would be inevitable, allowing the MART to serve as an incubator with the very best people to produce and then practice the very best ideas in medicine,” he said.

“With expanded space for patients and families, the MART offers a convenient access to Stony Brook Cancer’s experts, all of them in one location, whether you’re four years old or 84 years old.”

— Dr. Kenneth Kaushansky

Kaushansky said the building is more than medical professionals coming together and brainstorming.

“With expanded space for patients and families, the MART offers a convenient access to Stony Brook Cancer’s experts, all of them in one location, whether you’re 4 years old or 84 years old,” Kaushansky said.

The dean said since 2012 Dr. Yusuf Hannun, director of SBU Cancer Center, has assembled a dream team of researchers, physicians, staff members and educators dedicated to finding cures and compassionate care for SBU patients.

Hannun said the plan was to build a comprehensive cancer center on Long Island that conducts cutting-edge research to understand cancer and then design approaches to predict, diagnose, prevent and defeat cancer.

“The broad scope of activities that we conduct — research, education, clinical trials, prevention, patient care, survivorship and many others — is only possible in a setting of an academic medical center that can support this depth and breadth of activity,” he said.

SUNY Chancellor Kristina Johnson, who battled Hodgkin’s disease nearly 40 years ago, attended the event. As a cancer survivor, Johnson said she was happy to be at the ribbon cutting and wouldn’t be here today if it wasn’t for professionals that developed the treatment she had to undergo.

“I can’t wait to see what innovations are going to come out for the care and treatment of patients to come from the comprehensive team of cross-disciplinary researchers empowered by MART, and how this facility will change the way we educate physician-scientists here at Stony Brook University,” Johnson said.

Marcelo Lucero

REMEMBERING MARCELO LUCERO A DECADE AFTER HIS DEATH

Campus, community members to mark anniversary with Nov. 8 vigil at Stony Brook University

 Ten years to the date of the hate crime killing of Ecuadorian immigrant Marcelo Lucero, students, faculty and community members will gather at Stony Brook University for a night of remembrance and reflection.

“Our Town: Ten Years Later,” an educational vigil, will take place on Thursday, Nov. 8, from 7 to 9 p.m., in the university’s Students Activities Center (SAC) auditorium. Marcelo’s brother Joselo Lucero will address the crowd, along with Patchogue-Medford Schools Superintendent Dr. Michael Hynes and filmmaker Susan Hagedorn.

Six campus partners are sponsoring the vigil: the Undergraduate Student Government (main sponsor); the Hispanic Languages and Literature Dept.; Women’s, Gender and Sexuality Studies Dept.; Center for Civic Justice; Office of Multicultural Affairs; and Campus Residences.

The program will feature the screening of a special one-hour-long edited version of Deputized,Hagedorn’s documentary about the 2008 attack on Lucero by seven teens that intentionally sought Latinos to assault during a night of what they termed “beaner hopping.” A discussion and Q&A session will follow.

Remarks by Dr. Hynes, whose school district includes Patchogue Village, where Marcelo was slain, will begin the evening. The Lucero Award-winning video from the UN Plural+ Youth Video Festival on Migration, Diversity & Social Inclusion will be shown preceding Deputized.

Given the current national climate of division and distrust of immigrants, organizers say this year’s vigil is more important than ever to promote understanding of and respect for cultural differences. However, despite the international attention Marcelo’s fatal stabbing received and resulting calls for improved treatment of immigrants particularly by police, his brother’s story is not “political,” Joselo Lucero stressed.

“This is a human issue,” he said. “This is not about legal or illegal, documented or undocumented. This is about what happened to a human being. That’s what we will be remembering and realizing on November 8th.”

Co-organizer Ian Lesnick, assistant to the president and director of diversity affairs for the Undergraduate Student Government, added that the vigil also provides an opportunity for us “to reflect on ourselves as a society to see how we’ve changed and where we continue to grow.”

Marcelo and a friend were walking near the LIRR tracks in Patchogue when they were attacked by the seven youth. The killing sent shockwaves across Long Island and beyond, generated hundreds of news stories and sparked numerous community dialogues, a play, a novel and a PBS documentary .

The vigil is free of charge and open to the public. Free parking is available in the SAC lot. Upon driving onto the Stony Brook campus, follow signs to the Student Activities Center.

For information, contact 631-258-2016 or ilesnick@stonybrookusc.org.

Gábor Balázsi. Photo by Dmitry Nevozhay

By Daniel Dunaief

An especially hot July day can send hordes of people to Long Island beaches. A cooler July temperature, however, might encourage people to shop at a mall, catch a movie or stay at home and clean out clutter.

Similarly, genes in yeast respond to changes in temperature.

Gábor Balázsi, the Henry Laufer associate professor of physical and quantitative biology at Stony Brook University, recently published research in the Proceedings of the National Academy of Sciences on the effect of temperature changes on yeast genes.

“We are looking at single cells and at genetic systems and we can dissect and understand gene by gene with a high level of detail,” said Balázsi, who used synthetic genetic systems to allow him to dissect and understand how temperature affects these genes.

Understanding the basic science of how genes in individual cells respond to temperature differences could have broad applications. In agriculture, farmers might need to know how genes or gene circuits that provide resistance to a pathogen or drought tolerance react when the temperature rises or falls.

Similarly, researchers using genetically designed biological solutions to environmental problems, like cleanups at toxic spills, would need to understand how a change in temperature can affect their systems.

Lingchong You, an associate professor of biomedical engineering at Duke University, believes the research is promising.

“Understanding how temperature will influence the dynamics of gene circuits is intrinsically interesting and could serve as a foundation for the future,” You said. Researchers “could potentially design gene circuits to program the cell such that the cell will somehow remember its experience with the fluctuating temperatures,” which could provide clues about the experience of the cell.

Balázsi suggested the goal of his work is to understand the robustness of human control over cells in nonstandard conditions.

While other researchers have explored the effects of gene expression for hundreds of genes at different temperatures, Balázsi looked more precisely at single genes and human-made synthetic gene circuits in individual cells. He discovered various effects by inserting a two-gene circuit into yeast.

At the whole-cell level when temperatures rise from 30°C to 38°C, some cells continued growing, albeit at a slower rate, while others stopped growing and started to consume their proteins.

For the second type of cells, changing temperatures can lead to cell death. If the temperature comes down to normal levels soon enough, however, researchers can rescue those cells.

“How this decision happens is a question that should be addressed in the future,” Balázsi said.

While the dilution of all proteins slows down, the chemical reactions in which they participate speed up at a higher temperature, much like children who become more active after receiving sugar at a birthday party.

At another level, certain individual molecules change their movement between conformations at a higher temperature. Proteins wiggle more between different folding conformations even if they don’t change composition. This affects their ability to bind DNA.

Balázsi said he is fortunate that he works through the Laufer Center for Physical and Quantitative Biology, which partly supported the work, where he was able to find a collaborator to do molecular dynamic simulations. Based on the pioneering experiments of postdoctoral fellow Daniel Charlebois, with help from undergraduate researcher Sylvia Marshall, the team collected data for abnormal behaviors of well-characterized synthetic gene circuits. They worked with Kevin Hauser, a former Stony Brook graduate research assistant, who explained how the altered conformational movements affected how the protein and cells behaved.

The way proteins fold and move between conformations determines what they do.

Gábor Balázsi with his daughter Julianna at West Meadow Beach
Photo from Gábor Balázsi

Taking his observations and experiments further, Balázsi found that proteins that were unbound to a small molecule didn’t experience a change in their conformation. When they were linked up, however, they demonstrated a new behavior when heated. This suggests that understanding the effects of temperature on these genetic systems requires an awareness of the proteins involved, as well as the state of their interaction with other molecules.

While Balázsi explored several ways temperature changes affect the yeast proteins, he acknowledged that other levels or forces might emerge that dictate the way these proteins change.

Additionally, temperature changes represent just one of many environmental factors that could control the way the genetic machinery of a cell changes. The pH, or acidity, of a system might also change a gene or group of genes.

A main overarching question remains as to how much basic chemical and physical changes combine with biological effects to give predictable, observable changes in the behaviors of genes and living cells.

Balázsi may test other cell types. So far, he’s only looked at yeast cells. He would also like to know the order in which the various levels of reactions — from the whole cell to the molecular level — occur.

He is interested in cancer research and possibly defense applications and would like to take a closer look at the way temperature or other environmental factors impact human disease processes and progression or think about their relevance for homeland security or biological solutions to renewable energy.

Balázsi recognizes that he and others in this field have numerous hurdles to overcome to find acceptable appreciation for the application of synthetic gene circuits.

“It’s not so simple to engineer these cells reliably,” he said. “Some roadblocks need to be eliminated to convince people it’s feasible and useful.”

Balázsi suggested that the field of virology might benefit from pursuing some of these research questions. Viruses move from the environment or even from other hosts into humans. Avian influenza, for example, can begin inside a bird and wind up affecting people. These viruses “might have different expression patterns in birds versus humans,” he said.

Ultimately, he added, this kind of scientific pursuit is “multipronged and the applications are numerous.”

Above, Brian Colle, who enjoys surf fishing, with a false albacore that he caught at the Shinnecock Inlet. Photo by B. Colle

By Daniel Dunaief

In August of 2014, Islip experienced record rainfall, with over 13 inches coming down in a 24-hour stretch — more than the typical rainfall for an entire summer and a single day record for New York state. The rain required emergency rescues for motorists whose cars suddenly died after more than 5 inches of rain fell in a single hour.

What if, however, that rain had fallen just 50 miles west, in Manhattan, where the population density is much higher and where people travel to and from work on subways that can become flooded from storms that carry less precipitation?

An image of an ice crystal Colle examined during a Nor’easter. Image from B. Colle

Brian Colle, professor of atmospheric sciences and director of the Institute for Terrestrial and Planetary Atmospheres at the School of Marine and Atmospheric Sciences at Stony Brook University, is part of a group that is studying flood risks in the New York metro area during extreme storms that could bring heavy rains, storm surge or both. The team is exploring mitigation strategies that may help reduce flooding.

“The risk for an Islip event for somewhere in the NYC-Long Island area may be about one in 100 years (but this is being further quantified in this project), and this event illustrates that it is not a matter of whether it will occur in NYC, but a matter of when,” Colle explained in a recent interview.

The group, which is led by Brooklyn College, received $1.8 million in funding from New York City’s Department of Environmental Protection and the Mayor’s Office of Recovery & Resiliency. It also includes experts from The New School, the Stevens Institute of Technology and Colorado State University.

The co-principal investigators are Assistant Professor Brianne Smith and Professor Jennifer Cherrier, who are in the Department of Earth and Environmental Sciences at Brooklyn College–CUNY.

Smith, who had worked with Colle in the past, had recruited him to join this effort. They had “been wanting to do studies of flooding for New York City for a long time,” Smith said. “When the city came out with this” funding for research, Colle was “the first person I thought of.”

Malcolm Bowman, a distinguished service professor at Stony Brook University, holds his colleague, whom he has known for a dozen years, in high regard. Colle is “a leading meteorologist on regional weather patterns,” he wrote in an email. 

Colle is interested in the atmospheric processes that produce rainfall of 2 or 3 inches per hour. “It takes a unique part of the atmosphere to do that,” he said. The three main ingredients are lots of moisture, lift along a wind boundary, and an unstable atmosphere that allows air parcels, or a volume of air, to rise, condense and produce precipitation.

Representatives from the local airports, the subway systems and response units have been eager to get these predictions, so they can prepare mitigation efforts.

Brooklyn College – CUNY project co-leads Brianne Smith (left) and Jennifer Cherrier at Grand Army Plaza in Brooklyn in early September. Photo by John Mara

This group has taken an ambitious approach to understanding and predicting the course of future storms. Typically, scientists analyze storms using 100- to 200-kilometer grid spacing. In extreme rainfall events during coastal storms, scientists and city planners, however, need regional spacing of 20 kilometers. Looking at storms in finer detail may offer a more realistic assessment of local precipitation.

Researchers are anticipating more heavy rainfall events, akin to the one that recently caused flooding in Port Jefferson.

A warmer climate will create conditions for more heavy rains. Water vapor increases about 6 to 7 percent for every degree increase in Celsius. If the climate rises two to four degrees as expected by the end of the century, this would increase water vapor by 13 to 25 percent, Colle said.

The group includes experts from several disciplines. “Each of the scientists is highly aware of how integrative the research is,” Cherrier said. The researchers are asking, “How can we provide the best scientific foundation for the decisions” officials need to make. If, as predicted, the storms become more severe, there will be some “hard decisions to make.”

Smith suggested that a visible project led by women can encourage the next generation of students. Women undergraduates can appreciate the opportunity their female professors have to lead “cool projects,” she said. 

Raised from the time he was 4 in Ohio, Colle said he was a “typical weather geek” during his childhood. The blizzard of 1978 fascinated him. After moving to Long Island in 1999, Colle used to sit in a weather shed and collect ice crystals during nor’easters. He would study how the shape of these crystals changed during storms. An avid surf fisherman, Colle said there is “not a better place to observe weather” than standing near the water and fishing for striped bass, fluke, bluefish and false albacore. A resident of Mount Sinai, Colle lives with his wife Jennifer, their 16-year-old son Justin and their 13-year-old son Andrew.

As for his work on flood risks around the New York metro area, Colle said the group is producing monthly reports. The effort will end in December. “The urgency is definitely there,” he acknowledged. Heavy rainfall has increased the need to understand rain, particularly when combined with surge flooding.

A transportation study written over a decade ago describes storm surge and rainfall risk. That study, however, included a prediction of 1 to 2 inches of rainfall an hour, which is far less than the 5 inches an hour that hit Long Island in 2014.

“Once you start seeing that, there’s a lot of people who are nervous about that risk and want to get a best estimate of what could happen,” Colle said.

Cherrier described New York City as being “quite progressive” in gathering information and formulating data. “The city wants to be prepared as soon as possible.”

Stony Brook University President Dr. Samuel L. Stanley Jr. delivers his ninth state of the university address Oct. 3. Photo from Stony Brook University

As Stony Brook University President Dr. Samuel L. Stanley Jr. looks confidently to the future, the school’s budget deficit is still at the forefront of his mind.

On Oct. 3, Stanley delivered his ninth state of the university address on the Staller Center’s main stage to an auditorium full of faculty, staff, students and elected officials. During the speech, which lasted about an hour, the university president touched on several topics including enrollment growth, Stony Brook Medicine’s future and financial woes and successes — like the university’s positive economic impact on Long Island.

When it comes to tackling the budget deficit, Stanley did not specify the exact amount but said there is more work that needs to be done to lessen the financial shortfall. He said a hiring freeze still holds for 2018-19 because nothing has changed externally as the university has not received an increase of state support since 2010. He said fee increases and enrollment growth has helped alleviate some of the financial burdens, and the university is actively communicating with the state to seek an increase in allocations.

Stanley touted SBU’s presence as a driver for the local economy, citing about $7.2 billion generated from the hospital’s research; people hired and contracted; start-up companies involved with SBU’s incubator; and purchases of students and faculty in the area, the president said.

“We always take these things with a little grain of salt, but I think it’s an important thing that we need to talk about because again the state puts a significant investment into Stony Brook University,” he said. “We appreciate the investment we get from the state, but it’s really nice to talk about the return on that investment from the state.”

The university also saw positive results from The Campaign for Stony Brook fundraising efforts, which raised $630.7 million. He said many people ask him why money can’t be taken from those funds to help with the school’s budget deficit.

“Ninety-eight percent of that money raised is directly allocated to specific goals that our donors have on campus,” he said, adding the funds are usually put toward scholarships, endowed professorship, research projects or a specific campus building.

Stanley said the four-year graduation rate for the class entering in 2014 has reached 62 percent, which signifies a 17-point jump from a 45 percent graduation rate for the class entering in 2007. Among the factors he credited for the success is the Finish in 4 Grants Program. Initiated in spring 2015, the program assists students in good standing who are about to complete their studies but are confronted with personal circumstances that prevent it.

“We want to continue to build on this momentum, but it’s going to be important that we work very hard and continue to find the resources to support this very important program,” he said.

Stanley said a significant part of the university’s budget, $2.28 billion, is for Stony Brook Medicine.

“We are the destination, I believe, for quality care on Long Island,” he said. “We’re the only provider of a level one trauma center for Long Island. We have the only children’s hospital in Suffolk County.”

In the next few months, Stony Brook University Hospital will be opening the Medical and Research Translation building with a state-of-the-art cancer center, Stony Brook Children’s and Hospital Pavilion, and the Phillips Family Cancer Center in Southampton.

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