Stony Brook University SUNY Korea

June 3, 2021 STONY BROOK, NY, June 3, 2021 – A novel urine screening test that uses the protein Keratin 17 (K17) as a biomarker to detect new or recurrent bladder cancer may change diagnostics for a certain form of the disease called urothelial carcinoma (UC). The methodology behind the test stems from research at Stony Brook University led by Kenneth Shroyer, MD, PhD. The findings are reported in a paper published in the American Journal of Clinical Pathology.  Some 81,000 cases of bladder cancer are diagnosed in the United States each year according to the American Cancer Society. Accurate detection of bladder cancer, or urothelial carcinoma (UC), is often difficult, expensive and involves invasive testing. Going forward, this new method, based on the detection of K17 in urine specimens, could help guide treatment by improving diagnostic accuracy. “It is important to find new biomarkers to more accurately detect UC since standard methods used in most cytology labs are based primarily on microscopic details that do not always clearly distinguish cancer from benign cells,” explains Dr. Shroyer, the Marvin Kuschner Professor and Chair of Pathology at the Renaissance School of Medicine at Stony Brook University and inventor of the K17 test. Previously, Dr. Shroyer and his colleague, Dr. Luisa Escobar-Hoyos (an Assistant Professor at Yale), co-directed a team of Stony Brook University students and collaborators to demonstrate that K17 is a highly sensitive and specific biomarker for UC in tissue biopsy and surgical specimens. The current published study builds on these findings to show that K17 testing could also be performed as a non-invasive test on urine specimens. Using various urine sample sets, the Stony Brook team found that the urine K17 test detected UC in 35/36 (97 percent) of cases that were confirmed by biopsy, including 100 percent of cases with high-grade UC. From these results and other findings based on the testing, the authors conclude that K17 testing is a highly sensitive and specific diagnostic test for initial screening and for detection of recurrence across all grades of UC. Dr. Shroyer and his colleagues believe the potential of this test as a non-invasive way to detect UC will help to transform not only diagnostic practices but earlier treatment intervention and prognosis of UC. The K17 test is being developed commercially by KDx Diagnostics, Inc., a start-up biotech company, which has a license with The Research Foundation for The State University of New York. Recently, KDx has been awarded a breakthrough device designation from the Food and Drug Administration for its assay test with K17. For years, the Shroyer lab, in collaboration with Dr. Luisa Escobar-Hoyos, has been exploring K17 as a biomarker for various cancers, including UC and pancreatic cancer. Furthermore, the research team continues to advance the understanding of how K17, once thought to be only a structural protein, fundamentally impacts numerous hallmarks of cancer. Click here to read the original article

June 3, 2021 STONY BROOK, NY, June 3, 2021 —Stony Brook University Heart Institute is now offering its patients the latest generation of the Watchman FLX™ device, which provides protection from strokes for people who have atrial fibrillation (AFib), a type of arrhythmia or irregular heartbeat, that is not caused by a heart valve problem. Stony Brook is one of a select number of sites in New York State to offer the new Watchman FLX device. The procedure, which closes off the part of the heart where 90% of stroke-causing clots come from, will be done in Stony Brook University Hospital’s new Advanced Multifunctional Cath/EP Lab. The large, 845-square-foot multi-functional laboratory has been carefully designed and outfitted with state-of-the-art technology to allow the Heart Institute physicians to perform a full range of procedures. People with AFib, the most common type of heart rhythm disorder, have an increased risk of stroke by 5 times on average. Blood thinners are often prescribed to help prevent strokes but “some experience bleeding problems or have other reasons why blood thinners aren’t the best option,” explains Eric Rashba, MD, Director, Heart Rhythm Center at Stony Brook Heart Institute. The Watchman device, which is about the size of a quarter, provides an alternative to the lifelong use of blood thinners (anticoagulants) for people with AFib by blocking blood clots from leaving the heart and possibly causing a stroke.    The design of the newer, Watchman FLX device used by the Heart Institute offers significant advantages to the patient, including:   - Advanced safety due to the new framing of the device that allows for more long-term stability and a more complete seal - Enhanced procedural performance that allows the physician to better maneuver and position the device during the procedure - A broader size range to permit treatment of a wider range of patient anatomies    “At the Stony Brook Heart Rhythm Center, in the hands of our expert team, we are excited to bring this latest innovation to effectively provide protection equivalent to anticoagulants for preventing strokes and avoiding the risk of serious bleeding,” said Dr. Rashba. “It has saved lives and improved my patients’ quality of life.”   Click here to read the original article

June 2, 2021 More than 200 Stony Brook University administrators, faculty, staff and students participated in the May 5 virtual event, “Breaking Silence: A Public Forum on Anti-AAPI Racism.” The forum was held in response to the escalating violence, discrimination and harassment directed at Asians and Asian Americans, and in honor of Asian American and Pacific Islander (AAPI) Heritage Month, which recognizes the contributions and influence of Asian Americans and Pacific Islander Americans to the history, culture, and achievements of the United States. President Maurie McInnis opened the forum, saying, “I know that it is incredibly important that we take the time, not just this month, but year-round to talk about the pressures and prejudices that the AAPI community faces, and importantly, how we at Stony Brook University can respond to and support our colleagues and friends. We at Stony Brook are committed to ensuring that this university is always a place where the members of the AAPI community are supported, protected, and listened to.” Other remarks were delivered by Vice President for Equity and Inclusion and Chief Diversity Officer Judith Brown Clarke, Vice President for Student Affairs and Dean of Students Rick Gatteau, Dean of the College of Arts and Sciences Nicole Sampson, Professor of Applied Linguistics and Director of the Center for Multilingual and Intercultural Communication (MIC) Agnes He, and New York State Senator John Liu of Queens. He served as the event emcee. The forum was moderated by E.K. Tan, department chair, and Rosabel Ansari, interim graduate director, of the Department of Asian and Asian-American Studies. Forum participants spoke to denounce the scapegoating of Asian Americans for national crises, examined systemic racism against Asians and other minority groups in United States history, and promoted building anti-racist allyship. The event was held on Zoom and was open and free to all. Two videos were presented, created by Nerissa S. Balce, associate professor of Asian-American Studies, and Gary Mar, professor in the Department of Philosophy. Other faculty members who spoke to the history and effects of discrimination against Asian Americans included: James Mimura, Department of History; Crystal Fleming, Departments of Sociology and African Studies; Lori Flores, Department of History, and Charles Robbins, director of the Center for Changing Systems of Power. Student speakers included Judy Le and Khadija Saad. An open discussion was held among the participants, moderated by He and Heejeong Song, director of the Program in Korean Studies. Various on-campus and other resources were posted, questions were asked, personal experiences were shared and solutions proposed. The event was sponsored by the Department of Asian and Asian American Studies, the Center for Korean Studies, the Center for Multilingual and Intercultural Communication, the Japan Center at Stony Brook and the Mattoo Center for India Studies. The event was also co-sponsored by the Asian American Center Bridge, the Center for Changing Systems of Power, the Charles B. Wang Center, the College of Arts and Sciences, the Institute of Globalization Studies, the Office of the Dean of Students and the Office of Multicultural Affairs. Click here to read the original article

May 26, 2021 STONY BROOK, NY, May 26, 2021 – The accuracy of weather forecasting decreases with each additional day of forecasting and is limited in accuracy at two weeks. Now a new study published in Nature Communications and led by Hyemi Kim, PhD, Associate Professor in the School of Marine and Atmospheric Sciences (SoMAS) at Stony Brook University, highlights a way to improve weather forecasts beyond two weeks by using machine learning. Accurate weather forecasting has become increasingly important to society because of its socioeconomic value due to globalization, trade, travel, and the needs of policymakers and others such as risk managers. Reliable forecasts for weather conditions three-to-four weeks away (called the subseasonal range) can provide vital information about hazardous weather threats such as floods and heat waves. Professor Kim and colleagues focused on a phenomenon known as the Madden-Julian oscillation (MJO), a belt of thunderstorms that starts over the equatorial tropical Indian Ocean and moves slowly eastward toward the central Pacific Ocean, in a repetitious manner each year every 40 to 50 days. Scientists have used MJO as a key tool for three-to-four-week weather forecasting. However, computer modeling has not been able to simulate all aspects of MJO and therefore extended-range forecasts based on MJO information has a larger margin of error. The team combined state-of-the-art weather forecast models and observations with a machine learning process (a Deep Learning bias correction using all of the data) to forecast the MJO. With this Deep Learning bias correction, forecast errors in the MJO averaged over four weeks reduced by 80~90 percent. Professor Kim explains that computer models used for forecasting lose accuracy significantly when models try to reproduce MJO that crosses the Maritime Continent and moves eastward. Because of this, more model biases occur and predictions for global weather beyond two weeks becomes difficult. “Our study demonstrates that machine learning substantially reduces the MJO forecast errors from models, and this will help improve global extended range forecasts,” says Professor Kim. “Because we created a simple approach with machine learning, this method can be implemented into operational forecasts that are currently used for two-week weather forecasting and longer.” The researchers plan to apply their machine learning technique to test ways to improve forecasts of extreme weather events, such as hurricanes or heat waves in New York. The research was supported in part by the National Science Foundation (grant AGS-1652289). Click here to read the original article

May 24, 2021 On July 3, 2001, a research paper co-authored by Carol Carter, professor in the Department of Microbiology and Immunology at the Renaissance School of Medicine at Stony Brook, and a team of fellow researchers, was published. Its findings would open a new field of investigation into how pathogens escape from infected cells and reveal new opportunities for anti-viral drug development. This year marks the 20th anniversary of the discovery outlined in that paper, "Tsg101, a homologue of ubiquitin-conjugating (E2) enzymes, bind the L domain in HIV type 1 Pr55(Gag)." David Thanassi, professor and chair of the Department of Microbiology and Immunology, cites Carter’s work as an example of the transformative power of research in real-world applications. “The discovery described 20 years ago in Carol’s paper illustrates the power of basic research to generate unexpected insights and open new avenues for the development of therapeutic approaches to combat viral and other diseases,” Thanassi said. “It is particularly relevant to celebrate this milestone achievement now, given the ongoing COVID-19 viral pandemic. In the search for new treatments, many researchers are pursuing the now-accepted strategy, as embodied by Carol’s work, of targeting cellular factors to develop antiviral measures.” “I had come home from a meeting in the late 1990’s when the HIV pandemic was raging, much like COVID-19 is doing now, but with abysmal antivirals and no vaccine on the horizon,” Carter recalled. “The National Institute of Health (NIH) leadership said to researchers, ‘You need to come up with some strategies to circumvent rapidly emerging drug-resistance.’” As the HIV crisis raged, the World Health Organization (WHO) estimated that by 1999, 33 million people were living with HIV worldwide, and that 14 million had died of AIDS. The same year, then-president Bill Clinton declared HIV/AIDS a threat to U.S. national security and issued an executive order to assist developing countries in importing and producing generic HIV treatments. (UNAIDS, a United Nations program dedicated to worldwide HIV and AIDS response, estimates that 78 million people have become infected with HIV and 35 million have died from AIDS-related illnesses since the first cases were reported more than 35 years ago.) “Drug-resistance was emerging as a major threat because there were very few good drugs on hand,” said Carter. “It struck me that this was the time to entertain an idea that would have been laughed out of the room at an earlier time: the concept of targeting cellular instead of viral encoded gene products.” Carter said the latter puts pressure on viral evolution to select for resistant variants that can evade the drugs, a concern that is less likely to apply to cellular gene products. “Viruses exploit cells,” explained Carter. “Cells don’t make, maintain or change gene products for the convenience of the virus.” Stony Brook’s laboratory screened a library of “house-keeping genes” for any that were recognized by HIV, identified several, and focused on one called Tsg101 that showed itself early on to be differentially employed by the virus and host. In uninfected cells, Tsg101 plays an instrumental role in sending proteins the cell no longer wants to the “garbage pail,” compartments where such proteins are degraded. For example, Tsg101 ensures that proteins that signal continuous cell growth, as occurs in cancers, are removed from the cytoplasm. In contrast, in HIV-infected cells, Tsg101 is recruited to sites of virus assembly at the cell periphery. There, it still facilitates removal of the assemblages from the cytoplasm, however this recruitment permits the virus to exit into the extracellular space instead of a degradative chamber. Tsg101 stands for ‘Tumor Suppressor Protein #101.  “It was the 101st gene product reported to the Protein Data Bank with that description and initially thought to suppress tumor growth,” Carter said. “Learning that produced an ‘aha!’ moment because experiments that we had done by that point were indicating that HIV needed Tsg101 to get viral particles out of the cell and because we also knew HIV did not cause cancer. We’re still working on this, but the 20-year milestone demonstrates that HIV’s recruitment of Tsg101 was a great forecaster of the existence of virus-host interactions feasible to target for anti-viral drug development. Patents describing our translational effort have been granted or are pending.” In football terms, Tsg101 is the “quarterback” for the cellular team effort, also known as the ESCRT (endocytic sorting complexes required for trafficking) machinery that recognizes cargo coming into the cell and directs it to the proper subcellular destination, or “end zone.” Carter said that several laboratories both in the U.S. and around the globe are working on the ESCRT machinery and have established that several human viral pathogens encode L domains to recruit Tsg101 and depend on ESCRT for virus budding from cells. “Some labs are doing exquisite structural characterization of the ESCRT machinery components,” said Carter. “At this point, it has been discovered that ESCRT machinery is evolutionarily conserved from yeast to man. All species encode in their genomes identical or similar Tsg101 sequences that have remained essentially unchanged throughout evolution. This conservation indicates that the Tsg101 protein is unique and essential. It plays critical roles in cell division and neuronal cell pruning. Defects in the gene are embryonically lethal.” “This finding changed the course of the field and changed the course of the lab’s research,” said James Hurley, a structural biologist at Berkeley and one of the lead investigators of ESCRT machinery function. “I don’t think any other single paper has had as much impact on our lab’s research direction.” Hurley and Carter served together on National Institutes of Health (NIH) scientific advisory committees. Carter describes her research as both a rewarding adventure and a never-ending learning experience. “It’s been a fantastic journey,” said Carter. “Some of our compounds developed against HIV are able to inhibit replication of other human pathogens, including SARS CoV-2. It would be great if any of them proved to be useful therapeutics.” — Robert Emproto Click here to read the original article

May 18, 2021 A national team of researchers including Ira S. Cohen, MD, PhD, from the Renaissance School of Medicine at Stony Brook University, has identified a compound that prevents the lengthening of the heart’s electrical event, or action potential, which can cause a lengthening of the EKG’s Q-T interval and a dangerous and sometimes deadly arrhythmia called Torsades de Pointes. Many drugs that are effective against cancer, infections and other diseases, can induce a lengthening of the heart’s action potential as an adverse side effect, thus rendering these drugs unsafe or with risks outweighing their benefits for patients. This discovery may lead to a way to halt this dangerous side effect of commonly used drugs. The findings are published this week in PNAS. According to the American Heart Association, heart arrythmias contribute to about 200,000 to 300,000 sudden deaths a year, more than annual deaths from stroke, lung cancer or breast cancer. The drugs in question, as well as several that have been pulled from the market, cause a prolongation of the QT interval of the ECG (acquired Long Q-T Syndrome). Through both computational and experimental validation, the research team identified a compound named C28. They found that C28 not only prevents or reverses Q-T prolongation, it also does not cause any change on the normal action potential when used alone. The research demonstrates a significant step toward safer use and expanded therapeutic efficacy of certain medicines when taken in combination with C28. “These findings could prove ground-breaking in the effort to make some cancer drugs safer and bring other drugs back into the marketplace,” said Dr. Cohen, SUNY Distinguished Professor in the Department of Physiology and Biophysics, and Director of the Institute for Molecular Cardiology. “With many of these medications, there is a concentration of the drug that is acceptable, but at higher doses, it become dangerous. If C28 can eliminate the danger of QT prolongation, then these drugs can be used at higher concentrations, and in many cases, they can become more therapeutic.” Dr. Cohen, a renowned electrophysiologist, discovered components related to Long Q-T syndrome and has been researching the issue for decades in his Stony Brook laboratory. He discovered the steady state Na current as well as its slowly inactivating component. Together, these two currents are called persistent Na current. In collaboration with Richard Lin, MD, and Zhongju Lu, MD, PhD, he demonstrated that the persistent sodium current is a major cause of the dangerous Q-T prolongation in acquired Long Q-T syndrome. His lab includes investigations into the structure and function of potassium ion channels in the heart, initial research that has helped lead the research team to the identification of C28. Jianmin Cuil, PhD, co-author, head of the research team and Professor of Biomedical Engineering in the McKelvey School of Engineering in Washington University in St. Louis, worked previously with Dr. Cohen on cardiac arrhythmias as a graduate student at Stony Brook University from 1986 to 1994. The research team also includes Xiaoqin Zou, PhD, Professor of physics, biochemistry, and a member of the Dalton Cardiovascular Research Center and Institute for Data Science and Informatics at the University of Missouri-Columbia. The Methodology The team selected a specific target, IKs, for this latest work because it is one of the two potassium channels that are activated during the action potential: IKr (rapid) and IKs (slow). They wanted to determine if the prolongation of the QT interval could be prevented by compensating for the change in current that induces the Long QT Syndrome by enhancing IKs. They identified a site on the voltage-sensing domain of the IKs potassium ion channel that could be accessed by small molecules. Zou and colleagues used the atomic structure of the KCNQ1 unit of the IKs channel protein to computationally screen a library of a quarter of a million small compounds that targeted this voltage-sensing domain of the KCNQ1 protein unit. To do this, they developed software called MDock to test the interaction of small compounds with a specific protein in silico, or computationally. One by one, Zou and her lab docked the potential compounds with the protein KCNQ1 and compared the binding energy of each one. They selected about 50 candidates with very negative, or tight, binding energies. Cui and his lab then identified C28 using experiments out of the 50 candidates identified in silico by Zou’s lab. Dr. Cohen and colleagues tested the C28 compound in ventricular myocytes from a small mammal model that expresses the same IKs channel as humans. They found that C28 could prevent or reverse the drug-induced prolongation of the electrical signals across the cardiac cell membrane and minimally affected the normal action potentials at the same dosage. They also determined that there were no significant effects on atrial muscle cells, an important control for the drug’s potential use. While the researchers emphasize that C28 needs additional verification and testing, there is tremendous potential for this compound or others like it to help change cancer therapeutics as well as turn second line drugs into first-line drugs and return others previously taken off the market because of Q-T prolongation back onto the market. Click here to read the original article

May 12, 2021 Scientists at Stony Brook University, the University of Vermont and Dartmouth College have been studying mercury uptake into the food chain during the winter, and how mercury uptake may change in the future, as climate conditions change. The study, which was awarded $149,930 over two years by the Lake Champlain Sea Grant, began in May 2020 and will continue through February 2022, according to Roxanne Karimi, an adjunct assistant professor at Stony Brook University’s School of Marine and Atmospheric Sciences (SoMAS). Scientists worked through the pandemic to find out what happens to mercury, a common contaminant found in fish, as the fish food chain continues to operate during the winter. They have been collecting samples from Lake Champlain near the U.S.-Canadian border — at St. Albans Bay and Mississquoi Bay — attempting to find out whether mercury changes in chemical form and concentration in the water, lake sediments, and organisms that are in low in food chain, such as mussels. The information will indicate whether mercury is readily taken up into the food chain, including fish, during the winter compared to other seasons. “So far, we have found that methylmercury, the more toxic and biologically available form of mercury, occurs in the water — in dissolved form — in concentrations that are similar to those in other seasons,” Karimi said. “At this point, it is too early to tell whether there is a consistent pattern, or whether winter concentrations are consistently higher or lower than in other times of year.” Karimi noted that the predominant assumption was that mercury bioavailability decreases in winter due to lower temperatures, but this has not been adequately studied. “So far, our preliminary results counter that assumption, and our project will see how it ultimately holds up,” she said. “We will also examine how changes in winter climate conditions, such as changes in temperature and ice cover, might enhance or diminish mercury availability and uptake into the food chain in the future.” The scientists will also use data from the field to predict how fish mercury levels will change with climate. Key to answering this question is the ice cover during the winter, which is expected to decrease in thickness and duration as the climate warms. These factors influence how mercury and lake food chains function, and whether future climate conditions will enhance or diminish mercury buildup in fish in the future. The results from this project will provide the information necessary to predict changes in fish mercury levels, overall health value for human consumption, and inform fish monitoring and advisory policies. Karimi is the lead and sole investigator at Stony Brook, while SoMAS colleague Maureen Murphy provides outreach on the human health risks of mercury in fish to the public. The co-investigator is Andrew Schroth from Vermont, while Vivien Taylor at Dartmouth provides research support.   Click here to read the original article

May 7, 2021 Last Fall, the Office of the Vice President for Research, (OVPR) in partnership with the Institute for Engineering-Driven Medicine (IEDM) and the Clinical and Translational Science Center (CTSC) at Stony Brook University (SBU) launched the COVID-19 Research Collaboration Series. Each session focused on developing collaborations between researchers and included two talks about active COVID-19 research projects at Stony Brook University with an opportunity for discussion following the presentations. The series was announced and managed by the Office of Proposal Development (OPD) after confirming faculty interest in a series focused on collaborations for COVID-19 research projects. For each session, OPD paired two researchers around a common thematic discussion topic. The first session was held on November 5, 2020, and was followed by eight additional sessions, scheduled once every 2-4 weeks. The series concluded on April 29, 2021 with a special talk by guest speaker Dr. Jason McLellan from The University of Texas at Austin. “We launched this series as a follow up to a special initiative COVID-19 seed grant program to draw attention to the critical research that is addressing urgent healthcare challenges and the far-reaching social impacts of the pandemic in real time. Stony Brook University researchers are making incredible scientific advances in this space, and increasing collaborations are key to the continued progress of their research,” said Dr. Richard Reeder, Vice President for Research. The program received a terrific response from the Stony Brook University research community, with faculty participants from the College of Arts and Sciences, the College of Business, the College of Engineering and Applied Sciences, the School of Dental Medicine, the School of Health Technology and Management, the School of Nursing, the School of Medicine, and the School of Social Welfare. Seventy-two SBU faculty members registered for at least one session in the fall semester, and 80 SBU faculty members registered for the spring semester sessions. A few of the sessions were open to faculty from other State University of New York (SUNY) institutions and about 50 external faculty participated throughout the series. “Modern science is often done at the interfaces between traditional fields, especially for challenging problems like COVID-19. This series made it much easier to navigate the impressive breadth of research at Stony Brook and find collaborators with similar goals but complementary skills,” said Dr. Carlos Simmerling, Marsha Laufer Professor of Physical & Quantitative Biology. Recordings of select presentations are available for viewing on OPD’s Stony Brook Research Youtube Channel. Below is the full list of COVID-19 Research Collaboration Series sessions: Breaking Down COVID-19Thursday, November 5, 2020Talk 1: Computational models of the SARS-CoV-2 spike glycoprotein suggest possible routes to viral inactivation, Dr. Carlos SimmerlingTalk 2: Accelerating nanobody discovery to target SARS-CoV2, Dr. Ed LukVIDEO The Impact of COVID-19 on CommunitiesThursday, November 19, 2020Talk 1: The COVID-19 Pregnancy Experiences (COPE) Study: a prospective program of research on pandemic stress, perinatal stress, and their impacts on women and children, Dr. Heidi PreisTalk 2: Disability in the Time of COVID-19, Dr. Brooke EllisonVIDEO Predicting Disease Spread and SeverityThursday, December 10, 2020Talk 1: Classification and Severity Progression Measure of COVID-19 Patients Using Proteomic and Metabolomic Sera, Dr. Pawel PolakTalk 2: Monitoring novel coronavirus in sewage as an early warning system to detect hidden outbreaks and track disease prevalence in communities, Dr. Arjun VenkatesanVIDEO Developing COVID-19 TechnologiesMonday, December 14, 2020Talk 1: AI-enabled lung analyzer for Detection and Characterization of COVID-19, Dr. Jerome Liang VIDEOTalk 2: Personal smart phone-integrated virus sensors and mobile app for rapid and accurate saliva screening and option to share results with businesses before entering common space, Dr. Matthew Jacobs VIDEO Computational Approaches to Study COVID-19Thursday, January 28, 2021Talk 1: Meta Analysis of COVID-19 Combining Multiple Omics Data Sets, Dr. Wei Zhu VIDEOTalk 2: The Analysis of Binding SARS-CoV-2 to Various Substrates, Dr. Peng Zhang VIDEO Psychosocial Impact of COVID-19 and Implications for Well-BeingMonday, February 8, 2021Talk 1: Behavioral Underpinnings of Vaccine Hesitancy and Implications for Vaccine Acceptance, Dr. Stacey Finkelstein VIDEOTalk 2: Effect of the Coronavirus (COVID-19) Pandemic on the Academic, Career, Mental, Psychosocial, and Physical Functioning of the SBU Community, Dr. Brady D. Nelson VIDEO Models to Predict and Control COVID-19Thursday, February 25, 2021Talk 1: Using Demographic Pattern Analysis to Predict COVID-19 Fatalities on the US County Level, Dr. Klaus Mueller  VIDEOTalk 2: Pandemic Control in ECON-EPI Networks, Dr. Marina Azzimonti VIDEO Impacts of Social DistancingThursday, March 11, 2021Talk 1: The Impact of Social Distancing During the COVID-19 Outbreak on Mental Health and Substance Use Outcomes: Examining Risk and Protective Factors in Young Adult Populations in New York, Dr. Sana Malik & Dr. Ijeoma Opara VIDEOTalk 2: Psychosocial Impact of COVID-19-Induced Social Isolation (PICSI) on Youth with Autism Spectrum Disorder: A Longitudinal Study, Dr. Matthew Lerner & Alan H. Gerber VIDEO COVID-19 Life Cycle: From Viral Infection to Novel TherapeuticsMonday, March 22, 2021Talk 1: Viral Infection and Initiation of Thrombosis, Dr. Miriam RafailovichTalk 2: Targeted Degradation of SARS-CoV-2 Proteins, Dr. Peter TongeVIDEO Structure-based Design of Coronavirus Vaccine AntigensThursday, April 29, 2021Structure-based Design of Coronavirus Vaccine Antigens, Special guest speaker Dr. Jason S. McLellan, The University of Texas at AustinVIDEO Click here to read the original article

May 5, 2021 STONY BROOK, NY, May 5, 2021 – Stony Brook University has been ranked No. 39 among all U.S. universities in the QS US University Rankings 2021, moving up from No. 45 last year and placing in the top 5.5% nationwide. The University is also ranked as No. 5 among all colleges and universities in New York State. In addition to improving from #45 in 2020 to #39 in 2021, Stony Brook: Ranks #6 in the country on the diversity and internationalisation index Ranks #13 in the country among public universities Ranks as the #1 public university in New York The rankings are based on weighted scores in the categories of Employability, Diversity and Internationalization, Learning Experience and Research. Stony Brook’s strong showing is due in part to its high score in the category of Diversity and Internationalization, in which it ranks No. 6 nationally. This category includes the following indicators: gender pay gap, faculty gender diversity, ratio of undergraduates receiving Pell grants, students’ ethnicity, number of Fulbright students and ratio of international students. The QS World University Rankings: USA, is part of a subset of the QS World University Rankings, last published in June 2020, in which Stony Brook was ranked #373 globally and #68 in the U.S. The annual QS World University Rankings: USA is designed to assess how well universities are responding to the social, intellectual and economic challenges of our time. Universities are ranked according to research performance and career outcomes as well as a range of indicators assessing each institution’s social impact and attempts to foster equitability. Such indicators include gender pay gap, faculty gender diversity, ratio of undergraduate students receiving Pell Grants, and retention rate. The methodology also evaluates universities based on the efforts they are making to support the 17 UN Sustainable Development goals. Click here to read the original article

April 28, 2021 STONY BROOK, NY, April 28, 2021 – Scientists from Stony Brook University and the Max Planck Institute of Animal Behavior have pieced together a timeline of how brain and body size evolved in mammals over the last 150 million years. The findings, published in Science Advances, show that brain size relative to body size—long considered an indicator of animal intelligence—has not followed a stable scale over evolutionary time. The international team of 22 scientists, including biologists, evolutionary statisticians, and anthropologists, compared the brain mass of 1400 living and extinct mammals. For the 107 fossils examined—among them ancient whales and the most ancient Old World monkey skull ever found—they used endocranial volume data from skulls instead of brain mass data. The brain measurements were then analyzed along with body size to compare the scale of brain size to body size over deep evolutionary time. “A big surprise was that much of the variation in relative brain size of mammals that live today can be explained by changes that their ancestral lineages underwent following the mass extinction and other cataclysmic events,” says Jeroen Smaers, an evolutionary biologist, Associate Professor of Anthropology at Stony Brook University, and first author on the study. “This includes evolution of the biggest mammalian brains, such as the dolphins, elephants, and great apes, which all evolved their extreme proportions after the climate change event 23-33 million years ago.” According to the study, “big-brained” humans, dolphins, and elephants, for example, attained their proportions in different ways. Elephants increased in body size, but surprisingly, even more in brain size. Dolphins, on the other hand, generally decreased their body size while increasing brain size. Great apes showed a wide variety of body sizes, with a general trend towards increases in brain and body size. In comparison, ancestral hominins, which represent the human line, showed a relative decrease in body size and increase in brain size compared to great apes. The authors say that these complex patterns urge a re-evaluation of the deeply rooted paradigm that comparing brain size to body size for any species provides a measure of the species’ intelligence. Smaers points out: “At first sight, the importance of taking the evolutionary trajectory of body size into account may seem unimportant. After all, many of the big-brained mammals such as elephants, dolphins, and great apes also have a high brain-to-body size. But this is not always the case. The California sea lion, for example, has a low relative brain size, which lies in contrast to their remarkable intelligence.” By taking into account evolutionary history, the current study reveals that the California sea lion attained a low brain-to-body size because of the strong selective pressures on body size, most likely because aquatic carnivorans diversified into a semi-aquatic niche. In other words, they have a low relative brain size because of selection on increased body size, not because of selection on decreased brain size. “We’ve overturned a long-standing dogma that relative brain size can be equivocated with intelligence,” says Kamran Safi, a research scientist at the Max Planck Institute of Animal Behavior and senior author on the study. “Sometimes, relatively big brains can be the end result of a gradual decrease in body size to suit a new habitat or way of moving—in other words, nothing to do with intelligence at all. Using relative brain size as a proxy for cognitive capacity must be set against an animal’s evolutionary history and the nuances in the way brain and body have changed over the tree of life.” The study further showed that most changes in brain size occurred after two cataclysmic events in Earth’s history: the mass extinction 66 million years ago and a climatic transition 23-33 million years ago. The authors conclude that efforts to truly capture the evolution of intelligence will require increased effort toward examining neuroanatomical features, such as brain regions known for higher cognitive processes. “Brain-to-body size is of course not independent of the evolution of intelligence,” emphasizes Smaers. “But it may actually be more indicative of more general adaptions to large scale environmental pressures that go beyond intelligence.” Click here to read the original article

April 19, 2021 Department of Materials Science and Chemical Engineering Team Receives $2.4 Million ARPA-E Award The team in the Engineered Microstructures and Radiation Effects Laboratory (EMREL), led by Professor Lance Snead as the Principal Investigator (PI) and co-PI’s, Professor Jason Trelewicz and Professor David Sprouster, has been awarded $2.4 million from the U.S. Department of Energy Advanced Research Projects Agency-Energy (ARPA-E) program, an agency tasked with promoting and funding research and development of advanced energy technologies. All three investigators are part of the Department of Materials Science and Chemical Engineering, and Professor Trelewicz is also a core faculty member of the Institute for Advanced Computational Science. The award is part of a grant program focused on the development of fusion energy science and technologies that would lead to a safe, carbon-free, and abundant energy source for developed and emerging economies, specifically the joint Office of Fusion Energy and ARPA-E initiative Galvanizing Advances in Market-aligned Fusion for an Overabundance of Watts (GAMOW). “The ARPA-E award process is extremely competitive and requires demonstrating leading-edge research and solutions,” said Fotis Sotiropoulos, Dean, College of Engineering and Applied Sciences. “I’m incredibly proud of Lance and the EMREL team’s work in this important area of research for our College and the University.” The project, ENHANCED Shield: A Critical Materials Technology Enabling Compact Superconducting Tokamaks, addresses a key issue facing the next generation of small, high-field fusion reactors. Specifically, with the significant progress made in the development of High Temperature Superconductor (HTS), the magnetic field strength required to drive a fusion plasma has been greatly enhanced allowing for much smaller, more economic systems. However, as the system becomes smaller, damage to magnets becomes a serious concern.  This Stony Brook project aims to solve that problem through development of a new class of shield materials to protect the magnets, thus enabling compact fusion systems. According to Snead, the current superconducting magnets we know, the ones that work at cryogenic temperatures, are typically shielded by common engineering materials such as water and steel, perhaps with a bit of other materials layered in. The water, like any material with hydrogen, is good at shielding neutrons, while steel or heavy materials like lead are what you would use for X-rays or gamma rays.   “It’s all pretty low-tech but works just fine for the larger machines. The problem comes in when you don’t have a lot of real estate to work with and water is not a coolant option,” he says. The solution being proposed by the EMREL for compact fusion devices is to fabricate composited structures which simultaneously shield neutrons and gamma-rays.   The proposed innovation will pursue two classes of engineered composite materials, one with a metal matrix and one with a ceramic matrix. The metal matrix is considered a more mature technology and will be applied in lower temperature application while the ceramic matrix composite is targeting higher temperature application. Of note is that the ceramic matrix composite owes its base technology to a breakthrough made by the Stony Brook team under an ongoing ARPA-E grant work which demonstrated fabrication of dense magnesia materials at temperatures hundreds of degrees lower than previously seen. This has allowed, as taken advantage of here, the inclusion of high neutron absorbing metal hydride materials within a magnesia composite structure.     The team includes Professor Steve Zinkle in the Department of Nuclear Engineering at the University of Tennessee Knoxville and Dr. Ethan Peterson of the Massachusetts of Technology. The project is also joined by two privately funded commercial fusion ventures: Commonwealth Fusion Systems and Tokamak Energy. Click here to read the original article

April 15, 2021 The first two vaccines approved for battling COVID-19 in the United States use a relatively new approach — injections of simple packets containing mRNA, a genetic material that instructs our cells to make coronavirus spike proteins. But the technology for generating sufficient amounts of those mRNA packets dates back to the 1980s, when F. William Studier, a former adjunct professor of biochemistry at Stony Brook University who was, at the time, also a senior biophysicist at Brookhaven National Laboratory, developed a way to harness the molecular machinery of a very different virus. In the 1980s Studier, the late senior scientist John Dunn, and their group in Brookhaven Lab’s Biology Department completed sequencing and annotating the genome of the T7 bacteriophage. T7 is a virus that infects E. coli bacteria and commandeers those cells to make copies of the virus. Having the complete genome sequence helped the scientists understand how T7 genes and other elements work together to reproduce many copies of the virus. Shortly thereafter, Studier and his team found a way to direct T7’s prolific copying capability toward making things other than more T7s. They cloned the T7 RNA polymerase — the enzyme that transcribes DNA genes into messenger RNA (mRNA), which instructs cells which amino acids to link up to build a particular protein. The team then used this T7 RNA polymerase along with a powerful T7 promoter (a genetic element that serves as a “start” signal for gene transcription) to produce large amounts of RNA from almost any gene. These RNAs could be used directly, such as in mRNA-based vaccines, or delivered to ribosomes (cells’ protein-making factories) to be translated into proteins, as in the T7 expression system. At manufacturing plants run by Pfizer/BioNTech and Moderna, T7-derived promoters and enzymes crank out kilograms of spike-protein mRNA at a time — leaving our own cells to do the protein-making part after a dose of instructions is injected into our arms. “T7 was not a well-studied bacteriophage when I came to Brookhaven in 1964,” Studier said. “I was using it to study properties of DNA and decided also to study its molecular genetics and physiology. My goal, of course, was to understand as much as possible about T7 and how it works.”  Cloning the gene for T7 RNA polymerase in 1983 was particularly difficult, Studier noted. “Others had tried and failed. Companies had asked me if we had it,” he said. “We had the DNA sequence then, and I thought that I understood why the cloning had failed and how to remedy the problem.” Studier worked with others at Brookhaven Lab — Parichehre Davanloo, then a postdoctoral fellow, and Alan Rosenberg, a senior lab member — to tackle the challenge. Dunn purified the T7 RNA polymerase and showed that it produces large amounts of RNA. Barbara Moffatt, then a graduate student, worked with Studier to turn these discoveries into the T7 expression system. “The Brookhaven Lab patent attorney knew what we were doing and we filed what I think was the first patent at Brookhaven under the Bayh-Dole Act” — a law passed by Congress in 1980 that allowed institutions and grant recipients to patent and license rights to inventions stemming from government-funded research, Studier explained. The rest is history. The T7 expression system went on to become Brookhaven Lab’s most successful technology, with research labs around the world using it and hundreds of companies licensing the technology to make products. And although the patents have now expired, T7 is still the go-to system for biochemists everywhere. “I had wondered casually if T7 RNA polymerase might be involved in making the RNA vaccines,” mused Studier. “Basic research is almost always useful, and I’m pleased that my work has been helpful in obtaining powerful vaccines against this pandemic.” Click here to read the original article

“Toys are not really as innocent as they look. Toys and games are the prelude to serious ideas” – from “Power of Tens” Are you looking for meaningful ways to spend time while COVID-19 is ongoing? SUNY Korea FIT Professor Rachel Stuckey shared three of her favorite recommendations for all of you.   *To watch the YouTube video: Click here      

The recent commencement ceremony of SUNY Korea FIT students was  mentioned on the FIT NYC Website.       To read more, please check out the link below.       Click here

Video of FIT graduating students' exhibition is finally out! Check out the beautiful moments of the opening ceremony of the FIT AAS Exhibition. In the video, Jiwon Park, the winner of the FIT AAS Exhibition, introduces her work which is made up of 300 roses. Professor Bonkuk Koo gives the message to the graduating students that “no one, not even yourself can set limitations.”   YouTube: Click here