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  • richardmitnick 1:23 pm on December 11, 2017 Permalink | Reply
    Tags: , , Environmental Science From the Sky, Remote sensing, Susan Ustin, UC Davis,   

    From UC Davis: Women in STEM: “How Susan Ustin Helped Launch a New Field of Study and Why She Continues to Study the Earth from Above” 

    UC Davis bloc

    UC Davis

    1
    Susan L. Ustin, right, and Shruti Khanna, a postdoctoral student, demonstrate how to calibrate a field spectrometer, which helps interpret remote sensing data retrieved from satellites. (Jason Spyres/UC Davis)

    December 4, 2017
    Lisa Howard
    lehoward@ucdavis.edu

    When Susan L. Ustin began her career in remote sensing at UC Davis in the 1980s, her colleagues — mostly male — weren’t convinced that what she was doing was actually science.

    “They didn’t see the images as a visualization of data. To them, the images were just pretty pictures,” Ustin says.

    Ustin received a Ph.D. in botany from UC Davis in 1983. After that, she worked on campus for a number of years on nonpermanent funding until she was offered a faculty position in 1990. Although there weren’t many women in her field — it was mostly engineers and geologists in those days — she doesn’t think gender specifically played a factor in the time it took for her to get hired.

    “It was more a case that at the time, people didn’t think remote sensing was really science,” she says. “Trying to convince them that it was worthwhile seemed to be the biggest problem.” But she remembers being only the third woman hired as faculty in the Department of Land, Air and Water Resources.

    The idea of doing scientific research using data and images from airplanes, drones, and satellites may seem obvious to anyone who grew up with Google Earth, but more than 30 years ago the idea was still very new.

    A Los Angeles Times article published in 1987 about Ustin’s work introduces the then novel idea of tracking plant ecology via satellite. Imaging spectrometry, the article notes, “will enable researchers to better oversee global health by understanding the impact of human activities like destroying rain forests and causing pollution.” Another piece in the Los Angeles Times three years later describes how the cutting-edge science of remote sensing “may enable scientists to predict life-threatening global changes before they can be detected from the ground.”

    Remote sensing has fulfilled those predictions and more. It is now a key technology integrated into almost all aspects of modern life. Remote sensing is used for monitoring natural disasters, studying climate change, mapping soil types and forests, monitoring air pollution, forecasting weather, unearthing archaeological sites, detecting oil spills, determining moisture content of soil, documenting melting glaciers, predicting retails earnings by counting cars in parking lots, and much, much more.

    Ustin is now a world leader in the field of remote sensing. That she ended up pretty much building her own specialty was largely unintentional. “I noticed early in my career that women ended up peripheral. We ended up in the interdisciplinary areas instead of more central ones. You weren’t one of boys so you didn’t end up being a copy of the advisor,” she explains.

    “But then, it turned out that suddenly that peripheral area became an important area to be in. When it became apparent that remote sensing was going to be able to address some of the emerging environmental questions, I was well established. I was at the right time and the right place,” says Ustin.

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    Ustin and her team use AVIRIS hyperspectral data to assess forest structure and composition. This image from the Gifford Pinchot National Forest in Washington shows an old-growth mixed conifer forest with recent logging and clear-cut patches. Red shows soil, green shows vegetation, and blue is shade. (S. Ustin, And A. Trabucco, UC Davis)

    Environmental Science From the Sky

    Ustin wears several hats at UC Davis. She is a distinguished professor of environmental and resource sciences and the vice chair for the hydrology section in the Department of Land, Air and Water Resources. She is the director of the Center for Spatial Technology and Remote Sensing (CSTARS), a remote sensing lab. (If you’ve ever wondered about the satellite receiving dish on the roof of Academic Surge or the geostationary dish on Kemper Hall, those belong to CSTARS.) She’s the associate director of research for the John Muir Institute of the Environment.

    This year she was named a fellow of the prestigious American Geophysical Union, “For pioneering work in hyperspectral remote sensing that has improved our ability to understand and manage changes in terrestrial ecosystems.”

    She has an office downstairs in the John Muir Institute of the Environment, but her lab is upstairs in the renovated former beef barn, a cozy space with sloped ceilings that was once a hay loft. Most of the desks have multiple computer monitors.

    At any given time Ustin’s lab has a mixture of postdocs, undergraduates, international visitors and staff. Today several postdocs students are looking at images. What’s on the screen looks like what you’d see on Google satellite, California from the air, with different-colored gray squares and light-colored rectangles of the human-built environment — crops, housing developments, towns — and the occasional dark, curving shape of a river or a reservoir.

    Within those images, though, lie layers and layers of data that they use for studying a wide variety of projects. Over the years, Ustin and her lab have assessed remote sensing data from five continents for a wide variety of environmental issues.

    One of her lab’s current projects is monitoring invasive plant species in the California Delta. Another is tracking how forests that have been managed — by thinning or controlled burns — compare to untouched areas. “We ask questions like, is there evidence that the forest is healthier?” Ustin says. “Is there a difference if the control burn was 20 years ago versus five years ago? We are trying to figure out if any management techniques have resulted in a healthier forest than the uncontrolled surrounding forest.”

    Being able to manage the data from remote sensing has changed considerably since Ustin first started. In the 1980s, she describes how they used “homemade” computers and “homemade” software because nothing existed to process the data.

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    Susan Ustin looks at remote-sensing data in her lab at The Barn. A Google Scholar search for her work reveals almost 300 titles. She has published 130 scientific proceedings and written 34 book chapters. This year she was named a fellow of the prestigious American Geophysical Union.

    But now, she notes, ordinary computers can process the data, and there is a wide variety of graphic information systems software. Although she uses a lot of raw data, she notes many researchers who work in focused areas use data that has already been processed.

    “NASA processes a lot of sensor data nowadays instead of giving you the raw data,” Ustin says. “For example, you can get the leaf area index for the entire world.”

    What humans can see with their eyes is only a small portion of what sophisticated sensors can “see.” The visible spectrum — the portion of the electromagnetic spectrum visible to the human eye — is made up of wavelengths from about 390 nanometers (what we see as violet) up to about 700 nanometers (what we see as red). But sophisticated sensors can see a much wider range of the electromagnetic spectrum, and that data can reveal a tremendous amount of information.

    The data from the NASA satellites Ustin worked with in the 1980s, like the Landsat 3, used sensors that looked at just four areas of the spectrum — green, red and two different bands of infrared. Data from each band was collected for each pixel of the image. As technology improved, sensors continued to improve and are now able to pick up more and more spectral bands and create more data for smaller and smaller areas of the image, resulting in more fine-grained information. “Now the data we are working with has close to 500 bands per pixel,” Ustin says. The data can reveal everything from how well a crop is growing or where an invasive species is taking over an ecosystem to how fast a glacier is melting.

    Ustin’s work with this data, with remote sensing, has resulted in a tremendous amount of research. She has published 130 scientific proceedings and written 34 book chapters. She estimates she’s published over 200 articles in peer-reviewed journals. A Google Scholar search for her work reveals almost 300, with subjects in remote sensing, environmental sciences, geography, geology, vegetation, canopies and more. Her journal articles have titles like, “Marsh Loss Due to Cumulative Impacts of Hurricane Isaac and the Deepwater Horizon Oil Spill in Louisiana,” and “Remote sensing of canopy chemistry.”

    Her most cited article, with 824 citations, is from the January 1990 edition of Remote Sensing of Environment: “Vegetation in the deserts: 1. A regional measure of abundance from multispectral images.” The paper grew out of fieldwork she did in Owens Valley in the mid-1980s. It remains one of her favorite research projects.

    “It was pretty fun.” Ustin laughs. She and her fellow researchers stayed at the University of California’s White Mountain Research Center, in Bishop. They were there to map the amount of vegetation compared to the data from NASA’s Landsat-5 satellite.

    In the paper, they describe taking a method of analysis used by geologists and chemists, and applied it to remote sensing data. “We were trying to map the amount of vegetation,” Ustin says. “Mixture analysis was being used in totally different contexts, but it was the same general idea. You have a solution that’s a mixture of things, so how do you tell what’s in it?”

    Applying the new method worked. “It was pretty cool,” Ustin says. “We were able to estimate the vegetation cover fraction across the valley, from the valley floor up into the east side of the Sierras.” Their method ended up becoming a standard analysis in the field.

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    Susan Ustin in Northslope near Barrow Alaska, 2007. She was there for a graduate student research project looking at the carbon fluxes that happen when the lakes drain.

    Career Shaped by 1960s Culture and Counterculture

    Ustin is originally from Eugene, Oregon. In 1961, after graduating from high school, she moved to San Francisco with friends.

    This was few years after the peak of the Beat Generation in San Francisco, but North Beach was still a hangout for writers, artists and musicians. “You could go to coffee shops and they still had the sort of Beat stuff, and of course there was City Lights Bookstore,” Ustin says.

    She was drawn to the city’s vibrancy and activism. Integration was happening all over the country, and in San Francisco there were civil rights marches and demonstrations, as well as picketing of businesses — hotels, restaurants, car dealerships — that refused the hire African Americans.

    In the 1960s, there was also a growing awareness of the environmental damage happening to the planet. “People were worried about environmental degradation. Rachel Carson’s Silent Spring had come out,” Ustin says, referring to the landmark environmental book that called attention to the detrimental effects of pesticides like DDT, “and in the Bay Area there were a couple of oil spills that did a lot of damage to wildlife and birds.”

    She worked downtown, at the Emporium department store on Market Street. She married and had two sons. “I had a lot of friends. It was fun and exciting. Then came the Summer of Love,” Ustin says, talking about the hippy countercultural phenomenon that attracted an estimated 100,000 mostly young people to San Francisco’s Haight Ashbury district. “My husband thought it would be really fun to go off and be a hippy. We had two kids. So that’s when I decided to go back to school.”

    Ustin followed her interest in environmental issues and received a B.S. in biological sciences in 1974 and an M.S. in biological sciences in 1977, both from California State University Hayward. As a single mother, she notes she was able to attend because of Great Society programs that helped her financially and with childcare. Later on, she also received financial help that allowed her to pursue her Ph.D. at UC Davis. “At that time, California had state scholarships for graduate students. I got one of those and so I could attend,” Ustin says. In 1982, she married James Doyle, now a professor emeritus in the Department of Evolution and Ecology, and had her third son the following year.

    Ustin was studying plant physiological ecology — how plants respond to physical stresses — and in 1982, the year before she received her Ph.D. in botany, she began working with the Jet Propulsion Lab.

    “They were looking for someone who knew about plants and photosynthesis and how plants responded to environmental conditions for their new remote sensing program,” Ustin says. “At that point, remote sensing was very new and the people involved were usually from engineering or geology. They were looking for environmental ecologists, since most of the land is covered with plants and that’s what you see most of the time,” she says.

    And with that, she was hooked on remote sensing.

    A Different Perspective

    Ustin has no plans to retire, as of yet, although she admits she does less fieldwork than she used to. She laughs. “Now I send other people to do it.”

    One of the things she likes about what she does is that she doesn’t do the same thing every day. With every new project, there are new problems to solve.

    A major project Ustin is working on now is securing funding for collaboration with the Jet Propulsion Lab to launch a big data platform — an airplane that can collect data — with the most modern imaging technology available. The concept for this new airborne sensor system is that it will be dedicated to monitoring California agriculture and ecosystems, and therefore available when it is needed.

    She’s also looking for simpler new ways to collect remote sensing data at much lower altitudes, which explains the new drone sitting in a box in the corner of her office.

    “I have students that would like to fly them and I thought we would do a project at Russell Ranch,” the university’s 300-acre agricultural research facility just a few miles from the main campus.

    She sees new technology, like drones, being big game changers. “Instead of having to rely on a company or a government program, it suddenly puts the technology in everybody’s hands. You can collect the data yourself and have a lot more flexibility,” Ustin says. For example, not just relying on when the satellite comes over.

    She notes the camera in the drone she bought for her students isn’t particularly good, but that they could probably work with someone in Department of Engineering to build a sensor. Or they may use one of the new hyperspectral cameras that have many infrared bands. Or maybe a LIDAR device, a remote sensing method that uses light in the form of a pulsed laser. “There are lots of possibilities,” she says.

    “A lot of the farmers in the valley are starting to fly drones and they’re not doing complicated image analysis. They’re just looking at the spatial patterns. They’ll notice, yes, that part in that field — that’s where it’s really sandy and drains too fast. Or that part has too much clay and it doesn’t drain. Half the time, when they see it, they recognize what the problem is.”

    And this, to some extent, sums up why Ustin’s work is so significant.

    Remote sensing is not simply about collecting data from the air. It’s how seeing the data — seeing the world from above — helps people recognize what is happening. Problems can be identified and potentially mitigated or managed, everything from deforestation, excess nitrogen runoff, ecosystem degradation, dying forests, poor irrigation, invasive species and more.

    Environmental degradation still concerns her. “Temperatures are increasing. Glaciers all over the world are declining. Snow packs are declining. Precipitation in the Western United States has been declining for 30 years or more. All of these changes are going to have an impact on us,” she says.

    But to see the problems, it helps to look from above, whether from a few hundred feet up in the air with a drone or 23 miles above the Earth with a satellite.

    “We are too close, from our scale,” Ustin says. “Remote sensing gives you a different perspective. It’s easier to see the problems.”

    See the full article here .

    Please help promote STEM in your local schools.

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    UC Davis Campus

    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

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  • richardmitnick 7:45 pm on July 11, 2017 Permalink | Reply
    Tags: , , Neural Stem Cells Steered by Electric Fields in Rat Brain, , UC Davis   

    From UC Davis: “Neural Stem Cells Steered by Electric Fields in Rat Brain” 

    UC Davis bloc

    UC Davis

    July 11, 2017
    Andy Fell
    ahfell@ucdavis.edu

    Min Zhao
    minzhao@ucdavis.edu

    1
    Transplants of neural stem cells might be used to treat brain injuries, but how to get them to the right location? UC Davis researcher Min Zhao and Junfeng Feng, a neurosurgeon at Ren Ji Hospital, Shanghai, showed that they can steer transplanted stem cells (green, in inset on right) to one part of a rat’s brain using electrical fields. (Image: Junfeng Feng)

    Electric fields can be used to guide neural stem cells transplanted into the brain toward a specific location. The research, published July 11 in the journal Stem Cell Reports, opens possibilities for effectively guiding stem cells to repair brain damage.

    Professor Min Zhao at the University of California, Davis, School of Medicine’s Institute for Regenerative Cures studies how electric fields can guide wound healing. Damaged tissues generate weak electric fields, and Zhao’s research has shown how these electric fields can attract cells into wounds to heal them.

    “One unmet need in regenerative medicine is how to effectively and safely mobilize and guide stem cells to migrate to lesion sites for repair,” Zhao said. “Inefficient migration of those cells to lesions is a significant roadblock to developing effective clinical applications.”

    Junfeng Feng, a neurosurgeon at Ren Ji Hospital, Shanghai Jiao Tong University and Shanghai Institute of Head Trauma, visited Zhao’s lab to study how electric fields might guide stem cells implanted in the brain.

    Natural neural stem cells — cells that can develop into other brain tissues — are found deep in the brain, in the subventricular zone and hippocampus. To repair damage to the outer layers of the brain (the cortex), they have to migrate some distance, especially in the large human brain. Transplanted stem cells might also have to migrate some way to find an area of damage.

    Stem cells move ‘upstream’

    Feng and Zhao developed a model of stem cell transplants in rats. They placed human neural stem cells in the rostral migration stream — a pathway in the rat brain that carries cells toward the olfactory bulb, which governs the animal’s sense of smell. Cells move along this pathway partly carried by the flow of cerebrospinal fluid and partly guided by chemical signals.

    By applying an electric field within the rat’s brain, they found that they could get the transplanted stem cells to swim “upstream” against the fluid flow and natural cues and head for other locations within the brain.

    The transplanted stem cells were still in their new locations weeks or months after treatment.

    “Electrical mobilization and guidance of stem cells in the brain therefore provides a potential approach to facilitate stem cell therapies for brain diseases, stroke and injuries,” Zhao said.

    Additional authors on the paper are: at UC Davis, Lei Zhang, Jing Liu, Bruce Lyeth and Jan Nolta; Ji-Yao Jiang, Ren Ji Hospital, Shanghai Jiao Tong University and Shanghai Institute of Head Trauma; and Michael Russell, Aaken Laboratories, Davis. The work was supported by the California Institute for Regenerative Medicine with additional support from NIH, NSF and Research to Prevent Blindness Inc.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

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    UC Davis Campus

    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

     
  • richardmitnick 8:07 pm on June 12, 2017 Permalink | Reply
    Tags: , Artificial Cartilage Under Tension as Strong as Natural, “Scaffold-free” systems, Chondrocytes, , UC Davis   

    From UC Davis: “Artificial Cartilage Under Tension as Strong as Natural” 

    UC Davis bloc

    UC Davis

    June 12, 2017
    Andy Fell
    News and Media Relations
    530-752-4533
    ahfell@ucdavis.edu

    Kyriacos Athanasiou
    Biomedical Engineering
    (530) 752-1033
    athanasiou@ucdavis.edu

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    Lab-grown cartilage grown with tension (top) shows similar mechanical and chemical properties to natural cartilage, which allows our joints to move smoothly. The lower image shows computer modeling of strain distribution across the artificial tissue. (Athanasiou lab, UC Davis)

    Biomedical engineers at the University of California, Davis, have created a lab-grown tissue similar to natural cartilage by giving it a bit of a stretch. The tissue, grown under tension but without a supporting scaffold, shows similar mechanical and biochemical properties to natural cartilage. The results are published June 12 in the journal Nature Materials.

    Articular cartilage provides a smooth surface for our joints to move, but it can be damaged by trauma, disease or overuse. Once damaged, it does not regrow and is difficult to replace. Artificial cartilage that could be implanted into damaged joints would have great potential to help people regain mobility.

    Natural cartilage is formed by cells called chondrocytes that stick together and produce a matrix of proteins and other molecules that solidifies into cartilage. Bioengineers have tried to create cartilage, and other materials, in the lab by growing cells on artificial scaffolds. More recently, they have turned to “scaffold-free” systems that better represent natural conditions.

    The UC Davis team, led by Professor Kyriacos Athanasiou, Department of Biomedical Engineering, grew human chondrocytes in a scaffold-free system, allowing the cells to self-assemble and stick together inside a specially designed device. Once the cells had assembled, they were put under tension — mildly stretched — over several days. They showed similar results using bovine cells as well.

    “As they were stretched, they became stiffer,” said Jerry Hu, a research engineer and co-author on the study. “We think of cartilage as being strong in compression, but putting it under tension has dramatic effects.”

    The new material had a similar composition and mechanical properties to natural cartilage, they found. It contains a mix of glycoproteins and collagen, with crosslinks between collagen strands giving strength to the material.

    Experiments with mice show that the lab-grown material can survive in a physiological environment. The next step, Hu said, is to put the lab-grown cartilage into a load-bearing joint, to see if it remains durable under stress.

    “In this comprehensive study, we showed that we can finally engineer tissue that has the tensile and compressive characteristics of native tissue,” Athanasiou said. “The artificial cartilage that we engineer is fully biological with a structure akin to real cartilage. Most importantly, we believe that we have solved the complex problem of making tissues in the laboratory that are strong and stiff enough to take the extremely high loads encountered in joints such as the knee and hip.”

    Additional authors on the paper are: co-first authors Jennifer Lee and Le Huwe, Nikolaos Paschos and Ashkan Aryaei, all at UC Davis; and Courtney Gegg, now a graduate student at Stanford University. Athanasiou also holds an appointment as professor in the UC Davis Department of Orthopedic Surgery. The work was supported by grants from the National Institutes of Health.

    See the full article here .

    Please help promote STEM in your local schools.

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    Stem Education Coalition

    UC Davis Campus

    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

     
  • richardmitnick 7:39 pm on June 8, 2017 Permalink | Reply
    Tags: , , Food for fish and people, Rice fields as floodplains, Study: Floodplain Farm Fields Benefit Juvenile Salmon, UC Davis   

    From UC Davis: “Study: Floodplain Farm Fields Benefit Juvenile Salmon” 

    UC Davis bloc

    UC Davis

    June 7, 2017
    Nina Erlich-Williams
    541-230-1973
    nina@publicgoodpr.com

    Kat Kerlin
    UC Davis News and Media Relations
    530-752-7704
    kekerlin@ucdavis.edu

    1
    Rice fields managed as floodplains during winter can create surrogate wetland habitat for native fish. Photo: Carson Jeffres/UC Davis

    A new study offers a beacon of hope for a cease-fire in the Golden State’s persistent water wars.

    Floodplain Farm Fields Provide Novel Rearing Habitat for Chinook Salmon, published in the journal PLOS-ONE [ Jacob V. E. Katz , Carson Jeffres, J. Louise Conrad,Ted R. Sommer,Joshua
    Martinez, Steve Brumbaugh, Nicholas Corline, Peter B. Moyle] is based on the work by scientists from nonprofit group California Trout, UC Davis, and the California Department of Water Resources. The study provides further evidence that Central Valley farm fields that remain in active agricultural production can have environmental benefits for the state’s salmon populations.

    This surprising synergy runs counter to the usual California narrative where conflict over management of water and endangered species is the norm. This is particularly true in the State’s Central Valley, where more than 95 percent of former wetlands — critical habitat for native fish populations — have been leveed, drained and developed, primarily for farmland.

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    Juvenile salmon. Photo: Carson Jeffres/UC Davis

    Food for fish and people

    “This study demonstrates that the farm fields that now occupy the floodplain can not only grow food for people during summer, but can also produce food resources and habitat for native fish like salmon in winter,” said lead author Jacob Katz of California Trout. “Our work suggests that California does not always need to choose between its farms or its fish. Both can prosper if these new practices are put into effect, mimicking natural patterns on managed lands.”

    Approximately 10,000 small, hatchery-reared salmon, averaging less than 2 inches and weighing about a gram, were transplanted to a 5-acre field for several weeks between the fall rice harvest and spring planting. A subsample of the fish were tagged uniquely with electronic tags (similar to chips used to ID pets) to allow tracking of individual growth rates, which were among the highest ever recorded in freshwater in California.

    “By reconnecting rivers to floodplainlike habitat in strategic places around the Central Valley, we have the potential to help recover endangered salmon and other imperiled fish populations to self-sustaining levels,” said Ted Sommer, lead scientist for the California Department of Water Resources and a co-author on the study.

    Rice fields as floodplains

    Since 2012, a team of scientists has been examining how juvenile salmon use off-channel habitats, including off-season rice fields. The experiments provide evidence that rice fields managed as floodplains during winter can create “surrogate” wetland habitat for native fish.

    The team suggests that shallowly flooded fields function in similar ways to natural floods that once spread across the floodplain, supplying extremely dense concentrations of zooplankton — an important food for juvenile salmon. Foraging on these abundant and nutritious invertebrates, the young salmon grow extremely quickly, improving their chances of surviving their migration to sea and returning in three to five years as the large, adult fish.

    Since this original study, the team has continued to investigate how rice fields and other managed habitats could be improved to support salmon rearing.

    “This study shows that we can start focusing on solutions that support fish and people, instead of one or the other,” added Carson Jeffres of the UC Davis Center for Watershed Sciences, the second author on the report. “It’s a huge win-win.”

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    UC Davis Campus

    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

     
  • richardmitnick 3:39 pm on June 3, 2017 Permalink | Reply
    Tags: , , Howard University, , Nkechinyere Chidi-Ogbolu, UC Davis,   

    From UC Davis via USA Today College: Women in STEM: “She just graduated college and is starting her Ph.D. — and she’s only 18” Nkechinyere Chidi-Ogbolu 

    UC Davis bloc

    UC Davis

    1

    USA TODAY COLLEGE

    June 1, 2017
    Toni Airaksinen, Barnard College

    2
    Nkechinyere Chidi-Ogbolu is about to start working on her doctorate in biomedical engineering. And she’s just 18 years old. (Photo: Mercy Daniel-Aguebor)

    While many students have just graduated from high school, 18-year-old Nigeria native Nkechinyere Chidi-Ogbolu is not your typical teen.

    Chidi-Ogbolu just graduated summa cum laude from Howard University with a degree in chemical engineering — making her the youngest person to graduate from Howard this year, and one of the youngest in Howard’s history.

    3

    But that’s not all for Chidi-Ogbolu.

    She’s now preparing to start a Ph.D. program at the University of California-Davis after the summer ends. She’ll be studying biomedical engineering with a focus on creating and discovering new medicines.

    “I’ve always been interested in the medical field,” she told USA TODAY College. “But I want to have a broader scale of impact than in treating patients one-on-one.”

    Chidi-Ogbolu said she’s always been the youngest person in her classes. While most students from Nigeria graduate high school at the age of 16, Chidi-Ogbolu finished high school particularly early, at 14, since she skipped 5th grade and attended an accelerated high school.

    After high school, she left Nigeria for America and enrolled full-time at Howard University, a historically black university and her first-choice school.

    “I thought I would be more comfortable at the age going to a school with more people that looked like me and therefore I could more easily relate to,” said Chidi-Ogbolu. “Plus, they gave me a full scholarship, so that definitely helped.”

    Leaving her parents in Nigeria was difficult, but Chidi-Ogbolu wasn’t alone. Many of her extended family members live in America, including an aunt who lived not far from her dorm, and other family members in Texas and Alabama.

    She credited her family’s support for her ability to cope with her new surroundings.

    “I spoke to my mom almost every day on the phone — for over an hour almost every time. My dad and I talked really often too,” Chidi-Ogbolu says, adding that she spent most holidays with her aunts in America. “Talking to them definitely helped sometimes when things were overwhelming.”

    “My support system was a very big part of why I was able to stay very grounded during the whole journey,” she says.

    Her friends at Howard were very supportive of her too. Many of her them didn’t initially know how young she was, which gave rise to many moments of surprise.

    “People usually reacted with shock,” she says. “Then they became really protective.”

    With the blessings of her parents, Chidi-Ogbolu spent the summer after her junior year researching African weather patterns with Professor Paul Ullrich at UC-Davis. “While I was there, I decided that grad school was what I wanted to do.”

    She started working on her graduate school applications during her senior year. “I can’t say it was stress-free,” she jokes. Her hard work paid off on February 7, when she received her acceptance letter from UC-Davis.

    “It was definitely a wonderful moment,” she says.

    Prasant Mohapatra, UC Davis vice provost of graduate education, and dean of graduate studies, had this to say about Chidi-Ogbolu: “We are delighted to welcome Nkechinyere into the graduate education community at UC Davis. We hope to provide a dynamic educational experience that will deepen and expand her passion for advancing the field of biomedical engineering, and we are truly impressed by her future plans to help people worldwide through scientific research and innovation.”

    What’s next for her? This summer, she’s taking an advanced biology class at a local community college to prepare for her doctoral program. She’s also working on a book, provisionally titled Tales of an Uber Minor in College.

    While she says she’s super busy, she does set aside free time to relax. “I love watching movies and series, especially Korean ones, and I like to sing and do karaoke,” she says.

    Chidi-Ogbolu also has some advice for teens her age.

    “Don’t limit yourself because you think you can’t do it or because no one you know had done it,” she advises. “You can always be the exception to the rule and end up being exceptional.”

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    UC Davis Campus

    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

     
  • richardmitnick 4:26 pm on April 17, 2017 Permalink | Reply
    Tags: , , Pattern Discovery over Pattern Recognition: A New Way for Computers to See, UC Davis   

    From UC Davis: “Pattern Discovery over Pattern Recognition: A New Way for Computers to See” 

    UC Davis bloc

    UC Davis

    April 17th, 2017
    Andy Fell

    Jim Crutchfield wants to teach a machine to “see” in a new way, discovering patterns that evolve over time instead of recognizing patterns based on a stored template.

    It sounds like an easy task – after all, any animal with basic vision can see a moving object, decide whether it is food or a threat and react accordingly, but what comes easily to a scallop is a challenge for the world’s biggest supercomputers.

    Crutchfield, along with physics graduate student Adam Rupe and postdoc Ryan James, is designing these new machine learning systems to allow supercomputers to spot large-scale atmospheric structures, such as hurricanes and atmospheric rivers, in climate data. The UC Davis Complexity Sciences Center, which Crutchfield leads, was recently named as an Intel Parallel Computing Center and is collaborating with Intel Research, the Department of Energy’s National Energy Research Scientific Computing Center (NERSC) at the Lawrence Berkeley Lab, Stanford University, and University of Montreal. The entire Big Data Center project is led by Prabhat, leader of the Data And Analytics Services Group at the Berkeley lab.

    The team works on NERSC’s CORI II supercomputer, in the top five of the world’s fastest machines with over 600,000 CPU cores.

    2
    NERSC CRAY Cori II supercomputer

    Modern science is full of “big data.” For climate science, that includes both satellite- and ground-based measurements that span the planet, as well as “big” simulations.

    “We need new kind of machine learning to interpret very large data and planet-wide simulations,” Crutchfield said. Climate and weather systems evolve over time, so the machines need to be able to find patterns not only in space but over time.

    3
    UC Davis researchers plan to develop new tools so supercomputers can detect patterns in global climate simulations (NERSC/LBNL)

    “Dynamics are key to this,” Crutchfield said. Humans (and other visual animals) recognize dynamic changes very quickly, but it’s much harder for machines.

    Pattern Discovery is more than Pattern Recognition

    With existing technology, computers recognize patterns based on an existing template. That’s how voice recognition systems work, by comparing your voice to an existing catalog of sounds. These pattern recognition systems can be very useful but they can’t identify anything truly new – that isn’t represented in their template.

    Crutchfield and his team are taking a different approach, based on pattern discovery. They are working on algorithms that allow computers to identify structures in data without knowing what they are in advance.

    “Learning novel patterns is what humans are uniquely good at, but machines can’t do it,” he said.

    Using pattern discovery, a supercomputer would learn how to identify hurricanes or other features in climate and weather data. It might also identify new kinds of structures that are too complex for humans to perceive at all.

    While this application is in global climate modeling, Crutchfield hopes to make it a new paradigm for analyzing very large datasets.

    “Usually, you apply known models to interpret the data. To say that you will extract your model directly from the data is a radical claim,” he said.

    The collaboration is part of the Intel Parallel Computing Centers program, which provides funding to universities, institutions, and research labs to modernize key community codes used across a wide range of disciplines to run on industry-standard parallel architectures.

    More information

    Video: Global simulation of atmospheric water vapor produced by CORI supercomputer at NERSC

    See the full article here .

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  • richardmitnick 4:32 pm on April 10, 2017 Permalink | Reply
    Tags: , , , , MACS1423-z7p64, UC Davis   

    From UC Davis: “Long Ago and Far Away, an Average Galaxy” 

    UC Davis bloc

    UC Davis

    April 10, 2017
    Andy Fell

    1
    Astronomers used the gravity of a massive galaxy cluster as a lens to spot an incredibly distant galaxy, about 13.1 billion years in the past. They used the Hubble Space Telescope to find the galaxy and confirmed its age and distance with instruments at the Keck Observatory in Hawaii. Image credit: NASA/Keck/Austin Hoag/Marusa Bradac

    NASA/ESA Hubble Telescope

    Keck Observatory, Mauna Kea, Hawaii, USA

    Astronomers led by a graduate student at the University of California, Davis, have discovered one of the most distant galaxies in the universe, and it’s nothing out of the ordinary.

    “Other most distant objects are extremely bright and probably rare compared to other galaxies,” said Austin Hoag, a UC Davis graduate student in physics who is lead author on the paper, published April 10 in Nature Astronomy. “We think this is much more representative of galaxies of the time.”

    These ultradistant galaxies, seen as they were close to the beginning of the universe, are interesting to Hoag, UC Davis physics professor Marusa Bradac, and collaborators in the U.S., Australia and Europe because they fall within the “Epoch of Reionization,” a period about a billion years after the Big Bang when the universe became transparent.

    Reionization era and first stars, Caltech

    After the Big Bang, the universe was a cloud of cold, atomic hydrogen, which blocks light. The first stars and galaxies condensed out of the cloud and started to emit light and ionizing radiation. This radiation melted away the atomic hydrogen like a hot sun clearing fog, and the first galaxies spread their light through the universe.

    Much remains lost in the fog of reionization.

    “We have a before and an after, but not exactly a when,” Hoag said. There are also questions about what radiating objects drove reionization: Was it mostly young galaxies, or did objects such as black holes and gamma ray bursts contribute as well?

    Galaxy cluster is a giant lens in the sky

    The new object, named MACS1423-z7p64, is at a redshift of 7.6, putting it about 13.1 billion years in the past. (The farther away an object is, the farther its light is shifted into the red end of the spectrum, due to the expansion of the universe.) To find such faint, distant objects, the astronomers took advantage of a giant lens in the sky.

    As light passes by a massive object such as a galaxy cluster, its path gets bent by gravity, just as light gets bent passing through a lens. When the object is big enough, it can act as a lens that magnifies the image of objects behind it.

    Gravitational Lensing NASA/ESA

    Gravitational microlensing, S. Liebes, Physical Review B, 133 (1964): 835

    Hoag and colleagues are surveying the sky around massive galaxy clusters that are the right size and distance away to focus light from very distant galaxies. While it is similar to millions of other galaxies of its time, z7p64 just happened to fall into the “sweet spot” behind a giant galaxy cluster that magnified its brightness tenfold and made it visible to the team, using the Hubble Space Telescope. They were then able to confirm its distance by analyzing its spectrum with the Keck Observatory telescopes in Hawaii.

    The team plans to continue their survey of candidate galaxies with the Hubble and Keck telescopes. The upcoming launch of the James Webb Space Telescope, set for 2018, opens up new possibilities, Hoag said. The team is currently planning observations for the Webb telescope, which is bigger than Hubble and will allow astronomers to look at even more distant parts of the universe.

    “We will truly witness the birth of the first galaxies which will allow us to answer the longstanding question, of where did we come from,” Bradac said.

    Other authors on the paper are: at UC Davis, Kuang-Han Huang, Brian Lemaux and Julie He; Michele Trenti and Stephanie Bernard, University of Melbourne, Australia; Tommaso Treu, Louis E. Abramson, Charlotte Mason and Takahiro Morishita, UCLA; Kasper Schmidt, Leibniz-Institut für Astrophysik, Potsdam, Germany; Laura Pentericci, NAF Osservatorio Astronomico di Roma, Italy; and Tim Schrabback, Argelander-Institut für Astronomie, Bonn, Germany. The work was supported by NASA. The W.M. Keck Observatory is operated as a scientific partnership among the California Institute of Technology, the University of California and NASA and is made possible by the generous financial support of the W.M. Keck Foundation.

    Media contact(s)

    Marusa Bradac, UC Davis Physics, 530-752-6762 , marusa@physics.ucdavis.edu

    Austin Hoag, UC Davis Physics, athoag@ucdavis.edu

    Andy Fell, UC Davis News and Media Relations, 530-752-4533, ahfell@ucdavis.edu

    See the full article here .

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  • richardmitnick 4:52 pm on June 17, 2016 Permalink | Reply
    Tags: , , UC Davis, World’s First 1000-Processor Chip   

    From UC Davis: “World’s First 1,000-Processor Chip” 

    UC Davis bloc

    UC Davis

    June 17, 2016
    Andy Fell

    1
    This microchip with 1,000 processor cores was designed by graduate students in the UC Davis Department of Electrical and Computer Engineering. The chip is thought to be fastest designed in a university lab. No image credit.

    A microchip containing 1,000 independent programmable processors has been designed by a team at the University of California, Davis, Department of Electrical and Computer Engineering. The energy-efficient “KiloCore” chip has a maximum computation rate of 1.78 trillion instructions per second and contains 621 million transistors. The KiloCore was presented at the 2016 Symposium on VLSI Technology and Circuits in Honolulu on June 16.

    “To the best of our knowledge, it is the world’s first 1,000-processor chip and it is the highest clock-rate processor ever designed in a university,” said Bevan Baas, professor of electrical and computer engineering, who led the team that designed the chip architecture. While other multiple-processor chips have been created, none exceed about 300 processors, according to an analysis by Baas’ team. Most were created for research purposes and few are sold commercially. The KiloCore chip was fabricated by IBM using their 32 nm CMOS technology.

    Each processor core can run its own small program independently of the others, which is a fundamentally more flexible approach than so-called Single-Instruction-Multiple-Data approaches utilized by processors such as GPUs; the idea is to break an application up into many small pieces, each of which can run in parallel on different processors, enabling high throughput with lower energy use, Baas said.

    Because each processor is independently clocked, it can shut itself down to further save energy when not needed, said graduate student Brent Bohnenstiehl, who developed the principal architecture. Cores operate at an average maximum clock frequency of 1.78 GHz, and they transfer data directly to each other rather than using a pooled memory area that can become a bottleneck for data.

    The chip is the most energy-efficient “many-core” processor ever reported, Baas said. For example, the 1,000 processors can execute 115 billion instructions per second while dissipating only 0.7 Watts, low enough to be powered by a single AA battery. The KiloCore chip executes instructions more than 100 times more efficiently than a modern laptop processor.

    Applications already developed for the chip include wireless coding/decoding, video processing, encryption, and others involving large amounts of parallel data such as scientific data applications and datacenter record processing.

    The team has completed a compiler and automatic program mapping tools for use in programming the chip.

    Additional team members are Aaron Stillmaker, Jon Pimentel, Timothy Andreas, Bin Liu, Anh Tran and Emmanuel Adeagbo, all graduate students at UC Davis. The fabrication was sponsored by the Department of Defense and ARL/ARO Grant W911NF-13-1-0090; with support from NSF Grants 0903549, 1018972, 1321163, and CAREER Award 0546907; and SRC GRC Grants 1971 and 2321.

    See the full article here .

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  • richardmitnick 4:00 pm on June 15, 2016 Permalink | Reply
    Tags: , , , New Type of Meteorite Linked to Ancient Asteroid Collision, UC Davis   

    From UC Davis: “New Type of Meteorite Linked to Ancient Asteroid Collision” 

    UC Davis bloc

    UC Davis

    June 15, 2016
    Becky Oskin

    1
    The black, grainy meteorite embedded in rock from a Swedish quarry fell to Earth 470 million years ago. Chemically distinct from any meteorite yet discovered, it is likely debris from a massive collision in the asteroid belt. (Qing-zhu Yin, UC Davis).

    An ancient space rock discovered in a Swedish quarry is a type of meteorite never before found on Earth, scientists reported June 14 in the journal Nature Communications.

    “In our entire civilization, we have collected over 50,000 meteorites, and no one has seen anything like this one before,” said study co-author Qing-zhu Yin, professor of geochemistry and planetary sciences at the University of California, Davis. “Discovering a new type of meteorite is very, very exciting.”

    The new meteorite, called Ost 65, appears to be from the missing partner in a massive asteroid collision 470 million years ago. The collision sent debris falling to Earth over about a million years and may have influenced a great diversification of life in the Ordovician Period. One of the objects involved in this collision is well-known: It was the source of L-chondrites, still the most common type of meteorite. But the identity of the object that hit it has been a mystery.

    Ost 65 was discovered in Sweden’s Thorsberg quarry, source of more than 100 fossil meteorites. Measuring just under 4 inches wide, it looks like a gray cow patty plopped into a pristine layer of fossil-rich pink limestone. The Ost 65 rock is called a fossil meteorite because the original rock is almost completely altered except for a few hardy minerals — spinels and chromite. Analyses of chromium and oxygen isotopes in the surviving minerals allowed the researchers to conclude the Ost 65 meteorite is chemically distinct from all known meteorite types.

    By measuring how long Ost 65 was exposed to cosmic rays, the team established that it traveled in space for about a million years before it fell to Earth 470 million years ago. This timeline matches up with L-chondrite meteorites found in the quarry, leading the study authors to suggest the rock is a fragment of the other object from the Ordovician collision. The original object may have been destroyed during the collision, but it’s also possible that the remains are still out in space.

    Meteorites may have influenced evolution

    Researchers think that about 100 times as many meteorites slammed into Earth during the Ordovician compared with today, thanks to the massive collision in the asteroid belt. This rain of meteorites may have opened new environmental niches for organisms, thus boosting both the diversity and complexity of life on Earth.

    “I think this shows the interconnectedness of the entire solar system in space and time, that a random collision 470 million years ago in the asteroid belt could dictate the evolutionary path of species here on Earth,” Yin said.

    The study was led by Birger Schmitz, of Lund University in Sweden. Yin, of UC Davis, together with his postdoctoral fellow Matthew Sanborn, made the very precise measurement of chromium in tiny mineral grains within the meteorite. Researchers from the University of Hawaii at Manoa analyzed its oxygen isotopes.

    The new findings strengthen suspicions that more recent meteorite falls on Earth do not represent the full range of rocks drifting through the solar system. Yin said there is potential to better understand the history of our solar system by collecting meteorite fragments preserved in Earth’s ancient rocks. “If we can go back even further in time, we may eventually be able to find some of the true building blocks of Earth,” Yin said.

    The research was funded by NASA, the UC Office of the President and a European Research Council Advanced Grant.

    See the full article here .

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  • richardmitnick 9:43 pm on December 28, 2015 Permalink | Reply
    Tags: , , UC Davis   

    From UC Davis: “Turning the Tables on Hidden HIV” 

    Temp 1

    Thirty years ago, contracting HIV was a death sentence.

    The virus attacks the immune system, specifically T-cells, until immunity breaks down completely. Patients would eventually develop AIDS, and ultimately succumb to opportunistic infections.

    The development of highly active antiretroviral therapies or HAART changed all that, converting a deadly disease into a chronic one. As long as patients stayed on the drug regimen, they could live normal lifespans. Their immune systems would recover and viral levels would decline to nearly zero.

    But there’s a catch. Nearly zero is not the same as zero. HIV has a latency mode, during which the virus is dormant – evading both HAART and the body’s immune system. Remove HAART treatment, and the virus comes roaring back.

    That means a lifetime consuming powerful and expensive treatments – if one’s body and health status can tolerate them in the first place. And no one knows how the drugs will affect patients after 20, 30 or 40 years.

    “We’ve made great progress, but at the end of the day you still have more than 30 million people living with HIV,” says Satya Dandekar, professor and chair of the UC Davis Department of Medical Microbiology and Immunology. “Without drugs, the virus can come back at the same threat level for patients.

    “Actually eradicating HIV is extremely critical.”

    For decades, UC Davis researchers have worked with that ultimate goal in mind. Scientists have learned important details about how HIV operates along the way; for example, that it first attacks immune cells in the gut.

    But now we’ve reached a new stage in the battle against HIV. The goal is no longer to control the disease, but to cure it. Two UC Davis groups are beginning clinical trials in hopes of doing just that.

    Shock and kill

    It would be hard to overstate the significance of HIV latency. The virus’s ability to evade treatment has made it difficult, if not impossible, to cure. The challenge for clinicians is to identify a two-pronged strategy: shock the latent virus out of hibernation, and hit it with immune treatments to kill it.

    2
    No image credit found

    Dandekar, along with dermatologist Emanual Maverakis, are about to test the first part of that strategy. Just a few months ago, the Dandekar lab identified several agents that “wake up” HIV. One in particular, PEP005, has shown striking results. Even better, the drug is already approved by the U.S. Food and Drug Administration.

    “We found this was really effective at reactivating HIV and works beautifully with other latency reactivating agents,” says Dandekar. “The thing that’s really exciting is that the molecule is in the drug PICATO, which treats skin cancer. It’s already approved and being used by patients.”

    Now the UC Davis group hopes to extend PICATO’s uses to attacking HIV latency as well, and is launching a small clinical trial to test the drug’s safety in HIV patients. If the trial is successful, the team hopes to combine PICATO, and other drugs that reactivate HIV, with immunotherapies that would destroy the virus as it comes out of hiding.

    “It will have to be a combination,” says Dandekar. “Just reactivating HIV from latency won’t be enough. We need to position the patient so those reactivated cells can be cleared.”

    Reboot the system

    UC Davis researchers are moving another promising approach into clinical trials as well. It involves taking blood stem cells from patients, genetically engineering them with anti-HIV genes, and returning them to the patients – essentially “rebooting” their immune systems and empowering them to eradicate or adequately suppress remaining HIV on their own over the long term.

    “We are using our understanding of basic HIV biology to engineer each patient’s own stem cells to fight the virus,” says Joseph Anderson, an assistant adjunct professor who researches infectious diseases at the UC Davis Institute for Regenerative Cures, the university’s main stem cell research center. “We’re hoping that by reintroducing these cells in a bone marrow transplant, we can rebuild the immune system to resist HIV.”

    Temp 3

    Anderson and Mehrdad Abedi, a hematology professor and stem cell transplant specialist, are trying to replicate the treatment that cured Timothy Brown, also known as the “Berlin Patient.” Brown received a stem cell transplant from a donor whose genome contained an HIV-resistant mutation. That was seven years ago – and Brown remains HIV-free.

    Anderson, who has been investigating anti-HIV genes since he was a Ph.D. student, is using three different genes to attack the virus, each one hitting a different mechanism associated with HIV infection. Like the drug cocktails used for HAART, multiple attack vectors may reduce the virus’s ability to evade treatment.

    But a new key to the UC Davis team’s gene therapy strategy is also an improved viral vector that Anderson developed to help boost the treatment’s potency. The vector contains a gene that “tags” the surface of the stem cells that are HIV-resistant, allowing researchers to maximize their volume and potential power by culling out non-resistant cells before transplantation.

    Anderson and Abedi have received an $8.5 million grant from the state’s stem cell agency, the California Institute for Regenerative Medicine or CIRM, to conduct the trial. The study will test the engineered stem cells in patients with HIV-related lymphoma, since they already require bone marrow transplants to treat their cancer. This trial will also test the therapy’s safety.

    The team hopes the treatment will be a complete cure, but even a partial response would be great news for HIV patients.

    “Maybe we won’t be able to eradicate it in some patients,” said Anderson, “but hopefully we are giving them enough of an HIV-resistant immune system that they can live the rest of their lives without having to take the antiretroviral drugs.”

    See the full article here .

    Please help promote STEM in your local schools.

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    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

     
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