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  • richardmitnick 12:15 pm on March 22, 2019 Permalink | Reply
    Tags: Microsoft Quantum, National Quantum Initiative Act, Northwest Quantum Nexus, , Potential partners in academia and industry from across the Pacific Northwest, University of Washington   

    From University of Washington: “UW, Microsoft, Pacific Northwest National Laboratory establish new Northwest Quantum Nexus for a quantum revolution in science, technology” 

    U Washington

    From University of Washington

    March 21, 2019
    James Urton

    The University of Washington, the Pacific Northwest National Laboratory and Microsoft Quantum announced this week that they have joined forces in a new coalition to bring about a revolution in quantum research and technology.

    The Northwest Quantum Nexus was unveiled during a two-day summit at the UW, an event that included scientists and engineers from the three keystone institutions, as well as potential partners in academia and industry from across the Pacific Northwest.

    1
    Mary Lidstrom, UW vice provost for research, speaking at the Northwest Quantum Nexus summit on March 18, 2019.Andrea Starr/Pacific Northwest National Laboratory.

    “The technological and societal impact of the upcoming quantum revolution is going to be enormous,” said Mary Lidstrom, UW vice provost for research and professor of chemical engineering and microbiology. “The UW is thrilled to partner with Microsoft and PNNL in this Northwest Quantum Nexus.”

    In alignment with the National Quantum Initiative Act, the Northwest Quantum Nexus aims to develop a quantum-fluent workforce and economy in the Pacific Northwest region of the United States and Canada by accelerating research, technological development, education and training in the quantum information sciences, or QIS. Its objectives include:

    Forming cross-disciplinary research teams working across academia, government and industry toward scalable quantum computing — including quantum algorithms and programming — as well as research and development of quantum materials and devices
    Cultivating a workforce that is expert in quantum science, engineering and technology through education and training — including undergraduate and graduate education, curriculum development; and internships
    Promoting public-private partnerships as platforms to exchange knowledge and resources
    Translating QIS research to testbeds and relevant application areas such as sustainability and clean energy

    2
    2012 Nobel physics laureate David Wineland, a professor at the University of Oregon, speaks during the Northwest Quantum Nexus summit on March 18, 2019. In the early 1970s, Wineland was a UW postdoctoral researcher under Hans Dehmelt, who in 1989 became the first UW faculty member to win a Nobel Prize.Andrea Starr/Pacific Northwest National Laboratory.

    QIS disciplines include quantum computing, quantum communication, quantum sensing and quantum materials and devices. All of these applications and fields are designed around and enabled by the principles of quantum mechanics, including quantum superposition, which is the property of existing in several different configurations at the same time. For example, quantum computing uses the principles of quantum mechanics and quantum-mechanical processes to carry out computations, which could revolutionize fields from cryptography to molecular simulation. Quantum materials include materials in which new behaviors emerge from quantum interactions.

    As QIS technologies progress from research and development to applications in clean energy, sustainability, computing and communications, the Northwest Quantum Nexus seeks to boost the region’s quantum workforce as well as research and educational capacity, according to coalition members.

    “While there has been a long history of quantum research and education in the UW physics department, the landscape has changed recently,” said Kai-Mei Fu, associate professor of both physics and electrical and computer engineering. “People now see that you can harness the quantum nature of matter to realize new technologies.”

    “This change means a paradigm shift in education,” added Fu, who is also a faculty member in the UW’s Molecular Engineering & Sciences Institute. “Understanding quantum mechanics is no longer an academic question but a required skill for people to develop quantum materials, quantum devices, quantum systems and quantum algorithms.”

    These goals also offer opportunities to expand the Northwest Quantum Nexus. Summit attendees included dozens of scientists, engineers and administrators from the keystone partners, as well as potential partners from private companies, startups and universities from across the Pacific Northwest. Three members of Washington’s congressional delegation also attended the summit: Senator Maria Cantwell, Representative Derek Kilmer and Representative Adam Smith.

    The keystone partners have complementary strengths in QIS. For the past 15 years, Microsoft has been a major global driver of quantum computing research and software development. The PNNL’s research into QIS includes programming, algorithm development, materials synthesis and characterization, as well as applications in quantum chemistry and sensing.

    The UW has deep roots in quantum research and discovery. Two UW scientists have earned the Nobel Prize in Physics for QIS research — Hans Dehmelt in 1989 for developing ion traps and David Thouless in 2016 for theoretical work on topological phase transitions and topological phases of matter. Today, researchers across the UW — in the College of Engineering, the College of Arts & Sciences and the Institute for Nano-Engineered Systems — are at the forefront of QIS research. The university recently established UW Quantum X, which joins QIS research endeavors across the UW in fields such as quantum sensing, quantum computing, quantum communication and quantum materials and devices. Fu and Jim Pfaendtner, associate professor and chair of chemical engineering, serve as co-chairs of Quantum X.

    The three institutions also work together in QIS research and development. UW and PNNL scientists collaborate on quantum materials research through the Northwest Institute for Materials Physics, Chemistry and Technology. Scientists with Microsoft Quantum are teaching an undergraduate-level course on quantum computing algorithms in the UW’s Paul G. Allen School of Computer Science & Engineering. Microsoft and the PNNL have collaborated on a chemistry library will inform chemistry research relevant to quantum computing.

    The Northwest Quantum Nexus is a natural next step, according to the summit organizers.

    “The Northwest Quantum Nexus summit was an amazing success for UW Quantum X and our keystone partners Microsoft and the PNNL,” said Pfaendtner, who is also a faculty member in the UW’s Clean Energy Institute.

    “We are ready to roll up our sleeves and get to work competing for new private and public research funding, continuing UW’s long history of developing innovative and agile graduate and undergraduate education programs in the QIS field, and creating amazing new opportunities for our students and postdoctoral researchers.”

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    u-washington-campus
    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.
    So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 10:08 am on September 27, 2018 Permalink | Reply
    Tags: , , , , Rutgers Receives NSF Award to Continue Pioneering Ocean Initiative, , University of Washington,   

    From Rutgers University: “Rutgers Receives NSF Award to Continue Pioneering Ocean Initiative” 

    Rutgers smaller
    Our Great Seal.

    From Rutgers University

    September 25, 2018

    Dalya Ewais
    848-445-3153
    dalya.ewais@rutgers.edu

    The project delivers insight to researchers, policymakers and the public worldwide.

    The National Science Foundation this week announced it has awarded a five-year, $220 million contract to a coalition of academic and oceanographic research organizations, including Rutgers University–New Brunswick, to operate and maintain the Ocean Observatories Initiative [OOI].

    The coalition, led by the Woods Hole Oceanographic Institution with direction from the NSF, includes Rutgers, the University of Washington and Oregon State University.

    1

    The initiative includes platforms and sensors that measure physical, chemical, geological and biological properties and processes from the seafloor to the sea surface in key coastal and open-ocean sites of the Atlantic and Pacific. It was designed to address critical questions about the Earth-ocean system, including climate change, ecosystem variability, ocean acidification plate-scale seismicity and submarine volcanoes, and carbon cycling. The goal is to better understand the ocean and our planet.

    3
    The seafloor cable extends off the coast of Oregon and allows real-time communication with the deep sea. University of Washington

    Each institution will continue to operate and maintain the portion of project’s assets for which it is currently responsible. Rutgers will operate the cyberinfrastructure system that ingests and delivers data for the initiative.

    The initiative supports more than 500 autonomous instruments on the seafloor and on moored and free-swimming platforms that are serviced during regular, ship-based expeditions to the array sites. Data from each instrument is transmitted to shore, where it is freely available to users worldwide, including scientists, policy experts, decision-makers, educators and the general public.

    “Rutgers is proud to be a part of this transformative project that provides scientists and educators across the globe access to the richest source of real-time, in-water oceanographic data,” said David Kimball, interim senior vice president for research and economic development at Rutgers.

    Over the last three years, the Rutgers team led by Manish Parashar, director of the Rutgers Discovery Informatics Institute and Distinguished Professor of computer science, designed, built and operated the OOI’s cyberinfrastructure. The team also included Scott Glenn and Oscar Schofield, Distinguished Professors in the Department of Marine and Coastal Sciences and co-founders of Rutgers’ Center for Ocean Observing Leadership, who led the Rutgers data team.

    3
    From left to right: Manish Parashar, director of the Rutgers Discovery Informatics Institute and Distinguished Professor of computer science; Peggy Brennan-Tonetta, associate vice president for economic development at Rutgers’ Office of Research and Economic Development; and Ivan Rodero, project manager.
    Photo: Nick Romanenko/Rutgers University

    For the second phase of the OOI project, which begins on October 1 and runs for five years, Rutgers will receive about $6.6 million and will be responsible for maintaining the cyberinfrastructure and providing a network that allows 24/7 connectivity, ensuring sustained, reliable worldwide ocean observing data any time, any place, on any computer or mobile device. Peggy Brennan-Tonetta, associate vice president for economic development at Rutgers’ Office of Research and Economic Development, will serve as acting principal investigator.

    “Greater awareness and knowledge of the state of our oceans and the effects of their interrelated systems today is critical to a deeper understanding of our changing climate, marine and coastal ecosystems, atmospheric exchanges, and geodynamics. We are pleased to continue our involvement with this project that enables researchers to better understand the state of our oceans,” Brennan-Tonetta said.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    rutgers-campus

    Rutgers, The State University of New Jersey, is a leading national research university and the state’s preeminent, comprehensive public institution of higher education. Rutgers is dedicated to teaching that meets the highest standards of excellence; to conducting research that breaks new ground; and to providing services, solutions, and clinical care that help individuals and the local, national, and global communities where they live.

    Founded in 1766, Rutgers teaches across the full educational spectrum: preschool to precollege; undergraduate to graduate; postdoctoral fellowships to residencies; and continuing education for professional and personal advancement.

    As a ’67 graduate of University college, second in my class, I am proud to be a member of

    Alpha Sigma Lamda, National Honor Society of non-tradional students.

     
  • richardmitnick 2:17 pm on December 31, 2017 Permalink | Reply
    Tags: , , HiCRep method to accurately assess the reproducibility of data from Hi-C experiments, New insights into how the genome works inside of a cell, New statistical method for evaluating reproducibility in studies of genome organization" 2017, , Quite often correlation is treated as a proxy of reproducibility in many scientific disciplines but they actually are not the same thing, University of Washington, With the massive amount of data that is being produced in whole-genome studies it is vital to ensure the quality of the data   

    From Pennsylvania State University: “New statistical method for evaluating reproducibility in studies of genome organization” 2017 

    Penn State Bloc

    Pennsylvania State University

    03 October 2017
    Qunhua Li:
    qunhua.li@psu.edu
    (814) 863-7395

    Barbara K. Kennedy:
    bkk2@psu.edu
    (814) 863-4682

    Sam Sholtis

    A new, statistical method to evaluate the reproducibility of data from Hi-C — a cutting-edge tool for studying how the genome works in three dimensions inside of a cell — will help ensure that the data in these “big data” studies is reliable.

    1
    Schematic representation of the HiCRep method. HiCRep uses two steps to accurately assess the reproducibility of data from Hi-C experiments. Step 1: Data from Hi-C experiments (represented in triangle graphs) is first smoothed in order to allow researchers to see trends in the data more clearly. Step 2: The data is stratified based on distance to account for the overabundance of nearby interactions in Hi-C data. Credit: Li Laboratory, Penn State University

    “Hi-C captures the physical interactions among different regions of the genome,” said Qunhua Li, assistant professor of statistics at Penn State and lead author of the paper. “These interactions play a role in determining what makes a muscle cell a muscle cell instead of a nerve or cancer cell. However, standard measures to assess data reproducibility often cannot tell if two samples come from the same cell type or from completely unrelated cell types. This makes it difficult to judge if the data is reproducible. We have developed a novel method to accurately evaluate the reproducibility of Hi-C data, which will allow researchers to more confidently interpret the biology from the data.”

    The new method, called HiCRep, developed by a team of researchers at Penn State and the University of Washington, is the first to account for a unique feature of Hi-C data — interactions between regions of the genome that are close together are far more likely to happen by chance and therefore create spurious, or false, similarity between unrelated samples. A paper describing the new method appears in the journal Genome Research.

    “With the massive amount of data that is being produced in whole-genome studies, it is vital to ensure the quality of the data,” said Li. “With high-throughput technologies like Hi-C, we are in a position to gain new insight into how the genome works inside of a cell, but only if the data is reliable and reproducible.”

    Inside the nucleus of a cell there is a massive amount of genetic material in the form of chromosomes — extremely long molecules made of DNA and proteins. The chromosomes, which contain genes and the regulatory DNA sequences that control when and where the genes are used, are organized and packaged into a structure called chromatin. The cell’s fate, whether it becomes a muscle or nerve cell, for example, depends, at least in part, on which parts of the chromatin structure is accessible for genes to be expressed, which parts are closed, and how these regions interact. HiC identifies these interactions by locking the interacting regions of the genome together, isolating them, and then sequencing them to find out where they came from in the genome.

    2
    The HiCRep method is able to accurately reconstruct the biological relationship between different cell types, where other methods fail. Credit: Li Laboratory, Penn State University

    “It’s kind of like a giant bowl of spaghetti in which every place the noodles touch could be a biologically important interaction,” said Li. “Hi-C finds all of these interactions, but the vast majority of them occur between regions of the genome that are very close to each other on the chromosomes and do not have specific biological functions. A consequence of this is that the strength of signals heavily depends on the distance between the interaction regions. This makes it extremely difficult for commonly-used reproducibility measures, such as correlation coefficients, to differentiate Hi-C data because this pattern can look very similar even between very different cell types. Our new method takes this feature of Hi-C into account and allows us to reliably distinguish different cell types.”

    “This reteaches us a basic statistical lesson that is often overlooked in the field,” said Li. “Quite often, correlation is treated as a proxy of reproducibility in many scientific disciplines, but they actually are not the same thing. Correlation is about how strongly two objects are related. Two irrelevant objects can have high correlation by being related to a common factor. This is the case here. Distance is the hidden common factor in the Hi-C data that drives the correlation, making the correlation fail to reflect the information of interest. Ironically, while this phenomenon, known as the confounding effect in statistical terms, is discussed in every elementary statistics course, it is still quite striking to see how often it is overlooked in practice, even among well-trained scientists.“

    The researchers designed HiCRep to systematically account for this distance-dependent feature of Hi-C data. In order to accomplish this, the researchers first smooth the data to allow them to see trends in the data more clearly. They then developed a new measure of similarity that is able to more easily distinguish data from different cell types by stratifying the interactions based on the distance between the two regions. “This is like studying the effect of drug treatment for a population with very different ages. Stratifying by age helps us focus on the drug effect. For our case, stratifying by distance helps us focus on the true relationship between samples.”

    To test their method, the research team evaluated Hi-C data from several different cell types using HiCRep and two traditional methods. Where the traditional methods were tripped up by spurious correlations based on the excess of nearby interactions, HiCRep was able to reliably differentiate the cell types. Additionally, HiCRep could quantify the amount of difference between cell types and accurately reconstruct which cells were more closely related to one another.

    In addition to Li, the research team includes Tao Yang, Feipeng Zhang, Fan Song, Ross C. Hardison, and Feng Yue at Penn State; and Galip Gürkan Yardımcı and William Stafford Noble at the University of Washington. The research was supported by the U.S. National Institutes of Health, a Computation, Bioinformatics, and Statistics (CBIOS) training grant at Penn State, and the Huck Institutes of the Life Sciences at Penn State.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Penn State Campus

    WHAT WE DO BEST

    We teach students that the real measure of success is what you do to improve the lives of others, and they learn to be hard-working leaders with a global perspective. We conduct research to improve lives. We add millions to the economy through projects in our state and beyond. We help communities by sharing our faculty expertise and research.

    Penn State lives close by no matter where you are. Our campuses are located from one side of Pennsylvania to the other. Through Penn State World Campus, students can take courses and work toward degrees online from anywhere on the globe that has Internet service.

    We support students in many ways, including advising and counseling services for school and life; diversity and inclusion services; social media sites; safety services; and emergency assistance.

    Our network of more than a half-million alumni is accessible to students when they want advice and to learn about job networking and mentor opportunities as well as what to expect in the future. Through our alumni, Penn State lives all over the world.

    The best part of Penn State is our people. Our students, faculty, staff, alumni, and friends in communities near our campuses and across the globe are dedicated to education and fostering a diverse and inclusive environment.

     
  • richardmitnick 8:23 am on December 28, 2016 Permalink | Reply
    Tags: , , Radiology results on the internet, University of Washington   

    From U Washington: “Technology may bring radiologists closer to patients” 

    U Washington

    University of Washington

    12.21.2016
    Michael McCarthy

    Web access to radiology test results predicted to lead to more consultations between radiologists and patients

    1
    Dr. Christoph Lee views mammograms at UW Medicine radiology unit. Michael McCarthy

    As more patients gain access to the results of their X-rays and other radiology studies through hospital web portals, radiologists are likely to have more direct patient contact. This is the forecast of three physicians writing in the current issue of the Journal of the American College of Radiology.

    An increasing number of health systems are responding to patients’ demand to have rapid and convenient access to their health information. They have adopted patient web portals that allow patients to schedule appointments, refill prescriptions, email their health providers, and review their doctors’ notes, lab results, and radiology reports, write UW Medicine physicians Christoph I. Lee, a radiologist with Seattle Cancer Care Alliance, Joann G. Elmore, a UW professor of medicine, Division of General Internal Medicine, and Curtis P. Langlotz, professor of radiology at Stanford University School of Medicine in Palo Alto, California.

    Web access to medical notes and test results has been shown to be extremely popular with patients. They are particularly interested in their radiology reports. About half of patients click on and read the results of their imaging studies compared to just one-third clicking on their doctors’ notes, said Lee, the article’s lead author.

    This is a good trend, Lee added, because patients can learn a lot from these reports. The information in them can have a big impact on how patients understand their medical condition. In addition, access to the reports gives patients the opportunity to provide additional symptom information that can help radiologists improve their interpretation of study results.

    “Sometimes, the referring doctor may only give a two-word history with their request, say, ‘Abdominal pain,’” Lee explained. “Patients often offer more detail: for example, noting that they also have a recurring fever and unexplained weight loss. That’s invaluable information that helps us interpret the image.”

    But patient access also poses new challenges for radiologists, Lee pointed out,. For example, as more patients look at their radiology reports, it is likely more of them will want to contact radiologists with questions. That may prove difficult, as general radiologists often have to view, interpret and issue reports on 100 to 150 imaging studies a day. They are left with little time to meet with patients to review study results.

    One solution is to provide plain language summaries of radiology reports that patients can more easily understand.

    “Traditionally, radiology reports have been written for the doctor who referred the patient, who typically has a specific question he or she wants answered. As a result, the vocabulary we used in reports can be exoteric and can be difficult for patients to decipher,” Lee observed..

    But lay language summaries are likely to be only a first step, Lee went on to say.. “Eventually, we are going to evolve to have a system in which there are more direct radiologist-patient consultations in which patients, especially those with complex problems, come into the clinic, sit down with the radiologist, and review their imaging studies.”

    For some patients, such consultations will prove to be very helpful, Lee predicted. “When patients see their medical images, their clinical condition often becomes very real. It can be pretty powerful and affect their decision making. The saying ‘A picture is worth a thousand words’ is true.”

    Lee thinks most radiologists want to have more interaction with patients:. “Due to a fee-for-service payment system, we’ve been relegated to the backrooms because we have so many images to get through each day. But we are realizing that value is lost when we’re not more closely involved in the patient’s care. Currently, there is valuable information that is not being relayed or communicated directly to patients that should be, This information will help patients better understand their health and be more closely involved in their own care.”

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    u-washington-campus
    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us — the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 8:55 am on January 16, 2015 Permalink | Reply
    Tags: , , , University of Washington   

    From U Washington: “Tiny plant fossils a window into Earth’s landscape millions of years ago” 

    U Washington

    University of Washington

    January 15, 2015
    Michelle Ma

    Minuscule, fossilized pieces of plants could tell a detailed story of what the Earth looked like 50 million years ago.

    1
    A 49 million-year-old phytolith. Its curvy, large shape indicate the plant it came from grew in shady conditions. Scale bar is 10 micrometers.Regan Dunn, U of Wash.

    An international team led by the University of Washington has discovered a way to determine the tree cover and density of trees, shrubs and bushes in locations over time based on clues in the cells of plant fossils preserved in rocks and soil. Tree density directly affects precipitation, erosion, animal behavior and a host of other factors in the natural world. Quantifying vegetation structure throughout time could shed light on how the Earth’s ecosystems changed over millions of years.

    “Knowing an area’s vegetation structure and the arrangement of leaves on the Earth’s surface is key for understanding the terrestrial ecosystem. It’s the context in which all land-based organisms live, but we didn’t have a way to measure it until now,” said lead author Regan Dunn, a paleontologist at the UW’s Burke Museum of Natural History and Culture. Dunn completed this work as a UW doctoral student in the lab of Caroline Strömberg, the Estella B. Leopold associate professor in biology and curator of paleobotany at the Burke Museum.

    The findings are published Jan. 16 in the journal Science.

    The team focused its fieldwork on several sites in Patagonia, Argentina, which have some of the best-preserved fossils in the world and together represent 38 million years of ecosystem history (49-11 million years ago). Paleontologists have for years painstakingly collected fossils from these sites, and worked to precisely determine their ages using radiometric dating. The new study builds on this growing body of knowledge.

    2
    The researchers work in Miocene-aged deposits near Rio Chico in Chubut Province, Argentina.Regan Dunn, U of Wash.

    In Patagonia and other places, scientists have some idea based on ancient plant remains such as fossilized pollen and leaves what species of plants were alive at given periods in Earth’s history. For example, the team’s previous work documented vegetation composition for this area of Patagonia. But there hasn’t been a way to precisely quantify vegetation openness, aside from general speculations of open or bare habitats, as opposed to closed or tree-covered habitats.

    “Now we have a tool to go and look at a lot of different important intervals in our history where we don’t know what happened to the structure of vegetation,” said Dunn, citing the period just after the mass extinction that killed off the dinosaurs.

    “The significance of this work cannot be understated,” said co-author Strömberg. “Vegetation structure links all aspects of modern ecosystems, from soil moisture to primary productivity to global climate. Using this method, we can finally quantify in detail how Earth’s plant and animal communities have responded to climate change over millions of years, which is vital for forecasting how ecosystems will change under predicted future climate scenarios.”

    3
    Fossil phytoliths from a 40 million-year-old soil from the Sarmiento Formation, Gran Barranca, Chubut, Argentina. At the center is an epidermal phytolith indicative of open habitats by its smaller, less curvy shape. Scale bar is 10 micrometers.Regan Dunn, U of Wash.

    Work by other scientists has shown that the cells found in a plant’s outermost layer, called the epidermis, change in size and shape depending on how much sun the plant is exposed to while its leaves develop. For example, the cells of a leaf that grow in deeper shade will be larger and curvier than the cells of leaves that develop in less covered areas.

    Dunn and collaborators found that these cell patterns, indicating growth in shade or sun, similarly show up in some plant fossils. When a plant’s leaves fall to the ground and decompose, tiny silica particles inside the plants called phytoliths remain as part of the soil layer. The phytoliths were found to perfectly mimic the cell shapes and sizes that indicate whether or not the plant grew in a shady or open area.

    The researchers decided to check their hypothesis that fossilized cells could tell a more complete story of vegetation structure by testing it in a modern setting: Costa Rica.

    4
    Regan Dunn samples for phytoliths from the soil under a dense forest at Rincon de la Vieja National Park, Costa Rica.Melanie Conner, copyright Melanie Conner Photography

    Dunn took soil samples from sites in Costa Rica that varied from covered rainforests to grassy savannahs to woody shrub lands. She also took photos looking directly up at the tree canopy (or lack thereof) at each site, noting the total vegetation coverage.

    5
    This hemispherical photograph shows the tree canopy cover at a site in Santa Rosa National Park, Costa Rica. The corresponding forest profile (modified from Holdridge et al., 1971) gives a side profile of the forest’s density.Regan Dunn, U of Wash.

    Back in the lab, she extracted the phytoliths from each soil sample and measured them under the microscope. When compared with tree coverage estimated from the corresponding photos, Dunn and co-authors found that the curves and sizes of the cells directly related to the amount of shade in their environments. The researchers characterized the amount of shade as “leaf area index,” which is a standard way of measuring vegetation over a specific area.

    Testing this relationship between leaf area index and plant cell structures in modern environments allowed the team to develop an equation that can be used to predict vegetation openness at any time in the past, provided there are preserved plant fossils.

    “Leaf area index is a well-known variable for ecologists, climate scientists and modelers, but no one’s ever been able to imagine how you could reconstruct tree coverage in the past — and now we can,” said co-author Richard Madden of the University of Chicago. “We should be able to reconstruct leaf area index by using all kinds of fossil plant preservation, not just phytoliths. Once that is demonstrated, then the places in the world where we can reconstruct this will increase.”

    When Dunn and co-authors applied their method to 40-million-year-old phytoliths from Patagonia, they found something surprising — habitats lost dense tree cover and opened up much earlier than previously thought based on other paleobotanic studies. This is significant because the decline in vegetation cover occurred during the same period as cooling ocean temperatures and the evolution of animals with the type of teeth that feed in open, dusty habitats.

    The research team plans to test the relationship between vegetation coverage and plant cell structure in other regions around the world. They also hope to find other types of plant fossils that hold the same information at the cellular level as do phytoliths.

    Other co-authors are Matthew Kohn of Boise State University and Alfredo Carlini of Universidad Nacional de La Plata in Argentina.

    The research was funded by the National Science Foundation, the Geological Society of America, UW Biology and the Burke Museum.

    ###

    For more information, contact Dunn at dunnr@uw.edu or 206-685-0374.

    See the full article here.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    U Washington campus

    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us — the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 10:04 am on December 31, 2014 Permalink | Reply
    Tags: , , University of Washington   

    From U Washington: “Elusive ‘dark matter’ from human microbiome is revealed” 

    U Washington

    University of Washington

    12.23.2014
    HSNewsBeat

    A team of researchers including Jeff McLean of the University of Washington has published dramatic new findings on bacteria that are detectable but have evaded cultivation in the lab. Known as “microbial dark matter,” some are suspected culprits in the development of debilitating and chronic disease.

    In a paper published online in December’s Proceedings of the National Academy of Sciences, McLean and his colleagues reveal unprecedented molecular insights into the lifestyle and pathogenesis of Candidate Phylum TM7, a large group of related bacteria found in many environments in the world but which have previously eluded cultivation attempts.

    j
    Jeff McLean is acting associate professor of periodontics at the University of Washington.

    m
    Pictured are cells of TM7x (red), a member of the previously uncultivated TM7 phylum, attached to its partner species Actinomyces odontolyticus XH001 (white filamentous) isolated from the human oral cavity.

    TM7 has been among the estimated 40 to 60 percent of bacterial types in the human body that are uncultivated. It has been implicated in inflammatory mucosal diseases due to its increased abundance in patients with periodontitis.

    “I consider this the most exciting discovery in my 30-year microbiology research career,” said Wenyuan Shi of UCLA, one of the team’s leaders along with Xuesong He of UCLA and McLean, who collaborated as a member of the J. Craig Venter Institute before joining the UW School of Dentistry this year.

    The team’s discovery of how TM7 actually grows sheds significant light on the biological, ecological and medical importance of TM7 and could also help better understand how to grow other difficult bacteria. The TM7 phylotype or genetic cousin cultivated by the team – TM7x, a human bacterial form found in the oral cavity – is intriguing for its potential association with chronic inflammation of the digestive tract, vaginal disease and periodontitis.

    What sets TM7x apart is that it is a bacterium that lives on the surface of another bacterial strain, Actinomyces odontolyticus (XH001), yet TM7x also has a parasitic phase in which it kills the bacterium on which it lives.

    “Once the team grew and sequenced TM7x, revealing it has a very minimal genome with no biosynthetic pathways to make its own amino acids, and then captured images of this nano-sized bacteria growing on a larger bacterium, we could finally piece together how it makes a living in the human body,” said McLean. “This may be the first example of parasitic ectosymbiosis between two different bacteria – where one species lives on the surface of another species gaining essential nutrients and then decides to thank its host by attacking it.”

    “The uncultivable microbiota presents a fascinating ‘final frontier’ for dental microbiologists and is a high priority for the NIDCR research portfolio. Obligate epibionts such as TM7x provide a near-perfect case study of how co-cultivation strategies and a thorough appreciation for interspecies signaling can facilitate the recovery of these elusive organisms,” said Dr. R. Dwayne Lunsford, director of the microbiology program at the National Institute of Dental and Craniofacial Research.

    “Although culture-independent studies can give us a snap-shot of microbial diversity at a particular site, in order to truly understand physiology and virulence of an isolate, we must ultimately be able to grow and manipulate these bacteria in the lab.”

    Further investigations into TM7x will seek to reveal more about its unique relationship to XH001 and how this co-occurrence is responsible for mucosal diseases. Future findings could have implications for potential treatment and therapeutics.

    Other collaborators on this study include Renate Lux and Anna Edlund from the UCLA School of Dentistry; Shibu Yooseph, Adam P. Hall and Karen E. Nelson from the J. Craig Venter Institute; Su-Yang Liu and Genhong Cheng of the UCLA Department of Department of Microbiology, Immunology, and Molecular Genetics; Pieter C. Dorrestein, University of California at San Diego Departments of Chemistry and Biochemistry and Pharmacology; Eduardo Esquenazi, Sirenas Marine Discovery; and Ryan C. Hunter, University of Minnesota Department of Microbiology.

    See the full article here.

    Please help promote STEM in your local schools.

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    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us — the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 2:47 pm on December 10, 2014 Permalink | Reply
    Tags: , , , , , University of Washington   

    From astrobio.net: “Warmer Pacific Ocean could release millions of tons of seafloor methane” 

    U Washington

    University of Washington

    December 9, 2014
    Hannah Hickey

    Off the West Coast of the United States, methane gas is trapped in frozen layers below the seafloor. New research from the University of Washington shows that water at intermediate depths is warming enough to cause these carbon deposits to melt, releasing methane into the sediments and surrounding water.

    Researchers found that water off the coast of Washington is gradually warming at a depth of 500 meters, about a third of a mile down. That is the same depth where methane transforms from a solid to a gas. The research suggests that ocean warming could be triggering the release of a powerful greenhouse gas.

    b
    Sonar image of bubbles rising from the seafloor off the Washington coast. The base of the column is 1/3 of a mile (515 meters) deep and the top of the plume is at 1/10 of a mile (180 meters) deep.Brendan Philip / UW

    “We calculate that methane equivalent in volume to the Deepwater Horizon oil spill is released every year off the Washington coast,” said Evan Solomon, a UW assistant professor of oceanography. He is co-author of a paper to appear in Geophysical Research Letters.

    While scientists believe that global warming will release methane from gas hydrates worldwide, most of the current focus has been on deposits in the Arctic. This paper estimates that from 1970 to 2013, some 4 million metric tons of methane has been released from hydrate decomposition off Washington. That’s an amount each year equal to the methane from natural gas released in the 2010 Deepwater Horizon blowout off the coast of Louisiana, and 500 times the rate at which methane is naturally released from the seafloor.

    Dissociation of Cascadia margin gas hydrates in response to contemporary ocean warming
    Geophysical Research Letters | Dec. 5, 2014

    “Methane hydrates are a very large and fragile reservoir of carbon that can be released if temperatures change,” Solomon said. “I was skeptical at first, but when we looked at the amounts, it’s significant.”

    Methane is the main component of natural gas. At cold temperatures and high ocean pressure, it combines with water into a crystal called methane hydrate. The Pacific Northwest has unusually large deposits of methane hydrates because of its biologically productive waters and strong geologic activity. But coastlines around the world hold deposits that could be similarly vulnerable to warming.

    “This is one of the first studies to look at the lower-latitude margin,” Solomon said. “We’re showing that intermediate-depth warming could be enhancing methane release.”
    map of Washington coast

    The yellow dots show all the ocean temperature measurements off the Washington coast from 1970 to 2013. The green triangles are places where scientists and fishermen have seen columns of bubbles. The stars are where the UW researchers took more measurements to check whether the plumes are due to warming water.Una Miller / UW

    Co-author
    Una Miller, a UW oceanography undergraduate, first collected thousands of historic temperature measurements in a region off the Washington coast as part of a separate research project in the lab of co-author Paul Johnson, a UW professor of oceanography. The data revealed the unexpected sub-surface ocean warming signal.

    “Even though the data was raw and pretty messy, we could see a trend,” Miller said. “It just popped out.”

    The four decades of data show deeper water has, perhaps surprisingly, been warming the most due to climate change.

    “A lot of the earlier studies focused on the surface because most of the data is there,” said co-author Susan Hautala, a UW associate professor of oceanography. “This depth turns out to be a sweet spot for detecting this trend.” The reason, she added, is that it lies below water nearer the surface that is influenced by long-term atmospheric cycles.

    The warming water probably comes from the Sea of Okhotsk, between Russia and Japan, where surface water becomes very dense and then spreads east across the Pacific. The Sea of Okhotsk is known to have warmed over the past 50 years, and other studies have shown that the water takes a decade or two to cross the Pacific and reach the Washington coast.

    s
    Map of the Sea of Okhotsk

    “We began the collaboration when we realized this is also the most sensitive depth for methane hydrate deposits,” Hautala said. She believes the same ocean currents could be warming intermediate-depth waters from Northern California to Alaska, where frozen methane deposits are also known to exist.

    m
    The yellow dots show all the ocean temperature measurements off the Washington coast from 1970 to 2013. The green triangles are places where scientists and fishermen have seen columns of bubbles. The stars are where the UW researchers took more measurements to check whether the plumes are due to warming water.Una Miller / UW

    m
    Researchers used a coring machine to gather samples of sediment off Washington’s coast to see if observations match their calculations for warming-induced methane release. The photo was taken in October aboard the UW’s Thomas G. Thompson research vessel.Robert Cannata / UW

    Warming water causes the frozen edge of methane hydrate to move into deeper water. On land, as the air temperature warms on a frozen hillside, the snowline moves uphill. In a warming ocean, the boundary between frozen and gaseous methane would move deeper and farther offshore. Calculations in the paper show that since 1970 the Washington boundary has moved about 1 kilometer – a little more than a half-mile – farther offshore. By 2100, the boundary for solid methane would move another 1 to 3 kilometers out to sea.

    Estimates for the future amount of gas released from hydrate dissociation this century are as high as 0.4 million metric tons per year off the Washington coast, or about quadruple the amount of methane from the Deepwater Horizon blowout each year.

    Still unknown is where any released methane gas would end up. It could be consumed by bacteria in the seafloor sediment or in the water, where it could cause seawater in that area to become more acidic and oxygen-deprived. Some methane might also rise to the surface, where it would release into the atmosphere as a greenhouse gas, compounding the effects of climate change.
    researchers on ship

    2
    Evan Solomon (right) and Marta Torres (left, OSU) aboard the UW’s Thomas G. Thompson research vessel in October, with fluid samples from the seafloor that will help answer whether the columns of methane bubbles are due to ocean warming.Robert Cannata / UW

    Researchers now hope to verify the calculations with new measurements. For the past few years, curious fishermen have sent UW oceanographers sonar images showing mysterious columns of bubbles. Solomon and Johnson just returned from a cruise to check out some of those sites at depths where Solomon believes they could be caused by warming water.

    “Those images the fishermen sent were 100 percent accurate,” Johnson said. “Without them we would have been shooting in the dark.”

    Johnson and Solomon are analyzing data from that cruise to pinpoint what’s triggering this seepage, and the fate of any released methane. The recent sightings of methane bubbles rising to the sea surface, the authors note, suggests that at least some of the seafloor gas may reach the surface and vent to the atmosphere.

    The research was funded by the National Science Foundation and the U.S. Department of Energy. The other co-author is Robert Harris at Oregon State University.

    See the full article here.

    Please help promote STEM in your local schools.

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    Stem Education Coalition

    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us — the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 11:30 am on December 5, 2014 Permalink | Reply
    Tags: , , , , , University of Washington   

    From U Washington 

    U Washington

    University of Washington

    December 2, 2014
    Peter Kelley

    Planets orbiting close to low-mass stars — easily the most common stars in the universe — are prime targets in the search for extraterrestrial life.

    But new research led by an astronomy graduate student at the University of Washington indicates some such planets may have long since lost their chance at hosting life because of intense heat during their formative years.

    m
    Illustration of a low-mass, M dwarf star, seen from an orbiting rocky planet. NASA / JPL

    Low-mass stars, also called M dwarfs, are smaller than the sun, and also much less luminous, so their habitable zone tends to be fairly close in. The habitable zone is that swath of space that is just right to allow liquid water on an orbiting planet’s surface, thus giving life a chance.

    Planets close to their host stars are easier for astronomers to find than their siblings farther out. Astronomers discover and measure these worlds by studying the slight reduction in light when they transit, or pass in front of their host star; or by measuring the star’s slight “wobble” in response to the planet’s gravity, called the radial velocity method.

    But in a paper to be published in the journal Astrobiology, doctoral student Rodrigo Luger and co-author Rory Barnes, a UW research assistant professor, find through computer simulations that some planets close to low-mass stars likely had their water and atmospheres burned away when they were still forming.

    “All stars form in the collapse of a giant cloud of interstellar gas, which releases energy in the form of light as it shrinks,” Luger said. “But because of their lower masses, and therefore lower gravities, M dwarfs take longer to fully collapse — on the order of many hundreds of millions of years.”

    “Planets around these stars can form within 10 million years, so they are around when the stars are still extremely bright. And that’s not good for habitability, since these planets are going to initially be very hot, with surface temperatures in excess of a thousand degrees. When this happens, your oceans boil and your entire atmosphere becomes steam.”

    Also boding ill for the atmospheres of these worlds is the fact that M dwarf stars emit a lot of X-ray and ultraviolet light, which heats the upper atmosphere to thousands of degrees and causes gas to expand so quickly it leaves the planet and is lost to space, Luger said.

    “So, many of the planets in the habitable zones of M dwarfs could have been dried up by this process early on, severely decreasing their chance of actually being habitable.”

    A side effect of this process, Luger and Barnes write, is that ultraviolet radiation can split up water into its component hydrogen and oxygen atoms. The lighter hydrogen escapes the atmosphere more easily, leaving the heavier oxygen atoms behind. While some oxygen is clearly good for life, as on Earth, too much oxygen can be a negative factor for the origin of life.

    “Rodrigo has shown that this prolonged runaway greenhouse phase can produce huge atmospheres full of oxygen — like, 10 times denser than that of Venus and all oxygen,” said Barnes. “Searches for life often rely on oxygen as a tracer of extraterrestrial life — so the abiological production of such huge quantities of oxygen could confound our search for life on exoplanets.”

    Luger said the working title of their paper was Mirage Earths.

    “Because of the oxygen they build up, they could look a lot like Earth from afar — but if you look more closely you’ll find that they’re really a mirage; there’s just no water there.”

    The research was funded by NASA’s Astrobiology Institute, through the Virtual Planetary Laboratory, headquartered at the UW.

    See the full article here.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us — the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
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