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  • richardmitnick 9:21 am on May 25, 2017 Permalink | Reply
    Tags: "Unleashing the Power of Synthetic Proteins, , , , , U Washington   

    From Nautilus: “Unleashing the Power of Synthetic Proteins” 

    Nautilus

    Nautilus

    March 2017
    David Baker, Baker Lab, U Washngton, BOINC Rosetta@home project



    Dr. David Baker


    Rosetta@home project



    The opportunities for the design of synthetic proteins are endless.

    Proteins are the workhorses of all living creatures, fulfilling the instructions of DNA. They occur in a wide variety of complex structures and carry out all the important functions in our body and in all living organisms—digesting food, building tissue, transporting oxygen through the bloodstream, dividing cells, firing neurons, and powering muscles. Remarkably, this versatility comes from different combinations, or sequences, of just 20 amino acid molecules. How these linear sequences fold up into complex structures is just now beginning to be well understood (see box).

    Even more remarkably, nature seems to have made use of only a tiny fraction of the potential protein structures available—and there are many. Therein lies an amazing set of opportunities to design novel proteins with unique structures: synthetic proteins that do not occur in nature, but are made from the same set of naturally-occurring amino acids. These synthetic proteins can be “manufactured” by harnessing the genetic machinery of living things, such as in bacteria given appropriate DNA that specify the desired amino acid sequence. The ability to create and explore such synthetic proteins with atomic level accuracy—which we have demonstrated—has the potential to unlock new areas of basic research and to create practical applications in a wide range of fields.

    The design process starts by envisioning a novel structure to solve a particular problem or accomplish a specific function, and then works backwards to identify possible amino acid sequences that can fold up to this structure. The Rosetta protein modelling and design software identifies the most likely candidates—those that fold to the lowest energy state for the desired structure. Those sequences then move from the computer to the lab, where the synthetic protein is created and tested—preferably in partnership with other research teams that bring domain expertise for the type of protein being created.

    At present no other advanced technology can beat the remarkable precision with which proteins carry out their unique and beautiful functions. The methods of protein design expand the reach of protein technology, because the possibilities to create new synthetic proteins are essentially unlimited. We illustrate that claim with some of the new proteins we have already developed using this design process, and with examples of the fundamental research challenges and areas of practical application that they exemplify:

    2
    This image shows a designed synthetic protein of a type known as a TIM-barrel. Naturally occurring TIM-barrel proteins are found in a majority of enzymes, the catalysts that facilitate biochemical reactions in our bodies, in part because the circular cup-like or barrel shape at their core provides an appropriate space for the reaction to occur. The synthetic protein shown here has an idealized TIM-barrel template or blueprint that can be customized with pockets and binding sites and catalytic agents specific to particular reactants; the eight helical arms of the protein enhance the reaction space. This process can be used to design whole new classes of enzymes that do not occur in nature. Illustration and protein design prepared by Possu Huang in David Baker’s laboratory, University of Washington.

    Catalysts for clean energy and medicine. Protein enzymes are the most efficient catalysts known, far more so than any synthesized by inorganic chemists. Part of that efficiency comes from their ability to accurately position key parts of the enzyme in relation to reacting molecules, providing an environment that accelerates a reaction or lowers the energy needed for it to occur. Exactly how this occurs remains a fundamental problem which more experience with synthetic proteins may help to resolve.

    Already we have produced synthetic enzymes that catalyze potentially useful new metabolic pathways. These include: reactions that take carbon dioxide from the atmosphere and convert it into organic molecules, such as fuels, more efficiently than any inorganic catalyst, potentially enabling a carbon-neutral source of fuels; and reactions that address unsolved medical problems, including a potential oral therapeutic drug for patients with celiac disease that breaks down gluten in the stomach and other synthetic proteins to neutralize toxic amyloids found in Alzheimer’s disease.

    We have also begun to understand how to design, de novo, scaffolds that are the basis for entire superfamilies of known enzymes (Fig. 1) and other proteins known to bind the smaller molecules involved in basic biochemistry. This has opened the door for potential methods to degrade pollutants or toxins that threaten food safety.

    New super-strong materials. A potentially very useful new class of materials is that formed by hybrids of organic and inorganic matter. One naturally occurring example is abalone shell, which is made up of a combination of calcium carbonate bonded with proteins that results in a uniquely tough material. Apparently, other proteins involved in the process of forming the shell change the way in which the inorganic material precipitates onto the binding protein and also help organize the overall structure of the material. Synthetic proteins could potentially duplicate this process and expand this class of materials. Another class of materials are analogous to spider silk—organic materials that are both very strong and yet biodegradable—for which synthetic proteins might be uniquely suited, although how these are formed is not yet understood. We have also made synthetic proteins that create an interlocking pattern to form a surface only one molecule thick, which suggest possibilities for new anti-corrosion films or novel organic solar cells.

    Targeted therapeutic delivery. Self-assembling protein materials make a wide variety of containers or external barriers for living things, from protein shells for viruses to the exterior wall of virtually all living cells. We have developed a way to design and build similar containers: very small cage-like structures—protein nanoparticles—that self-assemble from one or two synthetic protein building blocks (Fig. 2). We do this extremely precisely, with control at the atomic level. Current work focuses on building these protein nanoparticles to carry a desired cargo—a drug or other therapeutic—inside the cage, while also incorporating other proteins of interest on their surface. The surface protein is chosen to bind to a similar protein on target cells.

    These self-assembling particles are a completely new way of delivering drugs to cells in a targeted fashion, avoiding harmful effects elsewhere in the body. Other nanoparticles might be designed to penetrate the blood-brain barrier, in order to deliver drugs or other therapies for brain diseases. We have also generated methods to design proteins that disrupt protein-protein interactions and proteins that bind to small molecules for use in biosensing applications, such as identifying pathogens. More fundamentally, synthetic proteins may well provide the tools that enable improved targeting of drugs and other therapies, as well as an improved ability to bond therapeutic packages tightly to a target cell wall.

    5
    A tiny 20-sided protein nanoparticle that can deliver drugs or other therapies to specific cells in the body with minimal side effects. The nanoparticle self-assembles from two types of synthetic proteins. Illustration and protein design prepared by Jacob Bale in David Baker’s laboratory, University of Washington.

    Novel vaccines for viral diseases. In addition to drug delivery, self-assembling protein nanoparticles are a promising foundation for the design of vaccines. By displaying stabilized versions of viral proteins on the surfaces of designed nanoparticles, we hope to elicit strong and specific immune responses in cells to neutralize viruses like HIV and influenza. We are currently investigating the potential of these nanoparticles as vaccines against a number of viruses. The thermal stability of these designer vaccines should help eliminate the need for complicated cold chain storage systems, broadening global access to life saving vaccines and supporting goals for eradication of viral diseases. The ability to shape these designed vaccines with atomic level accuracy also enables a systematic study of how immune systems recognize and defend against pathogens. In turn, the findings will support development of tolerizing vaccines, which could train the immune system to stop attacking host tissues in autoimmune disease or over-reacting to allergens in asthma.

    New peptide medicines. Most approved drugs are either bulky proteins or small molecules. Naturally occurring peptides (amino acid compounds) that are constrained or stabilized so that they precisely complement their biological target are intermediate in size, and are among the most potent pharmacological compounds known. In effect, they have the advantages of both proteins and small molecule drugs. The antibiotic cyclosporine is a familiar example. Unfortunately such peptides are few in number.

    We have recently demonstrated a new computational design method that can generate two broad classes of peptides that have exceptional stability against heat or chemical degradation. These include peptides that can be genetically encoded (and can be produced by bacteria) as well as some that include amino acids that do not occur in nature. Such peptides are, in effect, scaffolds or design templates for creating whole new classes of peptide medicines.

    In addition, we have developed general methods for designing small and stable proteins that bind strongly to pathogenic proteins. One such designed protein binds the viral glycoprotein hemagglutinin, which is responsible for influenza entry into cells. These designed proteins protect infected mice in both a prophylactic and therapeutic manner and therefore are potentially very powerful anti-flu medicines. Similar methods are being applied to design therapeutic proteins against the Ebola virus and other targets that are relevant in cancer or autoimmune diseases. More fundamentally, synthetic proteins may be useful as test probes in working out the detailed molecular chemistry of the immune system.

    Protein logic systems. The brain is a very energy-efficient logic system based entirely on proteins. Might it be possible to build a logic system—a computer—from synthetic proteins that would self-assemble and be both cheaper and more efficient than silicon logic systems? Naturally occurring protein switches are well studied, but building synthetic switches remains an unsolved challenge. Quite apart from bio-technology applications, understanding protein logic systems may have more fundamental results, such as clarifying how our brains make decisions or initiate processes.

    The opportunities for the design of synthetic proteins are endless, with new research frontiers and a huge variety of practical applications to be explored. In effect, we have an emerging ability to design new molecules to solve specific problems—just as modern technology does outside the realm of biology. This could not be a more exciting time for protein design.

    Predicting Protein Structure

    If we were unable to predict the structure that results from a given sequence of amino acids, synthetic protein design would be an almost impossible task. There are 20 naturally-occurring amino acids, which can be linked in any order and can fold into an astronomical number of potential structures. Fortunately the structure prediction problem is now well on the way toward being solved by the Rosetta protein modeling software.

    The Rosetta tool evaluates possible structures, calculates their energy states, and identifies the lowest energy structure—usually, the one that occurs in a living organism. For smaller proteins, Rosetta predictions are already reasonably accurate. The power and accuracy of the Rosetta algorithms are steadily improving thanks to the work of a cooperative global network of several hundred protein scientists. New discoveries—such as identifying amino acid pairs that co-evolve in living systems and thus are likely to be co-located in protein structures—are also helping to improve prediction accuracy.

    Our research team has already revealed the structures for more than a thousand protein families, and we expect to be able to predict the structure for nearly any protein within a few years. This is an important achievement with direct significance for basic biology and biomedical science, since understanding structure leads to understanding the function of the myriad proteins found in the human body and in all living things. Moreover, predicting protein structure is also the critical enabling tool for designing novel, “synthetic” proteins that do not occur in nature.

    How to Create Synthetic Proteins that Solve Important Problems

    6
    A graduate student in the Baker lab and a researcher at the Institute for Protein Design discuss a bacterial culture (in the Petri dish) that is producing synthetic proteins. Source: Laboratory of David Baker, University of Washington.

    Now that it is possible to design a variety of new proteins from scratch, it is imperative to identify the most pressing problems that need to be solved, and focus on designing the types of proteins that are needed to address these problems. Protein design researchers need to collaborate with experts in a wide variety of fields to take our work from initial protein design to the next stages of development. As the examples above suggest, those partners should include experts in industrial scale catalysis, fundamental materials science and materials processing, biomedical therapeutics and diagnostics, immunology and vaccine design, and both neural systems and computer logic. The partnerships should be sustained over multiple years in order to prioritize the most important problems and test successive potential solutions.

    A funding level of $100M over five years would propel protein design to the forefront of biomedical research, supporting multiple and parallel collaborations with experts worldwide to arrive at breakthroughs in medicine, energy, and technology, while also furthering a basic understanding of biological processes. Current funding is unable to meet the demands of this rapidly growing field and does not allow for the design and production of new proteins at an appropriate scale for testing and ultimately production, distribution, and implementation. Private philanthropy could overcome this deficit and allow us to jump ahead to the next generation of proteins—and thus to use the full capacity of the amino acid legacy that evolution has provided us.

    My BOINC

    See the full article here .

    Please help promote STEM in your local schools.

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    Stem Education Coalition

    Welcome to Nautilus. We are delighted you joined us. We are here to tell you about science and its endless connections to our lives. Each month we choose a single topic. And each Thursday we publish a new chapter on that topic online. Each issue combines the sciences, culture and philosophy into a single story told by the world’s leading thinkers and writers. We follow the story wherever it leads us. Read our essays, investigative reports, and blogs. Fiction, too. Take in our games, videos, and graphic stories. Stop in for a minute, or an hour. Nautilus lets science spill over its usual borders. We are science, connected.

     
  • richardmitnick 10:44 am on May 15, 2017 Permalink | Reply
    Tags: , , , Seattle Times, U Washington   

    From Seattle Times via U Washington: “What happens after a swarm of earthquakes strikes the Seattle region? Here’s what the experts say” 

    U Washington

    University of Washington

    1

    Seattle Times

    1
    Local seismologists aren’t sure whether the swarm of minor earthquakes near Bremerton, and other temblors, may signal the coming of a much larger event.

    May 12, 2017
    Bob Young

    After a flurry of minor earthquakes struck the Seattle area Thursday, local seismologists aren’t sure if the quakes will continue, or if they portend a more powerful and dangerous event to come.

    Concerns shifted from “Did you feel it?” to “What does it mean?” on Thursday after two morning earthquakes near Bremerton, one with a magnitude of 3.6, and another quake off Whidbey Island with a 3.4 magnitude.

    The Bremerton quakes were the latest in a swarm of 13 minor earthquakes that have hit the Kitsap Peninsula since May 3.

    A much smaller 1.7 magnitude quake was recorded Thursday near Granite Falls at 2:37 p.m.

    3

    Earthquakes registering between magnitudes 2.0 and 3.9 are considered minor.

    Seismologists at the University of Washington’s Pacific Northwest Seismic Network (PNSN) are particularly interested in whether the swarm might be related to the Seattle fault zone.

    The Seattle Fault is an area of thrust faults that run through Seattle and across the Puget Sound. The last time the fault ruptured in a big way was about 1,100 years ago. The resulting quake measured at least magnitude 7 and thrust up shorelines in West Seattle and Bainbridge Island by 20 feet or more. It also triggered a tsunami that swept through Puget Sound.

    In PNSN’s “Seismo blog” Thursday afternoon, Renate Hartog wrote that the Seattle Fault runs right through the area of the current swarm. But the quakes were deep, striking at about 25 kilometers.

    “But, remember, these earthquakes are very far below the surface and can therefore not be of any of the Seattle Fault strands,” Hartog wrote.

    See the full article here .

    You can help many citizen scientists in detecting earthquakes and getting the data to emergency services people in affected area.

    QCN bloc

    Quake-Catcher Network

    The Quake-Catcher Network is a collaborative initiative for developing the world’s largest, low-cost strong-motion seismic network by utilizing sensors in and attached to internet-connected computers. With your help, the Quake-Catcher Network can provide better understanding of earthquakes, give early warning to schools, emergency response systems, and others. The Quake-Catcher Network also provides educational software designed to help teach about earthquakes and earthquake hazards.

    After almost eight years at Stanford, and a year at CalTech, the QCN project is moving to the University of Southern California Dept. of Earth Sciences. QCN will be sponsored by the Incorporated Research Institutions for Seismology (IRIS) and the Southern California Earthquake Center (SCEC).

    The Quake-Catcher Network is a distributed computing network that links volunteer hosted computers into a real-time motion sensing network. QCN is one of many scientific computing projects that runs on the world-renowned distributed computing platform Berkeley Open Infrastructure for Network Computing (BOINC).

    BOINCLarge

    BOINC WallPaper

    The volunteer computers monitor vibrational sensors called MEMS accelerometers, and digitally transmit “triggers” to QCN’s servers whenever strong new motions are observed. QCN’s servers sift through these signals, and determine which ones represent earthquakes, and which ones represent cultural noise (like doors slamming, or trucks driving by).

    There are two categories of sensors used by QCN: 1) internal mobile device sensors, and 2) external USB sensors.

    Mobile Devices: MEMS sensors are often included in laptops, games, cell phones, and other electronic devices for hardware protection, navigation, and game control. When these devices are still and connected to QCN, QCN software monitors the internal accelerometer for strong new shaking. Unfortunately, these devices are rarely secured to the floor, so they may bounce around when a large earthquake occurs. While this is less than ideal for characterizing the regional ground shaking, many such sensors can still provide useful information about earthquake locations and magnitudes.

    USB Sensors: MEMS sensors can be mounted to the floor and connected to a desktop computer via a USB cable. These sensors have several advantages over mobile device sensors. 1) By mounting them to the floor, they measure more reliable shaking than mobile devices. 2) These sensors typically have lower noise and better resolution of 3D motion. 3) Desktops are often left on and do not move. 4) The USB sensor is physically removed from the game, phone, or laptop, so human interaction with the device doesn’t reduce the sensors’ performance. 5) USB sensors can be aligned to North, so we know what direction the horizontal “X” and “Y” axes correspond to.

    If you are a science teacher at a K-12 school, please apply for a free USB sensor and accompanying QCN software. QCN has been able to purchase sensors to donate to schools in need. If you are interested in donating to the program or requesting a sensor, click here.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.

    Earthquake safety is a responsibility shared by billions worldwide. The Quake-Catcher Network (QCN) provides software so that individuals can join together to improve earthquake monitoring, earthquake awareness, and the science of earthquakes. The Quake-Catcher Network (QCN) links existing networked laptops and desktops in hopes to form the worlds largest strong-motion seismic network.

    Below, the QCN Quake Catcher Network map
    QCN Quake Catcher Network map

    Meet The Quake-Catcher Network

    QCN bloc

    Quake-Catcher Network

    The Quake-Catcher Network is a collaborative initiative for developing the world’s largest, low-cost strong-motion seismic network by utilizing sensors in and attached to internet-connected computers. With your help, the Quake-Catcher Network can provide better understanding of earthquakes, give early warning to schools, emergency response systems, and others. The Quake-Catcher Network also provides educational software designed to help teach about earthquakes and earthquake hazards.

    After almost eight years at Stanford, and a year at CalTech, the QCN project is moving to the University of Southern California Dept. of Earth Sciences. QCN will be sponsored by the Incorporated Research Institutions for Seismology (IRIS) and the Southern California Earthquake Center (SCEC).

    The Quake-Catcher Network is a distributed computing network that links volunteer hosted computers into a real-time motion sensing network. QCN is one of many scientific computing projects that runs on the world-renowned distributed computing platform Berkeley Open Infrastructure for Network Computing (BOINC).

    The volunteer computers monitor vibrational sensors called MEMS accelerometers, and digitally transmit “triggers” to QCN’s servers whenever strong new motions are observed. QCN’s servers sift through these signals, and determine which ones represent earthquakes, and which ones represent cultural noise (like doors slamming, or trucks driving by).

    There are two categories of sensors used by QCN: 1) internal mobile device sensors, and 2) external USB sensors.

    Mobile Devices: MEMS sensors are often included in laptops, games, cell phones, and other electronic devices for hardware protection, navigation, and game control. When these devices are still and connected to QCN, QCN software monitors the internal accelerometer for strong new shaking. Unfortunately, these devices are rarely secured to the floor, so they may bounce around when a large earthquake occurs. While this is less than ideal for characterizing the regional ground shaking, many such sensors can still provide useful information about earthquake locations and magnitudes.

    USB Sensors: MEMS sensors can be mounted to the floor and connected to a desktop computer via a USB cable. These sensors have several advantages over mobile device sensors. 1) By mounting them to the floor, they measure more reliable shaking than mobile devices. 2) These sensors typically have lower noise and better resolution of 3D motion. 3) Desktops are often left on and do not move. 4) The USB sensor is physically removed from the game, phone, or laptop, so human interaction with the device doesn’t reduce the sensors’ performance. 5) USB sensors can be aligned to North, so we know what direction the horizontal “X” and “Y” axes correspond to.

    If you are a science teacher at a K-12 school, please apply for a free USB sensor and accompanying QCN software. QCN has been able to purchase sensors to donate to schools in need. If you are interested in donating to the program or requesting a sensor, click here.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.

    Earthquake safety is a responsibility shared by billions worldwide. The Quake-Catcher Network (QCN) provides software so that individuals can join together to improve earthquake monitoring, earthquake awareness, and the science of earthquakes. The Quake-Catcher Network (QCN) links existing networked laptops and desktops in hopes to form the worlds largest strong-motion seismic network.

    Below, the QCN Quake Catcher Network map
    QCN Quake Catcher Network map

    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 9:04 am on May 1, 2017 Permalink | Reply
    Tags: , , , U Washington   

    From U Washington: “Can early experiences with computers, robots increase STEM interest among young girls?” 

    U Washington

    University of Washington

    April 27, 2017
    Kim Eckart

    1
    Penn State/Flickr

    Girls start believing they aren’t good at math, science and even computers at a young age — but providing fun STEM activities at school and home may spark interest and inspire confidence.

    A study from the University of Washington’s Institute for Learning & Brain Sciences (I-LABS) finds that, when exposed to a computer-programming activity, 6-year-old girls expressed greater interest in technology and more positive attitudes about their own skills and abilities than girls who didn’t try the activity.

    The results suggest both a need and an opportunity for teaching computer science, in particular, in early elementary school, said Allison Master, a research scientist at I-LABS and the study’s lead author. Introducing concepts and skills when girls are young can boost their confidence and prompt interest in a field in which women today are underrepresented.

    “As a society, we have these built-in beliefs that are pushing boys toward certain activities more than girls. So our thought was, if you give equal experiences to boys and girls, what happens?” Master said. “We found that if you give them access to same opportunities, then girls and boys have the same response — equal interest and confidence.”

    The study, published online in the Journal of Experimental Child Psychology, involved 96 6-year-olds, evenly divided among boys and girls, who were randomly assigned one of three groups. In the first group, each child programmed a robot, then answered survey questions; in the second group, each played a storytelling card game, then answered the same questions, while those in the third group only answered the questions. The survey was designed to collect kids’ opinions of technology activities, like the robot, and their beliefs about whether girls or boys are better at computer programming and robotics.

    Programming, the researchers explained to the children, is “when you tell a computer or a robot or a phone what to do.”

    For the robot activity, children chose an animal-like robot. They first followed step-by-step instructions on a smartphone to “tell” it to move forward, backward, right or left, then chose the instructions themselves, effectively programming the phone to control the movements of the robots. The study found that after completing the robot activity, the boys and girls showed equal interest in technology and their own feelings of self-efficacy, or confidence in their own abilities.

    But when compared to the “control group” of children who played the card game or only answered the survey without playing a game, the difference was striking: The designed activity with the robot reduced the gender gap in technology interest by 42 percent, and the gap in self-efficacy by 80 percent.

    In other words, girls who programmed the robot were much more likely to express interest in programming and confidence in their own abilities to perform technology-related tasks than the girls who didn’t work with the robot.

    Co-author and I-LABS co-director Andrew Meltzoff said, “Experience in programming the robot movement was something that both boys and girls thought was fun. But the most important finding is that we brought the girls’ interest and motivation in STEM up to the level of the boys. This was a big impact for a brief, well-designed intervention. How long will it last? That’s an important question for future scientific experiments.”

    The findings suggest that incorporating more programming activities in the classroom or at home may ignite and sustain girls’ interest, Master said. Summer camps, after-school programs and other partner- or group-oriented activities present natural opportunities.

    “The important thing is to make activities accessible to all children in a fun way that also helps them build skills,” she said.

    The study’s robot activity did not, however, appear to change the children’s stereotypes about whether boys or girls are better at programming and robotics. While the girls who programmed the robot indicated greater confidence in their own abilities, that confidence did not alter their stereotypes, picked up from the culture, about girls and boys in general. The authors pointed to the potential of other experiences, such as meeting or seeing a woman programming a robot or working in a STEM field, for shifting these more deeply-held stereotypes.

    “Stereotypes get built up in our heads from many different sources and experiences, but perhaps if we give girls more experience doing these kinds of activities, that will give them more resources to resist those stereotypes,” Master said. “They might be able to say, ‘I can still be good at this and enjoy it, despite the cultural stereotypes.’” The researchers hope to test this in future studies.

    Researchers on the study also included Sapna Cheryan, associate professor in the Department of Psychology, along with Adriana Moscatelli of Play Works Studio in Seattle. The study was funded by the National Science Foundation.

    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 9:47 am on April 26, 2017 Permalink | Reply
    Tags: , , , U Washington   

    From U Washington: “With autism diagnoses on the rise, UW establishes clinic for babies” 

    U Washington

    University of Washington

    April 25, 2017
    Kim Eckart

    1
    Research scientist Tanya St. John works with a baby at the University of Washington Autism Center.

    To new parents, a baby’s every gurgle and glance are fascinating, from a smile at mom or dad to a reach for a colorful toy.

    But when a baby doesn’t look at parents and caregivers, imitate gestures and sounds, or engage in play, parents have questions. And a growing number are bringing their babies to the University of Washington Autism Center for answers.

    As autism diagnoses have increased over the years — an estimated one in 68 people has autism spectrum disorder — parents have looked for signs earlier in their children’s lives, especially if they have an older child with autism. While the average age for autism diagnosis in the United States is around 4 years, a growing body of research and practice suggests accurate assessment of children as young as 12 months old, though rare, is not only possible, but also useful.

    “Many people have an unfounded belief that you have to wait until 36 months of age to diagnose autism. That is not the case,” said Annette Estes, who directs the UW Autism Center and is a research affiliate at the Center on Human Development and Disability. “There is a great deal of value in diagnosing as soon as symptoms emerge — it gives parents a great deal of relief and allows appropriate intervention to begin.”

    With only a few infant autism clinics scattered around the country, families have brought their infants to the UW Autism Center from elsewhere in the United States, and in a few cases, the world, Estes said. The natural next step was to dedicate services to them.

    The center’s Infant Clinic, officially established this spring, provides four clinical psychologists to evaluate infants and toddlers up to 24 months of age, along with teams of behavior analysts to create a treatment plan with clinic- and home-based activities — just as would happen with older children. The difference, Estes explained, is the specific expertise with the infant population.

    The Autism Center, part of the UW Department of Speech & Hearing Sciences, has conducted a number of studies into the signs of autism and the effectiveness of intervention strategies. Earlier this year, Nature published findings from the center’s involvement in a North American effort that examined brain biomarkers in infants, including those with at least one autistic sibling. The study showed that magnetic resonance imaging (MRI) helped correctly identify 80 percent of babies who would go on to be diagnosed with autism at 2 years of age Researchers are wrapping up another study, focused on toddlers 12 to 24 months old, that looks at structured intervention activities versus a more play-based approach.

    That work bolsters the center’s diagnostic and treatment capacity with infants, Estes explained.

    For older infants and toddlers, psychologists focus on social and communication deficits, said Tanya St. John, a research scientist and clinical psychologist at the center. Typically-developing infants and toddlers spend time engaging and interacting with their caregivers, which helps them learn language and fosters their social development.

    “Children showing the early signs of autism don’t do those things as much as expected, or they don’t do them at all,” St. John said. “We look at a repertoire of other behaviors as well: Do they do the same thing over and over? Do they pick up a toy and inspect it closely? Do they have a hard time when you change activities?”

    It is less common to diagnose a very young child, St. John said, but when that happens, it’s typically because the symptoms are clear.

    “Most people are hesitant to give a diagnosis to a child who isn’t showing clear signs of ASD. We tend to give early diagnoses to children who meet all of the criteria for a diagnosis, and if they’re not, we take an assessment-and-monitoring approach, where we give parents specific recommendations based on the child’s current challenges, and then see the child back 3 to 6 months later,” she explained.

    Treatment would follow the same general trajectory, depending on the infant’s symptoms and development, as toddlers and older children. Specialists might work on communication, for instance, through strategies to encourage eye contact. As children age, they work with specialists on cognitive, social and motor skills, both individually and in peer groups. Much of the Autism Center’s approach is designed to give parents tools that they can use at home, Estes said.

    Spotting the signs of autism early is critical, she added, so that a family can connect with the right services, whether in the clinic or out in the community.

    A little over three years ago, the Autism Center accurately diagnosed its youngest client: a 10-month-old boy. Thanks to subsequent intervention activities, Estes said, he has developed communication skills, engages socially and is thriving in preschool.

    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 10:28 am on April 13, 2017 Permalink | Reply
    Tags: , , LiDAR, Technology to improve rockfall analysis on cliffs could save money lives, U Washington   

    From U Washington: “Technology to improve rockfall analysis on cliffs could save money, lives” 

    U Washington

    University of Washington

    April 11, 2017
    Jennifer Langston

    1
    This LiDAR image of a rock slope on Alaska’s Glenn Highway shows the “kinetic energy” of the slope, with red indicating a higher hazard from rockfalls.Matthew O’Banion/Oregon State University

    Pacific Northwest engineers have developed a new, automated technology to analyze the potential for rockfalls from cliffs onto roads and areas below, which should speed and improve this type of risk evaluation, help protect public safety and ultimately save money and lives.

    Called a “rockfall activity index,” the system is based on the powerful abilities of light detection and ranging, or LIDAR technology. It should expedite and add precision to what’s now a somewhat subjective, time-consuming process to determine just how dangerous a cliff is to the people, vehicles, roads or structures below it.

    This is a multimillion-dollar global problem, experts say, of significant concern to transportation planners.

    It’s a particular concern in the Pacific Northwest with its many mountain ranges, heavy precipitation, erosion of steep cliffs and unstable slopes, and thousands of roads that thread their way through that terrain. The evaluation system now most widely used around the world, in fact, was developed by the Oregon Department of Transportation more than 25 years ago.

    The new technology should improve on that approach, according to researchers who developed it from the University of Washington, Oregon State University and the University of Alaska Fairbanks. Findings were just published in Engineering Geology.

    “Transportation agencies and infrastructure providers are increasingly seeking ways to improve the reliability and safety of their systems, while at the same time reducing costs,” said Joe Wartman, associate professor of civil and environmental engineering at the University of Washington, and corresponding author of the study.

    “As a low-cost, high-resolution landslide hazard assessment system, our rockfall activity index methodology makes a significant step toward improving both protection and efficiency.”

    The new approach could replace the need to personally analyze small portions of a cliff at a time, looking for cracks and hazards, with analysts sometimes even rappelling down it to assess risks. LIDAR analysis can map large areas in a short period, and allow data to be analyzed by a computer.

    “Rockfalls are a huge road maintenance issue,” said co-author Michael Olsen, an associate professor of geomatics at Oregon State University.

    “Pacific Northwest and Alaskan highways, in particular, are facing serious concerns for these hazards. A lot of our highways in mountainous regions were built in the 1950s and 60s, and the cliffs above them have been facing decades of erosion that in many places cause at least small rockfalls almost daily. At the same time traffic is getting heavier, along with increasing danger to the public and even people who monitor the problem.”

    The study, based on some examples in southern Alaska, showed the new system could evaluate rockfalls in ways that very closely matched the dangers actually experienced. It produces data on the “energy release” to be expected from a given cliff, per year, that can be used to identify the cliffs and roads at highest risk and prioritize available mitigation budgets to most cost-effectively protect public safety.

    Tens of millions of dollars are spent each year in the U.S. on rock slope maintenance and mitigation.

    “This should improve and speed assessments, reduce the risks to people doing them, and hopefully identify the most serious problems before we have a catastrophic failure,” Olsen said.

    The technology is now complete and ready for use, researchers said, although they are continuing to develop its potential, possibly with the use of flying drones to expand the data that can be obtained.

    This research was supported by the UW-based Pacific Northwest Transportation Consortium, the National Science Foundation and the Alaska Department of Transportation and Public Facilities. Co-authors are Lisa Dunham, a UW graduate in civil and environmental engineering now at McMillen Jacobs Associates in Seattle; graduate assistant Matthew O’Banion at OSU; and Keith Cunningham, research assistant professor of remote sensing at the University of Alaska Fairbanks.

    For more information, contact Joe Wartman at wartman@uw.edu or 206-685-4806.

    See the full article here .

    Please help promote STEM in your local schools.

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    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 1:49 pm on April 3, 2017 Permalink | Reply
    Tags: , , , Slow slipping of Earth’s crust, U Washington   

    From U Washington: “Using a method from Wall Street to track slow slipping of Earth’s crust” 

    U Washington

    University of Washington

    March 28, 2017
    Hannah Hickey

    1
    A GPS station near Mount St. Helens in September 2014.Mike Gottlieb/UNAVCO

    Stock traders have long used specialized trackers to decide when to buy or sell a stock, or when the market is beginning to make a sudden swing.

    A new University of Washington study finds that the same technique can be used to detect gradual movement of tectonic plates, what are called “slow slip” earthquakes. These movements do not unleash damaging amounts of seismic energy, but scientists are just beginning to understand how they may be linked to the Big One.

    A new technique can quickly pinpoint slow slips from a single Global Positioning System station. It borrows the financial industry’s relative strength index , a measure of how quickly a stock’s price is changing, to detect slow slips within a string of GPS observations.

    The paper was published in December in the Journal of Geophysical Research: Solid Earth.

    “I’ve always had an interest in finance, and if you go to any stock ticker website there’s all these different indicators,” said lead author Brendan Crowell, a UW research scientist in Earth and space sciences. “This particular index stood out in its ease of use, but also that it needed no information — like stock volume, volatility or other terms — besides the single line of data that it analyzes for unusual behavior.”

    The study tests the method on more than 200 GPS stations that recorded slow slips between 2005 and 2016 along the Cascadia fault zone, which runs from northern California up to northern Vancouver Island.

    “Looking at the Cascadia Subduction Zone — which is the most-studied slow slip area in the world — was a good way to validate the methodology,” Crowell said.

    The results show that this simple technique’s estimates for the size, duration and travel distance for major slow slip events match the results of more exhaustive analyses of observations along the fault.

    Discovered in the early 2000s, slow slips are a type of silent earthquake in which two plates slip harmlessly past one another over weeks or months. In Cascadia the slipping runs backward from the typical motion along the fault. A slow slip slightly increases the chance of a larger earthquake. It also may be providing clues, which scientists don’t yet know how to decipher, to what is happening in the physics at the plate boundary.

    Regular earthquake monitoring relies on seismometers to track the shaking of the ground. That doesn’t work for slow slips, which do not release enough energy to send waves of energy through the Earth’s crust to reach seismometers.

    Instead, detection of slow slips relies on GPS data.

    “If you don’t have much seismic energy, you need to measure what’s happening with something else. GPS is directly measuring the displacement of the Earth,” Crowell said.

    At GPS stations, the same type of sensors used in smartphones are secured to steel pipes that are cemented at least 35 feet (about 10 meters, or three stories) into solid rock. By minimizing the noise, these stations can detect millimeter-scale changes in position at the surface, which can be used to infer movement deep underground.

    2
    Top: The eastward movement along the Cascadia fault (top), calculated relative strength index (middle), and slow-slip event probability (bottom) for a GPS station on southern Vancouver Island.Brendan Crowell/University of Washington

    Using these data to detect slow slips currently means comparing different GPS stations with complex data processing. But thanks to the efforts of stock traders who want to know quickly whether to buy or sell, the new paper shows that the relative strength index can detect a slow slip from a single one of the 213 GPS stations along the Cascadia Subduction Zone.

    The initial success suggests the method could have other geological applications.

    “I want to be able to use this for things beyond slow slip,” Crowell said. “We might use the method to look at the seismic effects of groundwater extraction, volcanic inflation and all kinds of other things that we may not be detecting in the GPS data.”

    The technique could be applied in places that are not as well studied as the Pacific Northwest, where geologic activity is already being closely monitored.

    “This works for stations all over the world — on islands, or areas that are pretty sparsely populated and don’t have a lot of GPS stations,” Crowell said.

    In related research, Crowell has used an Amazon Catalyst grant to integrate GPS, or geodetic, data into the ShakeAlert earthquake alert system. For really big earthquakes, detecting the large, slow shaking is not as accurate for pinpointing the source and size of the quake. It’s more accurate to use GPS to detect how much the ground has actually moved. Tracking ground motion also improves tsunami warnings. Crowell has used the grant to integrate the GPS data into the network’s real-time alerts, which are now in limited beta testing.

    Co-authors of the new paper are Yehuda Bock at Scripps Institution of Oceanography and Zhen Liu at NASA’s Jet Propulsion Laboratory. The research was funded by NASA and the Gordon and Betty Moore Foundation.

    See the full article here .

    You can help many citizen scientists in detecting earthquakes and getting the data to emergency services people in affected area.

    QCN bloc

    Quake-Catcher Network

    The Quake-Catcher Network is a collaborative initiative for developing the world’s largest, low-cost strong-motion seismic network by utilizing sensors in and attached to internet-connected computers. With your help, the Quake-Catcher Network can provide better understanding of earthquakes, give early warning to schools, emergency response systems, and others. The Quake-Catcher Network also provides educational software designed to help teach about earthquakes and earthquake hazards.

    After almost eight years at Stanford, and a year at CalTech, the QCN project is moving to the University of Southern California Dept. of Earth Sciences. QCN will be sponsored by the Incorporated Research Institutions for Seismology (IRIS) and the Southern California Earthquake Center (SCEC).

    The Quake-Catcher Network is a distributed computing network that links volunteer hosted computers into a real-time motion sensing network. QCN is one of many scientific computing projects that runs on the world-renowned distributed computing platform Berkeley Open Infrastructure for Network Computing (BOINC).

    BOINCLarge

    BOINC WallPaper

    The volunteer computers monitor vibrational sensors called MEMS accelerometers, and digitally transmit “triggers” to QCN’s servers whenever strong new motions are observed. QCN’s servers sift through these signals, and determine which ones represent earthquakes, and which ones represent cultural noise (like doors slamming, or trucks driving by).

    There are two categories of sensors used by QCN: 1) internal mobile device sensors, and 2) external USB sensors.

    Mobile Devices: MEMS sensors are often included in laptops, games, cell phones, and other electronic devices for hardware protection, navigation, and game control. When these devices are still and connected to QCN, QCN software monitors the internal accelerometer for strong new shaking. Unfortunately, these devices are rarely secured to the floor, so they may bounce around when a large earthquake occurs. While this is less than ideal for characterizing the regional ground shaking, many such sensors can still provide useful information about earthquake locations and magnitudes.

    USB Sensors: MEMS sensors can be mounted to the floor and connected to a desktop computer via a USB cable. These sensors have several advantages over mobile device sensors. 1) By mounting them to the floor, they measure more reliable shaking than mobile devices. 2) These sensors typically have lower noise and better resolution of 3D motion. 3) Desktops are often left on and do not move. 4) The USB sensor is physically removed from the game, phone, or laptop, so human interaction with the device doesn’t reduce the sensors’ performance. 5) USB sensors can be aligned to North, so we know what direction the horizontal “X” and “Y” axes correspond to.

    If you are a science teacher at a K-12 school, please apply for a free USB sensor and accompanying QCN software. QCN has been able to purchase sensors to donate to schools in need. If you are interested in donating to the program or requesting a sensor, click here.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.

    Earthquake safety is a responsibility shared by billions worldwide. The Quake-Catcher Network (QCN) provides software so that individuals can join together to improve earthquake monitoring, earthquake awareness, and the science of earthquakes. The Quake-Catcher Network (QCN) links existing networked laptops and desktops in hopes to form the worlds largest strong-motion seismic network.

    Below, the QCN Quake Catcher Network map
    QCN Quake Catcher Network map

    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 7:38 am on March 30, 2017 Permalink | Reply
    Tags: , , , U Washington   

    From U Washington: “Tackling resilience: Finding order in chaos to help buffer against climate change” 

    U Washington

    University of Washington

    March 29, 2017
    Michelle Ma

    1
    Lotus flowers on a delta island on the outer reaches of the Mississippi delta, which is in danger of drastically shrinking or disappearing. The islands are actually quite resilient, as seen in part by the vegetation growth. Britta Timpane-Padgham/NWFSC

    “Resilience” is a buzzword often used in scientific literature to describe how animals, plants and landscapes can persist under climate change. It’s typically considered a good quality, suggesting that those with resilience can withstand or adapt as the climate continues to change.

    But when it comes to actually figuring out what makes a species or an entire ecosystem resilient ― and how to promote that through restoration or management ― there is a lack of consensus in the scientific community.

    A new paper by the University of Washington and NOAA’s Northwest Fisheries Science Center aims to provide clarity among scientists, resource managers and planners on what ecological resilience means and how it can be achieved. The study, published this month in the journal PLOS ONE, is the first to examine the topic in the context of ecological restoration and identify ways that resilience can be measured and achieved at different scales.

    “I was really interested in translating a broad concept like resilience into management or restoration actions,” said lead author Britta Timpane-Padgham, a fisheries biologist at Northwest Fisheries Science Center who completed the study as part of her graduate degree in marine and environmental affairs at the UW.

    “I wanted to do something that addressed impacts of climate change and connected the science with management and restoration efforts.”

    Timpane-Padgham scoured the scientific literature for all mentions of ecological resilience, then pared down the list of relevant articles to 170 examined for this study. She then identified in each paper the common attributes, or metrics, that contribute to resilience among species, populations or ecosystems. For example, genetic diversity and population density were commonly mentioned in the literature as attributes that help populations either recover from or resist disturbance.

    Timpane-Padgham along with co-authors Terrie Klinger, professor and director of the UW’s School of Marine and Environmental Affairs, and Tim Beechie, research biologist at Northwest Fisheries Science Center, grouped the various resilience attributes into five large categories, based on whether they affected individual plants or animals; whole populations; entire communities of plants and animals; ecosystems; or ecological processes. They then listed how many times each attribute was cited, which is one indicator of how well-suited a particular attribute is for measuring resilience.

    2
    The Kissimmee River in central Florida. This ecosystem-scale restoration project began two decades ago and is used as an example in the study. South Florida Water Management District

    “It’s a very nice way of organizing what was sort of a confused body of literature,” Beechie said. “It will at least allow people to get their heads around resilience and understand what it really is and what things you can actually measure.”

    The researchers say this work could be useful for people who manage ecosystem restoration projects and want to improve the chances of success under climate change. They could pick from the ordered list of attributes that relate specifically to their project and begin incorporating tactics that promote resilience from the start.

    “Specifying resilience attributes that are appropriate for the system and that can be measured repeatably will help move resilience from concept to practice,” Klinger said.

    or example, with Puget Sound salmon recovery, managers are asking how climate change will alter various rivers’ temperatures, flow levels and nutrient content. Because salmon recovery includes individual species, entire populations and the surrounding ecosystem, many resilience attributes are being used to monitor the status of the fish and recovery of the river ecosystems that support them.

    The list of attributes that track resilience can be downloaded and sorted by managers to find the most relevant measures for the type of restoration project they are tackling. It is increasingly common to account for climate change in project plans, the researchers said, but more foresight and planning at the start of a project is crucial.

    “The threat of climate change and its impacts is a considerable issue that should be looked at from the beginning of a restoration project. It needs to be its own planning objective,” Timpane-Padgham said. “With this paper, I don’t want to have something that will be published and collect dust. It’s about providing something that will be useful for people.”

    No external funding was used for this study.

    Download the spreadsheet to find the best resilience measures for your project (click on the second file in the carousal titled Interactive decision support table)

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

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    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 10:56 am on February 16, 2017 Permalink | Reply
    Tags: , , , U Washington, Using (MRI) to study the brains of infants who have older siblings with autism   

    From U Washington: “Predicting autism: Researchers find autism biomarkers in infancy” 

    U Washington

    University of Washington

    February 15, 2017
    No writer credit

    By using magnetic resonance imaging (MRI) to study the brains of infants who have older siblings with autism, scientists were able to correctly identify 80 percent of the babies who would be subsequently diagnosed with autism at 2 years of age.

    Researchers from the University of Washington were part of a North American effort led by the University of North Carolina to use MRI to measure the brains of “low-risk” infants, with no family history of autism, and “high-risk” infants who had at least one autistic older sibling. A computer algorithm was then used to predict autism before clinically diagnosable behaviors set in. The study was published Feb. 15 in the journal Nature.

    This is the first study to show that it is possible to use brain biomarkers to identify which infants in a high-risk pool — that is, those having an older sibling with autism — will be diagnosed with autism spectrum disorder, or ASD, at 24 months of age.

    2
    Annette Estes, left, plays with a child at the UW Autism Center.Kathryn Sauber

    “Typically, the earliest we can reliably diagnose autism in a child is age 2, when there are consistent behavioral symptoms, and due to health access disparities the average age of diagnosis in the U.S. is actually age 4,” said co-author and UW professor of speech and hearing sciences Annette Estes, who is also director of the UW Autism Center and a research affiliate at the UW Center on Human Development and Disability, or CHDD. “But in our study, brain imaging biomarkers at 6 and 12 months were able to identify babies who would be later diagnosed with ASD.”

    The predictive power of the team’s findings may inform the development of a diagnostic tool for ASD that could be used in the first year of life, before behavioral symptoms have emerged.

    “We don’t have such a tool yet,” said Estes. “But if we did, parents of high-risk infants wouldn’t need to wait for a diagnosis of ASD at 2, 3 or even 4 years and researchers could start developing interventions to prevent these children from falling behind in social and communication skills.”

    People with ASD — which includes 3 million people in the United States — have characteristic social communication deficits and demonstrate a range of ritualistic, repetitive and stereotyped behaviors. In the United States, it is estimated that up to one out of 68 babies develops autism. But for infants with an autistic older sibling, the risk may be as high as one out of every five births.

    This research project included hundreds of children from across the country and was led by researchers at four clinical sites across the United States: the University of North Carolina-Chapel Hill, UW, Washington University in St. Louis and The Children’s Hospital of Philadelphia. Other key collaborators are at the Montreal Neurological Institute, the University of Alberta and New York University.

    3
    Stephen Dager.Marie-Anne Domsalla

    “We have wonderful, dedicated families involved in this study,” said Stephen Dager, a UW professor of radiology and associate director of the CHDD, who led the study at the UW. “They have been willing to travel long distances to our research site and then stay up until late at night so we can collect brain imaging data on their sleeping children. The families also return for follow-up visits so we can measure how their child’s brain grows over time. We could not have made these discoveries without their wholehearted participation.”

    Researchers obtained MRI scans of children while they were sleeping at 6, 12 and 24 months of age. The study also assessed behavior and intellectual ability at each visit, using criteria developed by Estes and her team. They found that the babies who developed autism experienced a hyper-expansion of brain surface area from 6 to 12 months, as compared to babies who had an older sibling with autism but did not themselves show evidence of autism at 24 months of age. Increased surface area growth rate in the first year of life was linked to increased growth rate of brain volume in the second year of life. Brain overgrowth was tied to the emergence of autistic social deficits in the second year.

    4
    MRI technician Mindy Dixon and Stephen Dager review a magnetic resonance spectroscopic image of a child’s brain chemistry.University of Washington

    The researchers input these data — MRI calculations of brain volume, surface area, and cortical thickness at 6 and 12 months of age, as well as sex of the infants — into a computer program, asking it to classify babies most likely to meet ASD criteria at 24 months of age. The program developed the best algorithm to accomplish this, and the researchers applied the algorithm to a separate set of study participants.

    Researchers found that, among infants with an older ASD sibling, the brain differences at 6 and 12 months of age successfully identified 80 percent of those infants who would be clinically diagnosed with autism at 24 months of age.

    If these findings could form the basis for a “pre-symptomatic” diagnosis of ASD, health care professionals could intervene even earlier.

    “By the time ASD is diagnosed at 2 to 4 years, often children have already fallen behind their peers in terms of social skills, communication and language,” said Estes, who directs behavioral evaluations for the network. “Once you’ve missed those developmental milestones, catching up is a struggle for many and nearly impossible for some.”

    Research could then begin to examine interventions on children during a period before the syndrome is present and when the brain is most malleable. Such interventions may have a greater chance of improving outcomes than treatments started after diagnosis.

    “Our hope is that early intervention — before age 2 — can change the clinical course of those children whose brain development has gone awry and help them acquire skills that they would otherwise struggle to achieve,” said Dager.

    The research team has gathered additional behavioral and brain imaging data on these infants and children — such as changes in blood flow in the brain and the movement of water along white matter networks — to understand how brain connectivity and neural activity may differ between high-risk children who do and don’t develop autism. In a separate study published Jan. 6 in Cerebral Cortex, the researchers identified specific brain regions that may be important for acquiring an early social behavior called joint attention, which is orienting attention toward an object after another person points to it.

    “These longitudinal imaging studies, which follow the same infants as they grow older, are really starting to hone in on critical brain developmental processes that can distinguish children who go on to develop ASD and those who do not,” said Dager. “We hope these ongoing efforts will lead to additional biomarkers, which could provide the basis for early, pre-symptomatic diagnosis and serve also to guide individualized interventions to help these kids from falling behind their peers.”

    The research was funded by the National Institutes of Health, Autism Speaks and the Simons Foundation.

    See the full article here .

    Please help promote STEM in your local schools.

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    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 4:29 pm on February 6, 2017 Permalink | Reply
    Tags: , , , U Washington, UW joins elite effort for better cancer tests in primary care   

    From U Washington: “UW joins elite effort for better cancer tests in primary care” 

    U Washington

    University of Washington

    01.31.2017
    Brian Donohue

    1
    Dr. Eunice Chen examines a patient at the UW Neighborhood Olympia Clinic. Clare McLean

    Primary-care doctors make first-line decisions about which patients – say, with an abnormal mole or a gastric complaint – should be referred out for cancer tests that are often expensive, invasive or difficult to schedule quickly.

    “That uncertainty is part of our everyday work as family doctors,” said Dr. Matthew Thompson, director of family medicine at the University of Washington School of Medicine and a practitioner at the UW Neighborhood Northgate Clinic in Seattle.

    3
    Dr. Matthew Thompson directs the family medicine program in the UW School of Medicine.

    So he’s jazzed about his department’s inclusion in an international effort that aspires to get better cancer diagnostics into primary-care doctors’ hands – to recognize cancers faster and reduce unwarranted referrals that wring patients’ emotions and wallets.

    “These technologies will take investment and development and testing, and I think primary care doctors will welcome that, as will our patients,” Thompson said.

    “CanTest,” a $6 million project funded by Cancer Research UK, makes UW Medicine a partner of the University of Cambridge and a handful of other elite research schools around the world; UW Family Medicine will direct its small share into the Primary Care Innovation Lab.

    “When the right test and technology comes up, we want to see which clinics in our WWAMI-based Practice & Research Network would be good sites for further studies,” Thompson said, referring to a group of 60 clinics across Washington, Wyoming, Alaska, Montana and Idaho.

    “Some of this is sharing; maybe there’s something that works in Australia or Denmark that we could be using here. How can we learn from each other across countries with the same kind of cancer issues?”

    4
    Technology aiming to screen for lung cancer with an exhalation is an example of a diagnostic pursued by this research grant. Owlstone Inc

    Over a five-year span of the grant, Cancer Research UK will train and support scientists to develop and share new screenings.

    “We want to nurture a new generation of researchers from a variety of backgrounds to work in primary-care cancer diagnostics, creating an educational melting pot to rapidly expand the field internationally,” said Dr. Fiona Walter, co- lead investigator at Cambridge.

    Dr. Willie Hamilton, co-lead researcher from the University of Exeter, said: “As a GP (general practitioner) myself, I know it can be frustrating to wait weeks for results before making any decisions for my patients. We’re trying to reduce this time by assessing ways that GPs could carry out these tests by themselves, as long as it’s safe and sensible to do so.”

    “We’re open to assessing many different tests, and we’re excited to hear from potential collaborators.”

    In addition to Hamilton, Walter and Thompson, the project’s senior faculty include Richard Neal, Yoryos Lyratzopoulos, Jon Emery, Hardeep Singh and Peter Vedsted. The Baylor College of Medicine in Houston is the only other U.S. site.

    See the full article here .

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    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 10:06 am on January 25, 2017 Permalink | Reply
    Tags: $279 million pledged for IHME to expand its work, , Bill & Melinda Gates Foundation, IHME, U Washington   

    From U Washington: “Bill & Melinda Gates Foundation boosts vital work of the UW’s Institute for Health Metrics and Evaluation” 

    U Washington

    University of Washington

    January 25, 2017
    Kayla Albrecht
    206-897-3792
    albrek7@uw.edu

    $279 million pledged for IHME to expand its work, highlighting UW’s position as global hub for improving population health worldwide.

    The Bill & Melinda Gates Foundation and University of Washington’s Institute for Health Metrics and Evaluation (IHME) announced today the foundation’s commitment to invest $279 million in IHME to expand its work over the next decade.

    The investment will allow IHME to build on its work providing independent health evidence to improve population health. The award complements other investments from the Gates Foundation to further the work of the University of Washington’s Population Health Initiative, which was launched in May 2016 and is establishing a university wide, 25-year vision to advance the health and well-being of people around the world.

    “IHME provides critical data about global health trends that can empower policymakers worldwide to identify better solutions in the fight against disease,” said Bill Gates, co-chair of the Bill & Melinda Gates Foundation.

    1
    An attendee at an Ebola workshop in Ghana reviews IHME data.Institute for Health Metrics and Evaluation

    Located within UW Medicine, IHME provides rigorous measurement and analysis of the world’s most prevalent and costly health problems and evaluates strategies to address them. The 10-year grant will fund IHME’s work to track how health resources are spent throughout the world, as well as innovations that identify future scenarios to allow decision-makers to better plan and set population health-related priorities. The funding will sustain IHME’s efforts as the coordinating center for the Global Burden of Disease project, the largest publishing collaboration in science, with more than 2,000 researchers worldwide. The grant also provides core support for IHME’s faculty, students, and staff.

    “IHME is deeply grateful for this funding and the foundation’s continued support,” said Dr. Christopher Murray, director of IHME. “Behind this grant is not simply a decision to continue outstanding research and analysis, but also an uncompromising commitment to use health metrics sciences to improve people’s lives.”

    “We are proud to support IHME and the University of Washington. We feel lucky that our local university is also on the leading edge of innovation globally, and we are grateful that it has chosen to innovate to help the poorest people in the world,” said Melinda Gates, co-chair of the Bill & Melinda Gates Foundation.

    The $279 million grant is the largest private donation in the university’s history and continues a long tradition of critical investments in the University of Washington by the Gates Foundation, which include grant awards across its academic disciplines including library science, global health, education, law and others. As of Jan. 25, 2017, the foundation has awarded the University of Washington over 250 grants totaling nearly $1.25 billion.

    “We’re thankful for this generous grant, which demonstrates the Gates Foundation’s high level of trust and confidence in IHME to deliver unsurpassed work on the world’s health challenges,” said UW President Ana Mari Cauce. “We share a vision – a world where all people can achieve their full potential – and through our partnerships we will improve the health and well-being of people here and around the globe.”

    IHME has grown from employing three individuals nine years ago to managing more than 300 faculty and staff today, while producing more than 200 scientific papers annually, and working closely with global and national institutions to improve health systems worldwide. Its findings are published in major scientific journals, policy reports, and online data visualizations. Moreover, IHME is now considered the trusted source for The World Bank, the United States Agency for International Development, The National Institutes of Health, the Wellcome Trust, and a range of other national and global organizations.

    Among its work, IHME publishes the annual Global Burden of Disease study (GBD), a systematic, scientific effort to quantify the magnitude of health loss from all major diseases, injuries, and risk factors by age, sex and population. With more than 2,000 collaborators in nearly 130 nations, the GBD examines 300-plus diseases and injuries and about 80 risk factors in every country, as well as sub-national assessments for China, Mexico, UK, Brazil, Japan, India, Saudi Arabia, Kenya and South Africa. In the U.S., 230 causes of death are estimated in every county in every state by census tract.

    The 2015 study, released in October, included more than 13 billion estimates of illnesses and injuries evaluated. (See: http://www.healthdata.org/news-release/increase-global-life-expectancy-offset-war-obesity-and-substance-abuse)

    See the full article here .

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