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  • richardmitnick 6:54 am on May 25, 2017 Permalink | Reply
    Tags: Applied Research & Technology, , , Rare Gene Mutations Inspire New Heart Drugs   

    From NYT: “Rare Gene Mutations Inspire New Heart Drugs” 

    New York Times

    The New York Times

    MAY 24, 2017

    Anna Feurer learned she had unusually low triglyceride levels after having bloodwork at a corporate health fair. The discovery prompted researchers to recruit her and her family for a research study of their genetic makeup. Credit Jess T. Dugan for The New York Times.

    What if you carried a genetic mutation that left you nearly impervious to heart disease? What if scientists could bottle that miracle and use it to treat everyone else?

    In a series of studies, the most recent published on Wednesday, scientists have described two rare genetic mutations that reduce levels of triglycerides, a type of blood fat, far below normal. People carrying these genes seem invulnerable to heart disease, even if they have other risk factors.

    Drugs that mimic the effects of these mutations are already on the way, and many experts believe that one day they will become the next blockbuster heart treatments. Tens of millions of Americans have elevated triglyceride levels. Large genetic studies have consistently suggested a direct link to heart disease.

    Added to the existing arsenal of cholesterol-reducers and blood pressure medications, the new medications “will drive the final nail in the coffin of heart disease,” predicted Dr. John Kastelein, a professor of vascular medicine at the University of Amsterdam who was not involved in the new research.

    These experimental triglyceride-reducers are in early stages of development, however, and human trials have only just begun. At the moment, the optimism of researchers is rooted less in clinical trial data than in the fact that nature has produced strong evidence they should work.

    People like Anna Feurer may be walking proof.

    In 1994, Mrs. Feurer, then 40, attended a health fair held by her employer, Ralston Purina, in St. Louis. She rolled up her sleeve and let a technician take blood to measure her cholesterol.

    Later, the company doctor called her in and told her that her triglyceride levels were almost inconceivably low. And so were her levels of LDL, which raises the risk of heart disease, and HDL, which is linked to a lower risk. The results were so unusual that he encouraged her to see a specialist.

    “It was all an accident,” Mrs. Feurer recalled in an interview. That her single blood sample could lead to new treatments is “definitely amazing.”

    She went to Dr. Gustav Schonfeld at Washington University in Saint Louis. He asked Mrs. Feurer if she and others in her family might participate in a research study. She agreed, recruiting her immediate family and even a few cousins and aunts.

    Some had strikingly low triglyceride levels, some had normal levels, and some were in between, Dr. Schonfeld found. He tried for years to locate the gene responsible but failed. (Dr. Schonfeld died in 2011.)

    In 2009, he sent Mrs. Feurer’s DNA to Dr. Sekar Kathiresan, a cardiologist at Massachusetts General Hospital. He discovered that she carried mutations in both copies of a gene, ANGPTL3, involved in triglyceride metabolism. (Each individual carries two copies of a given gene, one from each parent.)

    As it turned out, three of her nine siblings also had no working copy of the gene and extremely low triglyceride levels. Three others had one mutated gene and one normal gene; these siblings had low triglyceride levels, but nowhere near as low as those with no functioning gene.

    The other three siblings had inherited two normal ANGPTL3 genes and had normal triglyceride levels.

    “The big question was, ‘Does this loss-of-function mutation reduce coronary risk?’” Dr. Daniel Rader of the University of Pennsylvania, who is an author of three of the recently published studies, said.

    Dr. Nathan O. Stitziel, a cardiologist at Washington University in Saint Louis, said the evidence so far was that people with Mrs. Feurer’s mutation, at least, seemed to be protected.

    Dr. Stitziel and his colleagues scanned Mrs. Feurer’s coronary arteries and those of two siblings who also had two mutated ANGPTL3 genes. Each one was free of plaque, the researchers recently reported in the Journal of the American College of Cardiology.

    One sibling had been a heavy smoker, had high blood pressure and even had Type 2 diabetes, a powerful risk factor for heart disease. Yet there was no plaque in his arteries.

    Dr. Stitziel went on to lead an international group of researchers who looked for mutations that destroyed the gene in 180,180 people. It was a rare event, occurring in just one in 309 people.

    But Dr. Stitziel and his colleagues discovered the mutation reduced heart attack risk by a third.

    The second line of evidence for these drugs originated with a study of Old Order Amish in Lancaster, Pa. About 5 percent appeared to have arteries that were clear of plaque and low levels of triglycerides.

    As it turned out, these lucky people had inherited a single mutated copy of another gene related to triglyceride production, called ApoC3. Researchers wanted desperately to find people who had inherited two mutated copies to see whether short-circuiting the gene might be safe.

    They began by searching genetic data collected from more than 200,000 people around the world — but to no avail. Then the scientists tried a different tack, focusing on participants in a heart disease study in Pakistan, where first cousins often marry and mutations like these are more easily handed down.

    The strategy worked. After combing the world and turning up nothing, the investigators discovered more than 100 in Pakistan who had mutations in both ApoC3 genes. And these people were healthy, with low levels of triglycerides, researchers reported last month in the journal Nature.

    Now, with surprising speed, companies are starting to test experimental drugs that mimic a loss of ApoC3 by blocking the ApoC3 protein.

    In addition, two companies, Regeneron and Ionis Pharmaceuticals, are now testing drugs based on the mutations in the same gene that was found in the Feurer family, company scientists and academic researchers reported on Wednesday in The New England Journal of Medicine.

    Both companies reported that in preliminary studies, drugs based on these mutations reduced triglycerides in people with elevated levels. Both also reported studies of the drugs in mice showing the drugs protected the animals from heart disease.

    “The basic bottom line is that the reductions in triglycerides with these things is pretty unprecedented,” George Yancopoulos, president and chief scientific officer at Regeneron, said. Still, it’s not yet clear to what extent this will prevent heart attacks.

    Even more significant may be the way in which these drugs were identified. Finding people who are impervious to a disease like heart disease can open a door to letting the rest of the population share their genetic luck.

    “It’s a huge advance,” said Dr. Christie Mitchell Ballantyne, chief of cardiology and cardiovascular research at Baylor College of Medicine and a consultant for Regeneron (although not for the triglyceride studies). “That doesn’t mean it’s easy.”

    Still, he added, “what we are seeing is a new approach toward drug development.”

    See the full article here .

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  • richardmitnick 3:04 pm on May 24, 2017 Permalink | Reply
    Tags: Applied Research & Technology, , , Taiwan,   

    From Temblor: “M=5.0 Taiwan earthquake preceded by foreshock sequence” 



    May 24, 2017
    David Jacobson

    Southwestern Taiwan was hit by a M=5.0 earthquake today. This quake was preceded by a foreshock sequence that lasted approximately 33 hours. (Photo from: holidayssg.com)

    At 9:10 p.m. local time today (24 May), a M=5.0 earthquake struck western Taiwan near the city of Chiayi, which is home to over 250,000 people. This earthquake was preceded by a foreshock sequence of five earthquakes beginning approximately 33 hours earlier. The foreshock sequence began with a M=3.6, and culminated with another M=3.6 five minutes before the M=5.0. Most earthquakes are not preceded by a foreshock sequence, making this quake rare. At this stage, there have been no reports of damage, and according to the Taiwan Central Weather Bureau, moderate shaking was felt in the M=5.0, which can rock buildings, and cause slight damage. So, close to the epicenter, it is possible that minor damage was sustained. Should we hear any reports of damage, we will update this post.

    This Temblor map shows the location of the M=5.0 earthquake in Taiwan. In addition to the location from EMSC, the USGS location is also shown to illustrate the discrepancy in the catalogs. One of the earthquakes in the foreshock sequence is also shown.

    At this stage, there is a discrepancy between where the USGS and EMSC plot the location of today’s quake. The USGS has it in a stepover between the Chiuchiungkeng and Muchiliao-Liuchia faults, while EMSC has it just to the east of the Chiuchiungkeng Fault. The USGS location has been added to the Temblor map above so that this discrepancy can be seen (For any location outside the United States, Temblor shows EMSC data). The USGS has also produced a focal mechanism for this earthquake, which suggests both strike-slip and extensional components of slip, which is not consistent with the regional geology. Should a Taiwan focal mechanism come out, we will update this post.

    Based on the location shown in Temblor, this earthquake was likely associated with the Chiuchiungkeng Fault, a thrust fault within the southwestern foothills of Taiwan. Because of high slip rates associated with this fault, the region is believed to have a high probability of experiencing a large magnitude earthquake. This is verified when we look at the Taiwan Earthquake Model (see below). This model shows the likelihood of strong ground motion in the next 50 years.

    This figure shows the Taiwan Earthquake Model with recent earthquakes shown. This colors in the figure represent ground motion values (g) with a 10% likelihood in 50 years. This is the spectral acceleration at a period of 0.3 seconds (3.3 Hz).

    In addition to the Taiwan Earthquake Model, we can also consult the Global Earthquake Activity Rate (GEAR) model, to see what the likely earthquake magnitude is for this portion of Taiwan. This model, which uses global strain rates and seismicity since 1977, forecasts what the likely earthquake magnitude in your lifetime is for any location on earth. From the Temblor map below, one can see that a M=7.5 earthquake is likely in your lifetime. Such a quake could be devastating to the country, as a significant portion of the country’s agriculture is grown in southwestern Taiwan, and a large earthquake could damage valuable resources. Should anything change regarding the location or focal mechanism from today’s earthquake, we will update this post.

    This Temblor map shows the Global Earthquake Activity Rate (GEAR) model for Taiwan. What can be seen from this figure is that the area around today’s earthquake is susceptible to M=7.5+ quakes. Such an earthquake would be devastating to the area.

    European-Mediterranean Seismological Centre (EMSC)
    Taiwan Earthquake Model (TEM)
    Taiwan Central Weather Bureau

    See the full article here .

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    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).


    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

  • richardmitnick 2:42 pm on May 24, 2017 Permalink | Reply
    Tags: Applied Research & Technology, , , , New imaging technique aims to ensure surgeons completely remove cancer,   

    From Wash U: “New imaging technique aims to ensure surgeons completely remove cancer” 

    Wash U Bloc

    Washington University in St.Louis

    Caltech Logo


    May 17, 2017
    Tamara Bhandari

    A new imaging technique based on light and sound produces images doctors can use to distinguish cancerous breast tissue (below the dotted blue line) from normal tissue more quickly than is currently possible. Pathologists routinely inspect surgical specimens to make sure all cancerous tissue has been removed. The new technique (right) produces images as detailed and accurate as traditional methods (left), but in far less time. The researchers are working to make the technique fast enough to be used during a surgery, so patients don’t have to return for a second surgery. (Image: Terence T.W. Wong)

    Of the quarter-million women diagnosed with breast cancer every year in the United States, about 180,000 undergo surgery to remove the cancerous tissue while preserving as much healthy breast tissue as possible.

    However, there’s no accurate method to tell during surgery whether all of the cancerous tissue has been successfully removed. The gold-standard analysis takes a day or more, much too long for a surgeon to wait before wrapping up an operation. As a result, about a quarter of women who undergo lumpectomies receive word later that they will need a second surgery because a portion of the tumor was left behind.

    Now, researchers at Washington University School of Medicine in St. Louis and California Institute of Technology report that they have developed a technology to scan a tumor sample and produce images detailed and accurate enough to be used to check whether a tumor has been completely removed.

    Called photoacoustic imaging, the new technology takes less time than standard analysis techniques. But more work is needed before it is fast enough to be used during an operation.

    The research is published May 17 in Science Advances.

    “This is a proof of concept that we can use photoacoustic imaging on breast tissue and get images that look similar to traditional staining methods without any sort of tissue processing,” said Deborah Novack, MD, PhD, an associate professor of medicine, and of pathology and immunology, and a co-senior author on the study.

    The researchers are working on improvements that they expect will bring the time needed to scan a specimen down to 10 minutes, fast enough to be used during an operation. The current gold-standard method of analysis, which is based on preserving the tissue and then staining it to make the cells easier to see, hasn’t gotten any faster since it was first developed in the mid-20th century.

    For solid tumors in most parts of the body, doctors use a technique known as a frozen section to do a quick check of the excised lump during the surgery. They look for a thin rim of normal cells around the tumor. Malignant cells at the margins suggest the surgeon missed some of the tumor, increasing the chances that the disease will recur.

    But frozen sections don’t work well on fatty specimens like those from the breast, so the surgeon must finish a breast lumpectomy without knowing for sure how successful it was.

    “Right now, we don’t have a good method to assess margins during breast cancer surgeries,” said Rebecca Aft, MD, PhD, a professor of surgery and a co-senior author on the study. Aft, a breast cancer surgeon, treats patients at Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine.

    Currently, after surgery a specimen is sent to a pathologist, who slices it, stains it and inspects the margins for malignant cells under a microscope. Results are sent back to the surgeon within a few days.

    To speed up the process, the researchers took advantage of a phenomenon known as the photoacoustic effect. When a beam of light of the right wavelength hits a molecule, some of the energy is absorbed and then released as sound in the ultrasound range. These sound waves can be detected and used to create an image.

    “All molecules absorb light at some wavelength,” said co-senior author Lihong Wang, who conducted the work when he was a professor of biomedical engineering at Washington University’s School of Engineering & Applied Science. He is now at Caltech. “This is what makes photoacoustic imaging so powerful. Essentially, you can see any molecule, provided you have the ability to produce light of any wavelength. None of the other imaging technologies can do that. Ultrasound will not do that. X-rays will not do that. Light is the only tool that allows us to provide biochemical information.”

    The researchers tested their technique by scanning slices of tumors removed from three breast cancer patients. For comparison, they also stained each specimen according to standard procedures.

    The photoacoustic image matched the stained samples in all key features. The architecture of the tissue and subcellular detail such as the size of nuclei were clearly visible.

    “It’s the pattern of cells – their growth pattern, their size, their relationship to one another – that tells us if this is normal tissue or something malignant,” Novack said. “Overall, the photoacoustic images had a lot of the same features that we see with standard staining, which means we can use the same criteria to interpret the photoacoustic imaging. We don’t have to come up with new criteria.”

    Having established that photoacoustic techniques can produce usable images, the researchers are working on reducing the scanning time.

    “We expect to be able to speed up the process,” Wang said. “For this study, we had only a single channel for emitting light. If you have multiple channels, you can scan in parallel and that reduces the imaging time. Another way to speed it up is to fire the laser faster. Each laser pulse gives you one data point. Faster pulsing means faster data collection.”

    Aft, Novack and Wang are applying for a grant to build a photoacoustic imaging machine with multiple channels and fast lasers.

    “One day we think we’ll be able to take a specimen straight from the patient, plop it into the machine in the operating room and know in minutes whether we’ve gotten all the tumor out or not,” Aft said. “That’s the goal.”

    This work was supported by the National Institutes of Health, grant number DP1 EB016986 and R01 CA186567, and by Washington University’s Siteman Cancer Center’s 2014 Research Development Award.

    See the full article here .

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”

    Caltech campus

    Wash U campus
    Wash U campus

    Washington University’s mission is to discover and disseminate knowledge, and protect the freedom of inquiry through research, teaching, and learning.

    Washington University creates an environment to encourage and support an ethos of wide-ranging exploration. Washington University’s faculty and staff strive to enhance the lives and livelihoods of students, the people of the greater St. Louis community, the country, and the world.

  • richardmitnick 11:45 am on May 24, 2017 Permalink | Reply
    Tags: Applied Research & Technology, , HPC heard around the world,   

    From Science Node: “HPC heard around the world” 

    Science Node bloc
    Science Node

    19 May, 2017
    Tristan Fitzpatrick

    A new advanced computing alliance indicates cooperation and collaboration are alive and well in the global research community.

    It was an international celebration in Barcelona, Spain, as representatives from three continents met at PRACEdays17 to sign a memorandum of understanding (MoU), formalizing a new era in advanced research computing.

    On hand to recognize the partnership were John Towns, principal investigator of the Extreme Science and Engineering Discovery Environment (XSEDE), Serge Bogaerts, managing director of the Partnership for Advanced Computing in Europe (PRACE), and Masahiro Seki, president of the Japanese Research Organization for Information Science and Technology (RIST).


    “We are excited about this development and fully expect this effort will support the growing number of international collaborations emerging across all fields of scholarship,” says Towns.

    As steward of the US supercomputing infrastructure, XSEDE will share their socio-technical platform that integrates and coordinates the advanced digital services that support contemporary science across the country.

    See the full article here .

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    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

  • richardmitnick 10:50 am on May 24, 2017 Permalink | Reply
    Tags: , Applied Research & Technology, Engaging Diamonds for Next-Era Transistors,   

    From AIP: “Engaging Diamonds for Next-Era Transistors” 

    AIP Publishing Bloc

    American Institute of Physics

    by American Institute of Physics


    As consumers around the world have become increasingly dependent on electronics, the transistor, a semiconductor component central to the operation of these devices, has become a critical subject of scientific research. Over the last several decades, scientists and engineers have been able to both shrink the average transistor size and dramatically reduce its production costs. The current generation of smartphones, for example, relies on chips that each feature over 3.3 billion transistors.

    Most transistors are silicon-based and silicon technology has driven the computer revolution. In some applications, however, silicon has significant limitations. These include use in high power electronic devices and in harsh environments like the engine of a car or under cosmic ray bombardment in space. Silicon devices are prone to faltering and failing in difficult environments.

    Addressing these challenges, Jiangwei Liu, from Japan’s National Institute for Materials Sciences, and his colleagues describe new work developing diamond-based transistors this week in the journal Applied Physics Letters, from AIP Publishing.

    See the full article here .

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    AIP Building

    AIP serves a federation of physical science societies in a common mission to promote physics and allied fields.

  • richardmitnick 10:39 am on May 24, 2017 Permalink | Reply
    Tags: Applied Research & Technology, , , Synopsis: Capillary Effect in Grains Explained   

    From Physics: “Synopsis: Capillary Effect in Grains Explained” 

    Physics LogoAbout Physics

    Physics Logo 2


    May 23, 2017
    Michael Schirber

    Numerical simulations show that a previously observed capillary-like action in vibrating grain systems is due to convective motion of the grains.

    F. Fan et al., Phys. Rev. Lett. (2017)

    When a narrow tube is inserted into a bed of vibrating grains, the granular material rises up inside the tube, much like a liquid climbs through a thin straw. For liquids, this capillary, or wicking, action results from attractive interactions between the liquid molecules and the tube walls. But that explanation does not apply to grains—they do not stick to walls with enough force to defy gravity. New computer simulations show that the effect instead relies on friction-induced convective motion in the vibrating grains.

    Fengxian Fan, from the University of Shanghai for Science and Technology, and colleagues simulated a rectangular container partly filled with spherical grains (0.6 mm diameter). In the center of the container, a cylindrical tube (8 mm diameter) descended into the grains. When the tube was vibrated up and down, the simulated grains rose up the tube to a height of around 50 mm. But the effect disappeared when the team made the container walls frictionless. Wall friction causes a well-known convective motion in shaken grain systems (called the Brazil nut effect) in which grains at the walls are pushed downward, while grains in the center move up. The team showed that when the inserted tube vibrates, the resulting grain convection produces a pressure in the bottom of the tube that pushes material upwards. This understanding might help in the design and development of a grain pump that could transport grains along pipes for industrial processes.

    This research is published in Physical Review Letters.

    See the full article here .

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    Physicists are drowning in a flood of research papers in their own fields and coping with an even larger deluge in other areas of physics. How can an active researcher stay informed about the most important developments in physics? Physics highlights a selection of papers from the Physical Review journals. In consultation with expert scientists, the editors choose these papers for their importance and/or intrinsic interest. To highlight these papers, Physics features three kinds of articles: Viewpoints are commentaries written by active researchers, who are asked to explain the results to physicists in other subfields. Focus stories are written by professional science writers in a journalistic style and are intended to be accessible to students and non-experts. Synopses are brief editor-written summaries. Physics provides a much-needed guide to the best in physics, and we welcome your comments (physics@aps.org).

  • richardmitnick 10:17 am on May 24, 2017 Permalink | Reply
    Tags: Applied Research & Technology, , , Critical Thinking—Attained through Physics   

    From Cornell: “Critical Thinking—Attained through Physics” 

    Cornell Bloc

    Cornell University

    Jackie Swift

    Beatrice Jin

    Science is about experimentation, creativity, even play. The greatest breakthroughs have come from those who pushed the known limits to ask why, how, and ultimately what if. If this is how the best science is done, then why don’t we start giving students autonomy to explore and create in the lab early in their university training? If we do, Natasha G. Holmes, Physics, says that perhaps they’ll get a taste of what it means to be a scientist early enough that they’ll choose science as a career path.

    Holmes studies the teaching and learning of physics, especially in lab courses, but her work is applicable more broadly across many disciplines. “In the lab students have their hands on the equipment,” she says. “I’m looking at what they are getting or not getting out of that experience and also digging into what the lab space is actually good for. As a loftier, long-term goal, how can we provide students with transferable skills that will make them critical thinkers and good citizens?”

    A Tool for Assessing Critical Thinking Skills in Physics

    To shed light on those questions, Holmes is working on a project funded by the National Science Foundation to design a tool that can assess critical thinking. “This will be a closed response standardized test that allows any instructor to measure whether their students can think critically about a physics experiment,” Holmes says.

    Holmes and her coresearcher, Carl Wieman of Stanford University, began designing the assessment by gathering initial data from respondents at multiple universities. They asked them a series of open-ended questions about an introductory level mass-on-a-spring physics experiment conducted by a hypothetical group of people. Respondents answered questions about the hypothetical group’s methods and the data that the group collected. For instance, they were asked if they thought the data collected was reasonable, how well they felt the hypothetical group designed the experiment, and how well the group evaluated the model.

    “We were looking for the most common answers an introductory physics student would give,” Holmes explains. “But we also wanted to collect as many responses as we could from advanced physics majors, professors, and grad students to see the full spectrum of possible answers.” The researchers distilled the open-ended answers down into a multiple-choice test that can be given to students before they take a lab course and again afterward, to see how well they have learned the concepts.

    See the full article here .

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    Once called “the first American university” by educational historian Frederick Rudolph, Cornell University represents a distinctive mix of eminent scholarship and democratic ideals. Adding practical subjects to the classics and admitting qualified students regardless of nationality, race, social circumstance, gender, or religion was quite a departure when Cornell was founded in 1865.

    Today’s Cornell reflects this heritage of egalitarian excellence. It is home to the nation’s first colleges devoted to hotel administration, industrial and labor relations, and veterinary medicine. Both a private university and the land-grant institution of New York State, Cornell University is the most educationally diverse member of the Ivy League.

    On the Ithaca campus alone nearly 20,000 students representing every state and 120 countries choose from among 4,000 courses in 11 undergraduate, graduate, and professional schools. Many undergraduates participate in a wide range of interdisciplinary programs, play meaningful roles in original research, and study in Cornell programs in Washington, New York City, and the world over.

  • richardmitnick 9:06 am on May 24, 2017 Permalink | Reply
    Tags: Applied Research & Technology, How X-rays Helped to Solve Mystery of Floating Rocks, ,   

    From LBNL: “How X-rays Helped to Solve Mystery of Floating Rocks” 

    Berkeley Logo

    Berkeley Lab

    May 23, 2017
    Glenn Roberts Jr.
    (510) 486-5582

    Experiments at Berkeley Lab show scientists how pumice can remain buoyant for years.

    Pumice stones. (Credit: Berkeley Lab)

    It’s true—some rocks can float on water for years at a time. And now scientists know how they do it, and what causes them to eventually sink.

    X-ray studies at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have helped scientists to solve this mystery by scanning inside samples of lightweight, glassy, and porous volcanic rocks known as pumice stones. The X-ray experiments were performed at Berkeley Lab’s Advanced Light Source (ALS), an X-ray source known as a synchrotron.


    The surprisingly long-lived buoyancy of these rocks—which can form miles-long debris patches on the ocean known as pumice rafts that can travel for thousands of miles—can help scientists discover underwater volcano eruptions.

    In this 2006 satellite image, a large “raft” of floating pumice stones (beige) appears following a volcanic eruption in the Tonga Islands. (Credit: Jesse Alan/NASA Earth Observatory, Goddard Space Flight Center)

    And, beyond that, learning about its flotation can help us understand how it spreads species around the planet; pumice is nutrient rich and readily serves as a seafaring carrier of plant life and other organisms. Floating pumice can also be a hazard for boats, as the ashy mixture of ground-up pumice can clog engines.

    “The question of floating pumice has been around the literature for a long time, and it hadn’t been resolved,” said Kristen E. Fauria, a UC Berkeley graduate student who led the study, published in Earth and Planetary Science Letters.

    While scientists have known that pumice can float because of pockets of gas in its pores, it was unknown how those gases remain trapped inside the pumice for prolonged periods. If you soak up enough water in a sponge, for example, it will sink.

    “It was originally thought that the pumice’s porosity is essentially sealed,” Fauria said, like a corked bottle floating in the sea. But pumice’s pores are actually largely open and connected—more like an uncorked bottle. “If you leave the cap off and it still floats … what’s going on?”

    Some pumice stones have even been observed to “bob” in the laboratory—sinking during the evening and surfacing during the day.

    To understand what’s at work in these rocks, the team used wax to coat bits of water-exposed pumice sampled from Medicine Lake Volcano near Mount Shasta in Northern California and Santa María Volcano in Guatemala.

    VIDEO: This animation, produced from a series of X-ray microtomography images collected at Berkeley Lab’s Advanced Light Source, shows a cube-shaped sample of pumice (blue-gray) and pockets of trapped gases (other colors). The animation also shows liquid (at 18 seconds) that surrounds the gases. (Credit: Berkeley Lab, UC Berkeley)

    They then used an X-ray imaging technique at the ALS known as microtomography to study concentrations of water and gas—in detail measured in microns, or thousandths of a millimeter—within preheated and room-temperature pumice samples.

    The detailed 3-D images produced by the technique are very data-intensive, which posed a challenge in quickly identifying the concentrations of gas and water present in the pumice samples’ pores.

    To tackle this problem, Zihan Wei, a visiting undergraduate researcher from Peking University, used a data-analysis software tool that incorporates machine learning to automatically identify the gas and water components in the images.

    Concentrations of liquid and gas in samples of pumice stones are labeled in these images, produced by X-ray microtomography at Berkeley Lab’s Advanced Light Source. The images assisted researchers in identifying the mechanisms that enable pumice to float for prolonged periods. Heated pumice (shown in images at the top right and bottom right) samples contain a smaller volume of trapped gas than room-temperature samples. (Credit: UC Berkeley, Berkeley Lab)

    Researchers found that the gas-trapping processes that are in play in the pumice stones relates to “surface tension,” a chemical interaction between the water’s surface and the air above it that acts like a thin skin—this allows some creatures, including insects and lizards, to actually walk on water.

    “The process that’s controlling this floating happens on the scale of human hair,” Fauria said. “Many of the pores are really, really small, like thin straws all wound up together. So surface tension really dominates.”

    The team also found that a mathematical formulation known as percolation theory, which helps to understand how a liquid enters a porous material, provides a good fit for the gas-trapping process in pumice. And gas diffusion—which describes how gas molecules seek areas of lower concentration—explains the eventual loss of these gases that causes the stones to sink.

    Individual gas bubbles trapped in two pumice samples (labeled “ML01” and “SM01”) are shaded with different colors. The size and connectedness of the bubbles can vary widely within a sample. (Credit: UC Berkeley, Berkeley Lab)

    Michael Manga, a staff scientist in Berkeley Lab’s Energy Geosciences Division and a professor in the Department of Earth and Planetary Science at UC Berkeley who participated in the study, said, “There are two different processes: one that lets pumice float and one that makes it sink,” and the X-ray studies helped to quantify these processes for the first time. The study showed that previous estimates for flotation time were in some cases off by several orders of magnitude.

    “Kristen had the idea that in hindsight is obvious,” Manga said, “that water is filling up only some of the pore space.” The water surrounds and traps gases in the pumice, forming bubbles that make the stones buoyant. Surface tension serves to keep these bubbles locked inside for prolonged periods. The bobbing observed in laboratory experiments of pumice floatation is explained by trapped gas expanding during the heat of day, which causes the stones to temporarily float until the temperature drops.

    The X-ray work at the ALS, coupled with studies of small pieces of pumice floating in water in Manga’s UC Berkeley lab, helped researchers to develop a formula for predicting how long a pumice stone will typically float based on its size. Manga has also used an X-ray technique at the ALS called microdiffraction, which is useful for studying the origins of crystals in volcanic rocks.

    Dula Parkinson, a research scientist at Berkeley Lab’s ALS who assisted with the team’s microtomography experiments, said, “I’m always amazed at how much information Michael Manga and his collaborators are able to extract from the images they collect at ALS, and how they’re able to join that information with other pieces to solve really complicated puzzles.”

    See the full article here .

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  • richardmitnick 7:49 pm on May 23, 2017 Permalink | Reply
    Tags: Applied Research & Technology, , Georgia Straight, Rain Forest destruction by logging,   

    From UBC ia Georgia Straight: “Alys Granados: We have to protect all of the world’s rainforests, not just tropical rainforests” 

    U British Columbia bloc

    University of British Columbia


    Georgia Straight

    May 19th, 2017
    Alys Granados

    Logging on southern Vancouver Island. TJ Watt

    Most of us have heard about how rainforests are in trouble and the rapid rate at which we are losing these spectacular ecosystems, along with the incredible diversity of species that depend on them. Globally, most of these reports focus on tropical rainforests and there has been too little awareness about the fate of temperate rainforests. Close to home, very few know that the remaining old-growth forest on Vancouver Island is disappearing faster than natural tropical rainforests.

    Few of us have the opportunity to visit tropical forests in person, which can make us feel disconnected from the problems of deforestation and degradation of tropical countries. I am extremely lucky to have had the opportunity to work in tropical rainforests over the past seven years as part of my graduate work in wildlife ecology. Most of this has been in Sabah, Malaysian Borneo, where I investigated how selective logging disrupts interactions between trees and mammals.

    The loss of intact tropical forests continues to be a serious threat. The Food and Agriculture Organization of the United Nations (FAO) recently estimated that, globally, 10 percent of the remaining primary forests in tropical rainforest countries were lost between 1990 and 2015. These forests are home to many species that exist nowhere else on the planet and protecting their habitats is critical to their survival. Further, the livelihood of millions of people depends on intact forests and they play an important role in mitigating the effects of climate change by storing massive amounts of carbon.

    While all of this may be well known to many, few of us in Canada realize just how fast old-growth rainforest is being logged on Vancouver Island. I was very shocked to learn from recent Sierra Club B.C. data that over that same period (1990 to 2015), 30 percent of the remaining old-growth forest on Vancouver Island was logged. In other words, the rate of loss of so-called primary forests (forests that were largely undisturbed by human activity) on Vancouver Island is actually three times greater than in the tropics. In the past few years, the rate of old-growth logging on the Island has actually increased by 12 percent to 9,000 hectares per year (25 hectares a day).



    So what’s behind this forest loss? Similar to the tropics, logging plays a central role. One difference is that in many tropical countries logging often results in deforestation, while in other countries, such as Canada, logging generally leads to the replacement of rich ancient forests with even-aged young forest. Much of the old-growth forest on Vancouver Island has already been lost to clearcut logging and the remaining patches of old-growth (called variable retention by foresters) are too small to maintain enough habitat for species that depend on old-growth forest.

    In response to the Sierra Club data, the B.C. government stated that it is misleading to compare the problem in tropical countries to Vancouver Island because in British Columbia, logging companies are required by law to reforest logged areas. Although this is true, old-growth ecosystems with trees that are many hundreds of years of age are not growing back at a meaningful timescale and climate change means we will never see the same type of forest grow back in the first place.

    Species that rely on old-growth forest such, as the marbled murrelet, are negatively affected by the loss of old forest stands. In addition, the resulting large areas of young trees are not offering the type of habitat that most of the typical plants and animals on Vancouver Island depend on.

    Similar to tropical forests, coastal temperate forests play an important role storing carbon dioxide. In fact a single hectare of temperate rainforest can store up to 1,000 tonnes of carbon, a much greater amount than most tropical rainforests. Even if replanting is carried out, along the coast it can take centuries for reforested areas to reach a similar capacity in carbon-storage potential as that of intact old-growth forest stands.

    Tropical-forest loss rightfully deserves the attention it gets, and we are lucky here in B.C. to have equally amazing rainforest habitat. Given that we are living in a relatively rich part of the world compared to many tropical countries, it is remarkable that we are failing to do a better job of protecting the remaining rare and endangered ancient forests on Vancouver Island and inspire other parts of the world.

    (There is growing international pressure on the B.C. government to protect Vancouver Island’s endangered old-growth rainforest; see this release.)

    Coastal temperate rainforests exist only in very small areas on the planet and very little intact areas are left. Solutions exist, for example, in the Great Bear Rainforest north of Vancouver Island. Increasing the area of forest protected and halting destructive logging practices are both vital to ensuring the continued survival of these ecosystems and for a diverse economy. They should be a primary concern to us all.

    See the full article here .

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  • richardmitnick 5:53 am on May 23, 2017 Permalink | Reply
    Tags: Applied Research & Technology, , Discovery of an alga’s ‘dictionary of genes’ could lead to advances in biofuels and medicine, ,   

    From UCLA: “Discovery of an alga’s ‘dictionary of genes’ could lead to advances in biofuels, medicine” 

    UCLA bloc


    May 22, 2017
    Stuart Wolpert

    Inside the alga’s cells, showing the nucleus (purple), mitochondria (red), chloroplast (green) and lipids (yellow). Melissa Roth/HHMI and Andreas Walters/Berkeley Lab

    Plant biologists and biochemists from UCLA, UC Berkeley and UC San Francisco have produced a gold mine of data by sequencing the genome of a green alga called Chromochloris zofingiensis.


    Scientists have learned in the past decade that the tiny, single-celled organism could be used as a source of sustainable biofuel and that it produces a substance called astaxanthin, which may be useful for treating certain diseases. The new research could be an important step toward improving production of astaxanthin by algae and engineering its production in plants and other organisms.

    The study is published online in the journal Proceedings of the National Academy of Sciences.

    Chromochloris zofingiensis is one of the most prolific producers of a type of lipids called triacylglycerols, which are used in producing biofuels.

    Knowing the genome is like having a “dictionary” of the alga’s approximately 15,000 genes, said co-senior author Sabeeha Merchant, a UCLA professor of biochemistry. “From there, researchers can learn how to put the ‘words’ and ‘sentences’ together, and to target our research on important subsets of genes.”

    C. zofingiensis provides an abundant natural source for astaxanthin, an antioxidant found in salmon and other types of fish, as well as in some birds’ feathers. And because of its anti-inflammatory properties, scientists believe astaxanthin may have benefits for human health; it is being tested in treatments for cancer, cardiovascular disease, neurodegenerative diseases, inflammatory diseases, diabetes and obesity. Merchant said the natural version has stronger antioxidant properties than chemically produced ones, and only natural astaxanthin has been approved for human consumption.

    The study also revealed that an enzyme called beta-ketolase is a critical component in the production of astaxanthin.

    Algae absorb carbon dioxide and derive their energy from sunlight, and C. zofingiensis in particular can be cultivated on non-arable land and in wastewater. Harnessing it as a source for renewable and sustainable biofuels could lead to new ways to produce clean energy, said Krishna Niyogi, co-senior author of the paper and a scientist at the Department of Energy’s Lawrence Berkeley National Laboratory.

    Over the past decade-plus, Merchant said, research with algae, a small plant called rockcress, fruit flies and nematode worms — all so-called “model organisms” — has been advanced by other scientists’ determining their genome sequences.

    “They are called model organisms because we use what we learn about the operation of their cells and proteins as a model for understanding the workings of more complex systems like humans or crops,” she said. “Today, we can sequence the genome of virtually any organism in the laboratory, as has been done over the past 10 to 15 years with other model organisms.”

    Merchant, Niyogi and Matteo Pellegrini, a UCLA professor of molecular, cell and developmental biology and a co-author of the study, maintain a website that shares a wealth of information about the alga’s genome.

    During the study, the scientists also used soft X-ray tomography, a technique similar to a CT scan, to get a 3-D view of the algae cells , which gave them more detailed insights about their biology.

    Niyogi is also a UC Berkeley professor of plant and microbial biology and a Howard Hughes Medical Institute Investigator.


    The study’s other authors are researchers Shawn Cokus and Sean Gallaher and postdoctoral scholar David Lopez, all of UCLA; postdoctoral fellow Melissa Roth, and graduate students Erika Erickson, Benjamin Endelman and Daniel Westcott, all of Niyogi’s laboratory; and Carolyn Larabell, a professor of anatomy, and researcher Andreas Walter, both of UC San Francisco.

    The research was funded by the Department of Energy’s Office of Science, the Department of Agriculture’s National Institute of Food and Agriculture, the National Institute of General Medical Sciences of the National Institutes of Health, and the Gordon and Betty Moore Foundation.

    See the full article here .

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    We doubt the critics, reject the status quo and see opportunity in dissatisfaction. Our campus, faculty and students are driven by optimism. It is not naïve; it is essential. And it has fueled every accomplishment, allowing us to redefine what’s possible, time after time.

    This can-do perspective has brought us 12 Nobel Prizes, 12 Rhodes Scholarships, more NCAA titles than any university and more Olympic medals than most nations. Our faculty and alumni helped create the Internet and pioneered reverse osmosis. And more than 100 companies have been created based on technology developed at UCLA.

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