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  • richardmitnick 6:15 am on December 22, 2014 Permalink | Reply
    Tags: Applied Research & Technology, , ,   

    From MIT: “Trapping light with a twister” 


    MIT News

    December 22, 2014
    David L. Chandler | MIT News Office

    New understanding of how to halt photons could lead to miniature particle accelerators, improved data transmission.

    Researchers at MIT who succeeded last year in creating a material that could trap light and stop it in its tracks have now developed a more fundamental understanding of the process. The new work — which could help explain some basic physical mechanisms — reveals that this behavior is connected to a wide range of other seemingly unrelated phenomena.

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    Plot of radiative quality factor as a function of wave vector for a photonic crystal slab. At five positions, this factor diverges to infinity, corresponding to special solutions of Maxwell equations called bound states in the continuum. These states have enough energy to escape to infinity but remain spatially localized. Courtesy of the researchers

    The findings are reported in a paper in the journal Physical Review Letters, co-authored by MIT physics professor Marin Soljačić; postdocs Bo Zhen, Chia Wei Hsu, and Ling Lu; and Douglas Stone, a professor of applied physics at Yale University.

    Light can usually be confined only with mirrors, or with specialized materials such as photonic crystals. Both of these approaches block light beams; last year’s finding demonstrated a new method in which the waves cancel out their own radiation fields. The new work shows that this light-trapping process, which involves twisting the polarization direction of the light, is based on a kind of vortex — the same phenomenon behind everything from tornadoes to water swirling down a drain.

    In addition to revealing the mechanism responsible for trapping the light, the new analysis shows that this trapped state is much more stable than had been thought, making it easier to produce and harder to disturb.

    “People think of this [trapped state] as very delicate,” Zhen says, “and almost impossible to realize. But it turns out it can exist in a robust way.”

    In most natural light, the direction of polarization — which can be thought of as the direction in which the light waves vibrate — remains fixed. That’s the principle that allows polarizing sunglasses to work: Light reflected from a surface is selectively polarized in one direction; that reflected light can then be blocked by polarizing filters oriented at right angles to it.

    But in the case of these light-trapping crystals, light that enters the material becomes polarized in a way that forms a vortex, Zhen says, with the direction of polarization changing depending on the beam’s direction.

    Because the polarization is different at every point in this vortex, it produces a singularity — also called a topological defect, Zhen says — at its center, trapping the light at that point.

    Hsu says the phenomenon makes it possible to produce something called a vector beam, a special kind of laser beam that could potentially create small-scale particle accelerators. Such devices could use these vector beams to accelerate particles and smash them into each other — perhaps allowing future tabletop devices to carry out the kinds of high-energy experiments that today require miles-wide circular tunnels.

    The finding, Soljačić says, could also enable easy implementation of super-resolution imaging (using a method called stimulated emission depletion microscopy) and could allow the sending of far more channels of data through a single optical fiber.

    “This work is a great example of how supposedly well-studied physical systems can contain rich and undiscovered phenomena, which can be unearthed if you dig in the right spot,” says Yidong Chong, an assistant professor of physics and applied physics at Nanyang Technological University in Singapore who was not involved in this research.

    Chong says it is remarkable that such surprising findings have come from relatively well-studied materials. “It deals with photonic crystal slabs of the sort that have been extensively analyzed, both theoretically and experimentally, since the 1990s,” he says. “The fact that the system is so unexotic, together with the robustness associated with topological phenomena, should give us confidence that these modes will not simply be theoretical curiosities, but can be exploited in technologies such as microlasers.”

    The research was partly supported by the U.S. Army Research Office through MIT’s Institute for Soldier Nanotechnologies, and by the Department of Energy and the National Science Foundation.

    See the full article here.

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  • richardmitnick 8:45 am on December 20, 2014 Permalink | Reply
    Tags: Applied Research & Technology, , University of Leeds,   

    From Leeds: “Scientists observe the Earth grow a new layer under an Icelandic volcano” 

    Leeds

    University of Leeds

    15 December 2014
    No Writer Credit

    New research into an Icelandic eruption has shed light on how the Earth’s crust forms, according to a paper published today in Nature.

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    When the Bárðarbunga volcano, which is buried beneath Iceland’s Vatnajökull ice cap, reawakened in August 2014, scientists had a rare opportunity to monitor how the magma flowed through cracks in the rock away from the volcano.

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    The molten rock forms vertical sheet-like features known as dykes, which force the surrounding rock apart.

    Study co-author Professor Andy Hooper from the Centre for Observation and Modelling of Earthquakes, volcanoes and Tectonics (COMET) at the University of Leeds explained: “New crust forms where two tectonic plates are moving away from each other. Mostly this happens beneath the oceans, where it is difficult to observe.

    “However, in Iceland this happens beneath dry land. The events leading to the eruption in August 2014 are the first time that such a rifting episode has occurred there and been observed with modern tools, like GPS and satellite radar.”

    Although it has a long history of eruptions, Bárðarbunga has been increasingly restless since 2005. There was a particularly dynamic period in August and September this year, when more than 22,000 earthquakes were recorded in or around the volcano in just four weeks, due to stress being released as magma forced its way through the rock.

    Using GPS and satellite measurements, the team were able to track the path of the magma for over 45km before it reached a point where it began to erupt, and continues to do so to this day. The rate of dyke propagation was variable and slowed as the magma reached natural barriers, which were overcome by the build-up of pressure, creating a new segment.

    The dyke grows in segments, breaking through from one to the next by the build up of pressure. This explains how focused upwelling of magma under central volcanoes is effectively redistributed over large distances to create new upper crust at divergent plate boundaries, the authors conclude.

    As well as the dyke, the team found ‘ice cauldrons’ – shallow depressions in the ice with circular crevasses, where the base of the glacier had been melted by magma. In addition, radar measurements showed that the ice inside Bárðarbunga’s crater had sunk by 16m, as the volcano floor collapsed.

    COMET PhD student Karsten Spaans from the University of Leeds, a co-author of the study, added: “Using radar measurements from space, we can form an image of caldera movement occurring in one day. Usually we expect to see just noise in the image, but we were amazed to see up to 55cm of subsidence.”

    Like other liquids, magma flows along the path of least resistance, which explains why the dyke at Bárðarbunga changed direction as it progressed. Magma flow was influenced mostly by the lie of the land to start with, but as it moved away from the steeper slopes, the influence of plate movements became more important.

    Summarising the findings, Professor Hooper said: “Our observations of this event showed that the magma injected into the crust took an incredibly roundabout path and proceeded in fits and starts.

    “Initially we were surprised at this complexity, but it turns out we can explain all the twists and turns with a relatively simple model, which considers just the pressure of rock and ice above, and the pull exerted by the plates moving apart.

    The paper Segmented lateral dyke growth in a rifting event at Bárðarbunga volcanic system, Iceland is published in Nature on 15 December 2014.

    The research leading to these results has received funding from the European Community’s Seventh Framework Programme under Grant Agreement No. 308377 (Project FUTUREVOLC).

    Read the paper here: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14111.html

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    The University of Leeds was founded in 1904, but its origins go back to t­he nineteenth century with the founding of the Leeds School of Medicine in 1831 and then the Yorkshire College of Science in 1874.

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  • richardmitnick 6:35 am on December 20, 2014 Permalink | Reply
    Tags: Applied Research & Technology, , Ohio State University   

    From OSU: “Study Hints that Ancient Earth Made Its Own Water—Geologically” 

    OSU

    Ohio State University

    December 17, 2014
    Pam Frost Gorder

    A new study is helping to answer a longstanding question that has recently moved to the forefront of earth science: Did our planet make its own water through geologic processes, or did water come to us via icy comets from the far reaches of the solar system?

    The answer is likely “both,” according to researchers at The Ohio State University— and the same amount of water that currently fills the Pacific Ocean could be buried deep inside the planet right now.

    At the American Geophysical Union (AGU) meeting on Wednesday, Dec. 17, they report the discovery of a previously unknown geochemical pathway by which the Earth can sequester water in its interior for billions of years and still release small amounts to the surface via plate tectonics, feeding our oceans from within.

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    Wendy Panero

    In trying to understand the formation of the early Earth, some researchers have suggested that the planet was dry and inhospitable to life until icy comets pelted the earth and deposited water on the surface.

    Wendy Panero, associate professor of earth sciences at Ohio State, and doctoral student Jeff Pigott are pursuing a different hypothesis: that Earth was formed with entire oceans of water in its interior, and has been continuously supplying water to the surface via plate tectonics ever since.

    Researchers have long accepted that the mantle contains some water, but how much water is a mystery. And, if some geological mechanism has been supplying water to the surface all this time, wouldn’t the mantle have run out of water by now?

    Because there’s no way to directly study deep mantle rocks, Panero and Pigott are probing the question with high-pressure physics experiments and computer calculations.

    “When we look into the origins of water on Earth, what we’re really asking is, why are we so different than all the other planets?” Panero said. “In this solar system, Earth is unique because we have liquid water on the surface. We’re also the only planet with active plate tectonics. Maybe this water in the mantle is key to plate tectonics, and that’s part of what makes Earth habitable.”

    Central to the study is the idea that rocks that appear dry to the human eye can actually contain water—in the form of hydrogen atoms trapped inside natural voids and crystal defects. Oxygen is plentiful in minerals, so when a mineral contains some hydrogen, certain chemical reactions can free the hydrogen to bond with the oxygen and make water.

    Stray atoms of hydrogen could make up only a tiny fraction of mantle rock, the researchers explained. Given that the mantle is more than 80 percent of the planet’s total volume, however, those stray atoms add up to a lot of potential water.

    In a lab at Ohio State, the researchers compress different minerals that are common to the mantle and subject them to high pressures and temperatures using a diamond anvil cell—a device that squeezes a tiny sample of material between two diamonds and heats it with a laser—to simulate conditions in the deep Earth. They examine how the minerals’ crystal structures change as they are compressed, and use that information to gauge the minerals’ relative capacities for storing hydrogen. Then, they extend their experimental results using computer calculations to uncover the geochemical processes that would enable these minerals to rise through the mantle to the surface—a necessary condition for water to escape into the oceans.

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    This plate tectonics diagram from the Byrd Polar and Climate Research Center shows how mantle circulation delivers new rock to the crust via mid-ocean ridges. New research suggests that mantle circulation also delivers water to the oceans.

    In a paper now submitted to a peer-reviewed academic journal, they reported their recent tests of the mineral bridgmanite, a high-pressure form of olivine. While bridgmanite is the most abundant mineral in the lower mantle, they found that it contains too little hydrogen to play an important role in Earth’s water supply.

    Another research group recently found that ringwoodite, another form of olivine, does contain enough hydrogen to make it a good candidate for deep-earth water storage. So Panero and Pigott focused their study on the depth where ringwoodite is found—a place 325-500 miles below the surface that researchers call the “transition zone”—as the most likely region that can hold a planet’s worth of water. From there, the same convection of mantle rock that produces plate tectonics could carry the water to the surface.

    One problem: If all the water in ringwoodite is continually drained to the surface via plate tectonics, how could the planet hold any in reserve?

    For the research presented at AGU, Panero and Pigott performed new computer calculations of the geochemistry in the lowest portion of the mantle, some 500 miles deep and more. There, another mineral, garnet, emerged as a likely water-carrier—a go-between that could deliver some of the water from ringwoodite down into the otherwise dry lower mantle.

    If this scenario is accurate, the Earth may today hold half as much water in its depths as is currently flowing in oceans on the surface, Panero said—an amount that would approximately equal the volume of the Pacific Ocean. This water is continuously cycled through the transition zone as a result of plate tectonics.

    “One way to look at this research is that we’re putting constraints on the amount of water that could be down there,” Pigott added.

    Panero called the complex relationship between plate tectonics and surface water “one of the great mysteries in the geosciences.” But this new study supports researchers’ growing suspicion that mantle convection somehow regulates the amount of water in the oceans. It also vastly expands the timeline for Earth’s water cycle.

    “If all of the Earth’s water is on the surface, that gives us one interpretation of the water cycle, where we can think of water cycling from oceans into the atmosphere and into the groundwater over millions of years,” she said. “But if mantle circulation is also part of the water cycle, the total cycle time for our planet’s water has to be billions of years.”

    See the full article here.

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  • richardmitnick 5:50 am on December 20, 2014 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From Huff Post: “New Stonehenge Discovery Hailed As ‘Most Important In 60 Years'” 

    Huffington Post
    The Huffington Post

    Archaeologists studying Stonehenge and its environs say they’ve unearthed the remnants of an untouched, ancient encampment that dates back 6,000 years–a find that could rewrite British prehistory.

    s
    Stonehenge

    “This is the most important discovery at Stonehenge in over 60 years,” Professor Tim Darvill, a Bournemouth University archaeologist and a Stonehenge expert who was not involved in the new discovery, told the Telegraph. And as he told The Huffington Post in an email, the discovery overturns previous theories that “Stonehenge was built in a landscape that was not heavily used before about 3000 B.C.”

    But if scientists are buzzing about the discovery, they’re also bummed about a new government plan calling for the construction of a new tunnel underneath Stonehenge.

    The discovery was made during a dig at Blick Mead, a site about 1.5 miles from Stonehenge. Researchers found charcoal dating back to 4,000 B.C. and evidence of “possible structures,” according to a statement released by the university. They also unearthed burnt flint and tools, as well as the remains of aurochs–ancient cattle that served as food for ancient hunter-gatherers.

    The researchers plan further analysis on the artifacts but say they’re worried the tunnel construction could damage the site and get in the way of their work.

    “Blick Mead could explain what archaeologists have been searching for for centuries–an answer to the story of Stonehenge’s past,” David Jaques, the University of Buckingham archaeologist who discovered the encampment, told The Guardian. “But our only chance to find out about the earliest chapter of Britain’s history could be wrecked if the tunnel goes ahead.”

    Stonehenge, a prehistoric monument consisting of a ring of standing stones, is located eight miles north of Salisbury, England in Wiltshire. It has been listed as a World Heritage Site since 1986.

    See the full article here.

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    href=”http://www.dell.com/”>Dell

     
  • richardmitnick 8:43 pm on December 19, 2014 Permalink | Reply
    Tags: Applied Research & Technology, Computational Biology,   

    From Quanta: “Machine Intelligence Cracks Genetic Controls” 

    Quanta Magazine
    Quanta Magazine

    December 18, 2014
    Emily Singer

    Every cell in your body reads the same genome, the DNA-encoded instruction set that builds proteins. But your cells couldn’t be more different. Neurons send electrical messages, liver cells break down chemicals, muscle cells move the body. How do cells employ the same basic set of genetic instructions to carry out their own specialized tasks? The answer lies in a complex, multilayered system that controls how proteins are made.

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    Most genetic research to date has focused on just 1 percent of the genome — the areas that code for proteins. But new research, published today in Science, provides an initial map for the sections of the genome that orchestrate this protein-building process. “It’s one thing to have the book — the big question is how you read the book,” said Brendan Frey, a computational biologist at the University of Toronto who led the new research.

    Frey compares the genome to a recipe that a baker might use. All recipes include a list of ingredients — flour, eggs and butter, say — along with instructions for what to do with those ingredients. Inside a cell, the ingredients are the parts of the genome that code for proteins; surrounding them are the genome’s instructions for how to combine those ingredients.

    Just as flour, eggs and butter can be transformed into hundreds of different baked goods, genetic components can be assembled into many different configurations. This process is called alternative splicing, and it’s how cells create such variety out of a single genetic code. Frey and his colleagues used a sophisticated form of machine learning to identify mutations in this instruction set and to predict what effects those mutations have.

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    Olena Shmahalo/Quanta Magazine

    The researchers have already identified possible risk genes for autism and are working on a system to predict whether mutations in cancer-linked genes are harmful. “I hope this paper will have a big impact on the field of human genetics by providing a tool that geneticists can use to identify variants of interest,” said Chris Burge, a computational biologist at the Massachusetts Institute of Technology who was not involved in the study.

    But the real significance of the research may come from the new tools it provides for exploring vast sections of DNA that have been very difficult to interpret until now. Many human genetics studies have sequenced only the small part of the genome that produces proteins. “This makes an argument that the sequence of the whole genome is important too,” said Tom Cooper, a biologist at Baylor College of Medicine in Houston, Texas.

    Reading the Recipe

    The splicing code is just one part of the noncoding genome, the area that does not produce proteins. But it’s a very important one. Approximately 90 percent of genes undergo alternative splicing, and scientists estimate that variations in the splicing code make up anywhere between 10 and 50 percent of all disease-linked mutations. “When you have mutations in the regulatory code, things can go very wrong,” Frey said.

    “People have historically focused on mutations in the protein-coding regions, to some degree because they have a much better handle on what these mutations do,” said Mark Gerstein, a bioinformatician at Yale University, who was not involved in the study. “As we gain a better understanding of [the DNA sequences] outside of the protein-coding regions, we’ll get a better sense of how important they are in terms of disease.”

    Scientists have made some headway into understanding how the cell chooses a particular protein configuration, but much of the code that governs this process has remained an enigma. Frey’s team was able to decipher some of these regulatory regions in a paper published in 2010, identifying a rough code within the mouse genome that regulates splicing. Over the past four years, the quality of genetics data — particularly human data — has improved dramatically, and machine-learning techniques have become much more sophisticated, enabling Frey and his collaborators to predict how splicing is affected by specific mutations at many sites across the human genome. “Genome-wide data sets are finally able to enable predictions like this,” said Manolis Kellis, a computational biologist at MIT who was not involved in the study.

    Frey’s team used an approach called deep learning. Like any kind of machine-learning technique, the model tries to find a relationship between two sets of data. In this case, Frey’s team connected the human reference genome with rich data sets cataloging the amounts of different protein components in different tissues. (Just as two different cake recipes vary in their ratios of flour and sugar, brain cells and liver cells vary in how much of each protein they produce.) In essence, the algorithms trained a computational model to read instructions embedded in the DNA.

    While scientists already knew how to read some aspects of the splicing code, the new model is unique. It allows scientists to predict how a wide array of genetic components will interact. “This group took what we knew about splicing and put it into a computational framework where we can weight all [the variables],” Burge said.

    For example, researchers can use the model to predict what will happen to a protein when there’s a mistake in part of the regulatory code. Mutations in splicing instructions have already been linked to diseases such as spinal muscular atrophy, a leading cause of infant death, and some forms of colorectal cancer. In the new study, researchers used the trained model to analyze genetic data from people afflicted with some of those diseases. The scientists identified some known mutations linked to these maladies, verifying that the model works. They picked out some new candidate mutations as well, most notably for autism.

    One of the benefits of the model, Frey said, is that it wasn’t trained using disease data, so it should work on any disease or trait of interest. The researchers plan to make the system publicly available, which means that scientists will be able to apply it to many more diseases.

    A Broader Context

    The model also reveals that when it comes to the genome, “context is important, just like in English,” Frey said. “‘Cat’ means different things whether we’re talking about pets or construction equipment.” In the same way, how the cell interprets a set of splicing instructions depends on other nearby instructions. A string of DNA that means “make lots of component X” might mean “don’t make component X” when it’s sitting near a second set of instructions. “Whether a sequence has an effect depends on whether another sequence has an effect,” Frey said. “Without understanding that, it’s hard to predict how a pattern will affect splicing.”

    In addition, the model could help scientists reconsider known mutations, Burge said. Researchers already knew that some splicing instructions are found within protein-coding regions. In these cases, the same genetic sequence might code for both an ingredient and an instruction for what to do with it. (Consider whipped cream — it’s an ingredient, but it’s also in some ways an instruction.) A mutation in this protein-coding region might be dismissed as unimportant if it appears to do little or nothing to alter the corresponding protein. But when interpreted using the splicing code, that mutation might be found to have a profound effect by interfering with the splicing instructions. Frey’s group found many examples of these errors across the genome.

    Frey hopes the model will ultimately prove useful for personalized medicine. For example, doctors cannot yet determine whether healthy people with novel mutations are predisposed to diseases like cancer. With further validation, Frey’s model might help to answer this question. “We can analyze any mutation, even those that haven’t been identified yet,” Frey said. This allows researchers to predict whether a novel mutation is likely to be dangerous or harmless — in essence, performing a screening test. “I want to see it have a huge impact on medicine,” he said. “I want to translate this into practice.”

    See the full article, with video, here

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    Formerly known as Simons Science News, Quanta Magazine is an editorially independent online publication launched by the Simons Foundation to enhance public understanding of science. Why Quanta? Albert Einstein called photons “quanta of light.” Our goal is to “illuminate science.” At Quanta Magazine, scientific accuracy is every bit as important as telling a good story. All of our articles are meticulously researched, reported, edited, copy-edited and fact-checked.

     
  • richardmitnick 8:29 pm on December 19, 2014 Permalink | Reply
    Tags: Applied Research & Technology, , ,   

    From NSF- “Geomagnetic reversal: Understanding ancient flips and flops in Earth’s polarity” 

    nsf
    National Science Foundation

    December 19, 2014
    Ivy F. Kupec, (703) 292-8796 ikupec@nsf.gov

    Investigators
    Masako Tominaga
    Maurice Tivey
    William Sager

    Related Institutions/Organizations
    Woods Hole Oceanographic Institution

    Locations
    Western Pacific Seafloor , Hawaii

    Related Programs
    Marine Geology and Geophysics

    Imagine one day you woke up, and the North Pole was suddenly the South Pole.

    This geomagnetic reversal would cause your hiking compass to seem impossibly backwards. However, within our planet’s history, scientists know that this kind of thing actually has happened…not suddenly and not within human time scales, but the polarity of the planet has in fact reversed, which has caused scientists to wonder not only how it’s happened, but why.

    This week, as the National Science Foundation (NSF) research vessel R/V Sikuliaq continues its journey towards its home port in University of Alaska Fairbanks’ Marine Center in Seward, Alaska, she detours for approximately 35 days as researchers take advantage of her close proximity to the western Pacific Ocean’s volcanic sea floors. With the help of three types of magnetometers, they will unlock more of our planet’s geomagnetic history that has been captured in our Earth’s crust there.

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    Before leaving port, an undergraduate student acquires important control data with a gravitometer.

    “The geomagnetic field is one of the major physical properties of planet Earth, and it is a very dynamic property that can change from milliseconds to millions of years. It is always, always changing,” said the expedition’s chief scientist, Masako Tominaga, an NSF-funded marine geophysicist from Michigan State University. “Earth’s geomagnetic field is a shield, for example. It protects us from magnetic storms–bursts from the sun–so very pervasive cosmic rays don’t harm us. Our research will provide data to understand how changes in the geomagnetic field have occurred over time and give us very important clues to understand the planet Earth as a whole.”

    Flipping and flopping

    Reportedly, the last time, a geomagnetic reversal occurred was 780,000 years ago, known as the Brunhes-Matuyama reversal. Bernard Brunhes and Motonori Matuyama were the geophysicists who identified that reversal in 1906.

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    A supercomputer to model flow patterns in Earth’s liquid core.
    Dr. Gary A. GlatzmaierLos Alamos National LaboratoryU.S. Department of Energy.

    Researchers Tominaga, Maurice Tivey (from Woods Hole Oceanographic Institution) and William Sager (from University of Houston) have an interest that goes further back in history to the Jurassic period, 145-200 million years ago when a curious anomaly occurred. Scientists originally thought that during this time period, no geomagnetic reversals had happened at all. However, data–like the kind that Tominaga’s team will be collecting–revealed that in fact, the time period was full of reversals that occurred much more quickly.

    “We came to the conclusion that it was actually ‘flipping flopping,’ but so fast that it did not regain the full strength of the geomagnetic field of Earth like today’s strength. That’s why it was super, super low,” Tominaga explained. “The Jurassic period is very distinctive. We think that understanding this part of the geomagnetic field’s behavior can provide important clues for computer simulation where researchers have been trying to characterize this flipping and flopping. Our data could help predict future times when we might see this flipping flopping again.”

    Interestingly, historical records have shown points where the flipping seems likely to occur but then seems to change its mind, almost like a tease, where it returns to its original state. Those instances actually do occur on a shorter time scale than the full-fledged flipping and flopping. Again, scientists are looking for answers on why they occur as well.

    Better tools equal better data

    For approximately three decades, researchers like Tominaga have been probing this area of the western Pacific seafloor. With her cruise on R/V Sikuliaq, Tominaga and Tivey come with even more technology in hand.

    Thirty years ago, researchers didn’t have access to autonomous underwater vehicles (AUV) that could go to deeper, harder-to-reach ocean areas. However, that is just one of three ways Tominaga’s team will deploy three magnetometers during its time at sea. One magnetometer will work from aboard R/V Sikuliaq. Another will trail behind the ship, and the third will be part of the AUV.

    “The seafloor spreading at mid-ocean ridge occurred because of volcanic eruption over time. And when this molten lava formed the seafloor, it actually recorded ambient geomagnetic data. So when you go from the very young ocean seafloor right next to the mid-ocean ridge to very, very old seafloor away from the mid-ocean ridge, a magnetometer basically unveils changes in the geomagnetic field for us,” Tominaga said. “The closer we can get to the seafloor, the better the signal. That’s the rule of thumb for geophysics.”

    With the help of R/V Sikuliaq’s ship’s crew, Tominaga and Tivey, a cruise archivist who is also a computer engineer/scientist, and seven students (three of whom are undergraduates), the team will run daily operations 24 hours a day/seven days a week, deploying the magnetometers, collecting data and then moving on to the next site.

    Naturally, the weather can waylay even the best plans. “Our goal is always about the science, but the road likely will be winding,” Tominaga said. “The most enjoyable part of this work is to be able to work together with this extremely diverse group of people. The Sikuliaq crew, the folks at UAF and those connected to the ship from NSF have all been committed to seeing this research happen, which is incredibly gratifying…. When we make things happen together as a team, it is really rewarding.”

    Focus on fundamentals

    Not surprisingly, this kind of oceanographic research is among some of the most fundamental, serving as a foundation for other research where it might correlate or illuminate. Additionally, because the causes and impacts of these geomagnetic changes are unknown, connections to currents, weather patterns, and other geologic phenomenon can still be explored also.

    “NSF, along with the entire science community, has waited years for this unique state-of-the-art Arctic vessel, and the timing couldn’t be more critical,” said Rose DuFour, NSF program director. “Our hope is to use R/V Sikuliaq to help carry out the abundant arctic-based seagoing science missions that go beyond NSF-funded science and extend to those from other federal agencies, like Office of Naval Research as well.”

    Tominaga notes that another key part to the cruise’s mission is record keeping; it’s why an archivist is part of her team. He even will blog daily (with pictures). As foundational research, it’s important to “keep every single record intact,” and she believes this broadcasting daily narrative will assist in this effort. Additionally, the plan is to share the collected data as soon as possible with other researchers who can benefit from it as well. “Without going there, getting real data–providing ground truth–how do we know what is going on?” Tominaga said, explaining fieldwork’s importance.

    Tominaga is quite clear on what prompts her to keep one of the busiest fieldwork schedules, even during a season usually reserved for family and friends, sipping eggnog or champagne. “I was raised as a scientist/marine geophysicist, and I don’t just mean academically,” she said. “I really looked up to my mentors and friends and how they handed down what they know-so unselfishly. And when I was finishing my Ph.D., I realized that there will be a time I will hand down these things to the next generation. Now, as a professor at Michigan State University, I’m the one who has to pass the torch, if you will–knowledge, experience, and skills at sea. That’s what drives me.”

    See the full article here.

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    The National Science Foundation (NSF) is an independent federal agency created by Congress in 1950 “to promote the progress of science; to advance the national health, prosperity, and welfare; to secure the national defense…we are the funding source for approximately 24 percent of all federally supported basic research conducted by America’s colleges and universities. In many fields such as mathematics, computer science and the social sciences, NSF is the major source of federal backing.

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  • richardmitnick 4:24 pm on December 19, 2014 Permalink | Reply
    Tags: Applied Research & Technology, , , , ,   

    From SLAC: “First Direct Evidence that a Mysterious Phase of Matter Competes with High-Temperature Superconductivity” 


    SLAC Lab

    December 19, 2014

    SLAC Study Shows “Pseudogap” Phase Hoards Electrons that Might Otherwise Conduct Electricity with 100 Percent Efficiency

    Scientists have found the first direct evidence that a mysterious phase of matter known as the “pseudogap” competes with high-temperature superconductivity, robbing it of electrons that otherwise might pair up to carry current through a material with 100 percent efficiency.

    The result, led by researchers at Stanford University and the Department of Energy’s SLAC National Accelerator Laboratory, is the culmination of 20 years of research aimed at finding out whether the pseudogap helps or hinders superconductivity, which could transform society by making electrical transmission, computing and other areas much more energy efficient.

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    This illustration shows the complex relationship between high-temperature superconductivity (SC) and a mysterious phase called the pseudogap (PG). Copper oxide materials become superconducting when an optimal number of electrons are removed, leaving positively charged “holes,” and the material is chilled below a transition temperature (blue curve). This causes remaining electrons (yellow) to pair up and conduct electricity with 100 percent efficiency. Experiments at SLAC have produced the first direct evidence that the pseudogap competes for electrons with superconductivity over a wide range of temperatures at lower hole concentrations (SC+PG). At lower temperatures and higher hole concentrations, superconductivity wins out. (SLAC National Accelerator Laboratory)

    The new study definitively shows that the pseudogap is one of the things that stands in the way of getting superconductors to work at higher temperatures for everyday uses, said lead author Makoto Hashimoto, a staff scientist at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), the DOE Office of Science User Facility where the experiments were carried out. The results were published in Nature Materials.

    SLAC SSRL
    SSRL

    “Now we have clear, smoking-gun evidence that the pseudogap phase competes with and suppresses superconductivity,” Hashimoto said. “If we can somehow remove this competition, or handle it better, we may be able to raise the operating temperatures of these superconductors.”

    Tracking Down Electrons

    In the experiments, researchers used a technique called angle-resolved photoemission spectroscopy, or ARPES, to knock electrons out of a copper oxide material, one of a handful of materials that superconduct at relatively high temperatures – although they still have to be chilled to at least minus 135 degrees Celsius.

    Plotting the energies and momenta of the ejected electrons tells researchers how they were behaving when they were inside the material. In metals, for instance, electrons freely flow around and between atoms. In insulators, they stick close to their home atoms. And in superconductors, electrons leave their usual positions and pair up to conduct electricity with zero resistance and 100 percent efficiency; the missing electrons leave a characteristic gap in the researchers’ plots.

    But in the mid-1990s, scientists discovered another, puzzling gap in their plots of copper oxide superconductors. This “pseudogap” looked like the one left by superconducting electrons, but it showed up at temperatures too warm for superconductivity to occur. Was it a lead-in to superconducting behavior? A rival state that held superconductivity at bay? Where did it come from? No one knew.

    “It’s a complex, intimate relationship. These two phenomena likely share the same roots but are ultimately antagonistic,” said Zhi-Xun Shen, a professor at SLAC and Stanford and senior author of the study. “When the pseudogap is winning, superconductivity is losing ground.”

    Evidence of Competition

    Shen and his colleagues have been using ARPES to investigate the pseudogap ever since it showed up, refining their techniques over the years to pry more information out of the flying electrons.

    In this latest study, Hashimoto was able to find out exactly what was happening at the moment the material transitioned into a superconducting state. He did this by measuring not only the energies and momenta of the electrons, but the number of electrons coming out of the material with particular energies over a wide range of temperatures, and after the electronic properties of the material had been altered in various ways.

    He discovered clear, strong evidence that at this crucial transition temperature, the pseudogap and superconductivity are competing for electrons. Theoretical calculations by members of the team were able to reproduce this complex relationship.

    “The pseudogap tends to eat away the electrons that want to go into the superconducting state,” explained Thomas Devereaux, a professor at Stanford and SLAC and co-author of the study. “The electrons are busy doing the dance of the pseudogap, and superconductivity is trying to cut in, but the electrons are not letting that happen. Then, as the material goes into the superconducting state, the pseudogap gives up and spits the electrons back out. That’s really the strongest evidence we have that this competition is occurring.”

    Remaining Mysteries

    Scientists still don’t know what causes the pseudogap, Devereaux said: “This remains one of the most important questions in the field, because it’s clearly preventing superconductors from working at even higher temperatures, and we don’t know why.”

    But the results pave new directions for further research, the scientists said.

    “Now we can model the competition between the pseudogap and superconductivity from the theoretical side, which was not possible before,” Hashimoto said. “We can use simulations to reproduce the kinds of features we have seen, and change the variables within those simulations to try to pin down what the pseudogap is.”

    He added, “Competition may be only one aspect of the relationship between the two states. There may be more profound questions – for example, whether the pseudogap is necessary for superconductivity to occur.”

    In addition to SLAC and Stanford, researchers from Lawrence Berkeley National Laboratory, Osaka University, the National Institute of Advanced Industrial Science and Technology in Japan, the Japan Atomic Energy Agency, Tokyo Institute of Technology, University of Tokyo and Cornell University contributed to the study. The research was supported by the DOE Office of Science.

    See the full article here.

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    SLAC Campus
    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 4:01 pm on December 19, 2014 Permalink | Reply
    Tags: Applied Research & Technology, , ,   

    From: “Knee meniscus fixed using revolutionary stem cell procedure” 

    Cornell Bloc

    Cornell University

    Dec. 19, 2014
    Krishna Ramanujan

    Researchers report on a revolutionary new procedure that uses 3-D printing and the body’s stem cells to regenerate knee meniscus, a tissue lining that acts as a natural cushion between the femur and tibia.

    People with damaged menisci develop arthritis and are forced to limit their activity.

    The procedure, published online Dec. 10 in the journal Science Translational Medicine, has proved successful in sheep at Cornell University six months after surgery, though the researchers will monitor the sheep for a year to ensure the animals do not develop arthritis. Sheep menisci are structurally similar to those of humans, and clinical trials in humans could begin in two to three years.

    “Most middle-aged people who end up with a degenerate meniscus have it trimmed up [surgically], but if you lose more than 20 to 30 percent, then you are very prone to arthritis,” said Lisa Fortier, professor of large animal surgery at Cornell’s College of Veterinary Medicine and a co-author of the paper; she led the meniscus surgeries on sheep. “If everybody who needed it could replace their meniscus they could slow arthritis and maintain their full function,” Fortier added.

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    Lise Fortier checks the meniscus of a sheep that she operated on last summer, using a groundbreaking new procedure to regenerate knee meniscus. (Meg Goodale)

    The technique was developed by the paper’s senior author Jeremy Mao, professor of dental medicine at Columbia University Medical Center, and involves taking an MRI of the patient’s (in this case sheep’s) knee. Using a 3-D printer, Mao printed a biodegradable polyester scaffold in the exact shape of a patient’s meniscus. Through multiple lab experiments, Mao’s group discovered that two growth factors, when used in specific concentrations and at critical times, recruited the most stem cells for meniscal repair. The growth factors were then laced into the scaffold, allowing the body’s stem cells build a new meniscus four to six weeks after surgery.

    Currently, a torn meniscus requires replacement with cadaver tissue, which has a low success rate and can lead to disease and rejection, and synthetic menisci have proved ineffective and hard to fit properly in diversely built patients.

    Approximately a million people undergo meniscus surgeries each year in the United States.

    Co-authors include Scott Rodeo, orthopedic surgeon at the Hospital for Special Surgery, an affiliate of Weill Cornell Medical College; and Chang H. Lee, Chuanyong Lu and Cevat Erisken, all at Columbia University Medical Center.

    The study was funded by the National Institutes of Health, the Arthroscopy Association of North America, the American Orthopaedic Society for Sports Medicine and the Harry M. Zweig Foundation.

    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 3:06 pm on December 19, 2014 Permalink | Reply
    Tags: Applied Research & Technology, , ,   

    From Brown: “New technique reveals immune cell motion through variety of tissues” 

    Brown University
    Brown University

    December 18, 2014
    Kevin Stacey 401-863-3766

    Neutrophils, a type of white blood cell, are the immune system’s all-terrain vehicles. The cells are recruited to fight infections or injury in any tissue or organ in the body despite differences in the cellular and biochemical composition. Researchers from Brown University’s School of Engineering and the Department of Surgery in the Warren Alpert Medical School collaborated to devise a new technique for understanding how neutrophils move in these confined spaces.

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    Cell movement in 3-D tissue By placing neutrophils between two hydrogel sacks, researchers can mimic cell movement through 3-D tissue. Digital micrometers can change the characteristics — density, stiffness — of the medium through which the cells move. Frank lab/Brown University

    The technique involves two hydrogel sacks sandwiched together with a miniscule space in between. Neutrophils could be placed in that space, mimicking the confinement they experience within tissue. Time-lapse cameras measure how fast the cells move, and traction force microscopes determine the forces the cells exert on the surrounding gel.

    In a paper published in the Journal of Biological Chemistry, the researchers used the device to reveal new details about the motion of neutrophils. Bodily tissues are highly confined, densely packed, three-dimensional spaces that can vary widely in physical shape and elasticity. The researchers showed that neutrophils are sensitive to the physical aspects of their environment: They behave differently on flat surfaces than in confined three-dimensional space. Ultimately, the team hopes the system can be useful in screening drugs aimed at optimizing neutrophils to fight infection in specific tissue types.

    Traditionally, research on neutrophil motion in the lab is often done on two-dimensional, inflexible surfaces composed of plastic or glass. Those studies showed that neutrophils move using arm-like appendages called integrins. The cell extends the integrins, which grab onto to flat surfaces like tiny grappling hooks. By reeling those integrins back in, the cell is able to crawl along.

    Scientists thought that by inhibiting integrins, they could greatly reduce the cells’ ability to move through tissue. That, they thought, could be a good strategy for fighting autoimmune diseases in which neutrophils attack and damage healthy tissue.

    But in 2008, a landmark paper showed that neutrophils have a second mode of motion. The work showed that cells in which integrins had been disabled were still able to move through dense tissue.

    Christian Franck, assistant professor of engineering at Brown, and his colleagues wanted to learn more about this second mode of motion.

    “On flat 2-D surfaces there’s integrin-dependent motion, but in complicated 3-D materials there’s integrin-independent motion,” Franck said. “The question we were asking is can we find an in-vitro system that can recreate that integrin-independent motion, because you can’t get it in a regular petri dish.”

    Using their gel system and the traction force microscopes, Franck and his colleagues showed that, when confined, neutrophils exert force in several distinct spots. On the bottom of the cell, forces were generated in a way that was consistent with previous imaging of integrin engagement. But on the top of the cell, there was another source of force. The cell pushed on the upper gel surface with its nuclear lobe, the area of the cell where DNA resides.

    “It’s like a rock climber pushing against the walls of a canyon,” Franck said.

    To see if the force generated by the nuclear lobe was responsible for the cells’ ability to move without integrins, the researchers repeated the experiment with cells in which integrins were chemically inhibited. Sure enough, the cells were still able to move when confined between the gels. In fact, they were able to move faster.

    “We showed that physical confinement is the key feature to reproduce integrin-independent motion in a relatively simple setting,” Franck said. “That wasn’t possible previously on a flat surface.”

    The fact that confined cells actually move faster without their integrin suggests that even though integrins aren’t essential for the cells motion, they still play a regulatory role.

    “What we showed was that [use of integrins] is not black and white,” Franck said. “Even in this integrin-independent motion, integrins remain to regulate motion and force generation.”

    Now that they have a means of recreating how neutrophils travel through confined spaces in the lab, Franck and his team plan to do further experiments aimed at fine-tuning that motion. The system they’ve developed enables them to control the stiffness of the gel surfaces between which the cells travel, mimicking the varying stiffness of tissue in the body.

    “If motility is specific to a neutrophil being in a specific tissue, maybe we could attenuate its response,” Franck said. “Maybe we could make it move faster in the muscle and slower everywhere else, for example.”

    This new system enables testing of drugs aimed at doing just that. Such drugs could be of great benefit to people who have disorders of the immune system.

    Franck’s co-authors on the study were Jennet Toyjanova, Estefany Flores-Cortez, and Jonathan S. Reichner. The research was supported by the National Institutes of Health (grants GM066194 and AI101469), and by a Brown University seed grant.

    See the full article here.

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    Welcome to Brown

    Rhode Island Hall: Rhode Island Hall’s classical exterior was recently renovated with a modern interiorRhode Island Hall: Rhode Island Hall’s classical exterior was recently renovated with a modern interior

    Located in historic Providence, Rhode Island and founded in 1764, Brown University is the seventh-oldest college in the United States. Brown is an independent, coeducational Ivy League institution comprising undergraduate and graduate programs, plus the Alpert Medical School, School of Public Health, School of Engineering, and the School of Professional Studies.

    With its talented and motivated student body and accomplished faculty, Brown is a leading research university that maintains a particular commitment to exceptional undergraduate instruction.

    Brown’s vibrant, diverse community consists of 6,000 undergraduates, 2,000 graduate students, 400 medical school students, more than 5,000 summer, visiting and online students, and nearly 700 faculty members. Brown students come from all 50 states and more than 100 countries.

    Undergraduates pursue bachelor’s degrees in more than 70 concentrations, ranging from Egyptology to cognitive neuroscience. Anything’s possible at Brown—the university’s commitment to undergraduate freedom means students must take responsibility as architects of their courses of study.

     
  • richardmitnick 10:13 am on December 19, 2014 Permalink | Reply
    Tags: Applied Research & Technology, , ,   

    From ICL: “New study shows how some E. coli bacteria hijack key proteins to survive longer” 

    Imperial College London
    Imperial College London

    19 December 2014
    Laura Gallagher

    A new study shows how two strains of the intestinal bug E. coli manage to hijack host proteins used to control the body’s immune system.

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    The research, carried out by scientists at Imperial College London and published in the journal Nature Communications, shows how E. coli bacteria can block key human enzymes, in a way that has not previously been shown in any other biological context.

    The enzymes, known as kinases, are molecular switches that control processes such as immune responses to infection and cancers in humans. Better understanding how the E. coli bacteria interfere with kinases will provide valuable avenues for investigating new therapies.

    There are many different strains of E. coli. While some are good bacteria, others can cause symptoms ranging from mild diarrhoea and nausea to kidney failure and death. The two strains examined in this study are E. coli O157, which causes food-borne infections, and enteropathogenic E. coli (EPEC), which is a major cause of infantile diarrhoea in low-income countries.

    At present there are no vaccines or effective drugs to combat these infections – in fact antibiotic treatment of E. coli O157 infection can cause the invading bacteria to release more toxins, making the symptoms worse. Patients are treated with fluids and nutrients to enable their immune system to fight the infection.

    One reason why these strains are so dangerous is that they inject bacterial proteins into human cells. These proteins hijack the cell’s signalling network to promote their growth and survival, for example by preventing the host from recognising them as harmful bacteria.

    The new research found that E. coli O157 and EPEC inject a protein called EspJ which inhibits the kinases from signalling.

    “The way in which the EspJ protein blocks the activity of human kinases is completely novel,” says Professor Gad Frankel, from the MRC Centre for Molecular Bacteriology and Infection. “This study will help us better understand how pathogens are able to hijack cells and how they prevent the immune system from fighting the infection.”

    The team reached their conclusions after performing biochemical, mass spectrometry and cell biology assays. This study provides valuable new avenues of investigation: further research will look at whether EspJ-like proteins in other intestinal pathogens, such as Salmonella, behave in similar ways, and also what effect EspJ proteins in E. coli O157 might have on other types of kinases.

    The research was carried out by a team of scientists at Imperial College London, working in collaboration Albert-Ludwigs-Universität Freiburg, in Germany.

    See the full article here.

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    Imperial College London is a science-based university with an international reputation for excellence in teaching and research. Consistently rated amongst the world’s best universities, Imperial is committed to developing the next generation of researchers, scientists and academics through collaboration across disciplines. Located in the heart of London, Imperial is a multidisciplinary space for education, research, translation and commercialisation, harnessing science and innovation to tackle global challenges.

     
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