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    Bioscientists use mixed-reality headset, custom software to measure vegetation in the field

    Ecologists won’t always need expensive and bulky equipment to measure vegetation in the wild. Rice University scientists have discovered a modern heads-up display works pretty well.
    Rice researchers set up aMicrosoft HoloLens as a mixed-reality sensor to feed VegSense, their application to measure understory vegetation, plant life that grows between the forest canopy and floor.
    A proof-of-concept study by graduate student Daniel Gorczynski and bioscientistLydia Beaudrot shows VegSense could be a suitable alternative to traditional classical field measurements at a low cost.
    Their study in Methods in Ecology and Evolution shows the hardware-software combination excels at quantifying relatively mature trees in the wild, which is one measure of a forest’s overall health.
    Gorczynski came up with the idea to try HoloLens, commonly marketed as a productivity tool for manufacturing, health care and education. He developed the open-source software for the device and noted that while the combination is less effective at picking up saplings and small branches, there’s ample room for improvement.
    Gorczynski said he was introduced to mixed-reality sensing while an undergraduate at Vanderbilt University and recognized its potential for biological studies. “It seemed sort of like a natural fit,” he said. Gorczynski brought the idea to Beaudrot in 2019 shortly after his arrival at Rice. More

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    Using smartphones could help improve memory skills

    Using digital devices, such as smartphones, could help improve memory skills rather than causing people to become lazy or forgetful, finds a new study led by UCL researchers.
    The research, published in Journal of Experimental Psychology: General, showed that digital devices help people to store and remember very important information. This, in turn, frees up their memory to recall additional less important things.
    Neuroscientists have previously expressed concerns that the overuse of technology could result in the breakdown of cognitive abilities and cause “digital dementia.”
    However, the findings show that using a digital device as external memory not only helps people to remember the information saved into the device, but it also helps them to remember unsaved information too.
    To demonstrate this, researchers developed a memory task to be played on a touchscreen digital tablet or computer. The test was undertaken by 158 volunteers aged between 18 and 71.
    Participants were shown up to 12 numbered circles on the screen, and had to remember to drag some of these to the left and some to the right. The number of circles that they remembered to drag to the correct side determined their pay at the end of the experiment. One side was designated ‘high value’, meaning that remembering to drag a circle to this side was worth 10 times as much money as remembering to drag a circle to the other ‘low value’ side. More

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    Advancing dynamic brain imaging with AI

    MRI, electroencephalography (EEG) and magnetoencephalography have long served as the tools to study brain activity, but new research from Carnegie Mellon University introduces a novel, AI-based dynamic brain imaging technology which could map out rapidly changing electrical activity in the brain with high speed, high resolution, and low cost. The advancement comes on the heels of more than thirty years of research that Bin He has undertaken, focused on ways to improve non-invasive dynamic brain imaging technology.
    Brain electrical activity is distributed over the three-dimensional brain and rapidly changes over time. Many efforts have been made to image brain function and dysfunction, and each method bears pros and cons. For example, MRI has commonly been used to study brain activity, but is not fast enough to capture brain dynamics. EEG is a favorable alternative to MRI technology however, its less-than-optimal spatial resolution has been a major hindrance in its wide utility for imaging.
    Electrophysiological source imaging has also been pursued, in which scalp EEG recordings are translated back to the brain using signal processing and machine learning to reconstruct dynamic pictures of brain activity over time. While EEG source imaging is generally cheaper and faster, specific training and expertise is needed for users to select and tune parameters for every recording. In new published work, He and his group introduce a first of its kind AI-based dynamic brain imaging methodology, that has the potential of imaging dynamics of neural circuits with precision and speed.
    “As part of a decades-long effort to develop innovative, non-invasive functional neuroimaging solutions, I have been working on a dynamic brain imaging technology that can provide precision, be effective and easy to use, to better serve clinicians and researchers,” said Bin He, professor of biomedical engineering at Carnegie Mellon University.
    He continues, “Our group is the first to reach the goal by introducing AI and multi-scale brain models. Using biophysically inspired neural networks, we are innovating this deep learning approach to train a neural network that can precisely translate scalp EEG signals back to neural circuit activity in the brain without human intervention.”
    In He’s study, which was recently published in Proceedings of the National Academy of Sciences(PNAS), the performance of this new approach was evaluated by imaging sensory and cognitive brain responses in 20 healthy human subjects. It was also rigorously validated in identifying epileptogenic tissue in a cohort of 20 drug-resistant epilepsy patients by comparing AI based noninvasive imaging results with invasive measurements and surgical resection outcomes.
    Results wise, the novel AI approach outperformed conventional source imaging methods when precision and computational efficiency are considered.
    “With this new approach, you only need a centralized location to perform brain modeling and training deep neural network,” explained He. “After collecting data in a clinical or research setting, clinicians and researchers could remotely submit the data to the centralized well trained deep neural networks and quickly receive accurate analysis results. This technology could speed up diagnosis and assist neurologists and neurosurgeons for better and faster surgical planning.”
    As a next step, the group plans to conduct larger clinical trials in efforts to bring the research closer to clinical implementation.
    “The goal is for efficient and effective dynamic brain imaging with simple operation and low cost,” explained He. “This AI-based brain source imaging technology makes it possible.”
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    Materials provided by College of Engineering, Carnegie Mellon University. Original written by Sara Vaccar. Note: Content may be edited for style and length. More

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    Engineers repurpose 19th-century photography technique to make stretchy, color-changing films

    Imagine stretching a piece of film to reveal a hidden message. Or checking an arm band’s color to gauge muscle mass. Or sporting a swimsuit that changes hue as you do laps. Such chameleon-like, color-shifting materials could be on the horizon, thanks to a photographic technique that’s been resurrected and repurposed by MIT engineers.
    By applying a 19th-century color photography technique to modern holographic materials, an MIT team has printed large-scale images onto elastic materials that when stretched can transform their color, reflecting different wavelengths as the material is strained.
    The researchers produced stretchy films printed with detailed flower bouquets that morph from warm to cooler shades when the films are stretched. They also printed films that reveal the imprint of objects such as a strawberry, a coin, and a fingerprint.
    The team’s results provide the first scalable manufacturing technique for producing detailed, large-scale materials with “structural color” — color that arises as a consequence of a material’s microscopic structure, rather than from chemical additives or dyes.
    “Scaling these materials is not trivial, because you need to control these structures at the nanoscale,” says Benjamin Miller, a graduate student in MIT’s Department of Mechanical Engineering. “Now that we’ve cleared this scaling hurdle, we can explore questions like: Can we use this material to make robotic skin that has a human-like sense of touch? And can we create touch-sensing devices for things like virtual augmented reality or medical training? It’s a big space we’re looking at now.”
    The team’s results appear today in Nature Materials. Miller’s co-authors are MIT undergraduate Helen Liu, and Mathias Kolle, associate professor of mechanical engineering at MIT. More

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    Quantum control for advanced technology: Past and present

    One of the cornerstones of the implementation of quantum technology is the creation and manipulation of the shape of external fields that can optimise the performance of quantum devices. Known as quantum optimal control, this set of methods comprises a field that has rapidly evolved and expanded over recent years.
    A new review paper published in EPJ Quantum Technology and authored by Christiane P. Koch, Dahlem Center for Complex Quantum Systems and Fachbereich Physik, Freie Universität Berlin along with colleagues from across Europe assesses recent progress in the understanding of the controllability of quantum systems as well as the application of quantum control to quantum technologies. As such, it lays out a potential roadmap for future technology.
    While quantum optimal control builds on conventional control theory encompassing the interface of applied mathematics, engineering, and physics, it must also factor in the quirks and counter-intuitive nature of quantum physics.
    This includes superposition, the concept that a quantum system can exist in multiple states at one time, one of the keys to the advanced computing power of machines that rely on quantum bits — or qubits.
    Ultimately the main goal of quantum optimal control is to make emerging quantum technologies operate at their optimal performance and reach physical limits.
    “Each device architecture comes with specific limits but these limits are often not attained by more traditional ways to operate the device,” Koch says. “Using pulse shaping may push the devices to the limits in terms of accuracy or operation speed that is fundamentally possible.”
    The authors of this review consider factors in the discipline including the extent to which a quantum system can be established, controlled and observed without causing this superposition to collapse, something which seriously impedes the stability of quantum computers.
    The review also suggests that just as conventional engineers have a control theoretical framework to rely on, the training of future “quantum engineers” may require a similar framework which is yet to be developed.
    A quantum system that unifies theory and experiment is one of the current research goals of the field with the authors pointing out that this will also form the basis for the development of optimal control strategies.
    As well as assessing the recent progress towards this goal, the team lay out some of the roadblocks that may lie ahead for the field. Roadblocks that will need to be overcome if a quantum technological future is to be manifested.
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    Materials provided by Springer. Note: Content may be edited for style and length. More

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    Fiddler crab eye view inspires researchers to develop novel artificial vision

    Artificial vision systems find a wide range of applications, including self-driving cars, object detection, crop monitoring, and smart cameras. Such vision is often inspired by the vision of biological organisms. For instance, human and insect vision have inspired terrestrial artificial vision, while fish eyes have led to aquatic artificial vision. While the progress is remarkable, current artificial visions suffer from some limitations: they are not suitable for imaging both land and underwater environments, and are limited to a hemispherical (180°) field-of-view (FOV).
    To overcome these issues, a group of researchers from Korea and USA, including Professor Young Min Song from Gwangju Institute of Science and Technology in Korea, have now designed a novel artificial vision system with an omnidirectional imaging ability, which can work in both aquatic and terrestrial environments. Their study was made available online on 12 July 2022 and published in Nature Electronics on 11 July 2022.
    “Research in bio-inspired vision often results in a novel development that did not exist before. This, in turn, enables a deeper understanding of nature and ensure that the developed imaging device is both structurally and functionally effective,” says Prof. Song, explaining his motivation behind the study.
    The inspiration for the system came from the fiddler crab (Uca arcuata), a semiterrestrial crab species with amphibious imaging ability and a 360° FOV. These remarkable features result from the ellipsoidal eye stalk of the fiddler crab’s compound eyes, enabling panoramic imaging, and flat corneas with a graded refractive index profile, allowing for amphibious imaging.
    Accordingly, the researchers developed a vision system consisting of an array of flat micro-lenses with a graded refractive index profile that was integrated into a flexible comb-shaped silicon photodiode array and then mounted onto a spherical structure. The graded refractive index and the flat surface of the micro-lens were optimized to offset the defocusing effects due to changes in the external environment. Put simply, light rays traveling in different mediums (corresponding to different refractive indices) were made to focus at the same spot.
    To test the capabilities of their system, the team performed optical simulations and imaging demonstrations in air and water. Amphibious imaging was performed by immersing the device halfway in water. To their delight, the images produced by the system were clear and free of distortions. The team further showed that the system had a panoramic visual field, 300o horizontally and 160o vertically, in both air and water. Additionally, the spherical mount was only 2 cm in diameter, making the system compact and portable.
    “Our vision system could pave the way for 360° omnidirectional cameras with applications in virtual or augmented reality or an all-weather vision for autonomous vehicles,” speculates Prof. Song excitedly.
    Story Source:
    Materials provided by GIST (Gwangju Institute of Science and Technology). Note: Content may be edited for style and length. More

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    A roadmap for the future of quantum simulation

    A roadmap for the future direction of quantum simulation has been set out in a paper co-authored at the University of Strathclyde.
    Quantum computers are hugely powerful devices with a capacity for speed and calculation which is well beyond the reach of classical, or binary, computing. Instead of a binary system of zeroes and ones, it operates through superpositions, which may be zeroes, ones or both at the same time.
    The continuously-evolving development of quantum computing has reached the point of having an advantage over classical computers for an artificial problem. It could have future applications in a wide range of areas. One promising class of problems involves the simulation of quantum systems, with potential applications such as developing materials for batteries, industrial catalysis and nitrogen fixing.
    The paper, published in Nature, explores near- and medium-term possibilities for quantum simulation on analogue and digital platforms to help evaluate the potential of this area. It has been co-written by researchers from Strathclyde, the Max Planck Institute of Quantum Optics, Ludwig Maximilians University in Munich, Munich Center for Quantum Science and Technology, the University of Innsbruck, the Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, and Microsoft Corporation.
    Professor Andrew Daley, of Strathclyde’s Department of Physics, is lead author of the paper. He said: “There has been a great deal of exciting progress in analogue and digital quantum simulation in recent years, and quantum simulation is one of the most promising fields of quantum information processing. It is already quite mature, both in terms of algorithm development, and in the availability of significantly advanced analogue quantum simulation experiments internationally.
    “In computing history, classical analogue and digital computing co-existed for more than half a century, with a gradual transition towards digital computing, and we expect the same thing to happen with the emergence of quantum simulation. More

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    Electrical bacteria may help clean oil spills and curb methane emissions

    The small motorboat anchors in the middle of the Chesapeake Bay. Shrieks of wintering birds assault the vessel’s five crew members, all clad in bright orange flotation suits. One of the crew slowly pulls a rope out of the water to retrieve a plastic tube, about the length of a person’s arm and filled with mud from the bottom of the bay. As the tube is hauled on board, the stench of rotten eggs fills the air.

    “Chesapeake Bay mud is stinky,” says Sairah Malkin, a biogeochemist at the University of Maryland Center for Environmental Science in Cambridge who is aboard the boat. The smell comes from sulfuric chemicals called sulfides within the mud. They’re quite toxic, Malkin explains.

    Malkin and her team venture out onto the bay every couple of months to sample the foul muck and track the abundance of squiggling mud dwellers called cable bacteria. The microbes are living wires: Their threadlike bodies — thinner than a human hair — can channel electricity.

    Sairah Malkin, of the University of Maryland Center for Environmental Science, cuts holes in a large sediment coring tube to sample mud collected from the bottom of the Chesapeake Bay.Clara Fuchsman

    Cable bacteria use that power to chemically rewire their surroundings. While some microbes in the area produce sulfides, the cable bacteria remove those chemicals and help prevent them from moving up into the water column. By managing sulfides, cable bacteria may protect fish, crustaceans and other aquatic organisms from a “toxic nightmare,” says Filip Meysman, a biogeochemist at the University of Antwerp in Belgium. “They’re kind of like guardian angels in these coastal ecosystems.”

    Now, scientists are studying how these living electrical filaments might do good in other ways. Laboratory experiments show that cable bacteria can support other microbes that consume crude oil, so researchers are investigating how to encourage the bacteria’s growth to help clean up oil spills. What’s more, researchers have shown that cable bacteria could help slash emissions of a potent greenhouse gas — methane — into the atmosphere.

    There’s plenty of evidence that cable bacteria exert a strong influence over their microbial neighbors, Meysman says. The next step, he says, is to figure out how to channel that influence for the greater good.

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    Electric life

    Under the microscope, cable bacteria resemble long sausage links. Their multicellular bodies can grow up to 5 centimeters long. Embedded in the envelope of each cell are parallel “wires” of conductive proteins, which the bacteria use to channel electrons. According to Meysman, the wires are more conductive than the semi­conductors found in electronics.

    About a decade ago, a team of scientists first discovered cable bacteria, in sediment collected from the bottom of Denmark’s Aarhus Bay. Since then, cable bacteria have been found on at least four continents, in streams, lakes, estuaries and coastal environments. “Name me a country, and I’ll show you where the cable bacteria are,” Meysman says.

    Most often, cable bacteria nestle shallow in the sediment, with one end positioned near the surface where there is oxygen and the other end plugged into deeper, sulfide-rich zones. Using their filamentous bodies as electrical conduits, cable bacteria snatch electrons from sulfides on one end and off-load them to oxygen — an eager electron acceptor — at the other, says Nicole Geerlings, a biogeochemist at Utrecht University in the Netherlands. Similar to how batteries charge and release energy by transferring electrons between an anode and cathode, cable bacteria power themselves by channeling electrons, she says. “The electron transport gives [cable bacteria] energy.”

    This unique lifestyle allows cable bacteria to survive in an environment that many organisms could not endure.

    A cable bacterium (right) has a multicellular, segmented body that can grow up to 5 centimeters. Electrically conductive, parallel fibers (visible in the close-up at left) encase the body.From left: N. Geerlings/Utrecht Univ.; Silvia Hidalgo Martinez/Univ. of Antwerp

    Toxic fire wall

    In 2015, Malkin, Meysman and colleagues reported that cable bacteria may help to counteract the onset of euxinia — a fatal buildup of sulfides in oxygen-starved bodies of water. Euxinia can trigger mass die-offs of fish, crustaceans and other aquatic life.

    The lethal phenomenon can occur after fertilizers or sewage are washed into the sea or lakes. That flow of nutrients can trigger algal blooms. When those nutrients are depleted, the blooms die, and large quantities of organic matter sink and accumulate on the sediment. Microbes then decompose the dead material, devouring much of the oxygen in the surrounding water in the process. When oxygen levels become critically low, sulfides may begin to leak from the sediment into the water, giving rise to euxinia.

    Sediments near the bottom of this core sample, taken from the Chesapeake Bay, are probably dark due to the presence of sulfides, while sediments near the top are lighter because cable bacteria have removed the sulfides.S. Malkin

    While studying cable bacteria in a brackish body of water in the Netherlands, Malkin and colleagues discovered a thin layer of rust coating the lake’s bottom. As the cable bacteria pulled electrons from sulfides, converting the noxious chemicals into less-harmful sulfates, the water within the sediment became more acidic, which dissolved some minerals containing iron. The now-mobile iron percolated upward in the sediment, until it interacted with oxygen to form rust.

    This layer of rust could capture sulfides that would otherwise flow into the water, acting as a “fire wall” that could delay euxinia for over a month, or even prevent it altogether, the researchers reported. Even when the cable bacteria’s population dropped, the rust layer persisted, protecting other aquatic creatures from sulfide exposure. The rust may explain why even though instances of nutrient pollution, algal blooms and oxygen depletion are relatively common, reports of euxinia are rare.

    Oil cleanup

    Some researchers are trying to harness the bacteria’s electrical abilities to tackle another devastating threat to coastal ecosystems — oil spills.

    When an oil spill happens in a body of water, booms, skimmers or sorbents are often deployed to limit the spread of hydrocarbons on the surface. But oil may also wash onto beaches, mix with sediments in shallow waters and aggregate onto sinking particles of organic debris, hitching a ride to the seafloor.

    Cleaning up oil at the bottom of the sea is a difficult job, says Ugo Marzocchi, a biogeochemist at Aarhus University in Denmark. “I am not aware of a very effective way to remove hydrocarbons from the seafloor,” he says. “In inland freshwater systems, what is generally done is to dig out the sediments,” he says, an expensive strategy that would be even more costly at sea.

    [embedded content]
    Electrical cable bacteria (white filaments) emerge from the seafloor sediment (at bottom) stretching their bodies to reach a zone of oxygen in the water. The stringy organisms use the oxygen to offload electrons they’ve harvested from harmful sulfides found in the sediment. As sulfide concentrations go down, the water becomes more habitable to microbes that can clean up oil spills.

    Some soil-dwelling microorganisms can use hydrocarbons to fuel their metabolism, and researchers have been studying how some of these oil burners might assist in the cleanup of contaminated sediments. But as they break down hydrocarbons, the microbes generate those concerning sulfides, which are detrimental to the microbes’ own survival, Marzocchi says. In other words, the microbes can help clean up the oil for only so long before they’re overwhelmed by their own toxic waste.

    Cable bacteria might be just the solution, Marzocchi thought. In 2016, researchers reported finding evidence of the electrical microbes in a tar oil-contaminated groundwater aquifer in Germany. Knowing that cable bacteria could occupy sediments contaminated with hydrocarbons, Marzocchi and colleagues reasoned that these bacteria might be able to assist oil-burning microbes and accelerate oil cleanup.

    The researchers filled several containers with oil-contaminated sediment from Aarhus Bay — which contained naturally occurring oil-eating bacteria. The group then injected a few containers with cable bacteria and monitored the degree of hydrocarbon degradation in all of the containers over seven weeks. By the end of the test, the concentration of alkanes — a type of hydrocarbon — in the sediment with cable bacteria had dropped from 0.125 milligrams per gram of sediment to 0.086 milligrams per gram — a 31 percent drop. That’s 23 percentage points more than the 9 percent decrease in the control samples. Cable bacteria helped accelerate the metabolic activity of their oil-eating neighbors by converting the toxic sulfides into sulfates. The sulfates didn’t harm the oil-eating microbes — in fact, they used the chemicals as fuel.

    The researchers are now trying to develop methods to promote cable bacteria growth in the field and see if it’s possible to enhance their effect on oil degradation. One catch is that in oil-contaminated sediment, oxygen is quickly used up by the microbes that break down hydrocarbons. That’s a problem since cable bacteria need access to oxygen. Salts that slowly release oxygen or nitrate — which cable bacteria can use in place of oxygen — might help spur the electrical organisms’ growth at oil spills. But more work is needed to identify the right chemical components and dosage, Marzocchi says.

    Meanwhile, scientists are investigating how cable bacteria might help reduce emission of another hydrocarbon — one that accumulates in the sky.

    Methane at the root

    Colorless, odorless methane is the simplest hydrocarbon (SN: 8/15/20, p. 8). It consists of a single carbon atom attached to a quartet of hydrogen atoms. And it’s a potent greenhouse gas — more than 25 times as effective at trapping heat in the atmosphere as carbon dioxide.

    One major source of methane is rice paddies (SN: 9/25/21, p. 16). During the growing season, rice farmers typically flood their fields to help stave off weeds and pests. Methane-producing microbes — aptly named methanogens — thrive in these waterlogged soils. Paddy-dwelling methanogens are so prolific that rice fields are estimated to generate about 11 percent of all human-induced methane emissions.

    But cable bacteria like paddies too. In 2019, Vincent Scholz, a microbiologist at Aarhus University, and colleagues reported that cable bacteria could flourish among the roots of rice plants and several other aquatic plant species.

    In an experiment, pots of rice plants grown in soils with cable bacteria (right) developed orange layers of rust and emitted less methane than pots without cable bacteria (left).V.V. Scholz/Aarhus Univ.

    That discovery inspired the researchers to investigate how the bacteria interact with methanogens in soils that grow rice. The team grew its own rice plants — some potted in soils with cable bacteria, and some without — and monitored methane emissions.

    To the researchers’ surprise, adding cable bacteria reduced rice soil methane emissions by 93 percent. In the process of removing electrons from sulfides, the bacteria generate sulfates, which other microbes can use as fuel. These sulfate-consuming microbes outcompeted methanogens for nutrients such as hydrogen and acetate in the rice soils, the researchers found. The results were “quite amazing,” Scholz says, though the effectiveness of the electrical microbes in real rice fields has yet to be tested.

    There are signs that cable bacteria are already plugged into real rice paddy soils. After analyzing genetic data collected from rice paddies in the United States, India, Vietnam and China, Scholz and colleagues reported in 2021 the presence of cable bacteria at sites in all four countries. Scholz is in Northern California this summer studying how cable bacteria live in rice fields and whether they’re already impacting methane emissions. He is also exploring ways to introduce cable bacteria to rice fields where they don’t yet exist or enhance the microbes’ numbers in fields where they do.

    There is still much to discover about how the wispy electrical conductors influence our world, Malkin says. Back in the Chesapeake Bay, she and colleagues have found that cable bacteria tend to flourish in the spring, a surge that has also been observed in the Netherlands. The findings add to a growing body of work that suggests cable bacteria are opportunistic organisms that interact with their environments in similar ways all around the world.

    If cable bacteria are already hard at work across the planet, then a bit of coaxing from researchers may be all it takes to turn the mud-dwelling creatures into the most helpful neighbors that a living thing could ask for. More