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    SeqScreen can reveal 'concerning' DNA

    It’s a given that certain bacteria and viruses can cause illness and disease, but the real culprits are the sequences of concern that lie within the genomes of these microbes.
    Calling them out is about to get easier.
    Years of work by Rice University computer scientists and their colleagues have led to an improved platform for DNA screening and pathogenic sequence characterization, whether naturally occurring or synthetic, before they have the chance to impact public health.
    Computer scientist Todd Treangen of Rice’s George R. Brown School of Engineering and genomic specialist Krista Ternus of Signature Science LLC led the study that produced SeqScreen, a program to accurately characterize short DNA sequences, often called oligonucleotides.
    Treangen said SeqScreen is intended to improve the detection and tracking of a wide range of pathogenic sequences.
    “SeqScreen is the first open-source software toolkit that is available for synthetic DNA screening,” Treangen said. “Our program improves upon the previous state of the art for companies, individuals and government agencies for their DNA screening practices.”
    The study, which began as high-risk, high-payoff research funded by the National Intelligence Agency’s IARPAprogram in 2017, appears in the journal Genome Biology. More

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    Magnetic superstructures resonate with global 6G developers

    Osaka Metropolitan University researchers observed unprecedented collective resonance motion in chiral helimagnets that allow a boost in current frequency bands.
    When will 6G be a reality? The race to realize sixth generation (6G) wireless communication systems requires the development of suitable magnetic materials. Scientists from Osaka Metropolitan University and their colleagues detected an unprecedented collective resonance at high frequencies in a magnetic superstructure called a chiral spin soliton lattice (CSL), revealing CSL-hosting chiral helimagnets as a promising material for 6G technology. The study was published in Physical Review Letters.
    Future communication technologies require expanding the frequency band from the current few Gigahertz (GHz) to over 100 GHz. Such high frequencies are not yet possible given that existing magnetic materials used in communication equipment can only resonate and absorb microwaves up to approximately 70 GHz with a practical-strength magnetic field. Addressing this gap in knowledge and technology, the research team led by Professor Yoshihiko Togawa from Osaka Metropolitan University delved into the helicoidal spin superstructure CSL. “CSL has a tunable structure in periodicity, meaning it can be continuously modulated by changing the external magnetic field strength,” explained Professor Togawa. “The CSL phonon mode, or collective resonance mode ― when the CSL’s kinks oscillate collectively around their equilibrium position ― allows frequency ranges broader than those for conventional ferromagnetic materials.” This CSL phonon mode has been understood theoretically, but never observed in experiments.
    Seeking the CSL phonon mode, the team experimented on CrNb3S6, a typical chiral magnetic crystal that hosts CSL. They first generated CSL in CrNb3S6 and then observed its resonance behavior under changing external magnetic field strengths. A specially designed microwave circuit was used to detect the magnetic resonance signals.
    The researchers observed resonance in three modes, namely the “Kittel mode,” the “asymmetric mode,” and the “multiple resonance mode.” In the Kittel mode, similar to what is observed in conventional ferromagnetic materials, the resonance frequency increases only if the magnetic field strength increases, meaning that creating the high frequencies needed for 6G would require an impractically strong magnetic field. The CSL phonon was not found in the asymmetric mode, either.
    In the multiple resonance mode, the CSL phonon was detected; in contrast to what is observed with magnetic materials currently in use, the frequency spontaneously increases when the magnetic field strength decreases. This is an unprecedented phenomenon that will possibly enable a boost to over 100 GHz with a relatively weak magnetic field — this boost is a much-needed mechanism for achieving 6G operability.
    “We succeeded in observing this resonance motion for the first time,” noted first author Dr. Yusuke Shimamoto. “Due to its excellent structural controllability, the resonance frequency can be controlled over a wide band up to the sub-terahertz band. This wideband and variable frequency characteristic exceeds 5G and is expected to be utilized in research and development of next-generation communication technologies.”
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    Scientists conceptualize a species 'stock market' to put a price tag on actions posing risks to biodiversity

    So far, science has described more than 2 million species, and millions more await discovery. While species have value in themselves, many also deliver important ecosystem services to humanity, such as insects that pollinate our crops.
    Meanwhile, as we lack a standardized system to quantify the value of different species, it is too easy to jump to the conclusion that they are practically worthless. As a result, humanity has been quick to justify actions that diminish populations and even imperil biodiversity at large.
    In a study, published in the scholarly open-science journal Research Ideas and Outcomes, a team of Estonian and Swedish scientists propose to formalize the value of all species through a conceptual species ‘stock market’ (SSM). Much like the regular stock market, the SSM is to act as a unified basis for instantaneous valuation of all items in its holdings.
    However, other aspects of the SSM would be starkly different from the regular stock market. Ownership, transactions, and trading will take new forms. Indeed, species have no owners, and ‘trade’ would not be about transfer of ownership rights among shareholders. Instead, the concept of ‘selling’ would comprise processes that erase species from some specific area — such as war, deforestation, or pollution.
    “The SSM would be able to put a price tag on such transactions, and the price could be thought of as an invoice that the seller needs to settle in some way that benefits global biodiversity,” explains the study’s lead author Prof. Urmas Kõljalg (University of Tartu, Estonia).
    Conversely, taking some action that benefits biodiversity — as estimated through individuals of species — would be akin to buying on the species stock market. Buying, too, has a price tag on it, but this price should probably be thought of in goodwill terms. Here, ‘money’ represents an investment towards increased biodiversity.
    “By rooting such actions in a unified valuation system it is hoped that goodwill actions will become increasingly difficult to dodge and dismiss,” adds Kõljalg.
    Interestingly, the SSM revolves around the notion of digital species. These are representations of described and undescribed species concluded to exist based on DNA sequences and elaborated by including all we know about their habitat, ecology, distribution, interactions with other species, and functional traits.
    For the SSM to function as described, those DNA sequences and metadata need to be sourced from global scientific and societal resources, including natural history collections, sequence databases, and life science data portals. Digital species might be managed further by incorporating data records of non-sequenced individuals, notably observations, older material in collections, and data from publications.
    The study proposes that the SSM is orchestrated by the international associations of taxonomists and economists.
    “Non-trivial complications are foreseen when implementing the SSM in practice, but we argue that the most realistic and tangible way out of the looming biodiversity crisis is to put a price tag on species and thereby a cost to actions that compromise them,” says Kõljalg.
    “No human being will make direct monetary profit out of the SSM, and yet it’s all Earth’s inhabitants — including humans — that could benefit from its pointers.”
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    Math model predicts efficacy of drug treatments for heart attacks

    Researchers used mice to develop a mathematical model of a myocardial infarction, popularly known as a heart attack.
    The new model predicts several useful new drug combinations that may one day help treat heart attacks, according to researchers at The Ohio State University.
    Typically caused by blockages in the coronary arteries — or the vessels that supply blood to the heart — these cardiovascular events are experienced by more than 800,000 Americans every year, and about 30% end up dying. But even for those who survive, the damage these attacks inflict on the muscles of the heart is permanent and can lead to dangerous inflammation in the affected areas of the heart.
    Treatment to restore blood flow to these blocked passages of the heart often includes surgery and drugs, or what’s known as reperfusion therapy. Nicolae Moise, lead author of the study and a postdoctoral researcher in biomedical engineering at Ohio State, said the study uses mathematical algorithms to assess the efficacy of the drugs used to combat the potentially lethal inflammation many patients experience in the aftermath of an attack.
    “Biology and medicine are starting to become more mathematical,” Moise said. “There’s so much data that you need to start integrating it into some kind of framework.” While Moise has worked on other mathematical models of animal hearts, he said that the framework detailed in the current paper is the most detailed schematic of myocardial infarctions in mice ever made.
    The research is published in the Journal of Theoretical Biology.
    Represented by a series of differential equations, the model Moise’s team created was made using data from previous animal studies. In medicine, differential equations are often used to monitor the growth of diseases in graph form. More

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    Next gen television and computer screens: Creating optically active polymers

    A scientist from the Faculty of Pure and Applied Sciences at the University of Tsukuba developed a method for producing electrically conductive polymers that assume a helical configuration. By using a liquid crystal as a template, he was able to produce optically active polymers that can convert light into a circular polarization. This approach may help lower the cost of smart displays.
    Walking into an electronic store these days can be an overwhelming experience if you happen to wander into the television aisle. The sizes of TVs have significantly expanded in recent years, while the prices have dropped. This is mainly due to the adoption of organic light emitting devices (OLEDs), which are carbon-based polymers that can glow at tunable optical wavelengths. These conjugated polymers, which have alternating single and double bonds, are both electrically conductive, and have colors that can be controlled by chemical doping with other molecules. Their oxidation state can also be rapidly switched using an electric voltage, which affects their coloration. However, future advancement may require new materials that can take advantage of other kinds of optical properties, such as circular polarization.
    Now, a researcher from the University of Tsukuba has introduced a technique for creating polymers locked into a helical configuration, using a sacrificial liquid crystal template. “Polymers that both have optical activity and luminescent function can emit circularly polarized light,” author Professor Hiromasa Goto says. For this process, the liquid crystal molecules were originally in a straight configuration. The addition of monomer molecules caused the liquid crystals to twist into a helical configuration. This imprints a “chirality” or handedness to the structure, making it oriented either clockwise or counterclockwise. An electric voltage was applied, which triggered polymerization of the monomers. The liquid crystal template was then removed, leaving a polymer frozen in a helical shape. By breaking the mirror symmetry, the polymer has the ability to convert linearly polarized light into a circular polarization. The furan rings in the polymer not only contribute to the electrical conductivity, they also help stabilize the helical structure. “The pi-stacking interactions between the rings allows the polymer to aggregate into a highly ordered chiral system,” Professor Goto says. The resulting polymer was tested using circular dichroism absorption spectroscopy and was found to have strong optical activity at visible wavelengths. Future applications of this process may include cheaper and more energy efficient electronic displays.
    This work was supported by the Japan Society for the Promotion of Science (JSPS), Grants-in-Aid for Scientific Research (Magnetic Properties of Magneto-Optically Active Helical Polymers, No. 20K05626).
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    Electrically conductive paints and other polymer alloys now produced easily

    Medical devices, cars, and many advanced technologies contain innumerable delicate components that are held together by electrically conductive polymers, such as polyaniline. For several decades, synthesis of polyaniline for industrial electronics applications has faced a major limitation: what solvent best facilitates synthesis? This abstract question is important for minimizing the cost and complexity of polyaniline production and facilitating useful properties such as shaping. The ability to use a range of cheap, low-boiling-point solvents would greatly assist versatile polymer processing modes such as inkjet printing, but had remained elusive until now.
    In a study recently published in Polymer-Plastics Technology and Materials, researchers from the University of Tsukuba and collaborating partners have synthesized polyaniline in various common solvents. This improved ability to synthesize and process polyaniline will greatly simplify production and lower manufacturing costs.
    “Polyaniline is an extremely versatile polymer in routine and advanced technologies, but restrictions on which solvents can be used for synthesis have long hindered this versatility,” explains Professor Hiromasa Goto, senior author. “Our discovery of how to facilitate polymerization in diverse solvents will be useful in basic research and industrial applications.”
    The researchers produced polyaniline from aniline sulfate in a single step when they added a small quantity of iodine to the reaction mixture. Many solvents were compatible with this procedure, including nontoxic ethanol as well as dichloromethane. Extensive instrumental characterizations demonstrated that the polyaniline produced by this method exhibited the crystallinity and electrical properties as if it had been prepared by conventional methods.
    “A particularly exciting result is the ease of preparing industrially useful polymer alloys, such as blends with polystyrene or cellulose derivatives,” says Professor Goto. “Electrically conductive paint, advanced rubber blends, and other materials are now straightforward to prepare, which we expect will facilitate product development in diverse fields.”
    What is it about the added iodine that facilitates polyaniline production? The researchers propose that iodine is an electron-acceptor dopant that facilitates production of localized polarons, which is critical to the subsequent polymerization by radical chain reactions.
    The results of this study will help make polyaniline more compatible with inkjet printing and other useful processing technologies, and thus simplify production of printed circuit boards and other common components of modern electronics. By focusing on the rather abstract topic of solvent compatibility, many routine and advanced technologies will be easier to make at lower cost.
    This work was supported by the Japan Society for the Promotion of Science (JSPS, Grants-in-Aid for Scientific Research (KAKENHI) [20K05626].
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    Training virtually can reduce psychosocial stress and anxiety

    Previous research has described how virtual training produces acute cognitive and neural benefits. Building on those results, a new study suggests that a similar virtual training can also reduce psychosocial stress and anxiety.
    Researchers from Tohoku University’s Smart-Aging Research Center (IDAC) published their findings in the International Journal of Environmental Research and Public Health on May 23, 2022.
    Physical exercise benefits our overall well-being. But for some — such as neurological patients, people suffering from cardiovascular disease, and hospitalized patients — physical exercise is not feasible, or even too dangerous. However, similar effects may be brought about using Immersive Virtual Reality (IVR).
    Despite initially designed for entertainment, IVR has attracted interest from the academic community because of its potential use for clinical purposes, since it allows the user to experience a virtual world through a virtual body.
    In the researchers’ previous study, they found that looking at a moving virtual body displayed in first-person perspective induces physiological changes. Heart rates increased/decreased coherently with the virtual movements, even though the young participants remained still. Consequently, acute cognitive and neural benefits occurred, just like after real physical activity.
    In a followup study, the same benefits were also found on healthy elderly subjects after 20-minute sessions occurring twice a week for six weeks.
    In the current study, the researchers explored the effect on stress, adding another level to the beneficial effects of virtual training. Young healthy subjects, while sitting still, experienced a virtual training displayed from the first-person perspective, creating the illusion of ownership over movements.
    The avatar ran at 6.4 km/h for 30 minutes. Before and after the virtual training, the researchers induced and assessed the psychosocial stress response by measuring the salivary alpha-amylase — a crucial biomarker indicating the levels of neuroendocrine stress. Similarly, they distributed a subjective questionnaire for anxiety.
    The results showed a decreased psychosocial stress response and lower levels of anxiety after the virtual training, comparable to what happens after real exercise.
    “Psychosocial stress represents the stress experienced in frequent social situations such as social judgment, rejection, and when our performances get evaluated,” says Professor Dalila Burin, who developed the study. “While a moderate amount of exposure to stress might be beneficial, repeated and increased exposure can be detrimental to our health. This kind of virtual training represents a new frontier, especially in countries like Japan, where high performance demands and an aging population exist.”
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    Researchers change the game when it comes to activity tracking

    The creation of high-resolution extrusion printing — think 3D printing but with ink that conducts electricity — has enabled UBC researchers to explore the potential of wearable human motion devices.
    Wearable technology — smartwatches, heart monitors, sleep aid devices, even step counters — have become part of everyday life. And researchers with UBC Okanagan’s Nanomaterials and Polymer Nanocomposites Laboratory, have created even smaller, lighter and highly-accurate sensors that can be integrated into clothing and equipment.
    In collaboration with Drexel University and the University of Toronto, the UBCO research team is exploring a high-resolution extrusion printing approach to develop tiny devices with dual functionality — electromagnetic interference (EMI) shields and a body motion sensor.
    Tiny and lightweight, these EMI shields can have applications in the health care, aerospace and automotive industries, explains Dr. Mohammad Arjmand, Assistant Professor and Canada Research Chair in Advanced Materials and Polymer Engineering at UBC Okanagan’s School of Engineering.
    Using a two-dimensional inorganic nanomaterial called MXene, alongside a conductive polymer, Dr. Arjmand’s team has customized a conductive ink with a number of properties that make it easier to adapt into wearable technologies.
    “Advanced or smart materials that provide electrical conductivity and flexibility are highly sought-after,” he says. “Extrusion printing of these conductive materials will allow for macro-scale patterning, meaning we can produce different shapes or geometries, and the product will have outstanding architecture flexibility.”
    Currently, manufacturing technologies of these functional materials are mostly limited to laminated and unsophisticated structures that don’t enable the integration of monitoring technologies, explains doctoral student Ahmadreza Ghaffarkhah.
    “These printed structures can be seeded with micro-cracks to develop highly sensitive sensors. Tiny cracks in their structures are used to track small vibrations in their surroundings,” says Ghaffarkhah. “These vibrations can monitor a multitude of human activities, including breathing, facial movements, talking as well as the contraction and relaxation of a muscle.”
    By going back to the drawing board, the UBCO researchers were able to address a major challenge encountered by extrusion printing. Previously, the technology didn’t allow for high-enough printing resolution, so it was difficult to manufacture highly precise structures.
    “Compared to conventional manufacturing technologies, extrusion printing offers customization, reduction in materials waste, and rapid production, while opening up numerous opportunities for wearable and smart electronics,” explains Dr. Arjmand. “As extrusion printing techniques improve, it is opening the door to many unique innovations.”
    The researchers continue to investigate additional applications for extrusion printing inks that go beyond EMI shields and wearable electronics.
    The research was published in Carbon, with financial support from a Natural Sciences and Engineering Research Council of Canada Alliance Grant and Zentek Limited. More