Tech

Researchers at the University of Rochester and Cornell University have taken an important step toward developing a communications network that exchanges information across long distances by using photons, mass-less measures of light that are key elements of quantum computing and quantum communications systems.

The research team has designed a nanoscale node made out of magnetic and semiconducting materials that could interact with other nodes, using laser light to emit and accept photons.

The development of such a quantum network--designed to take advantage of the physical properties of light and matter characterized by quantum mechanics--promises faster, more efficient ways to communicate, compute, and detect objects and materials as compared to networks currently used for computing and communications.

Described in the journal Nature Communications, the node consists of an array of pillars a mere 120 nanometers high. The pillars are part of a platform containing atomically thin layers of semiconductor and magnetic materials.

The array is engineered so that each pillar serves as a location marker for a quantum state that can interact with photons and the associated photons can potentially interact with other locations across the device--and with similar arrays at other locations. This potential to connect quantum nodes across a remote network capitalizes on the concept of entanglement, a phenomenon of quantum mechanics that, at its very basic level, describes how the properties of particles are connected at the subatomic level.

"This is the beginnings of having a kind of register, if you like, where different spatial locations can store information and interact with photons," says Nick Vamivakas, professor of quantum optics and quantum physics at Rochester.

Toward 'miniaturizing a quantum computer'

The project builds on work the Vamivakas Lab has conducted in recent years using tungsten diselenide (WSe2) in so-called Van der Waals heterostructures. That work uses layers of atomically thin materials on top of each other to create or capture single photons.

The new device uses a novel alignment of WSe2 draped over the pillars with an underlying, highly reactive layer of chromium triiodide (CrI3). Where the atomically thin, 12-micron area layers touch, the CrI3 imparts an electric charge to the WSe2, creating a "hole" alongside each of the pillars.

In quantum physics, a hole is characterized by the absence of an electron. Each positively charged hole also has a binary north/south magnetic property associated with it, so that each is also a nanomagnet

When the device is bathed in laser light, further reactions occur, turning the nanomagnets into individual optically active spin arrays that emit and interact with photons. Whereas classical information processing deals in bits that have values of either 0 or 1, spin states can encode both 0 and 1 at the same time, expanding the possibilities for information processing.

"Being able to control hole spin orientation using ultrathin and 12-micron large CrI3, replaces the need for using external magnetic fields from gigantic magnetic coils akin to those used in MRI systems," says lead author and graduate student Arunabh Mukherjee. "This will go a long way in miniaturizing a quantum computer based on single hole spins. "

Still to come: Entanglement at a distance?

Two major challenges confronted the researchers in creating the device.

One was creating an inert environment in which to work with the highly reactive CrI3. This was where the collaboration with Cornell University came into play. "They have a lot of expertise with the chromium triiodide and since we were working with that for the first time, we coordinated with them on that aspect of it," Vamivakas says. For example, fabrication of the CrI3 was done in nitrogen-filled glove boxes to avoid oxygen and moisture degradation.

The other challenge was determining just the right configuration of pillars to ensure that the holes and spin valleys associated with each pillar could be properly registered to eventually link to other nodes.

And therein lies the next major challenge: finding a way to send photons long distances through an optical fiber to other nodes, while preserving their properties of entanglement.

"We haven't yet engineered the device to promote that kind of behavior," Vamivakas says. "That's down the road."

OAK BROOK, Ill. - A recently developed data science pathway for fourth-year radiology residents will help prepare the next generation of radiologists to lead the way into the era of artificial intelligence and machine learning (AI-ML), according to a special report published in Radiology: Artificial Intelligence.

AI-ML has the potential to transform medicine by delivering better and more efficient healthcare. Applications in radiology are already arriving at a staggering rate. Yet organized AI-ML curricula are limited to a few institutions and formal training opportunities are lacking.

Three senior radiology residents at Brigham and Women's Hospital (BWH) in Boston recently helped devise a data science pathway to provide a well-rounded introductory experience in AI-ML for fourth-year residents. The pathway combines formal instruction with practical problem-solving in collaboration with data scientists.

"Across the nation there are a number of radiology residency programs that are trying to figure out how to integrate AI into their training," said the paper's co-lead author Walter F. Wiggins, M.D., Ph.D. "We thought that perhaps our experience would help other programs figure out ways to integrate this type of training into either their elective pathways or their more general residency curriculum."

The pathway provides an immersion into AI-ML through a flexible schedule of educational, experiential and research activities at the Massachusetts General Hospital (MGH) & BWH Center for Clinical Data Science (CCDS). Dr. Wiggins and his resident colleagues, M. Travis Caton, M.D., and Kirti Magudia, M.D., Ph.D., were exposed to all aspects of AI-ML application development, including data curation, model design, quality control and clinical testing. The residents contributed to model and tool development at multiple stages, and their work during the pilot period led to 12 accepted abstracts for presentation at national meetings. Feedback from the pilot project resulted in the establishment of a formal AI-ML curriculum for future residents.

"Radiologists have always had to manage, analyze and process data in order to be able to do their work," Dr. Wiggins said. "We already have the underlying skill sets and infrastructure that we can tap into to allow residents with an interest in AI and ML to really develop and become leaders in applying these skills clinically."

The pathway provided ample opportunities for the residents to work directly with data scientists to better understand how they approach image analysis problems with ML tools. This communication, in turn, helped the data scientists better understand how radiologists approach a radiology problem in a clinical setting. The data scientists could be easily implemented in clinical practice.

"An important component of a curriculum like this is to learn the language the data scientists speak and teach them a little bit about the language that we as radiologists speak so that we can have better, more effective collaborations," Dr. Wiggins said. "Going through that process over several different projects was where I think I gained the best experience throughout all of this."

Dr. Wiggins credited Katherine Andriole, Ph.D., director of Research Strategy and Operations at the CCDS, and Michael H. Rosenthal, M.D., Ph.D., for their guidance and feedback as mentors of the project.

Earlier this year, Dr. Wiggins accepted a position as clinical director of AI at Duke Radiology in Durham, North Carolina, where he hopes to utilize some of the lessons he learned from the pathway development process.

"I also hope that people from other institutions might read this manuscript and find something useful for integrating into their residency curricula or for developing specialized pathways for informatics and/or data science," he said.

A new Tel Aviv University study compares the effects of two types of disposable dishes on the marine environment -- regular plastic disposable dishes and more expensive bioplastic disposable dishes certified by various international organizations -- and determines that the bioplastic dishes had a similar effect on marine animals as regular plastic dishes. Moreover, the study finds that bioplastic does not degrade rapidly in the marine environment.

The research was led by research student Guillermo Anderson and Prof. Noa Shenkar of the School of Zoology at the George S. Wise Faculty of Life Sciences and the Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University. The study was published online on August 20, 2020, in the journal Environmental Pollution. It will be published in the print version of the journal in January 2021.

"People buy expensive disposable dishes and utensils with the special bioplastic standard seal of compliance on the assumption that they are being environmentally responsible," Prof. Shenkar says. "Our study proves that while this may be good for their conscience, it can still damage the environment."

Environmental pollution caused by plastics in general and at sea in particular is a well-known crisis. According to various assessments, some 350 million tons of plastic goods are produced every single year, half of which is disposable dishes and utensils thrown away after a single use. Plastic is a very durable polymer made of chemicals derived from fossil fuels. Marine animals ingest plastic microparticles containing toxic additives that are integral to these harmful microparticles.

"In recent decades, substances called 'bioplastics' came on the market," Anderson explains. "Bioplastics are made of natural, renewable materials, and biodegrade relatively fast under certain conditions. Disposable dishes and utensils made of bioplastics were granted various international standard seals and are marketed to consumers as environmentally friendly. We wanted to test the supposedly environmentally friendly disposable dishes to see if they do, in fact, meet expectations."

The study compared disposable cups made of regular plastic and bioplastic and their effects on ascidians, a type of a marine invertebrate; examined the extent, if any, to which these marine invertebrates were capable of digesting particles of the regular plastics and bioplastics; then observed the recruitment of marine organisms to the materials.

At least in the short term, both types of plastic have a similar detrimental effect, Prof. Shenkar says. "Bioplastics are made of natural materials and, in that sense, they are more beneficial environmentally speaking. But they may also contain toxins just like regular plastic dishes and they do not biodegrade quickly in the aquatic habitat. In fact, the standard appearing on the label is dated. It doesn't refer at all to different kinds of plastic additives and speaks of biodegrading within 180 days, but that is specifically under conditions available only in industrial composting settings."

There is a huge number of human problems that scientists and engineers have solved by drawing ideas directly from mechanisms found in other lifeforms, from Velcro to Japan's famous bullet trains, the Shinkansen. Thus, it should not come as a surprise to know that many remarkable advances in anti-reflective coating were inspired by the peculiar biostructures found in moth eyes.

As mainly nocturnal animals that wish to stay hidden from surrounding predators, moths have evolved to develop eyes that are non-reflective. Their eyes have a periodic nanometric structure that makes the eye surface graded, as opposed to polished. This causes most incident light to bend at the surface and therefore, be transmitted through the eye instead of being reflected off it. This nanoscale arrayed structure is so effective that researchers have tried to mimic it using other materials to create anti-reflective coatings with varying degrees of success.

However, in spite of the recent progress in nanoscience that allows the adoption of this idea for various practical applications, there are still barriers to overcome in terms of scalability and cost of manufacturing. To tackle these problems, scientists from Tokyo University of Science and Geomatec Co., Ltd., Japan, have been working on a novel strategy to produce moth-eye nanostructures and transparent films. In their latest study, published in Micro and Nano Engineering, they present a promising method to fabricate moth-eye molds and films at large scales.

Though this research team had previously succeeded in creating moth-eye molds made of glassy carbon etched with an oxygen ion beam, this approach was not scalable. "Producing glassy carbon substrates requires the use of powder metallurgy technology, which is difficult to use to produce molds with a large area," explains Professor Jun Taniguchi from Tokyo University of Science, "To overcome this limitation, we tried using only a thin layer of glassy carbon deposited on top a large regular glass substrate."

Moreover, to make this new strategy feasible, the team opted this time to use an inductively coupled plasma (ICP) system as opposed to the previously used electron-cyclotron resonance ion source. While both devices can etch glassy carbon using a concentrated beam of oxygen ions, ICP technology produces a wider ion beam irradiation range, which is more suitable for working on large-area structures.

After testing with different ICP parameters, the researchers determined that a two-step ICP etching process was best to obtain a high-quality nanostructured mold. Then, they used this mold to produce a transparent film with a moth-eye nanostructure using a UV-curable resin.

The optical properties of this film were remarkable; its reflectance toward light in the visible range was only 0.4%, ten times lower than that of a similar film without the moth-eye nanostructure. What's more, the transmittance of light through the material was also increased, meaning that no trade-off in optical properties occurred as a result of using the film to reduce reflected light.

Mr Hiroyuki Sugawara, Chief Technical Officer at Geomatec, highlights the many possible applications of such anti-reflective films if it were possible to produce them at the meter scale: "We could use these films to improve visibility in flat panel displays, digital signs, and the transparent acrylic plates used everywhere since the start of the COVID-19 pandemic. Moreover, anti-reflective coating could also be an efficient way to improve the performance of solar panels."

This study showcases how to expand the uses of biologically inspired structures by making their fabrication more easily scalable. Let us hope these technological advances help us preserve nature so that we can keep obtaining useful ideas from other species.

Scientists at Swansea University have developed a very sensitive method to detect the tiny signatures of so called 'charge traps' in organic semiconductors.

The research, published in Nature Communications and supported by the Welsh Government through the European Regional Development Fund, may change views about what limits the performance of organic solar cells, photodetectors and OLEDs.

Organic semiconductors are materials mainly made of carbon and hydrogen which can be flexible, low weight and colourful.

They are the key components in OLED displays, solar cells and photodetectors that can distinguish different colours and even mimic the rods and cones of the human eye.

The efficiency of organic solar cells to convert sunlight to electricity has recently reached 18 % and the race is on to really understand the fundamentals of how they work.

Lead author Nasim Zarrabi, a PhD student at Swansea University said: "For a long time, we guessed that some charges that are generated by the sunlight can be trapped in the semiconductor layer of the solar cell, but we've never really been able to prove it.

"These traps make solar cells less efficient, photodetectors less sensitive and an OLED TV less bright, so we really need a way to study them and then understand how to avoid them - this is what motivates our work and why these recent findings are so important."

Research lead, Dr Ardalan Armin, a Sêr Cymru II Rising Start Fellow commented: "Ordinarily, traps are 'dead ends' so to speak; in our study we see them also generating new charges rather than annihilating them completely.

"We'd predicted this could maybe happen, but until now did not have the experimental accuracy to detect these charges generated via traps."

Dr Oskar Sandberg, the theorist behind the work said that he has been waiting for such experimental accuracy for several years.

"What we observed experimentally has been known in silicon and gallium arsenide as intermediate band solar cells, in organic solar cells it has never been shown that traps can generate charges," he said.

"The additional charges generated by the traps is not beneficial for generating lots of electricity because it is very tiny.

"But it is sufficient to be able to study these effects and maybe find ways to control them in order to make genuine improvements in device performance."

DALLAS - Nov. 4, 2020 - A mutation in the gene that causes cystic fibrosis may accelerate heart function decline in those with Duchenne muscular dystrophy (DMD), a new study by UT Southwestern researchers suggests. The findings, published online recently in the Journal of the American Heart Association, could help doctors develop new strategies to preserve heart function in this population, potentially extending patients' lives.

DMD, caused by a mutation on the X chromosome, affects 1 of every 3,500 to 5,000 boys worldwide. This mutation results in the failure to produce dystrophin, a protein that protects muscle cells from damage, which in turn causes progressive muscle weakness. Although patients with DMD can suffer a variety of neuromuscular and lung complications, the cause of death - usually before age 35 - is typically cardiomyopathy, or weakness of the heart muscle.

All DMD patients eventually develop cardiomyopathy. But how early it develops and how progressive it manifests varies considerably, explains Pradeep Mammen, M.D., associate professor in the department of internal medicine's division of cardiology at UTSW, who runs a cardiology clinic specifically for patients with DMD and other neuromuscular disorders.

The reason for this variability has been unknown. However, Mammen and his colleagues suspected that it might result from an additional genetic variation, which may synergistically worsen heart function in DMD patients, accelerating the underlying cardiomyopathy.

To search for genetic variants that might have this effect, Mammen and his team recruited 22 male patients with DMD from their clinic and 12 female carriers, mostly mothers of patients. (Carriers were included in the study since they often also develop cardiomyopathy.) Cardiac function was assessed in 32 of these volunteers using either cardiac magnetic resonance imaging (cMRI), echocardiography, or cardiac computed tomography. Each volunteer also submitted blood to check for additional markers of cardiac function and to perform whole exome sequencing, a genetic test that reads all protein-making genes in the body.

In DMD patients with the worst cardiac function, the researchers identified a few candidate genes that might exacerbate their cardiomyopathy. But one in particular, a switch in a single unit of the cystic fibrosis transmembrane regular (CFTR) gene known as a "missense" mutation, stood out due to its role in heart cells. This gene, which causes cystic fibrosis when both the body's copies carry a different characteristic mutation, is responsible for creating channels in heart cells that let bicarbonate in and regulate cell electrolyte levels.

DMD patients with the missense mutation in a single copy of this gene had a variety of markers of worse heart function compared with those who didn't, including lower left ventricular ejection fraction, larger end-diastolic volume, and higher levels of a blood protein called N-terminal pro-B-type natriuretic peptide.

Although it is unknown how this CFTR mutation exerts its effects, Mammen says doctors who treat these patients might eventually test for this mutation to identify DMD patients who need more aggressive cardiac care at a younger age. Currently, DMD patients receive a range of interventions as cardiomyopathy develops and worsens, ranging from drugs (including ACE inhibitors, beta blockers, and mineralocorticoid receptor agonists) to left ventricular assist devices. Although patients typically begin receiving cardiac care in their teens to early 20s, patients carrying the CFTR mutation may benefit from starting aggressive care earlier to prevent heart damage.

"Even with new strategies to treat these patients on the horizon, such as genome editing that could convert DMD to a less severe form known as Becker's muscular dystrophy, cardiomyopathy will continue to be a patient's most serious and life-ending consequence," says Mammen, who holds the Alfred W. Harris, M.D., Professorship in Cardiology. "Finding ways to help preserve heart function over time could offer new hope for patients with DMD."

HOUSTON - (Nov. 3, 2020) - A thin coating of the 2D nanomaterial hexagonal boron nitride is the key ingredient in a cost-effective technology developed by Rice University engineers for desalinating industrial-strength brine.

More than 1.8 billion people live in countries where fresh water is scarce. In many arid regions, seawater or salty groundwater is plentiful but costly to desalinate. In addition, many industries pay high disposal costs for wastewater with high salt concentrations that cannot be treated using conventional technologies. Reverse osmosis, the most common desalination technology, requires greater and greater pressure as the salt content of water increases and cannot be used to treat water that is extremely salty, or hypersaline.

Hypersaline water, which can contain 10 times more salt than seawater, is an increasingly important challenge for many industries. Some oil and gas wells produce it in large volumes, for example, and it is a byproduct of many desalination technologies that produce both freshwater and concentrated brine. Increasing water consciousness across all industries is also a driver, said Rice's Qilin Li, co-corresponding author of a study about Rice's desalination technology published in Nature Nanotechnology.

"It's not just the oil industry," said Li, co-director of the Rice-based Nanotechnology Enabled Water Treatment Center (NEWT). "Industrial processes, in general, produce salty wastewater because the trend is to reuse water. Many industries are trying to have 'closed loop' water systems. Each time you recover freshwater, the salt in it becomes more concentrated. Eventually the wastewater becomes hypersaline and you either have to desalinate it or pay to dispose of it."

Conventional technology to desalinate hypersaline water has high capital costs and requires extensive infrastructure. NEWT, a National Science Foundation (NSF) Engineering Research Center (ERC) headquartered at Rice's Brown School of Engineering, is using the latest advances in nanotechnology and materials science to create decentralized, fit-for-purpose technologies for treating drinking water and industrial wastewater more efficiently.

One of NEWT's technologies is an off-grid desalination system that uses solar energy and a process called membrane distillation. When the brine is flowed across one side of a porous membrane, it is heated up at the membrane surface by a photothermal coating that absorbs sunlight and generates heat. When cold freshwater is flowed across the other side of the membrane, the difference in temperature creates a pressure gradient that drives water vapor through the membrane from the hot to the cold side, leaving salts and other nonvolatile contaminants behind.

A large difference in temperature on each side of the membrane is the key to membrane desalination efficiency. In NEWT's solar-powered version of the technology, light-activated nanoparticles attached to the membrane capture all the necessary energy from the sun, resulting in high energy efficiency. Li is working with a NEWT industrial partner to develop a version of the technology that can be deployed for humanitarian purposes. But unconcentrated solar power alone isn't sufficient for high-rate desalination of hypersaline brine, she said.

"The energy intensity is limited with ambient solar energy," said Li, a professor of civil and environmental engineering. "The energy input is only one kilowatt per meter square, and the production rate of water is slow for large-scale systems."

Adding heat to the membrane surface can produce exponential improvements in the volume of freshwater that each square foot of membrane can produce each minute, a measure known as flux. But saltwater is highly corrosive, and it becomes more corrosive when heated. Traditional metallic heating elements get destroyed quickly, and many nonmetallic alternatives fare little better or have insufficient conductivity.

"We were really looking for a material that would be highly electrically conductive and also support large current density without being corroded in this highly salty water," Li said.

The solution came from study co-authors Jun Lou and Pulickel Ajayan in Rice's Department of Materials Science and NanoEngineering (MSNE). Lou, Ajayan and NEWT postdoctoral researchers and study co-lead authors Kuichang Zuo and Weipeng Wang, and study co-author and graduate student Shuai Jia developed a process for coating a fine stainless steel mesh with a thin film of hexagonal boron nitride (hBN).

Boron nitride's combination of chemical resistance and thermal conductivity has made its ceramic form a prized asset in high-temperature equipment, but hBN, the atom-thick 2D form of the material, is typically grown on flat surfaces.

"This is the first time this beautiful hBN coating has been grown on an irregular, porous surface," Li said. "It's a challenge, because anywhere you have a defect in the hBN coating, you will start to have corrosion."

Jia and Wang used a modified chemical vapor deposition (CVD) technique to grow dozens of layers of hBN on a nontreated, commercially available stainless steel mesh. The technique extended previous Rice research into the growth of 2D materials on curved surfaces, which was supported by the Center for Atomically Thin Multifunctional Coatings, or ATOMIC. The ATOMIC Center is also hosted by Rice and supported by the NSF's Industry/University Cooperative Research Program.

The researchers showed that the wire mesh coating, which was only about one 10-millionth of a meter thick, was sufficient to encase the interwoven wires and protect them from the corrosive forces of hypersaline water. The coated wire mesh heating element was attached to a commercially available polyvinylidene difluoride membrane that was rolled into a spiral-wound module, a space-saving form used in many commercial filters.

In tests, researchers powered the heating element with voltage at a household frequency of 50 hertz and power densities as high as 50 kilowatts per square meter. At maximum power, the system produced a flux of more than 42 kilograms of water per square meter of membrane per hour -- more than 10 times greater than ambient solar membrane distillation technologies -- at an energy efficiency much higher than existing membrane distillation technologies.

Li said the team is looking for an industry partner to scale up the CVD coating process and produce a larger prototype for small-scale field tests.

"We're ready to pursue some commercial applications," she said. "Scaling up from the lab-scale process to a large 2D CVD sheet will require external support."

NEWT is a multidisciplinary engineering research center launched in 2015 by Rice, Yale University, Arizona State University and the University of Texas at El Paso that was recently awarded a five-year renewal grant for $16.5 million by the National Science Foundation. NEWT works with industry and government partners to produce transformational technology and train engineers who are ready to lead the global economy.

Ajayan is Rice's Benjamin M. and Mary Greenwood Anderson Professor in Engineering, MSNE department chair and a professor of chemistry. Lou is a professor and associate department chair in MSNE and a professor of chemistry.

WASHINGTON, November 3, 2020 -- Squids and other cephalopods use a form of jet propulsion that is not well understood, especially when it comes to their hydrodynamics under turbulent flow conditions. Discovering their secrets can help create new designs for bioinspired underwater robots and vehicles that need to operate within this environment.

Researchers in Scotland, the U.S., and China are exploring the fundamental mechanism behind squids' pulsed-jet propulsion. In Physics of Fluids, from AIP Publishing, the group describes their numerical study of the jet propulsion of cephalopods with turbulent flow considered for the first time. Among their discoveries, they found that thrust production and efficiency are underestimated within laminar, or nonturbulent, flows.

The model for this research is a 2D squidlike swimmer that has a flexible mantle body with a pressure chamber and a nozzle that serves as the inlet and outlet of water. An external force, which mimics the squid muscle's constriction, is applied on the flexible mantle surface of the model.

"As a result, the internal volume of the body decreases and water inside the chamber is ejected to form a jet flow," said Yang Luo, one of the authors and a research assistant at the University of Strathclyde in Glasgow, Scotland. "The squid is propelled forward by the strong jet in the opposite direction, then the mantle inflates automatically as a result of stored elastic energy. During inflation of the mantle, water is sucked into the chamber and gets ejected during the next mantle deflation."

Jet propulsion can be more efficient when turbulent flow is considered, according to Luo. The group also discovered symmetry-breaking instability of vortices around the jetter, which sends out jets of water, after several continuous jet cycles.

"This may help provide a better understanding of why burst-and-coast swimming is used by juvenile and adult squids that operate within turbulent flows more frequently compared with squid hatchlings that operate within laminar flows," said Luo.

Beyond jet propulsion, juvenile and adult squids also rely on fin oscillation on their heads for swimming quite often. The group found this burst-and-coast style may help squids avoid the symmetry-breaking instability of the surrounding flow vortex that could cause thrust and efficiency deterioration.

"The findings of our work about the mechanism of symmetry-breaking instability provides guidance for the design of squid-inspired underwater robots and vehicles," said Luo. "Continuous jet propulsion may not be favorable, and specific measures are needed to mitigate the effect of this instability during the design of jet propulsion-inspired underwater vehicles or propulsors via active control of body deformation to change the evolution of the internal vortices pattern."

Will we see new jet propulsion-based submarines soon?

"It's difficult to determine at this point," Luo said. "But as a relatively less extensively studied form of underwater propulsion, it is advantageous in terms of a straightforward mechanism for effective instantaneous escape and high maneuverability. This makes it promising for integrating with typical thruster propulsion to achieve on-demand maneuverability."

Many people have had the experience of being poked in the back by a plastic tag while trying on clothes in a store. That is just one example of radio frequency identification technology, which has become a mainstay not just in retail but also in manufacturing, logistics, transportation, health care and more. Other tagging systems include the scannable barcode and the QR code.

Despite their near ubiquity, these object tagging systems have their shortcomings: They may be too large or inflexible for certain applications, they are easily damaged or removed, and they may be impractical to apply in high quantities. But recent advancements in DNA-based data storage and computation offer new possibilities for creating a tagging system that is smaller and lighter than conventional methods.

That's the point of Porcupine, a new molecular tagging system introduced by University of Washington and Microsoft researchers. These tags can be programmed and read within seconds using a portable nanopore device. In a new paper published Nov. 3 in Nature Communications, the team describes how dehydrated strands of synthetic DNA can take the place of bulky plastic or printed barcodes. Building on recent developments in DNA sequencing technologies and raw signal processing tools, the team's inexpensive and user-friendly design forgoes the need for access to specialized labs and equipment.

"Molecular tagging is not a new idea, but existing methods are still complicated and require access to a lab, which rules out many real-world scenarios," said lead author Kathryn Doroschak, a UW doctoral student in the Paul G. Allen School of Computer Science & Engineering. "We designed the first portable, end-to-end molecular tagging system that enables rapid, on-demand encoding and decoding at scale, and which is more accessible than existing molecular tagging methods."

Instead of radio waves or printed lines, the Porcupine tagging scheme relies on a set of distinct DNA strands called molecular bits, or "molbits" for short, that incorporate highly separable nanopore signals to ease later readout. Each individual molbit comprises one of 96 unique barcode sequences combined with a longer DNA fragment selected from a set of predetermined sequence lengths. Under the Porcupine system, the binary zeros and ones of a digital tag are signified by the presence or absence of each of the 96 molbits.

"We wanted to prove the concept while achieving a high rate of accuracy, hence the initial 96 barcodes, but we intentionally designed our system to be modular and extensible," said co-author Karin Strauss, senior principal research manager at Microsoft Research and affiliate professor in the Allen School. "With these initial barcodes, Porcupine can produce roughly 4.2 billion unique tags using basic laboratory equipment without compromising reliability upon readout."

Although DNA is notoriously expensive to read and write, Porcupine gets around this by prefabricating the fragments of DNA. In addition to lowering the cost, this approach has the added advantage of enabling users to arbitrarily mix existing strands to quickly and easily create new tags. The molbits are prepared for readout during initial tag assembly and then dehydrated to extend the shelf life of the tags. This approach protects against contamination from other DNA present in the environment while simultaneously reducing readout time later.

Another advantage of the Porcupine system is that molbits are extremely tiny, measuring only a few hundred nanometers in length. In practical terms, this means each molecular tag is small enough to fit over a billion copies within one square millimeter of an object's surface. This makes them ideal for keeping tabs on small items or flexible surfaces that aren't suited to conventional tagging methods. Invisible to the naked eye, the nanoscale form factor also adds another layer of security compared to conventional tags.

"Unlike existing inventory control methods, DNA tags can't be detected by sight or touch. Practically speaking, this means they are difficult to tamper with," said senior author Jeff Nivala, a research scientist at the Allen School. "This makes them ideal for tracking high-value items and separating legitimate goods from forgeries. A system like Porcupine could also be used to track important documents. For example, you could envision molecular tagging being used to track voters' ballots and prevent tampering in future elections."

To read the data in a Porcupine tag, a user rehydrates the tag and runs it through a portable nanopore device. To demonstrate, the researchers encoded and then decoded their lab acronym, "M-I-S-L," reliably and within a few seconds using the Porcupine system. As advancements in nanopore technologies make them increasingly affordable, the team believes molecular tagging could become an increasingly attractive option in a variety of real-world settings.

"Porcupine is one more exciting example of a hybrid molecular-electronic system, combining molecular engineering, new sensing technology and machine learning to enable new applications," said co-author Luis Ceze, a professor in the Allen School.

The virus that causes COVID-19 was present in New York City long before the city's first case of the disease was confirmed on March 1, researchers at the Icahn School of Medicine at Mount Sinai report. Their study found that more than 1.7 million New Yorkers--about 20 percent of the city's population--have already been infected with the virus, known as SARS-CoV-2, and that the infection fatality rate of the virus is close to 1 percent, ten times deadlier than the flu.

Results of the retrospective surveillance study of more than 10,000 plasma samples taken from the beginning of February to July will be published in Nature on Tuesday, November 3 at 5AM ET.

A sharp rise in infections in New York City occurred in the week ending March 8, followed by a significant increase of COVID-19 deaths during the week ending March 15. New York State implemented a stay-at-home order March 22, after which daily case numbers in New York City started to plateau and then decreased in April and May.

Very little testing capacity was available at the beginning of the local epidemic in early March, but, "We now know there were many asymptomatic and mild to moderate cases that likely went undetected," said Emilia Mia Sordillo, MD, PhD, Associate Professor of Pathology, Molecular and Cell Based Medicine, Director of Clinical Microbiology, an attending physician in Infectious Diseases at the Icahn School of Medicine and the Mount Sinai Health System, and a senior author on the paper. "In this study, we aimed to understand the dynamics of infection in the general population and in people seeking urgent care."

The study findings are based on a dataset of 10,691 plasma samples from Mount Sinai Health System patients obtained and tested between the weeks ending February 9 and July 5. The first group included 4,101 samples from patients seen in Mount Sinai's emergency departments and from patients that were admitted to the hospital for urgent care. This group, termed the "urgent care" group, served as a positive control group designed to detect increasing SARS-CoV-2 infections in individuals with moderate to severe COVID-19 as the local epidemic progressed. The second group of 6,590 samples, termed the "routine care" group, were obtained from patients at OB/GYN visits, labor and deliveries, oncology-related visits, hospitalizations due to elective surgeries and transplant surgeries, preoperative medical assessments and related outpatient visits, cardiology office visits, and other regular office/treatment visits. Researchers reasoned that these samples might resemble the general population more closely because the purposes for these scheduled visits were unrelated to acute SARS-CoV-2 infection. The urgent care group comprised 45.5 percent females while the routine care group included 67.6 percent females. The majority of individuals in the urgent care group were over 61 years of age while the routine care group had a more balanced age distribution that more closely resembled the general population adult population.

To estimate true infection rates, researchers measured the presence of antibodies to past SARS-CoV-2 infections, rather than the presence of the virus, in weekly intervals. The antibody test used in this research--an enzyme-linked immunosorbent assay (ELISA)-- was developed and launched at Mount Sinai and is able to detect the presence or absence of antibodies to SARS-CoV-2, as well as the titer (level) of antibodies an individual has. The high sensitivity and specificity of this test--meaning that the rate of false negatives and false positives is low--allowed it to be among the first to receive emergency use authorization from New York State and the U.S. Food and Drug Administration.

"Our two-step ELISA test confirms the presence and level antibodies. The use of two sequential tests reduces the false positive rate and favors high specificity resulting in a sensitivity of 95 percent and a specificity of 100 percent," said Viviana Simon, MD, PhD, Professor of Microbiology, and Medicine; a member of the faculty of the Global Health and Emerging Pathogens Institute at the Icahn School of Medicine; and a senior author on the paper.

Seroprevalence increased at different rates in both groups, rising sharply in the urgent care group. Notably, seropositive samples were found as early as mid-February (several weeks before the first official cases) and leveled out at slightly above 20 percent in both groups after the epidemic wave subsided by the end of May. From May to July, seroprevalence and antibody titers stayed stable, suggesting lasting antibody levels in the population.

"Our data suggests that antibody titers are stable over time, that the seroprevalence in the city is around 22 percent, that at least 1.7 million New Yorkers have been infected with SARS-CoV-2 so far, and that the infection fatality rate is 0.97 percent after the first epidemic wave in New York City," said Florian Krammer, PhD, Mount Sinai Professor in Vaccinology at the Icahn School of Medicine and corresponding author on the paper. "We show that the infection rate was relatively high during the first wave in New York but is far from seroprevalence that might indicate community immunity (herd immunity). Knowing the detailed dynamics of the seroprevalence shown in this study is important for modeling seroprevalence elsewhere in the country."

The aim of the EU Nitrates Directive is to reduce nitrates leaking into the environment in order to prevent pollution of water supplies. The widely accepted view is that this will also help protect threatened plant species which can be damaged by high levels of nutrients like nitrates in the soil and water. However, an international team of researchers including the Universities of Göttingen, Utrecht and Zurich, has discovered that many threatened plant species will actually suffer because of this policy. The results were published in Nature Ecology and Evolution.

Nitrogen, in the form of nitrates, is an important nutrient for plant species. However, an overabundance can harm plant biodiversity: plant species that thrive on high levels of nitrates can displace other species adapted to low levels. "Despite this, it is not enough simply to reduce the level of nitrates," says co-author Julian Schrader, researcher in the Biodiversity, Macroecology and Biogeography Group at the University of Göttingen. "Such a policy can even backfire and work against the protection of threatened plant species if other nutrients are not taken into account."

In addition to nitrogen, plants also need phosphorus and potassium to grow. The researchers discovered that the ratio of these nutrients in the soil is important. They showed that when the concentration of nitrogen in the soil is reduced, without simultaneously reducing the concentration of phosphates, plant species that are already threatened, could disappear.

"Many threatened plant species in Europe are found in places where phosphate concentrations are low," Schrader explained. If nitrogen concentrations decrease, as a result of effective environmental policies, then the relative concentration of phosphorous increases. This means that threatened species come under even more pressure. Threatened species are particularly sensitive to changes in nutrient concentrations and should, according to the researchers, be better protected.

The results of this research have significant consequences for the current EU Nitrate Directive. The authors advocate the introduction of an EU Phosphate Directive in addition to the existing EU Nitrate Directive.

Scientists have developed an AI tool to analyse how proteins move and interact which is faster and more accurate than humans, according to a study published today in eLife.

The software, which is freely available, dramatically speeds up the study of protein dynamics and makes it accessible to research teams across the world, rather than limited to a few laboratories with specialist expertise.

Proteins are the workhorses of our cells, and their movement controls a vast array of biological processes. Studying the choreography of proteins - how they move around and interact with each other - is an essential part of understanding fundamental biology. One of the main tools for studying protein motion is called single molecule Förster Resonance Energy Transfer (smFRET). This works by labelling two or more parts of the molecule with a different fluorescent tag, and when the two tags are in close proximity, the change in fluorescence can be detected by a microscope. In this way, the movement of proteins can be visualised and measured down to the nanometre level.

"Some of the challenges with smFRET include the very large data that are produced, and the steps that researchers need to take to process the images before analysis," explains lead author Johannes Thomsen, who carried out this study as a Research Assistant at the University of Copenhagen, Denmark, and has since graduated with a PhD. "Machine learning technologies, especially deep neural networks, have significantly improved our ability to understand large datasets without the need for human intervention. We wanted to see whether employing these technologies to smFRET data would allow automated, fast characterisation of protein motions, independently of human experts."

The team chose to use a type of deep learning called deep neural networks (DNN). Deep learning is a unique branch of machine learning that takes the raw form of the data and looks for patterns with no prior 'knowledge'. It has the advantage of learning useful features from raw data without time-intensive pre-processing, and offers a 'less opinionated' evaluation of the data, compared with the more subjective analysis by humans. DNN has a further advantage in that it can learn to recognise important aspects of the data and then classify it into groups. Although developing a DNN is a computationally intensive process that can take time, once trained the model can be used easily, and by non-experts, in any computer.

The tool, DeepFRET, imports raw microscope images, locates the two different fluorescence signals, corrects for background noise and, with limited human help, produces a chart showing the motion of the molecules within the sample. When tested with simulated and real data, its accuracy at detecting meaningful patterns from the data was more than 95%, outperforming human operators and yet only needing 1% of the time. The evaluation time for DeepFRET on a single piece of data (a trace) was around 50 milliseconds, whereas human reviewers spent an average of five seconds per trace.

"We have developed a machine learning method that can automatically, rapidly and reproducibly analyse recordings of the choreography of protein motions, with simple user interface that works on different operating systems," concludes senior author Nikos Hatzakis, Associate Professor at the University of Copenhagen, and Affiliate Associate Professor at the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen. "The method works equally to or better than existing methods, and requires only minimal contribution by humans. It therefore offers a tool for people with limited expertise, which we hope will contribute to the standardisation and rapid expansion of this field of study."

A team of chemists from RUDN University synthesized new organosilicon compounds containing terbium and europium ions. These complexes have an unusual cage-like crystal structure that contains four metal ions. The team was the first to study the magnetic and photophysical properties of such compounds and to observe their magnetic phase transition and luminescence properties. The results of the work were published in Chemistry - A European Journal.

Cakelike Metal-containing silsesquioxanes (CLMSs) are complex organo-inorganic compounds that contain carbon, silicon, and metal atoms bound with each other. Chemists are interested in CLMSs because their molecules can form various cagelike structures and extended 3D derivatives. Different molecular structures and metal atoms give silsesquioxanes special physical properties, for example, making them promising catalysts for important organic synthesis reactions. A team of chemists from RUDN University obtained four new metal-containing silsesquioxanes and studied their luminescence and magnetic properties.

Complexes obtained by the team are based on the lanthanide metals, namely, terbium and europium. Lanthanide compounds are known for their unusual magnetic and optical properties: the former make them an excellent source for the production of contrast agents for medical applications, and the latter - materials for electroluminescent devices. However, until this work, these properties had never been studied in detail for lanthanide-containing cage silsesquioxanes. Compounds obtained by the team have an unusual structure that has never been observed before, with prism-shaped cage including central core with four lanthanide atoms. This central layer is coordinated by two cyclic silsesquioxane fragments, solvent molecules, and organic (phosphorus- or nitrogen-containing) cations. Notably, terbium compounds synthesized by the team were the first-ever silsesquioxanes to contain this metal.

"Until recently, only two types of lanthanide CLMSs had been known and had undergone X-ray diffraction study. The first type was cubane siloxane compounds - cube-shaped structures with a lanthanide atom in each corner. The second was the so-called sandwiches: two siloxane fragments with a layer of lanthanide ions and alkaline metals laying between them. Both types were only considered as unusual structural types and/or catalytic system models, and their optical and magnetic properties were largely understudied," said Dr. Alexey Bilyachenko, a Deputy Head of the Joint Institute for Chemical Research at RUDN University.

To obtain new compounds, the team developed a two-step reaction. First, a reactive substance (sodium phenylsiloxanolate) was synthesized. Second, the so-called self-assembly reaction took place: sodium phenylsiloxanolate (in the presence of organic cations) formed a regular structure due to coordination to lanthanide ions. X-ray diffraction analysis allowed to establish the structure of the products and identified fourmembered siloxane cycles in their structures. Previously, such cycles have only been observed in titanium- and cobalt-based CLMSs.

Magnetic properties of lanthanide-based silsesquioxanes were investigated for the first time. The terbium-based compound demonstrated the magnetic spin flip effect (i.e. the switch from antiferromagnetic behaviour into a ferromagnetic one).

To study the optical properties of the substances, the team subjected them to photoexcitation under the influence of UV or visible blue light. The compounds demonstrated characteristic luminescence: europium-containing substances provided red emission, while terbium-containing ones provided a green one. Therefore, these compounds turned out to be the first CLMSs with magnetic and luminescent properties studied in detail.

Coral reefs are hotspots of biodiversity. As they can withstand heavy storms, they offer many species a safe home, and at the same time, they protect densely populated coastal regions as they level out storm-driven waves. However, how can these reefs that are made up of often very fragile coral be so stable? A team of researchers from Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) and the University of Bayreuth have now discovered that a very specific type of 'cement' is responsible for this - by forming a hard calcareous skeleton, coralline red algae stabilise the reefs, and have been doing so for at least 150 million years.

The wide variety of life they support is immediately apparent on images of tropical coral reefs. Their three-dimensional scaffolding provides a habitat for a large number of species. However, the skeletons of the coral are often so fragile that they would not be able to withstand heavy storms by themselves. Even if scientists have long suspected that coralline red algae provide support to reefs with their calcareous skeletons, this is the first time that this link has been proven.

Coralline red algae have been supporting coral reefs for at least 150 million years

The researchers from FAU and the University of Bayreuth were able to prove this supporting function by analysing more than 700 fossilised reefs from 150 million years of the Earth's history. 'The coralline red algae form a calcareous skeleton and cement the coral reefs together,' explains Dr. Sebastian Teichert from the Chair of Palaeoenvironmental Research at FAU. 'However, several crises over the course of millions of years have limited their capacity to do so.'

Successful adaptive strategies against plant grazers

These crises include the evolution of plant grazing marine animals such as sea urchins and parrot fishes who have repeatedly decimated populations of coralline red algae over the course of time. The algae, however, developed defence mechanisms such as special growth forms in order to defend themselves against their attackers. 'The algae have adapted so well that they now even benefit from these plant grazers,' says Teichert. 'They rid the coralline red algae of damaging growth such as green algae, allowing it to grow unhindered.' This means coralline red algae are more successful at supporting coral reefs today than ever before in the Earth's history.

The extent to which climate change affects the supporting role of coralline red algae is not yet known. Any deterioration to their living conditions would not only affect the coral and other inhabitants of reefs, but also humans, as coral reefs level out storm-driven waves and make an important contribution to coastal protection. They also provide a nursery habitat for several fish and shellfish which are an important source of food.

Pacemakers and other implantable cardiac devices used to monitor and treat arrhythmias and other heart problems have generally had one of two drawbacks - they are made with rigid materials that can't move to accommodate a beating heart, or they are made from soft materials that can collect only a limited amount of information.

Researchers led by a mechanical engineer from the University of Houston have reported in Nature Electronics a patch made from fully rubbery electronics that can be placed directly on the heart to collect electrophysiological activity, temperature, heartbeat and other indicators, all at the same time.

Cunjiang Yu, Bill D. Cook Associate Professor of Mechanical Engineering at UH and corresponding author for the paper, said the device marks the first time bioelectronics have been developed based on fully rubbery electronic materials that are compatible with heart tissue, allowing the device to solve the limitations of previous cardiac implants, which are mainly made out of rigid electronic materials.

"For people who have heart arrhythmia or a heart attack, you need to quickly identify the problem," Yu said. "This device can do that." Yu is also a principle investigator with the Texas Center for Superconductivity at UH.

In addition to the ability to simultaneously collect information from multiple locations on the heart - a characteristic known as spatiotemporal mapping - the device can harvest energy from the heart beating, allowing it to perform without an external power source. That allows it to not just track data for diagnostics and monitoring but to also offer therapeutic benefits such as electrical pacing and thermal ablation, the researchers reported.

Yu is a leader in the development of fully rubbery electronics with sensing and other biological capabilities, including for use in robotic hands, skins and other devices. The epicardial bioelectronics patch builds upon that with a material with mechanical properties that mimic cardiac tissue, allowing for a closer interface and reducing the risk that the implant could damage the heart muscle.

"Unlike bioelectronics primarily based on rigid materials with mechanical structures that are stretchable on the macroscopic level, constructing bioelectronics out of materials with moduli matching those of the biological tissues suggests a promising route towards next-generational bioelectronics and biosensors that do not have a hard-soft interface for the heart and other organs," the researchers wrote. "Our rubbery epicardial patch is capable of multiplexed ECG mapping, strain and temperature sensing, electrical pacing, thermal ablation and energy harvesting functions."