Computers Math

Genetically encoded reporter proteins have been a mainstay of biotechnology research, allowing scientists to track gene expression, understand intracellular processes and debug engineered genetic circuits.
But conventional reporting schemes that rely on fluorescence and other optical approaches come with practical limitations that could cast a shadow over the field’s future progress. Now, researchers at the University of Washington and Microsoft have created a “nanopore-tal” into what is happening inside these complex biological systems, allowing scientists to see reporter proteins in a whole new light.
The team introduced a new class of reporter proteins that can be directly read by a commercially available nanopore sensing device. The new system ? dubbed “Nanopore-addressable protein Tags Engineered as Reporters” or “NanoporeTERs” ? can detect multiple protein expression levels from bacterial and human cell cultures far beyond the capacity of existing techniques.
The study was published Aug. 12 in Nature Biotechnology.
“NanoporeTERs offer a new and richer lexicon for engineered cells to express themselves and shed new light on the factors they are designed to track. They can tell us a lot more about what is happening in their environment all at once,” said co-lead author Nicolas Cardozo, a doctoral student with the UW Molecular Engineering and Sciences Institute. “We’re essentially making it possible for these cells to ‘talk’ to computers about what’s happening in their surroundings at a new level of detail, scale and efficiency that will enable deeper analysis than what we could do before.”
For conventional labeling methods, researchers can track only a few optical reporter proteins, such as green fluorescent protein, simultaneously because of their overlapping spectral properties. For example, it’s difficult to distinguish between more than three different colors of fluorescent proteins at once. In contrast, NanoporeTERs were designed to carry distinct protein “barcodes” composed of strings of amino acids that, when used in combination, allow at least ten times more multiplexing possibilities. More

The old adage “never let them see you sweat,” doesn’t apply in the electrical and computer engineering lab of Rose Faghih, assistant professor of electrical and computer engineering in the University of Houston Cullen College of Engineering. In fact, Faghih seeks sweat, the kind that beads on your upper lip when you’re nervous — skin conductance response (SCR) as the change in sweat activity is scientifically called. It is through that measure that Faghih is reporting the ability to monitor stress and even help lower it.
To collect and study these physiological signals of stress, Faghih’s research team has built a new closed-loop technology by placing two electrodes on smartwatch-type wearables. Once the signal for stress is detected, a reminder is sent through the smartwatch, for example, to listen to relaxing music to calm down. Thus, the loop is closed as the detected stress launches the subtle suggestion.
“This study is one of the very first steps toward the ultimate goal of monitoring brain responses using wearable devices and closing the loop to keep a person’s stress state within a pleasant range,” reports Faghih in the journal IEEE Xplore.
Electrodermal activity (i.e., the electrical conductivity of the skin) carries important information about the brain’s cognitive stress. Faghih uses signal processing techniques to track the hidden stress state and design an appropriate control algorithm for regulating the stress state and closing the loop. The results of the research illustrate the efficiency of the proposed approach and validate its feasibility of being implemented in real life.
“To the best of our knowledge, this research is one of the very first to relate the cognitive stress state to the changes in SCR events and design the control mechanism to close the loop in a real-time simulation system,” said UH doctoral student and lead study author Fekri Azgomi, who accomplished the task of closed-loop cognitive stress regulation in a simulation study based on experimental data.
Due to the increased ubiquity of wearable devices capable of measuring cognitive stress-related variables, the proposed architecture is an initial step toward treating cognitive disorders using non-invasive brain state decoding.
“The final results verify that the proposed architecture has great potential to be implemented in a wrist-worn wearable device and used in daily life,” said Faghih.
Stress is a worldwide issue that can result in catastrophic health and financial complications. A recent Gallup poll found that more than one in three adults (35%) worldwide said they experienced stress during “a lot of the day yesterday.”
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Materials provided by University of Houston. Original written by Laurie Fickman. Note: Content may be edited for style and length. More

Scientists have taken the clearest picture yet of electronic particles that make up a mysterious magnetic state called quantum spin liquid (QSL).
The achievement could facilitate the development of superfast quantum computers and energy-efficient superconductors.
The scientists are the first to capture an image of how electrons in a QSL decompose into spin-like particles called spinons and charge-like particles called chargons.
“Other studies have seen various footprints of this phenomenon, but we have an actual picture of the state in which the spinon lives. This is something new,” said study leader Mike Crommie, a senior faculty scientist at Lawrence Berkeley National Laboratory (Berkeley Lab) and physics professor at UC.
“Spinons are like ghost particles. They are like the Big Foot of quantum physics — people say that they’ve seen them, but it’s hard to prove that they exist,” said co-author Sung-Kwan Mo, a staff scientist at Berkeley Lab’s Advanced Light Source. “With our method we’ve provided some of the best evidence to date.”
A surprise catch from a quantum wave
In a QSL, spinons freely move about carrying heat and spin — but no electrical charge. To detect them, most researchers have relied on techniques that look for their heat signatures. More

To train robots how to work independently but cooperatively, researchers at the University of Cincinnati gave them a relatable task: move a couch.
If you’ve ever helped someone move furniture, you know it takes coordination — simultaneously pushing or pulling and reacting based on what your helper is doing. That makes it an ideal problem to examine collaboration between robots, said Andrew Barth, a doctoral student in UC’s College of Engineering and Applied Science.
“It’s a good metaphor for cooperation,” Barth said.
In the Intelligent Robotics and Autonomous Systems Lab of UC aerospace engineering professor Ou Ma, student researchers developed artificial intelligence to train robots to work together to move a couch — or in this case a long rod that served as a stand-in — around two obstacles and through a narrow door in computer simulations.
“We made it a little more difficult on ourselves. We want to accomplish the task with as little communication as possible among the robots,” student Barth said.
He was lead author of a study on the project published in the journal Intelligent Service Robotics. Professor Ma, UC doctoral student Yufeng Sun and UC senior research associate Lin Zhang were co-authors. More

New research published in the journal Clinical Psychological Science reveals that teenagers (ages 13-17) in low socioeconomic settings who spend a moderate amount of time online after a stressful experience deal with adversity far better than those who spend many hours online or avoid digital technology altogether.
“Adolescents are smart, and they make use of technology to their own advantage. Because adolescents in disadvantaged settings tend to have fewer local supports, the study sought to find out whether online engagement helped reduce their stress,” said lead author Kathryn Modecki with Griffith University’s Menzies Health Institute and School of Applied Psychology. “There has been a tendency to assume that technology use by teens is negative and harmful, but such a broad assumption isn’t borne out by what we know about the developmental stage of adolescence.”
To gather firsthand data on teens and technology, the researchers provided iPhones to more than 200 adolescents living in low socioeconomic settings. The teens were instructed to report on their technology use, stressors, and emotions five times a day for a week while using the iPhones exactly as they would use personal smartphones. The data were used to compare the emotional states of adolescents who used technology moderately, excessively, or not at all when coping with stress.
The results revealed that adolescents who engaged with technology in moderation in the hours after a stressful situation bounced back more readily and experienced smaller surges in negative emotions, like sadness and worry, compared to adolescents who didn’t use technology or who routinely used technology as a coping mechanism.
“We found a just-right ‘Goldilocks’ effect in which moderate amounts of online coping helped mitigate surges in negative emotions and dips in happiness,” said Modecki. “In the face of daily stressors, when adolescents engaged in emotional support seeking, they experienced better short-term stress relief.”
According to the researchers, the online space serves not just as a short-term distraction but as a resource for adolescents to find support and information about what is troubling them. By leveling the playing field for accessing that information and support, this coping strategy may be especially pertinent for teens in low-income settings.
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Materials provided by Association for Psychological Science. Note: Content may be edited for style and length. More

Researchers from the Graduate School of Engineering, Osaka City University have succeeded in storing electricity with the voltage generated from the conversion phenomenon of ferromagnetic resonance (FMR) using an ultra-thin magnetic film of several tens of nanometers.
The research was conducted under the leadership of Prof. Eiji Shikoh. “We are interested in efficiently using the Earth’s natural resources to harvest energy,” states the professor, “and capturing the energy from electromagnetic waves that surround us through the electromotive force (EMF) they generate in magnetic films under FMR shows potential as one such way.” Their research was published in the journal AIP Advances.
Ferromagnetic resonance is a state in which applying electromagnetic waves and an electrostatic magnetic field to a magnetic media causes the electromagnets inside the media to undergo precession at the same frequency as that of the electromagnetic waves. As a technique, it is often used to probe the magnetic properties of a variety of media, from bulk ferromagnetic materials to nano-scale magnetic thin films.
“Research has shown that an EMF is generated in a ferromagnetic metal (FM) that is under FMR,” states Yuta Nogi, first author of the study, “and we explored energy storage possibilities using two FMs that are highly durable, well understood, and thus commonly used in FMR research — an iron-nickel (Ni80Fe20) and iron-cobalt (Co50Fe50) alloy thin film.”
First, the team confirmed the two alloy films generated electricity under ferromagnetic resonance and found that Ni80Fe20 generated about 28 microvolts while Co50Fe50 generated about 6 microvolts of electricity. To store the electricity, they used an electron spin resonance device to pressurize the electromagnetic wave, and the electromagnet of the device for the static magnetic field. Connecting a storage battery directly to the membrane of the sample via a conductor, the team observed that both FM samples successfully stored energy after being in a state of FMR for 30 minutes. However, as the resonance time extended, the amount of energy stored with the iron-nickel alloy film did not change while the iron-cobalt alloy film saw a steady increase.
“This is due to the respective magnetic field ranges for the FMR excitation,” concludes Prof. Shikoh. Upon investigating the different energy storage characteristics of the thin films, the team found when they were in the same thermal states during the experiments, Co50Fe50 could maintain FMR in a detuned condition, while Ni80Fe20 was outside the FMR excitation range. “By appropriately controlling the thermal conditions of the FM film,” continues the professor, “EMF generation under ferromagnetic resonance can be used as an energy harvesting technology.”
Another interesting point about this research is that the team focused on EMF generation itself, independent of its origin. This means that as long as the FMR conditions are met, energy can be stored from electromagnetic waves we interact with daily — for example the Wi-Fi at your favorite café.
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Materials provided by Osaka City University. Note: Content may be edited for style and length. More

Mathematicians at the Center for Advanced Mathematics for Energy Research Applications (CAMERA) at Lawrence Berkeley National Laboratory (Berkeley Lab) have developed a mathematical algorithm to decipher the rotational dynamics of twisting particles in large complex systems from the X-ray scattering patterns observed in highly sophisticated X-ray photon correlation spectroscopy (XPCS) experiments.
These experiments — designed to study the properties of suspensions and solutions of colloids, macromolecules, and polymers — have been established as key scientific drivers to many of the ongoing coherent light source upgrades occurring within the U.S. Department of Energy (DOE). The new mathematical methods, developed by the CAMERA team of Zixi Hu, Jeffrey Donatelli, and James Sethian, have the potential to reveal far more information about the function and properties of complex materials than was previously possible.
Particles in a suspension undergo Brownian motion, jiggling around as they move (translate) and spin (rotate). The sizes of these random fluctuations depend on the shape and structure of the materials and contain information about dynamics, with applications across molecular biology, drug discovery, and materials science.
XPCS works by focusing a coherent beam of X-rays to capture light scattered off of particles in suspension. A detector picks up the resulting speckle patterns, which contain several tiny fluctuations in the signal that encode detailed information about the dynamics of the observed system. To capitalize on this capability, the upcoming coherent light source upgrades at Berkeley Lab’s Advanced Light Source (ALS), Argonne’s Advanced Photon Source (APS), and SLAC’s Linac Coherent Light Source are all planning some of the world’s most advanced XPCS experiments, taking advantage of the unprecedented coherence and brightness.
But once you collect the data from all these images, how do you get any useful information out of them? A workhorse technique to extract dynamical information from XPCS is to compute what’s known as the temporal autocorrelation, which measures how the pixels in the speckle patterns change after a certain passage of time. The autocorrelation function stitches the still images together, just as an old-time movie comes to life as closely related postcard images fly by.
Current algorithms have mainly been limited to extracting translational motions; think of a Pogo stick jumping from spot to spot. However, no previous algorithms were capable of extracting “rotational diffusion” information about how structures spin and rotate — information that is critical to understanding the function and dynamical properties of a physical system. Getting to this hidden information is a major challenge. More

The COVID-19 pandemic may be the deadliest viral outbreak the world has seen in more than a century. But statistically, such extreme events aren’t as rare as we may think, asserts a new analysis of novel disease outbreaks over the past 400 years.
The study, appearing the week of Aug. 23 in the Proceedings of the National Academy of Sciences, used a newly assembled record of past outbreaks to estimate the intensity of those events and the yearly probability of them recurring.
It found the probability of a pandemic with similar impact to COVID-19 is about 2% in any year, meaning that someone born in the year 2000 would have about a 38% chance of experiencing one by now. And that probability is only growing, which the authors say highlights the need to adjust perceptions of pandemic risks and expectations for preparedness.
“The most important takeaway is that large pandemics like COVID-19 and the Spanish flu are relatively likely,” said William Pan, Ph.D., associate professor of global environmental health at Duke and one of the paper’s co-authors. Understanding that pandemics aren’t so rare should raise the priority of efforts to prevent and control them in the future, he said.
The study, led by Marco Marani, Ph.D., of the University of Padua in Italy, used new statistical methods to measure the scale and frequency of disease outbreaks for which there was no immediate medical intervention over the past four centuries. Their analysis, which covered a murderer’s row of pathogens including plague, smallpox, cholera, typhus and novel influenza viruses, found considerable variability in the rate at which pandemics have occurred in the past. But they also identified patterns that allowed them to describe the probabilities of similar-scale events happening again.
In the case of the deadliest pandemic in modern history — the Spanish flu, which killed more than 30 million people between 1918 and 1920 — the probability of a pandemic of similar magnitude occurring ranged from 0.3% to 1.9% per year over the time period studied. Taken another way, those figures mean it is statistically likely that a pandemic of such extreme scale would occur within the next 400 years. More