Culture

The outermost reaches of our solar system are a strange place--filled with dark and icy bodies with nicknames like Sedna, Biden and The Goblin, each of which span several hundred miles across.

Two new studies by researchers at the University of Colorado Boulder may help to solve one of the biggest mysteries about these far away worlds: why so many of them don't circle the sun the way they should.

The orbits of these planetary oddities, which scientists call "detached objects," tilt and buckle out of the plane of the solar system, among other unusual behaviors.

"This region of space, which is so much closer to us than stars in our galaxy and other things that we can observe just fine, is just so unknown to us," said Ann-Marie Madigan, an assistant professor in the Department of Astrophysical and Planetary Sciences (APS) at CU Boulder.

Some researchers have suggested that something big could be to blame--like an undiscovered planet, dubbed "Planet 9," that scatters objects in its wake.

But Madigan and graduate student Alexander Zderic prefer to think smaller. Drawing on exhaustive computer simulations, the duo makes the case that these detached objects may have disrupted their own orbits--through tiny gravitational nudges that added up over millions of years.

The findings, Madigan said, provide a tantalizing hint to what may be going on in this mysterious region of space.

"We're the first team to be able to reproduce everything, all the weird orbital anomalies that scientists have seen over the years," said Madigan, also a fellow at JILA. "It's crazy to think that there's still so much we need to do."

The team published its results July 2 in the Astronomical Journal and last month in the Astronomical Journal Letters.

Power to the asteroids

The problem with studying the outer solar system, Madigan added, is that it's just so dark.

"Ordinarily, the only way to observe these objects is to have the sun's rays smack off their surface and come back to our telescopes on Earth," she said. "Because it's so difficult to learn anything about it, there was this assumption that it was empty."

She's one of a growing number of scientists who argue that this region of space is far from empty--but that doesn't make it any easier to understand.

Just look at the detached objects. While most bodies in the solar system tend to circle the sun in a flat disk, the orbits of these icy worlds can tilt like a seesaw. Many also tend to cluster in just one slice of the night sky, a bit similar to a compass that only points north.

Madigan and Zderic wanted to find out why. To do that, they turned to supercomputers to recreate, or model, the dynamics of the outer solar system in greater detail than ever before.

"We modeled something that may have once existed in the outer solar system and also added in the gravitational influence of the giant planets like Jupiter," said Zderic, also of APS.

In the process, they discovered something unusual: the icy objects in their simulations started off orbiting the sun like normal. But then, over time, they began to pull and push on each other. As a result, their orbits grew wonkier until they eventually resembled the real thing. What was most remarkable was that they did it all on their own--the asteroids and minor planets didn't need a big planet to throw them for a loop.

"Individually, all of the gravitational interactions between these small bodies are weak," Madigan said. "But if you have enough of them, that becomes important."

Earth times 20

Madigan and Zderic had seen hints of similar patterns in earlier research, but their latest results provide the most exhaustive evidence yet.

The findings also come with a big caveat. In order to make Madigan and Zderic's theory of "collective gravity" work, the outer solar system once needed to contain a huge amount of stuff.

"You needed objects that added up to something on the order of 20 Earth masses," Madigan said. "That's theoretically possible, but it's definitely going to be bumping up against people's beliefs."

One way or another, scientists should find out soon. A new telescope called the Vera C. Rubin Observatory is scheduled to come online in Chile in 2022 and will begin to shine a new light on this unknown stretch of space.

"A lot of the recent fascination with the outer solar system is related to technological advances," Zderic said. "You really need the newest generation of telescopes to observe these bodies."

Researchers at McMaster University who study how the brain processes sound have discovered the common practice of using artificial tones in perception experiments could mean scientists are overlooking important and interesting discoveries in the field of brain research.

The research, published recently in the journal Scientific Reports, is the culmination of a decade of rigorous analysis, in which the team reviewed one thousand auditory experiments published in several leading journals.

They found nearly 90 per cent of sounds used in these experiments have no connection to the natural world.

"Many theories and models derived from the use of artificial tone beeps in research experiments fail to describe the actual listening processes," says Michael Schutz, lead author and associate professor of Music Cognition and Percussion at McMaster.

Schutz's interdisciplinary background plays an important role in this project. A percussionist by training, he directs the McMaster University Percussion Ensemble and is an active performing musician. This regular immersion in professional music-making has tuned his ears to the complexities of sound--and the lack thereof in artificial tones.

His research team in the MAPLE lab team has repeatedly shown crucial differences in the processing of natural versus artificial sounds, raising questions about the degree to which tone beeps can actually properly test the auditory system.

"Although useful in experiments as they are 'controlled,' tone beeps are unnatural. Nothing in the natural world sounds like them," he says.

His team focuses in particular on the property of amplitude envelope, or the shape of the sound, which they have repeatedly shown plays a crucial role in perception. Their survey of auditory experiments found it was often not even considered or even adequately documented in hundreds of experiments.

The implications are not only theoretical, but also practical, says researchers.

For instance, artificial tones figure prominently in assessing the fit of hearing aids and cochlear implants, yet users frequently find listening to be problematic in natural environments. Researchers suggest unnatural sounds in research of this nature can have implications for our understanding of sensory integration in children with Autism Spectrum Disorder.

Although these children often struggle with integration of speech sounds, research using tone beeps has often failed to replicate those deficits. Given his expertise in studying the perception of natural sounds versus tone beeps, autism researchers at the University of Rochester Medical Centre approached Schutz about using his paradigm to close the gap between lab-based findings and real-world listening which is filled with rich, dynamically changing sounds.

In contrast to the complexity of natural sounds, tone beeps are incredibly impoverished, says Schutz.

"Think of the simplistic sounds we hear every day at the checkout counter, the auditory alerts of a truck backing up or the alarm of a medical device. By showing that these flat, artificial sounds are ubiquitous in research it is easier to understand how they have inadvertently become ingrained into design standards," he says.

Schutz is currently working with an international team to improve auditory alarm design of medical devices, which are often poorly designed and draw upon artificial tones which can create numerous problems in the operating of emergency rooms in hospitals, where they go off frequently, are missed altogether, keep patients awake, among other issues.

He suggests the soundscape of a hospital is jarring and there is tremendous room for improvement, which might include alarms that use musical tones.

"We believe we can improve these sounds and reduce overall annoyance, without sacrificing detectability."

ST. LOUIS, MO, July 7, 2020 - Growth and development of all organisms depends on coordinated regulation of gene expression in time and space, and this is largely controlled by non-coding sequences in the genome. A major challenge in genomics-enabled crop improvement is functional annotation of cis-regulatory elements in crop genomes and the ability to harness these sequences, either through breeding or biotechnology, to fine-tune target pathways with minimal disruption to the complex networks in which they reside.

A team of researchers led by Andrea Eveland, Ph.D., assistant member, Donald Danforth Plant Science Center, has mapped out the non-coding, 'functio nal' genome in maize during an early developmental window critical to formation of pollen-bearing tassels and grain-bearing ears.

Integrating information on chromatin structure, transcript profiles, and genome-wide association studies, their analyses provide a comprehensive look into the regulation of inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential. This study by Parvathaneni and Bertolini et al., "The regulatory landscape of early maize inflorescence development", was published on July 6, 2020 in the journal, Genome Biology.

"We have a good idea of the major controllers of inflorescence development in maize from years of classical genetics studies" said Eveland. "But simply removing their function or expressing them constitutively usually does not result in higher-yielding corn. We need to learn how to adjust their expression precisely in space and time to achieve optimal outputs. This study serves as a foundation for doing that."

Over the past century, hybrid-based breeding and improvement in maize has led to selection of smaller tassels that intercept less light and sequester less resources, and larger, more productive ears. Since the tassel and ear develop by a common developmental program, further improvement of ear traits will require decoupling of this program, for example, by tassel- or ear-specific regulatory elements. Understanding how the same genes are regulated differently in tassel and ear, and using this specificity to control one over the other, will enhance breeding efforts in maize.

Eveland's research focuses on the developmental mechanisms that control plant architecture traits in cereal crops. Specifically, she investigates how plant organs are formed from stem cells, and how variation in the underlying gene regulatory networks can precisely modulate plant form. Her team integrates both computational and experimental approaches to explore how perturbations to these gene networks can alter morphology, both within a species and across the grasses, with the ultimate goal of defining targets for improving grain yield in cereals.

In addition to Eveland's team, co-authors include researchers from Florida State University, the University of California at Davis, and the University of Illinois Urbana-Champaign. The collaborative research was funded by the National Science Foundation PGRP in awards to Eveland and co-author Alexander Lipka, Ph.D. (UIUC) to identify regulatory variation for improving maize yield traits, and to Hank Bass, Ph.D. (FSU) to apply techniques in chromatin profiling to important agronomic crop species.

Ribonucleic acid, or RNA, is part of our genetic code and present in every cell of our body. The best known form of RNA is a single linear strand, of which the function is well known and characterized. But there is also another type of RNA, so-called "circular RNA", or circRNA, which forms a continuous loop that makes it more stable and less vulnerable to degradation. CircRNAs accumulate in the brain with age. Still, the biological functions of most circRNAs are not known and are a riddle for the scientific community. Now scientists from the Max Planck Institute for Biology of Ageing have come one step closer to answer the question what these mysterious circRNAs do: one of them contributes to the ageing process in fruit flies.

Carina Weigelt and other researchers in the group led by Linda Partridge, Director at the Max Planck Institute for Biology of Ageing, used fruit flies to investigate the role of the circRNAs in the ageing process. "This is unique, because it is not very well understood what circRNAs do, especially not in an ageing perspective. Nobody has looked at circRNAs in a longevity context before", says Carina Weigelt who conducted the main part of the study. She continues: "Now we have identified a circRNA that can extend lifespan of fruit flies when we increase it, and it is regulated by insulin signaling".

Specific circRNA influences lifespan via insulin signalling

The insulin pathway regulates ageing, metabolism, reproduction and growth in worms, flies and humans. When this pathway is blocked by different methods, for instance by using genetically modified flies that lack insulin, the flies live longer. But it is not known how exactly this happens. The scientists now believe that part of the answer could lie with the circRNAs. They found a specific circRNA, called circSulfateless (circSfl), that behaved differently compared to other circRNAs. CircSfl was expressed at much higher levels in the long-lived fruit flies that lacked insulin as compared to normal flies. Furthermore, when flies were genetically manipulated to have higher level of circSfl, these flies also lived longer. These findings show that not only is circSfl dependent on insulin - circSfl itself can also directly influence the lifespan of fruit flies.

In the cells the necessary proteins that the body needs for all sorts of functions are made from normal linear RNAs, but generally not from circular RNAs. Again, the scientists found another difference between circSfl and other circular RNAs: a protein is indeed made from circSfl. The exact function of this protein is not known, but Carina Weigelt says: " The circSfl protein is similar but not identical to the classical Sfl protein originating from the linear Sfl RNA. We don't know exactly how the circSfl-derived protein influences ageing, but perhaps it interacts with similar proteins as the regular Sfl protein."

What does this mean for ageing research? Carina Weigelt says: "We want to understand how ageing works and why the flies lacking insulin are long-lived. It seems like one of the mechanisms is circSfl. We now want to further investigate the ageing process by looking at other circular RNAs also in other animals." Because circular RNAs also accumulate in the mammalian brain, these findings most likely also have important implications for humans.

Astrophysicists of Far Eastern Federal University (FEFU) with colleagues from Russia and oversea have revealed that large and dense particles with irregular shapes possess a 10-μm silicate feature introduced in lots of comets and protoplanetary discs. The outcome based on 15 examples of olivine silicate studied doesn't meet Mie theory provisions applied for comet particles modelling and capable of helping to reconsider the results of data. A related article appears in Icarus.

A silicate feature of a measured space object unfolds as a series of peaks in a certain region of the infrared spectrum. They are typical for silicates, minerals forming the mass of Earth rocks. The group of peaks lays in the spectrum at wavelengths of 9.2, 10.0, 10.5, 11.2 and 11.9 micrometres. Since they are all close to a wavelength of 10 microns, the phenomenon got a name as "a ten-micron silicate feature".

Studying the spectrum of protoplanetary disks and comets with a silicate feature, many scientists use the Mie theory for modeling. The theory restricts the size and shape of particles, suggesting that particle shall show a silicate feature only if it is spherical and of a size smaller than 1 micrometer, or bigger which comes along with a porous structure or constitution of individual small fragments.

"Yet such a structure of particles does not correspond to what we see in high-precision images took during the study of comet 67P / Churyumov-Gerasimenko, and is not in agreement with a part of the ground-based studies, which allows us to draw up a number of questions to the modeling method." Ekaterina Chornaya said, a Ph.D. student at the FEFU School of Natural Sciences. "We set up an experiment to find out whether it is possible to reproduce the silicate feature in sufficiently large olivine particles, which can be represented as analogues of cosmic dust. The selected particles had a size much more than 1 micron and a dense structure, which already put off the restrictions of the Mie theory. The olivine particles were not porous and did not consist of separate small fragments, but we have proved that they also have a silicate feature."

The outcome of the experiment puts aside the restriction of the mandatory sphericity and size of particles with a ten-micron silicate feature. It can significantly affect our knowledge about comets and deep space.

Young astrophysicists from FEFU University Ekaterina Chornaya and Anton Kochergin have been studying the microphysical properties of cometary dust for several years. They investigate the principles of cosmic dust particles motion considering solar radiation affect and conduct laboratory experiments with comet dust particles analogues. The purpose of the research is to shed light on the evolutionary processes of the solar system. This is the basic research direction that many scientific groups around the world are engaged in.

The practical measurements (polarimetry and photometry of comets) FEFU scientists carry out on the base of the Ussuriysk Astrophysical Observatory of the Institute of Applied Astronomy of the Russian Academy of Sciences.

Olivine particles were investigated using the latest equipment on the base of the research and educational center "Nanocenter" run in FEFU.

In a new study published in the Journal of Child Psychology and Psychiatry, Candice Alfano, University of Houston professor of psychology and director of the Sleep and Anxiety Center of Houston, reports the results from an innovative, experimental study showing inadequate nighttime sleep alters several aspects of children's emotional health.

Although plenty of correlational research links inadequate sleep with poor emotional health, experimental studies in children are rare. Alfano and her team studied 53 children ages 7-11 over more than a week. The children completed an in-lab emotional assessment twice, once after a night of healthy sleep and again after two nights where their sleep was restricted by several hours.

"After sleep restriction, we observed changes in the way children experience, regulate and express their emotions," reports Alfano. "But, somewhat to our surprise, the most significant alterations were found in response to positive rather than negative emotional stimuli."

The multi-method assessment had children view a range of pictures and movie clips eliciting both positive and negative emotions while the researchers recorded how children responded on multiple levels. In addition to subjective ratings of emotion, researchers collected respiratory sinus arrhythmias (a non-invasive index of cardiac-linked emotion regulation) and objective facial expressions. Alfano points out the novelty of these data. "Studies based on subjective reports of emotion are critically important, but they don't tell us much about the specific mechanisms through which insufficient sleep elevates children's psychiatric risk."

Alfano highlights the implications of her findings for understanding how poor sleep might "spill over" into children's everyday social and emotional lives. "The experience and expression of positive emotions are essential for children's friendships, healthy social interactions and effective coping. Our findings might explain why children who sleep less on average have more peer-related problems," she said.

Another important finding from the study is that the impact of sleep loss on emotion was not uniform across all children. Specifically, children with greater pre-existing anxiety symptoms showed the most dramatic alterations in emotional responding after sleep restriction.

According to Alfano, these results emphasize a potential need to assess and prioritize healthy sleep habits in emotionally vulnerable children.

In a new study published in Cell, "RNA sensing by gut Piezo1 is essential for systemic serotonin synthesis", a research team led by Kenta Maruyama M.D., Ph.D. from National Institute for Physiological Sciences (NIPS) explored the role of Piezo1, a mechano-sensing receptor, in the sensing of bacterial RNA. They found that gut Piezo1 stimulated by bacterial RNA was pivotal for the production of serotonin, an important hormone that regulates gut and bone homeostasis.

Serotonin is critical for normal functioning of the central and peripheral nervous system to control emotion, peristalsis and blood pressure. The two production origins of serotonin include brain neurons and the gut enterochromaffin cells. Notably, serotonin does not cross the blood-brain barrier and 90% of the body's total serotonin is secreted by enterochromaffin cells, establishing gut as the major source of peripheral serotonin. Most of the gut-derived serotonin is absorbed by platelets that release it after a various stimulation. This then leads to the activation of several biological phenomena, such as gut peristalsis and bowel inflammation. Interestingly, it has been reported that small fraction of gut-derived serotonin acts as a hormone. For instance, bone forming osteoblasts function is inhibited by serotonin. Notably, gut specific deletion of tryptophan hydroxylase-1 (Tph-1), a synthase that generates serotonin from tryptophan, leads to the high bone mass phenotype. Despite the pleiotropic functions of gut-derived serotonin in various biological phenomena, the molecular mechanisms controlling serotonin production remain largely unexplored.

Sensation of the mechanical forces in the gut is critical for normal peristalsis, but their molecular mechanisms are elusive. The mechanosensitive Piezo1 cation channel was recently identified, which is expressed in various tissues and is critical for mechano-transduction in vascular development, red blood cell volume control and blood pressure homeostasis. Despite the importance of Piezo1 in mechano-sensation, its function in gut remains to be explored.

In this study, NIPS research team demonstrated that microbiome-derived single-stranded RNA (ssRNA) induces serotonin production from the gut enterochromaffin cells via Piezo1 in the absence of mechanical force. The intestinal epithelium-specific deletion of Piezo1 causes impaired gut peristalsis, mild manifestations of experimental colitis, and increases bone mass accompanied by low serum serotonin levels. The researchers further found that mouse fecal extracts contain large amounts of RNA and purified fecal RNA activates Piezo1. Strikingly, RNase A, a ssRNA degrading enzyme, abolishes the ligand activity of fecal RNA and successfully suppresses serum serotonin level and increases bone mass by infusion to the colon. These findings indicate that targeting gut ssRNA can be a good strategy for modulating the gut-derived serotonin associated pathophysiology.

Astronomers can go their whole career without finding a new object in the sky. But for Lina Necib, a postdoctoral scholar in theoretical physics at Caltech, the discovery of a cluster of stars in the Milky Way, but not born of the Milky Way, came early - with a little help from supercomputers, the Gaia space observatory, and new deep learning methods.

Writing in Nature Astronomy this week, Necib and her collaborators describe Nyx, a vast new stellar stream in the vicinity of the Sun, that may provide the first indication that a dwarf galaxy had merged with the Milky Way disk. These stellar streams are thought to be globular clusters or dwarf galaxies that have been stretched out along its orbit by tidal forces before being completely disrupted.

The discovery of Nyx took a circuitous route, but one that reflects the multifaceted way astronomy and astrophysics are studied today.

FIRE in the Cosmos

Necib studies the kinematics -- or motions -- of stars and dark matter in the Milky Way. "If there are any clumps of stars that are moving together in a particular fashion, that usually tells us that there is a reason that they're moving together."

Since 2014, researchers from Caltech, Northwestern University, UC San Diego and UC Berkeley, among other institutions, have been developing highly-detailed simulations of realistic galaxies as part of a project called FIRE (Feedback In Realistic Environments). These simulations include everything scientists know about how galaxies form and evolve. Starting from the virtual equivalent of the beginning of time, the simulations produce galaxies that look and act much like our own.

Mapping the Milky Way

Concurrent to the FIRE project, the Gaia space observatory was launched in 2013 by the European Space Agency. Its goal is to create an extraordinarily precise three-dimensional map of about one billion stars throughout the Milky Way galaxy and beyond.

"It's the largest kinematic study to date. The observatory provides the motions of one billion stars," she explained. "A subset of it, seven million stars, have 3D velocities, which means that we can know exactly where a star is and its motion. We've gone from very small datasets to doing massive analyses that we couldn't do before to understand the structure of the Milky Way."

The discovery of Nyx involved combining these two major astrophysics projects and analyzing them using deep learning methods.

Among the questions that both the simulations and the sky survey address is: How did the Milky Way become what it is today?

"Galaxies form by swallowing other galaxies," Necib said. "We've assumed that the Milky Way had a quiet merger history, and for a while it was concerning how quiet it was because our simulations show a lot of mergers. Now, with access to a lot of smaller structures, we understand it wasn't as quiet as it seemed. It's very powerful to have all these tools, data and simulations. All of them have to be used at once to disentangle this problem. We're at the beginning stages of being able to really understand the formation of the Milky way."

Applying Deep Learning to Gaia

A map of a billion stars is a mixed blessing: so much information, but nearly impossible to parse by human perception.

"Before, astronomers had to do a lot of looking and plotting, and maybe use some clustering algorithms. But that's not really possible anymore," Necib said. "We can't stare at seven million stars and figure out what they're doing. What we did in this series of projects was use the Gaia mock catalogues."

The Gaia mock catalogue, developed by Robyn Sanderson (University of Pennsylvania), essentially asked: 'If the FIRE simulations were real and observed with Gaia, what would we see?'

Necib's collaborator, Bryan Ostdiek (formerly at University of Oregon, and now at Harvard University), who had previously been involved in the Large Hadron Collider (LHC) project, had experience dealing with huge datasets using machine and deep learning. Porting those methods over to astrophysics opened the door to a new way to explore the cosmos.

"At the LHC, we have incredible simulations, but we worry that machines trained on them may learn the simulation and not real physics," Ostdiek said. "In a similar way, the FIRE galaxies provide a wonderful environment to train our models, but they are not the Milky Way. We had to learn not only what could help us identify the interesting stars in simulation, but also how to get this to generalize to our real galaxy."

The team developed a method of tracking the movements of each star in the virtual galaxies and labelling the stars as either born in the host galaxy or accreted as the products of galaxy mergers. The two types of stars have different signatures, though the differences are often subtle. These labels were used to train the deep learning model, which was then tested on other FIRE simulations.

After they built the catalogue, they applied it to the Gaia data. "We asked the neural network, 'Based on what you've learned, can you label if the stars were accreted or not?'" Necib said.

The model ranked how confident it was that a star was born outside the Milky Way on a range from 0 to 1. The team created a cutoff with a tolerance for error and began exploring the results.

This approach of applying a model trained on one dataset and applying it to a different but related one is called transfer learning and can be fraught with challenges. "We needed to make sure that we're not learning artificial things about the simulation, but really what's going on in the data," Necib said. "For that, we had to give it a little bit of help and tell it to reweigh certain known elements to give it a bit of an anchor."

They first checked to see if it could identify known features of the galaxy. These include "the Gaia sausage" -- the remains of a dwarf galaxy that merged with the Milky Way about six to ten billion years ago and that has a distinctive sausage-like orbital shape.

"It has a very specific signature," she explained. "If the neural network worked the way it's supposed to, we should see this huge structure that we already know is there."

The Gaia sausage was there, as was the stellar halo -- background stars that give the Milky Way its tell-tale shape -- and the Helmi stream, another known dwarf galaxy that merged with the Milky Way in the distant past and was discovered in 1999.

First Sighting: Nyx

The model identified another structure in the analysis: a cluster of 250 stars, rotating with the Milky Way's disk, but also going toward the center of the galaxy.

"Your first instinct is that you have a bug," Necib recounted. "And you're like, 'Oh no!' So, I didn't tell any of my collaborators for three weeks. Then I started realizing it's not a bug, it's actually real and it's new."

But what if it had already been discovered? "You start going through the literature, making sure that nobody has seen it and luckily for me, nobody had. So I got to name it, which is the most exciting thing in astrophysics. I called it Nyx, the Greek goddess of the night. This particular structure is very interesting because it would have been very difficult to see without machine learning."

The project required advanced computing at many different stages. The FIRE and updated FIRE-2 simulations are among the largest computer models of galaxies ever attempted. Each of the nine main simulations -- three separate galaxy formations, each with slightly different starting point for the sun -- took months to compute on the largest, fastest supercomputers in the world. These included Blue Waters at the National Center for Supercomputing Applications (NCSA), NASA's High-End Computing facilities, and most recently Stampede2 at the Texas Advanced Computing Center (TACC).

The researchers used clusters at the University of Oregon to train the deep learning model and to apply it to the massive Gaia dataset. They are currently using Frontera, the fastest system at any university in the world, to continue the work.

"Everything about this project is computationally very intensive and would not be able to happen without large-scale computing," Necib said.

Future Steps

Necib and her team plan to explore Nyx further using ground-based telescopes. This will provide information about the chemical makeup of the stream, and other details that will help them date Nyx's arrival into the Milky Way, and possibly provide clues on where it came from.

The next data release of Gaia in 2021 will contain additional information about 100 million stars in the catalogue, making more discoveries of accreted clusters likely.

"When the Gaia mission started, astronomers knew it was one of the largest datasets that they were going to get, with lots to be excited about," Necib said. "But we needed to evolve our techniques to adapt to the dataset. If we didn't change or update our methods, we'd be missing out on physics that are in our dataset."

The successes of the Caltech team's approach may have an even bigger impact. "We're developing computational tools that will be available for many areas of research and for non-research related things, too," she said. "This is how we push the technological frontier in general."

New Haven, Conn. -- Teens are getting licensed to drive later than they used to and missing critical safety training as a result, according to Yale researchers.

In a study in the July 2 edition of the Journal of Adolescent Health, researchers at Yale identified some of the factors contributing to delaying driving licensure, or DDL, and pointed to policy changes that could expand safety training regardless of age.

When teens delay getting their driver's licenses, said lead author Dr. Federico E. Vaca, professor of emergency medicine and director of the Yale Developmental Neurocognitive Driving Simulation Research Center (DrivSim Lab), they age out of these safety measures which are not required after a person turns 18. "On the day I turned 16, I was at the DMV getting my license," said Vaca. "Now, that's not happening. We wanted to know, why not?"

The study found that race, socioeconomic status, and parenting are all important factors.

From 2006 to 2016, the proportion of high school seniors with driver's licenses fell from 81% to 72%, and at least 70% of eligible adolescents delay licensing by at least one year, the study noted. These delays affect the extent to which these young drivers participate a program known as Graduated Driver Licensing (GDL), requirements that young drivers must meet before they have a fully independent license. The GDL program, some version of which exists in all 50 states, typically requires 16-year-olds to log a certain number of hours of practice driving with a parent or guardian during a learner's permit stage, and later restricts late-night driving and driving with young passengers. Many states also include restrictions on cell phone use in the car as part of the GDL.

"These are key restrictions," said Vaca. "All the epidemiology shows that the later you drive at night, the more dangerous it is. "Once you get past 9 or 10 p.m., the fatal crash rate goes up. We also know from the literature that, for young drivers, the risk of fatal crashes also goes up with the number of passengers in the car."

GDL addresses these facts, and the programs have been successful in promoting safer driving, Vaca said. After GDL programs were introduced in the U.S. in the mid-nineties, fatal crashes among teens declined by 74% among 16-year-olds, by 61% among 17-year-olds, by 55% among 18-year-olds, and by 45% among 19-year-olds.

The researchers found that certain racial, ethnic, and socioeconomic groups are delaying licensure at higher rates -- in particular Latino and black teens. Using data from the National Institutes of Health's NEXT Generation Health Study, which followed a cohort of 10th grade students into adulthood, the Yale researchers found that Latino teens were 4.5 times as likely as white teens to delay getting their licenses by over two years and black teens were 2.3 times as likely.

Furthermore, they found that teens whose parents' highest educational degree level was high school were 3.7 times more likely to delay by over two years than those whose parents had a college degree. Teens from poor families were 4.4 times as likely to delay for more than two years compared to those from affluent families. Teens who perceived that their mothers were actively involved in their lives and monitoring their behaviors were less likely to delay their driving licensure. A similar effect was not seen with fathers.

When young people don't start driving until their early 20s, said Vaca, they are navigating a much more complicated world, where exposure to alcohol and drugs -- a major contributor to crash risk -- is considerably higher than for teens.

"If you haven't gone through GDL, you're not gradually exposed to nighttime driving and typically not gradually exposed to driving with several passengers where you progressively learn to manage the occupant space while driving," Vaca said.

Vaca said that in addition to missing safety instruction, which results in more crashes and fatalities among vulnerable populations, some teens who delay licensure miss out on employment, education, and other opportunities.

One solution, Vaca said, can be found by looking to GDL policies in other countries, such as Australia and the United Kingdom, where GDL restrictions are applied to novice drivers of all ages before a full license is issued.

"Motor vehicle crashes are the leading cause of death for young people," Vaca said. "It's important that they get sufficient supervised practice driving as well as gradual exposure to a variety of driving conditions and learn how to safely navigate them."

Flavonoids from a specific line of corn act as anti-inflammatory agents in the guts of mice with an inflammatory-bowel-disease-like condition, according to a team of researchers who said flavonoid-rich corn should be studied to determine its potential to provide a protective effect on human health.

The researchers bred a novel line of corn at Penn State's Russell E. Larson Agricultural Research Center to produce compounds called flavan-4-ols. The team then conducted an experiment with mice to judge the effect of those powerful antioxidant compounds on induced inflammation of the colon.

"In this study, we utilized two corn lines­ -- one containing flavan-4-ols and one lacking flavan-4-ols -- to investigate the anti-inflammatory property of that flavonoid," said Surinder Chopra, professor of maize genetics in the College of Agricultural Sciences, Penn State. "They are near isogenic lines, meaning that their genetic makeups are identical except for a few specific genetic loci that are responsible for generation of the flavonoids."

According to the researchers, inflammatory bowel disease, often referred to as IBD, is a chronic intestinal inflammatory condition that awaits safe and effective preventive strategies. Naturally occurring flavonoid compounds are promising therapeutic candidates against IBD due to their great antioxidant potential and ability to reduce inflammation and leaky gut syndrome.

A growing number of epidemiological studies show that diets rich in fruits and vegetables, which contain a significant amount of flavonoids, have been associated with reduced risk of hypertension, cardiovascular disease, type 2 diabetes and other chronic diseases such as inflammatory bowel disease. In addition to their anti-inflammatory properties, naturally occurring flavonoids are safer than standard drugs.

In the study, researchers obtained seeds for an inbred corn line from the National Seed Storage Laboratory at Fort Collins, Colorado, and for a corn genetic stock containing genes required for the flavonoid pathway. After back-crossing the plants, the resulting hybrid possesses a higher antioxidant capacity than conventional lines -- a promising trait that could be introduced into elite cultivars to increase dietary benefits, according to Chopra.

Mice in the study with the induced-IBD syndrome were divided into four groups. One group was fed a control, or standard, diet. The second and third groups' diets were supplemented with corn containing flavan-4-ols at 15% and 25%. The fourth group was fed a diet supplemented with a genetically related corn that did not contain the flavonoids.

In findings recently published in Nutrients, researchers reported that mice consuming a corn-based diet with flavan-4-ols exhibited alleviated IBD-like symptoms resulting from the protective effect of flavonoids against colonic inflammation by restoring intestinal barrier function. The study, spearheaded by Binning Wu and Rohil Bhatnagar, doctoral candidates in Penn State's Department of Plant Science, provides a rationale for breeding for flavonoid-enriched cultivars for better dietary benefits.

The idea that flavonoids coming from grains may promote human health is a new one, noted Lavanya Reddivari, assistant professor of food science at Purdue University, who helped guide the study. She and Chopra began collaborating on research related to antioxidant compounds in crop plants about five years ago when she was a faculty member at Penn State.

"Most of the epidemiological studies focus on flavonoid-enriched fruits, especially berries," she said. "However, grains contain a high concentration of bound flavonoids that are thought to exert better antioxidant activity and prolonged presence in systemic circulation, compared to free-form flavonoids, due to their slower and continuous release during digestion and microbial fermentation. These results suggest the feasibility of a human intervention study with flavonoid-rich corn to investigate its protective effects."

Many of the most promising medicines under development are proteins, often antibodies, to help patients fight disease. These proteins must be purified as part of the manufacturing process -- a task that can be tricky and result in costly waste.

Scientists have struggled to directly measure the movement of proteins, known as protein diffusion, in materials that include both solid and liquid components. They have also disagreed on how movement at the surface of the material contributes to protein movement when using ion-exchange chromatography, a laboratory and manufacturing method for separating materials based on their charge. Proteins can creep into the pores of resin beads used to perform ion-exchange chromatography and bind on the walls, based on charge.

Now, a team of engineers from the University of Delaware, with a collaborator from pharmaceutical company Amgen, has shown that surface diffusion in protein transport into ion-exchange beads depends on adsorption affinity -- a measure of attraction between the two materials. By exploiting this relationship, the team developed a procedure to purify a monoclonal antibody -- a type of molecule that mediates immunity -- with productivity 43% higher than usual.

The team's results were published in the Proceedings of the National Academy of Sciences in March. The paper's authors include Ohnmar Khanal, a doctoral student in chemical engineering; Vijesh Kumar, postdoctoral fellow in chemical engineering; Fabrice Schlegel, a principal engineer at Amgen; and Abraham Lenhoff, Allan P. Colburn Professor of Chemical Engineering.

"We present a very strong case for the significance of surface diffusion, and we use multiple approaches to corroborate its importance through a simple technique that can be implemented right away," said Khanal.

The team used chromatography, mechanistic modeling, confocal microscopy and small-angle neutron scattering. The latter was performed at the National Center for Neutron Research at the National Institute for Standards and Technology.

By understanding and exploiting protein surface diffusion in ion-exchange chromatography, researchers can build upon this work and develop methods to reduce waste during the expensive drug manufacturing process.

"Ion-exchange chromatography of proteins is an absolutely key operation in biopharmaceutical manufacturing," said Lenhoff.

Kumar and Lenhoff are now working on a separate project funded by the National Institute for Innovation in Biopharmaceutical Manufacturing, based at the University of Delaware, to develop mathematical models of chromatography, which could enable more efficient ways of designing and developing manufacturing processes.

Researchers can also build upon this new fundamental understanding of protein diffusion and perhaps apply it to other problems. Protein diffusion on surfaces is an important phenomenon inside the body, too. Movement and fibrillation of amyloid-ß in the brain has been associated with neurogenerative diseases, for example, and protein surface diffusion can affect the performance of biosensors.

"This is an example of how fundamental research can lead to practical applications and significant improvements in those practical applications," said Lenhoff.

And it all started with a brainstorm, where Khanal suggested more in-depth investigation of surface diffusion's relationship to binding affinity on the charged surfaces using complementary tools.

"When we started this, we never thought we would go this far," said Kumar. "It started as a very small idea."

A patient and family walk into a doctor's office. They hope that the latest tests will reveal what is causing the patient's illness and end the diagnostic odyssey they have been going through for years. Having an accurate diagnosis also means that maybe there is a treatment that at least can alleviate the patient's condition.

At Baylor College of Medicine, Dr. Sarah Elsea and her colleagues have been working on improving their ability to identify the genetic cause of undiagnosed conditions. Their study appears in the journal Genetics in Medicine.

"About nine of every 10 patients that are referred to us have neurological conditions, such as developmental delay and intellectual disability, for which they don't have a diagnosis," said Elsea, professor of molecular and human genetics at Baylor and corresponding author of the work.

To identify the genetic cause of undiagnosed conditions, the researchers look for potentially defective genes in the patient's genome. They use whole-exome sequencing, which analyzes all the genes that encode proteins. A gene may have many variants that encode slightly different versions of the same protein that still carry their function normally. But some variants may encode defective proteins that can cause disease. The challenging part is determining whether the variant of a particular gene that is found in a patient is causing the disease.

"In some cases, the variant is missing all or a large portion of the gene, which results in a non-functional protein. This suggests that the variant is involved in the disease. However, most genetic variants involve changes in a single building block of the DNA. That one 'misspelled' gene sequence may or may not result in a defective or less functional protein, and we need other mechanisms, such as untargeted metabolomics, to determine if that genetic change causes disease," said Elsea, who also is the senior director of biochemical genetics at Baylor Genetics.

Enter untargeted metabolomics

Elsea and her colleagues used untargeted metabolomics to provide an additional level of information to help them determine whether the genetic variant they found in the patient was actually causing the condition.

"Untargeted metabolomics lets us look at the function of the protein encoded by the gene variant in the patient to explore metabolic abnormalities that may be associated with the variant," Elsea said.

In the current study, the researchers integrated whole-exome sequencing and targeted metabolomics to analyze the data of a group of 170 patients. They were pleased to find that the metabolomics data informed 44 percent of the cases.

"The analysis let us reclassify nine variants as likely benign, 15 variants as likely causing disease and three as disease-causing variants. Metabolomics data confirmed a clinical diagnosis in 21 cases," Elsea said. "Our analysis is extremely helpful not only for confirming that a variant causes the condition, but also to rule out variants as the cause of disease. Having a more accurate diagnosis may help identify a better treatment for the condition and also provides important information for the family regarding recurrence risk."

This analysis also aids with the diagnosis of patients that may have a mild form of a disease, because the analysis is broad and very sensitive and shows the effects of the variant in entire metabolic pathways.

"We have been able to identify a few cases with milder diseases. Before our integrated analysis, we would not have diagnosed those cases with the disease, but we can now because metabolomics revealed metabolic abnormalities that we could link to the gene variant in the patient," Elsea said. "This approach has improved diagnostics substantially and also increased our understanding of these conditions and the range of clinical manifestations that we might see in patients."

The researchers hope that their integrated multi-omics analysis will help other patients by providing a diagnosis, clarifying previous suspected diagnoses or monitoring their treatment.

Researchers from the University of Houston, in collaboration with others, have designed a "catch and kill" air filter that can trap the virus responsible for COVID-19, killing it instantly.

Zhifeng Ren, director of the Texas Center for Superconductivity at UH, collaborated with Monzer Hourani, CEO of Medistar, a Houston-based medical real estate development firm, and other researchers to design the filter, which is described in a paper published in Materials Today Physics.

The researchers reported that virus tests at the Galveston National Laboratory found 99.8% of the novel SARS-CoV-2, the virus that causes COVID-19, was killed in a single pass through a filter made from commercially available nickel foam heated to 200 degrees Centigrade, or about 392 degrees Fahrenheit. It also killed 99.9% of the anthrax spores in testing at the national lab, which is run by the University of Texas Medical Branch.

"This filter could be useful in airports and in airplanes, in office buildings, schools and cruise ships to stop the spread of COVID-19," said Ren, MD Anderson Chair Professor of Physics at UH and co-corresponding author for the paper. "Its ability to help control the spread of the virus could be very useful for society." Medistar executives are is also proposing a desk-top model, capable of purifying the air in an office worker's immediate surroundings, he said.

Ren said the Texas Center for Superconductivity at the University of Houston (TcSUH) was approached by Medistar on March 31, as the pandemic was spreading throughout the United States, for help in developing the concept of a virus-trapping air filter.

Luo Yu of the UH Department of Physics and TcSUH along with Dr. Garrett K. Peel of Medistar and Dr. Faisal Cheema at the UH College of Medicine are co-first authors on the paper.

The researchers knew the virus can remain in the air for about three hours, meaning a filter that could remove it quickly was a viable plan. With businesses reopening, controlling the spread in air conditioned spaces was urgent.

And Medistar knew the virus can't survive temperatures above 70 degrees Centigrade, about 158 degrees Fahrenheit, so the researchers decided to use a heated filter. By making the filter temperature far hotter - about 200 C - they were able to kill the virus almost instantly.

Ren suggested using nickel foam, saying it met several key requirements: It is porous, allowing the flow of air, and electrically conductive, which allowed it to be heated. It is also flexible.

But nickel foam has low resistivity, making it difficult to raise the temperature high enough to quickly kill the virus. The researchers solved that problem by folding the foam, connecting multiple compartments with electrical wires to increase the resistance high enough to raise the temperature as high as 250 degrees C.

By making the filter electrically heated, rather than heating it from an external source, the researchers said they minimized the amount of heat that escaped from the filter, allowing air conditioning to function with minimal strain.

A prototype was built by a local workshop and first tested at Ren's lab for the relationship between voltage/current and temperature; it then went to the Galveston lab to be tested for its ability to kill the virus. Ren said it satisfies the requirements for conventional heating, ventilation and air conditioning (HVAC) systems.

"This novel biodefense indoor air protection technology offers the first-in-line prevention against environmentally mediated transmission of airborne SARS-CoV-2 and will be on the forefront of technologies available to combat the current pandemic and any future airborne biothreats in indoor environments," Cheema said.

Hourani and Peel have called for a phased roll-out of the device, "beginning with high-priority venues, where essential workers are at elevated risk of exposure (particularly schools, hospitals and health care facilities, as well as public transit environs such as airplanes)."

That will both improve safety for frontline workers in essential industries and allow nonessential workers to return to public work spaces, they said.

Microalgae could provide an alternative source of healthy omega-3 fatty acids for humans while also being more environmentally friendly to produce than popular fish species. This is the result of a new study by scientists from Martin Luther University Halle-Wittenberg (MLU). The study was recently published in the Journal of Applied Phycology and offers an initial indication of the environmental effects of producing microalgae in Germany.

Microalgae have been the focus of several decades of research - initially as a raw material for alternative fuels, but more recently as a source of nutrients in the human diet. They are mainly produced in open ponds in Asia; however, these ponds are at risk of potential contamination. Also, some species of algae are easier to cultivate in closed systems, so-called photobioreactors. "We wanted to figure out whether microalgae produced in photobioreactors in Germany could provide a more environmentally friendly source of essential nutrients than fish," says Susann Schade from the Institute of Agricultural and Nutritional Sciences at MLU. Up to now, photobioreactors had usually only been compared to pond cultivation and they often scored worse due to their higher environmental impacts. "However, little research has been done on the precise extent of the environmental impacts of algae produced for human consumption, especially under climatic conditions such as those found in Germany," adds Schade.

For their study, the researchers developed a model to determine location-specific environmental impacts. "One of the things we did was to compare the carbon footprint of nutrients from microalgae and fish. We also analysed how much both food sources increase the acidification and eutrophication in water bodies," explains Dr Toni Meier, head of the Innovation Office nutriCARD at MLU. The researchers were able to show that microalgae farming has a similar impact on the environment as fish production. "However, if we compare the environmental effects in relation to the amount of omega-3 fatty acids produced, fish from aquaculture comes off far worse," says Schade. One advantage of algae cultivation is its low land consumption; even infertile soils can be used. In contrast, both open ponds and the cultivation of feed for aquaculture require very large areas of land. In particular, fish species that are popular in Germany, such as salmon and pangasius, are primarily produced through aquaculture and therefore put the environment under a considerable amount of pressure. However, even fishing wild Alaska pollack had poorer values than microalgae for all environmental indicators.

"Microalgae should not and cannot completely replace fish as a food source. But if microalgae could be established as a common food, it would be another excellent environmentally friendly source of long-chain omega-3 fatty acids," explains Meier. Several algae are already used as a food supplement in powder or tablet form and as an additive to foods such as pasta or cereals. It would be a way to reduce the current gap in the global supply of omega-3 fatty acids. At the same time, it would provide considerable relief to the world's oceans.

Washington, DC - July 7, 2020 - According to findings published this week in mBio, Nissle, a strain of Escherichia coli, is harmless to intestinal tissue and may protect the gut from enterohemorrhagic E. coli, a pathogen that produces Shiga toxin.

E. coli has gotten a bad rap because a few pathogenic strains can cause severe, even life-threatening, symptoms. But for more than a century, the commensal strain Nissle has been used as a probiotic and, more recently, to treat intestinal disorders including ulcerative colitis.

Researchers at the University of Cincinnati wanted to understand whether Nissle could also protect intestinal tissue against EHEC and other pathogens. They studied the probiotic's protective effects using human intestinal organoids, or HIOs, which are experimental models of real tissue derived from stem cells.  

The researchers first injected the HIOs with Nissle and observed that the bacterium was harmless: It did not damage the epithelial barrier, formed by the protective outer layer of the organoid. Next, in separate experiments, they injected HIOs with enterohemorrhagic E. coli or EHEC. This pathogen produces Shiga toxin, which sickens millions and kills thousands of people--mainly children--every year. The EHEC quickly broke down the epithelial barrier in the HIOs.  

Then, the researchers pre-treated HIOs with Nissle and, 12 hours later, injected them with EHEC. This is where the Nissle proved to be protective: Even though the EHEC proliferated in the organoid tissue, it did not destroy the epithelial barrier. During the same time, the Nissle population declined rapidly in the tissue. The researchers observed the same effects when they injected pre-treated HIOs with uropathogenic E. coli, the strain responsible for the majority of urinary tract infections.  

"Basically, the Nissle was killed by the pathogenic bacteria, but it made the intestine able to withstand damage better," said molecular geneticist Alison Weiss, Ph.D., who worked on the study together with Suman Pradhan, Ph.D., a research associate in Weiss's lab.  

The results suggest Nissle may confer benefits not by inhibiting the pathogenic strains directly, but instead by harnessing defense mechanisms in the cell itself, and that the probiotic may help prevent severe EHEC infections. However, the results also suggest that Nissle can be vulnerable to phages from the Shiga toxin, which would limit the probiotic's usefulness as a therapeutic. Weiss cautioned that more studies are needed to better understand the complex interactions of bacterial species in a real-world setting.  

Weiss's research focuses on bacteria that produce the Shiga toxin, like EHEC. "It's really bad," she said. "My whole career, I've been interested in preventing pediatric pathogens. Once these kids get EHEC, all you can do is give them fluids and support them. There's nothing else we can do."  

Weiss is excited by the potential of using HIOs as a model for better understanding intestinal conditions. "They're a huge breakthrough," she said. "A lot of intestinal pathogens are species-specific, and organoids are really good for looking at early events."  

Organoids offer at least one other major advantage over mice, she added. "Mice are awful. They pee and bite and scratch," she said. "The little organoids don't complain at all."