Culture

The ability to read is foundational to education, but prolonged school closures and distance learning due to the pandemic have imposed unique challenges on the teaching of many fundamental skills. When in-person classes resume, many students will likely need a period of catch-up learning, especially those who lag behind in basic reading skills.

New research published in the journal Psychological Science shows that people who were taught to read by receiving explicit instructions on the relationship between sounds and spelling experienced a dramatic improvement compared to learners who discovered this relationship naturally through the reading process. These results contribute to an ongoing debate about how best to teach children to read.

A team of researchers from Royal Holloway, University of London, tested both techniques on a group of 48 adults who, over an intensive two-week period, were taught to read a new language that was printed in unfamiliar symbols.

One half of the participants learned spelling-to-sound and spelling-to-meaning regularities solely through experience with reading the novel words during training. The other half received a brief session of explicit instruction on these regularities before training commenced. At the end of the two-week period, both groups were given reading tests to gauge how well they had learned the new language.

"Our results were really striking. By the end of the two weeks, virtually all learners who had received explicit instruction were able to read words printed in the unfamiliar symbols," said Kathleen Rastle, a researcher at Royal Holloway and lead author on the paper.

In contrast, despite up to 18 hours of experience with the new language, less than 25% of the "discovery learners" reached the same standard, and some showed very poor learning.

"Reading is the foundation for children's learning throughout their schooling; for this reason, the learning loss that we are seeing is very concerning and has the potential for lifelong consequences," said Rastle. "The provision of evidence-based instructional methods has never been more important. Our research highlights the significance of explicit instruction in ensuring that all pupils have the opportunity to develop strong reading skills."

COLUMBIA, Mo. - While physical activity is important for everyone, research has shown people with developmental disabilities do not exercise as often as their typically developed peers. In an effort to close this disparity, a researcher at the University of Missouri recently created fitness picture books that help youth with autism exercise more frequently while offering low-income families a simple resource for workout motivation when outdoor fitness equipment might not be accessible.

"There is so much research geared toward helping individuals with autism improve their academic performance, social skills and communication skills, but we also need to remember how important physical activity is for living a healthy lifestyle," said Lorraine Becerra, an assistant teaching professor at the MU College of Education. "There are numerous health benefits of exercise, such as pumping blood in your body, better sleep and reduced risk of obesity. Also, if we can get kids with autism more physically engaged, they are more likely to run around and play with their peers, so there are other aspects of their life we can improve as well."

Becerra is also a behavior analyst at the Thompson Center for Autism and Neurodevelopmental Disorders. Since some of her former clients with autism had body mass indexes that had risen to unhealthy levels due to excessive sedentary behavior, their caregivers asked Becerra to develop creative ways to encourage their children to exercise more.

So, in a recent research study, Becerra created fitness picture books that contained step-by-step images of various exercises, such as jumping jacks, bear crawls and lunges. The picture books were successfully utilized to increase the amount of time the individuals with autism engaged in physical activity.

Having previously worked in low-income school districts with limited financial resources, Becerra understands the need to find cost-efficient methods to help kids with autism exercise more frequently.

"It's important to remember that some schools might not have a jungle gym or many age-appropriate resources for kids to play with," Becerra said. "The great thing about the picture books is they provide simple, engaging exercises that can be done in a wide variety of settings, like a school playground, backyard or even an empty field at a park. It is also a quick and easy way for caregivers or teachers to provide organized structure during flexible free time, such as during recess."

With recent advancements in technology and entertainment, youth are increasingly spending more of their time sitting in front of televisions, tablets and personal electronic devices. Becerra is passionate about reminding youth -- particularly individuals on the autism spectrum -- about the importance of scheduling time for physical activity.

"These lifelong habits start when you are young," Becerra said. "Making time to run around and establish those exercise routines early in life will help youth maintain those habits in their adolescent and adult years."

Marine protected areas (MPAs) around O?ahu do not adequately protect populations of herbivorous reef fishes that eat algae on coral reefs. That is the primary conclusion of a study published in Coral Reefs by researchers from the University of Hawai?i at Mānoa School of Ocean and Earth Science and Technology (SOEST).

There are over 20 species of herbivorous fishes and ten species of herbivorous urchins commonly observed on Hawaiian reefs. These species eat algae that grows on reefs, a process called herbivory, that contributes to the resilience of coral reefs by preventing algae dominance that can lead to overgrowth of corals.

The team of researchers found that of the four marine protected areas around O?ahu they assessed in the study, three did not provide biologically significant benefits for herbivorous fish populations compared to reefs outside the areas.

"Marine protected areas are a fishery management tool to limit or prevent fishing to help the recovery and maintenance of fish abundance and biomass inside the MPA," said senior author Erik Franklin, Associate Research Professor at the Hawai?i Institute of Marine Biology in SOEST. "An effective MPA should lead to a considerably higher abundance and biomass of fishes inside the MPA boundaries that would otherwise be caught by fishers but that wasn't what our study found."

Other factors influencing the biomass of herbivorous fishes included habitat complexity and depth, suggesting that environmental characteristics of coral reefs may have had a greater impact on herbivorous fish populations than MPA protection.

Importance for Hawai?i

As part of the Sustainable Hawai?i Initiative, the State of Hawai?i's Division of Aquatic Resources leads the Marine 30x30 Initiative, which committed to effectively manage Hawaii's nearshore waters with 30 percent established as marine management areas by 2030. Currently, five percent of waters within state jurisdiction, which is within three nautical miles of shore, have some form of marine management, but no-take MPAs that ban fishing only make up less than one-half of one percent of the nearshore waters. To attain the stated goal of the 30x30 Initiative would require an expansion of marine managed areas to include an additional 25 percent of Hawai?i state waters.

"Our results suggest that prior to an expansion of MPAs in Hawaiian waters, more effort should be directed to effectively manage the existing MPAs to see if they meet the desired management objectives," said lead author and UH Mānoa's Marine Biology Graduate Program graduate student Noam Altman-Kurosaki. "The addition of more MPAs throughout the state that have similar performance to the O?ahu MPAs would just lead to a series of paper parks that don't provide biologically significant conservation benefits while decreasing fishing opportunities."

Study details

Franklin said the research resulted in a comparative analysis of herbivorous fish and urchin populations inside and outside of O?ahu MPAs that demonstrated biologically insignificant differences in fish biomass between the MPAs and reference areas, except for one site, Hanauma Bay. The analyses used statistical methods to assess the effects of protecting population within MPAs and the influence that differences in benthic habitats contributed to the results.

Large carnivores are generally sensitive to ecosystem changes because their specialized diet and position at the top of the trophic pyramid is associated with small population sizes. This in turn leads to lower genetic diversity in top predators compared to animals lower down the food chain. Genetic diversity is very important for a species' ability to survive and adapt to future changes.

Extraordinary genetic diversity in an extraordinary cat

In this study, the researchers sequenced the complete genome of 53 African leopards and compared them to the Amur leopards and other big cat species. To their surprise, the researchers found that the genetic diversity of African leopards is extremely high: Almost four times higher than the Amur leopard's, twice as high as the lion's and almost five times higher than the cheetah's.

Patrícia Pečnerová, postdoc at the Department of Biology and one of the shared first authors, explains:

- "The exceptional genetic diversity is likely a result of the leopard's ability to avoid population crashes and reductions. We found that during hundreds of thousands of years, African leopard populations remained large. We think that this reflects the versatility of the species, feeding on a wider variety of prey than any of the other large predators."

Roaming every habitat in Africa - but for how long?

The high genetic diversity of the African leopards is not the only surprise hidden in the leopard genomes. They also show fewer genetic barriers within the continent of Africa than other mammal species.

Kristian Hanghøj, one of the corresponding authors of the study explains:

- "We believe that during evolutionary history the leopard roamed the African continent more freely than almost any other mammal species, exchanging genetic material throughout. It has a unique ability to succeed in almost any habitat and climate and neither rain forests, nor deserts seem to have blocked the movements of leopards over the millennia."

The surprising findings demonstrate how the ecology of a species - such as how 'picky' it is about habitat and prey, can influence its genomic variation. The exceptionally high genetic diversity could give the African leopard an advantage in coping with environmental challenges, including climate change and habitat destruction.

However, habitat fragmentation is a severe threat to all large animals, even those as adept at coping with human presence as the leopard. The human-made changes to natural habitats are occurring at a pace that is likely too fast for almost any wild animal species to adapt to, and previous studies have shown that African leopards have lost 48-67% of their natural habitat over the last 300 years.

- "To place our results into a greater context, we emphasize that the African leopard is also facing severe threats to its survival, despite being sort of an evolutionary success", finishes Patrícia Pečnerová.

Born in food web ecology, the concept of trophic levels -- the hierarchy of who eats who in the natural world -- is an elegant way to understand how biomass and energy move through a natural system. It's only natural that the idea found its way into the realm of aquaculture, where marine and freshwater farmers try to maximize their product with efficient inputs.

"It's often used as a measure of how sustainable it is to harvest or consume that species," said Rich Cottrell(link is external), a postdoctoral researcher at UC Santa Barbara's National Center for Ecological Analysis & Synthesis (NCEAS). As plants (level 1) become food to plant eaters (level 2), who in turn are consumed by carnivores (level 3) and so on, the amount of energy required to support the same weight of organisms increases, he explained. As a result, species at levels 4 or 5, such as tuna, require far more energy per pound than would species in the lower trophic levels. It's the same reason vegetarian diets are often considered to be more sustainable than meat-eating ones.

"In the same manner, trophic level measures are now being recommended in policy settings for use as an indicator of the sustainability of fish farming, or aquaculture," Cottrell said. The lower the trophic level, the more sustainable the species is considered to be, and so policy often calls for more farming of low-trophic species.

However, argue Cottrell and fellow aquaculture experts in a paper(link is external) published in the journal Reviews in Aquaculture, at this time of increasing complexity and sophistication in the aquaculture sector, the same simplicity that makes trophic levels attractive as a measure of sustainability also makes them insufficient.

The causes for that have largely to do with how today's farmed fish are fed.

"Most of the fish and invertebrates that we farm for food are produced using human-made feeds," Cottrell explained. "But these feeds are constantly changing, and so the meaning of farmed trophic levels is changing through time." For instance, he pointed out, salmon are considered to be at a higher trophic level because their naturally carnivorous diets would require large amounts of fishmeal and oil, but advances in feed and manufacturing have reduced the proportion of fish-based ingredients to 10-15% in modern salmon diets. Meanwhile, herbivorous species such as carp and tilapia have been found to respond favorably to small amounts of fishmeal in their feed.

"In reality, they're now farmed at similar trophic levels," Cottrell said. "The line between 'low' and 'high' trophic levels will continue to blur with innovation."

The trophic level concept misses still another important aspect of aquaculture sustainability in the realm of feed and resource efficiency, or how efficiently the farmed animals convert what they are fed into edible food.

"This is not well explained by trophic level," Cottrell said, adding that despite their high trophic placement, many carnivorous farmed fish could be more feed-efficient than their naturally carnivorous counterparts. And because aquaculture is increasingly turning to agriculture to provide replacements for fishmeal and oil, the promise of sustainability might be an empty one.

"Replacing fish-based ingredients with crops has led to a dramatic reduction in the trophic level of fed aquaculture species, but we know very little about how sustainable it is to increase pressure on global agricultural systems," he said.

As the global aquaculture sector strives to meet the growing demand for farmed seafood, the researchers say it's time to rethink the use of trophic levels as a rule for and measure of sustainability. Stipulating low trophic level aquaculture recommendations may not be successful in promoting greater sustainability, Cottrell said. Boosting the supply of mussels, for instance, may not fulfill increasing demand for shrimp or salmon.

"It behooves us to find a way to ensure that for high-demand products, we produce these in the most environmentally efficient and socially responsible way possible," he said. "Trophic levels will not get us there."

Fortunately, there are efforts at more nuanced sustainability assessments, such as voluntary certifications through the Aquaculture Stewardship Council or Best Aquaculture Practices, which examine the impacts of aquaculture at the farm level and through supply chains.

"Greater support for these programs and incentives for producers from various regions and production systems to join them would be a far more robust way to strengthen the sustainability of the aquaculture sector going forward," Cottrell said.

A University of Oklahoma-led study published in 2020 revealed that both area and plant growth of paddy rice is significantly related to the spatial-temporal dynamics of atmospheric methane concentration in monsoon Asia, where 87% of the world's paddy rice fields are situated. Now, the same international research team has released a follow-up discussion paper in the journal Nature Communications. In this paper, the team identifies the limits and insufficiency of the major greenhouse emission database (EDGAR) in estimating paddy rice methane emissions.

"Methane emission from paddy rice fields contribute to the rising of atmospheric methane concentration (XCH4), one of the greenhouse gases for global warming and climate change," said Xiangming Xiao, a professor in the Department of Microbiology and Plant Biology, College of Arts and Sciences. "In this paper, our team highlighted the needs and pathways to improve this dataset, which could lead to substantial improvement in understanding and modeling methane emission, atmospheric transport and chemistry over monsoon Asia and the globe."

OU researchers developed annual paddy rice maps at 500-meter spatial resolution and quantified the spatial-temporal changes in rice paddy area in monsoon Asia during 2000-2015. Xiao said these annual maps are the first of their kind and could be used to further improve simulations of models that estimate methane emission from paddy rice fields.

EL PASO, Texas - A study by physiology researchers at The University of Texas at El Paso found that El Paso's stay-at-home ordinance due to the COVID-19 pandemic had positive effects on the health and well-being of the region's residents.

Despite a shutdown of gyms and movement restrictions on non-essential activities, residents increased their fitness activity and closely monitored their food and nutrition intake, said Cory M. Smith, Ph.D., assistant professor of kinesiology in UTEP's College of Health Sciences and the study's principal investigator.

More than 1,300 El Paso and Las Cruces, New Mexico, residents participated in Smith's COVID-19 Survival Survey during the month of September 2020. Questions focused on their personal changes in physical activity, nutritional habits, and changes in thoughts and attitudes toward common hygiene practices and emergency preparedness in response to the COVID-19 pandemic and the El Paso County's Work Safe, Stay Home order that went into effect March 24, 2020.

According to the data, 37% of participants said they improved their exercise practices by changing their exercise focus, exercising more and trying new fitness activities, and 15% said they increased their outdoor recreation activities. Forty-five percent of residents responded that they increased self-monitoring of their food intake.

"We hypothesized that people were going to exercise less during the pandemic after gyms and fitness facilities were shut down," said Smith, director of UTEP's Human and Environmental Physiology Laboratory (HEPL). "But when we began to evaluate the data, we found some hidden health benefits of the pandemic. People were exercising more and eating better. Hopefully, this data will give us a better understanding of how people react during a public health crisis and how we can better prepare for future public health emergencies."

Smith attributed the study's positive health outcomes to people's increased awareness of the risk factors associated with COVID-19, a highly contagious respiratory illness caused by the SARS-CoV-2 virus.

Before El Paso implemented the stay-at-home order, 39% of participants reported a high level of concern for contracting COVID-19 compared with 50% of individuals who reported a low level of concern for catching coronavirus. Eleven percent indicated they were not concerned.

After the order went into effect, the number of respondents who had a high level of concern for contracting COVID-19 increased to 57%. Individuals who reported a low level of concern for the virus dropped to 39%, and 4% of participants reported no concern.

The survey revealed that residents who felt sick were more likely to stay home and not go to work, school, or social events after the stay-at-home order. In addition, the implementation of the Stay at Home Ordinance increased handwashing and sanitizing frequency in 92% of individuals.

Data on changes in employment, nutrition habits and physical activity are also included in the survey.

Smith planned to share the results with the City of El Paso. He said data could be used to improve community protocols to better enforce public safety guidelines in the event of a future pandemic.

Researchers at the University of Maryland School of Medicine (UMSOM) co-authored a study, published today in the journal Science, that details the sequencing of 64 full human genomes. This reference data includes individuals from around the world and better captures the genetic diversity of the human species. Among other applications, the work will enable population-specific studies on genetic predispositions to human diseases as well as the discovery of more complex forms of genetic variation.

Twenty years ago this month, the International Human Genome Sequencing Consortium announced the first draft of the human genome reference sequence. The Human Genome Project, as it was called, required 11 years of work and involved more than 1000 scientists from 40 countries. This reference, however, did not represent a single individual, but instead was a composite of humans that could not accurately capture the complexity of human genetic variation.

Building on this, scientists have conducted several sequencing projects over the last 20 years to identify and catalog genetic differences between an individual and the reference genome. Those differences usually focused on small single base changes and missed larger genetic alterations. Current technologies now are beginning to detect and characterize larger differences - called structural variants - such as insertions of new genetic material. Structural variants are more likely than smaller genetic differences to interfere with gene function.

The new finding in Science announced a new and significantly more comprehensive reference dataset that was obtained using a combination of advanced sequencing and mapping technologies. The new reference dataset reflects 64 assembled human genomes, representing 25 different human populations from across the globe. Importantly, each of the genomes was assembled without guidance from the first human genome composite. As a result, the new dataset better captures genetic differences from different human populations.

"We've entered a new era in genomics where whole human genomes can be sequenced with exciting new technologies that provide more substantial and accurate reads of the DNA bases," said study co-author Scott Devine, PhD, Associate Professor of Medicine at UMSOM and faculty member of IGS. "This is allowing researchers to study areas of the genome that previously were not accessible but are relevant to human traits and diseases."

Institute of Genome Science (IGS)'s Genome Resource Center (GRC) was one of three sequencing centers, along with Jackson Labs and the University of Washington, that generated the data using a new sequencing technology that was developed recently by Pacific Biosciences. The GRC was one of only five early access centers that was asked to test the new platform.

Dr. Devine helped to lead the sequencing efforts for this study and also led the sub-group of authors who discovered the presence of "mobile elements" (i.e., pieces of DNA that can move around and get inserted into other areas of the genome). Other members of the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine are among the 65 co-authors. Luke Tallon, PhD, Scientific Director of the Genomic Resource Center, worked with Dr. Devine to generate one of the first human genome sequences on the Pacific Bioscences platform that was contributed to this study. Nelson Chuang, a graduate student in Dr. Devine's lab also contributed to the project.

"The landmark new research demonstrates a giant step forward in our understanding of the underpinnings of genetically-driven health conditions," said E. Albert Reece, MD, PhD, MBA, Executive Vice President for Medical Affairs, UM Baltimore, and the John Z. and Akiko K. Bowers Distinguished Professor and Dean, University of Maryland School of Medicine. "This advance will hopefully fuel future studies aimed at understanding the impact of human genome variation on human diseases."

Psychologists have long found that people behave differently than when they learn of peers' actions. A new study by computer scientists found that when individuals in an experiment about autonomous vehicles were informed that their peers were more likely to sacrifice their own safety to program their vehicle to hit a wall rather than hit pedestrians who were at risk, the percentage of individuals willing to sacrifice their own safety increased by approximately two-thirds.

As computer scientists train machines to act as people's agents in all sorts of situations, the study's authors indicate that the social component of decision-making is often overlooked. This could be of great consequence, note the paper's authors who show that the trolly problem -long shown to be the scenario moral psychologists turn to--is problematic. The problem, the authors indicate, fails to show the complexity of how humans make decisions.

Jonathan Gratch, one of the paper's author, the principal investigator for this project, and a computer scientist at the USC Institute for Creative Technologies, says existing models assume that in high stakes life and death decisions, people think differently than they actually do. He indicates that there are not moral absolutes for human decision-making but rather "it is more nuanced," says Gratch.

The researchers conducted four separate simulation experiments to understand how people might process and act on the moral dilemmas they would face as an operator of a driverless car. The first three experiments focused on human behavior when faced with risk to themselves and others in the event of negative scenario in which the vehicle would have to be programmed to either the car to hit the wall or hit five pedestrians. The authors prove that participants would use severity of injury to self and the risk to others as guideposts for decision-making. They found that the higher the risk to pedestrians; the more likely people were likely to self -sacrifice their own health. In addition, the level of risk to pedestrians did not to have to be as high as for the operator of the autonomous vehicle to sacrifice their own well-being.

In the fourth experiment, the researchers added a social dimension telling participants what peers had opted to do in the same situation. In one simulation, the knowledge that peers chose to risk their own health changed the participants' responses, rising from 30 percent who were willing to risk their health to 50 percent. But this can go both ways cautions Gratch. "Technically there are two forces at work. When people realize their peers don't care, this pulls people down to selfishness. When they realize they care, this pulls them up."

The research has implications for autonomous vehicles including drones and boats, as well as robots that are programmed by humans. The authors suggest that it is important for manufacturers to have an awareness of how humans actually make decisions in life or death situations. In addition, the authors imply that transparency in how machines are programmed as well as relinquishing controls to the human drivers so that they might change settings prior to these life and death situations are important for the public. They also suggest it is important for legislators to be aware of how vehicles might be programmed. Lastly, given the human susceptibility to conform to social norms, the authors believe that public health campaigns related to how peers programmed their autonomous vehicles for self-sacrifice might influence future owners to change their vehicle settings to be more oriented to protecting others from injury and choose self-sacrifice.

The COVID-19 virus holds some mysteries. Scientists remain in the dark on aspects of how it fuses and enters the host cell; how it assembles itself; and how it buds off the host cell.

Computational modeling combined with experimental data provides insights into these behaviors. But modeling over meaningful timescales of the pandemic-causing SARS-CoV-2 virus has so far been limited to just its pieces like the spike protein, a target for the current round of vaccines.

A new multiscale coarse-grained model of the complete SARS-CoV-2 virion, its core genetic material and virion shell, has been developed for the first time using supercomputers. The model offers scientists the potential for new ways to exploit the virus's vulnerabilities.

"We wanted to understand how SARS-CoV-2 works holistically as a whole particle," said Gregory Voth, the Haig P. Papazian Distinguished Service Professor at the University of Chicago. Voth is the corresponding author of the study that developed the first whole virus model, published November 2020 in the Biophysical Journal.

"We developed a bottom-up coarse-grained model," said Voth, "where we took information from atomistic-level molecular dynamics simulations and from experiments." He explained that a coarse-grained model resolves only groups of atoms, versus all-atom simulations, where every single atomic interaction is resolved. "If you do that well, which is always a challenge, you maintain the physics in the model."

The early results of the study show how the spike proteins on the surface of the virus move cooperatively.

"They don't move independently like a bunch of random, uncorrelated motions," Voth said. "They work together."

This cooperative motion of the spike proteins is informative of how the coronavirus explores and detects the ACE2 receptors of a potential host cell.

"The paper we published shows the beginnings of how the modes of motion in the spike proteins are correlated," Voth said. He added that the spikes are coupled to each other. When one protein moves another one also moves in response.

"The ultimate goal of the model would be, as a first step, to study the initial virion attractions and interactions with ACE2 receptors on cells and to understand the origins of that attraction and how those proteins work together to go on to the virus fusion process," Voth said.

Voth and his group have been developing coarse-grained modeling methods on viruses such as HIV and influenza for more than 20 years. They 'coarsen' the data to make it simpler and more computationally tractable, while staying true to the dynamics of the system.

"The benefit of the coarse-grained model is that it can be hundreds to thousands of times more computationally efficient than the all-atom model," Voth explained. The computational savings allowed the team to build a much larger model of the coronavirus than ever before, at longer time-scales than what has been done with all-atom models.

"What you're left with are the much slower, collective motions. The effects of the higher frequency, all-atom motions are folded into those interactions if you do it well. That's the idea of systematic coarse-graining."

The holistic model developed by Voth started with atomic models of the four main structural elements of the SARS-CoV-2 virion: the spike, membrane, nucleocapsid, and envelope proteins. These atomic models were then simulated and simplified to generate the complete course-grained model.

The all-atom molecular dynamics simulations of the spike protein component of the virion system, about 1.7 million atoms, were generated by study co-author Rommie Amaro, a professor of chemistry and biochemistry at the University of California, San Diego.

"Their model basically ingests our data, and it can learn from the data that we have at these more detailed scales and then go beyond where we went," Amaro said. "This method that Voth has developed will allow us and others to simulate over the longer time scales that are needed to actually simulate the virus infecting a cell."

Amaro elaborated on the behavior observed from the coarse-grained simulations of the spike proteins.

"What he saw very clearly was the beginning of the dissociation of the S1 subunit of the spike. The whole top part of the spike peels off during fusion," Amaro said.

One of the first steps of viral fusion with the host cell is this dissociation, where it binds to the ACE2 receptor of the host cell.

"The larger S1 opening movements that they saw with this coarse-grained model was something we hadn't seen yet in the all-atom molecular dynamics, and in fact it would be very difficult for us to see," Amaro said. "It's a critical part of the function of this protein and the infection process with the host cell. That was an interesting finding."

Voth and his team used the all-atom dynamical information on the open and closed states of the spike protein generated by the Amaro Lab on the Frontera supercomputer, as well as other data. The National Science Foundation (NSF)-funded Frontera system is operated by the Texas Advanced Computing Center (TACC) at The University of Texas at Austin.

"Frontera has shown how important it is for these studies of the virus, at multiple scales. It was critical at the atomic level to understand the underlying dynamics of the spike with all of its atoms. There's still a lot to learn there. But now this information can be used a second time to develop new methods that allow us to go out longer and farther, like the coarse-graining method," Amaro said.

"Frontera has been especially useful in providing the molecular dynamics data at the atomistic level for feeding into this model. It's very valuable," Voth said.

The Voth Group initially used the Midway2 computing cluster at the University of Chicago Research Computing Center to develop the coarse-grained model.

The membrane and envelope protein all-atom simulations were generated on the Anton 2 system. Operated by the Pittsburgh Supercomputing Center (PSC) with support from National Institutes of Health, Anton 2 is a special-purpose supercomputer for molecular dynamics simulations developed and provided without cost by D. E. Shaw Research.

"Frontera and Anton 2 provided the key molecular level input data into this model," Voth said.

"A really fantastic thing about Frontera and these types of methods is that we can give people much more accurate views of how these viruses are moving and carrying about their work," Amaro said.

"There are parts of the virus that are invisible even to experiment," she continued. "And through these types of methods that we use on Frontera, we can give scientists the first and important views into what these systems really look like with all of their complexity and how they're interacting with antibodies or drugs or with parts of the host cell."

The type of information that Frontera is giving researchers helps to understand the basic mechanisms of viral infection. It is also useful for the design of safer and better medicines to treat the disease and to prevent it, Amaro added.

Said Voth: "One thing that we're concerned about right now are the UK and the South African SARS-CoV-2 variants. Presumably, with a computational platform like we have developed here, we can rapidly assess those variances, which are changes of the amino acids. We can hopefully rather quickly understand the changes these mutations cause to the virus and then hopefully help in the design of new modified vaccines going forward."

Timothy Callaghan, PhD, and Alva Ferdinand, DrPH, JD, from the Southwest Rural Health Research Center at Texas A&M University School of Public Health, joined colleagues in the first national study of how often people in urban and rural areas in the United States follow COVID-19 guidelines. These include public health best practices like wearing masks in public, sanitizing homes and work areas, maintaining physical distancing, working from home and avoiding dining in restaurants or bars.

The research team used a survey of 5,009 U.S. adults that closely matched the makeup of the country's population as a whole. The survey asked how often participants followed COVID-19 prevention recommendations and collected data on political ideology, perceived risk of getting COVID-19, whether participants had been tested for the disease, and how trusting of medical experts subjects were. They also collected data on demographic factors like age, gender, race, education, income and religiosity and used respondent ZIP code to determine whether they lived in a rural or urban area.

The research team found rural Americans were less likely than their urban counterparts to report following most of the recommended prevention behaviors. The two most notable differences were in wearing face coverings in public and in working from home. They also found smaller but significant differences in avoiding restaurants, changing travel plans and disinfecting homes and work areas, with rural residents again being less likely to follow recommendations. Other measures like social distancing, hand washing and canceling social engagements showed no significant differences between rural and urban-dwelling Americans.

When including political ideology and social factors in their analysis, the researchers found that some factors were associated with the likelihood of following recommendations. Older respondents and people who were more concerned about COVID-19 were more likely to follow at least some of the recommendations, as were those with greater educational attainment and higher income. People with a more conservative political ideology were less likely to follow prevention guidelines and women were more likely to follow them than men. However, living in a rural area remained a strong influence on following public health recommendations.

Given the limited access to high quality medical care in rural areas, these behaviors could lead to negative, yet avoidable, health outcomes in rural America. Finding ways to improve the adoption of COVID-19 prevention behaviors in rural areas is therefore critical, "something that targeted messaging might help to achieve," Callaghan said. "Public health efforts that consider factors like trust of medical experts and political ideology when reaching out to different groups could be key."

DETROIT (February 25, 2021) - Researchers at Henry Ford Health System, as part of a national asthma collaborative, have identified a gene variant associated with childhood asthma that underscores the importance of including diverse patient populations in research studies.

The study is published in the print version of the American Journal of Respiratory and Critical Care Medicine.

For 14 years researchers have known that a casual variant for early onset asthma resides on chromosome 17, which holds one of the most highly replicated and significant genetic associations with asthma. Henry Ford researchers acknowledged they would not have identified it in this study without a diverse patient population that included African Americans, many from the metro Detroit area.

"This study is one of the best examples that demonstrates diversity matters in genetic research," said L. Keoki Williams, M.D., MPH, the study's senior author and co-Director of Henry Ford's Center for Individualized and Genomic Medicine Research. "African Americans have greater variation in their genome due to their African ancestry and this allowed us to pin-point a variant on chromosome 17 which has eluded asthma researchers for over a decade."

In an accompanying editorial written by researchers at the Harvard Medical School, the authors wrote that divergent genealogical histories can facilitate gene discovery. "In a time when our society is attempting to confront the ills of racial discrimination, including the ongoing racial disparities in healthcare, it is imperative that future studies are more inclusive to ensure that all peoples benefit equally in the post-genome era."

According to the National Center for Health Statistics, more than 41 million Americans had asthma in 2019, of which 18.5% were children less than 18 years of age. As a group, African Americans have some of the highest rates of asthma in the U.S. - 17.6% vs. 9.3% for African American children and non-Hispanic white children, respectively, and 15.2% vs. 13.8% for African American adults and non-Hispanic white adults, respectively.

The Henry Ford-led study was conducted in collaboration with researchers Esteban Burchard, M.D., MPH, at the University of California San Francisco (UCSF) and Hakon Hakonarson, M.D., Ph.D., at the Children's Hospital of Philadelphia (CHOP). It was part of the Asthma Translational Genomics Collaborative and the National Heart Lung and Blood Institute's Trans-Omics for Precision Medicine (TOPMed) program, a nationwide effort to use cutting-edge genetic technologies to better understand common, yet complex, diseases.

The study is believed to be the largest to date using whole genome sequencing for asthma research. It included 5,630 African American participants with and without asthma from the Henry Ford, UCSF and CHOP cohorts. Participants from Henry Ford were part of the Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity, or SAPPHIRE.

"African Americans have been represented in less than 3% of these types of studies, yet make up 13% of the U.S. population," said Hongsheng Gui, Ph.D., a Henry Ford researcher and study co-author. "Another reason to have diverse study populations is that many of the genetic risk markers found in one population group don't replicate in other population groups. However, the variant that we found appears to confer the same magnitude of asthma risk in both African Americans and non-Hispanic white Americans."

The variant that was identified resides in a gene called gasdermin-B, abbreviated GSDMB. Researchers found that the "protective" variant caused alternative splicing or editing of the final gene, resulting in a messenger RNA sequence missing exons 6 and 7. Researchers believe that this finding will help focus efforts to understand how this particular gene affects a child's risk of developing asthma.

Preterm labor comprises 12.7% of all pregnancies. Although the overall rate of pregnancy is decreasing, the occurrence of premature birth due to preterm labor in south korea has been increasing over the past 7 years. Not only is preterm birth accountable for about a half of all neonatal mortality cases, the neurological deficits in surviving premature infants often lead to problems later in life, such as developmental disorders and respiratory complications. Currently, preterm labor is detected only when expecting mothers experience abnormal symptoms, or when they undergo a routine test like abdominal ultrasound or a laboratory test for vaginal secretions. It is difficult to detect preterm labor early, and there are few treatment options available other than pharmaceutical agents such as anti-contraction medications, with which side effects are of concern.

The Korea Institute of Science and Technology (KIST) announced that in collaboration with the research team led by Ki Hoon Ahn, Professor at the Department of OB/GYN, Korea University Anam Hospital and Dr. Soo Hyun Lee, the team at KIST Brain Science Institute (BSI) developed a non-invasive electroceutical for the early detection and simultaneous treatment of preterm labor.

While preterm labor is generally known to have various causes, including naturally occurring early contractions and premature rupture of membranes, a final symptom is irregular uterine contractions. The KIST research team developed a donut-shaped electrode that is inserted into the cervix to sense the signals of uterine contractions in real time, making the early diagnosis of preterm labor possible. Moreover, after sensing the signal of uterine contractions, the electrode can generate an electrical signal, thus functioning as an electroceutical to suppress uterine contractions by relaxing uterine muscles via sympathetic nerve stimulation.

The research team tested the safety and functioning of this electroceutical system for preterm labor detection and treatment using preterm-labor mouse and pig models, and confirmed that electrical stimulation generated from the system could delay and inhibit uterine contractions.

Professor Ki Hoon Ahn of Korea University Anam Hospital said, "Although new drug research and development (R&D) has been actively performed worldwide, the efficacy was not sufficient enough and there were side effects. We developed this system because there was a clinical need for a medical equipment with a novel mechanism." He also added that, "Infant mortality and the occurrence of sequelae due to preterm labor are expected to drastically decrease with the use of the first-ever medical device controlling uterine contractions."

Soo Hyun Lee, PhD, of KIST, contributed by saying that, "The donut-shaped electroceutical is not a therapy based on the existing pharmaceuticals, but a therapeutic tool to inhibit uterine contractions via electrical stimulation, and is likely to be developed further as a new concept-based medical technology." He added that, "The research was initiated as a project of the KIST-Korea University Anam Hospital Translation Research Center. In near future, we plan to conduct clinical research with government research grants, like an interagency program for medical device R&D."

The total amount of data generated worldwide is expected to reach 175 ZB (Zettabytes; 1 ZB equals 1 billion Terabytes) by 2025. If 175 ZB were stored on Blu-ray disks, the disk stack would be 23 times the distance to the Moon. We face the urgent need to develop storage technologies that can accommodate this enormous amount of data.

The demand to store ever-increasing volumes of information has resulted in the widespread implementation of data centers for Big Data. These centers consume massive amounts of energy (about 3% of global electricity supply) and rely on magnetization-based hard disk drives with limited storage capacity (up to 2 TB per disk) and lifespan (up to 3-5 years). Laser-enabled optical data storage is a promising and cost-effective alternative for meeting this unprecedented demand. However, the diffractive nature of light has limited the size of the information bits that can be reached and, as a result, the storage capacity of the optical disks.

Researchers at USST, RMIT and NUS have now overcome this limitation by using earth-rich lanthanide-doped upconversion nanoparticles and graphene oxide flakes. This unique material platform enables low-power optical writing nanoscale information bits (nanoscale refers to sizes of 1-100 nanometers, where one nanometer is one billionth of a meter).

A much-improved data density can be achieved for an estimated storage capacity of 700 TB on a 12-cm optical disk, comparable to a storage capacity of 28,000 Blu-ray disks. Furthermore, the technology uses inexpensive continuous-wave lasers, reducing operating costs compared to traditional optical writing techniques using expensive and bulky pulsed lasers.

This technology also offers the potential for optical lithography of nanostructures in carbon based chips that are highly required in next-generation nanophotonic devices.

The impact

Optical data storage has advanced remarkably over the last decades, but the optical disk storage capacity is still limited to a few Terabytes.

The developed sub-diffraction optical writing technology can produce an optical disk with the largest storage capacity of all available optical devices.

While advances are needed to optimize the technology, the results open new avenues to address the global challenge of data storage. The technology is suited to the mass production of optical disks, so that the potential is enormous.

This ground-breaking technology could offer a cheaper and sustainable solution for the next generation of high-capacity optical data storage while enabling the energy-efficient nanofabrication of flexible graphene based electronics.

Liquid structures - liquid droplets that maintain a specific shape - are useful for a variety of applications, from food processing to cosmetics, medicine, and even petroleum extraction, but researchers have yet to tap into these exciting new materials' full potential because not much is known about how they form.

Now, a research team led by Berkeley Lab has captured real-time high-resolution videos of liquid structures taking shape as nanoparticle surfactants (NPSs) - soap-like particles just billionths of a meter in size - jam tightly together, side by side, to form a solid-like layer at the interface between oil and water.

Their findings, recently featured on the cover of Science Advances , could help researchers better optimize liquid structures to advance new biomedical applications such as reconfigurable microfluidics for drug discovery and all-liquid robotics for targeted cancer drug delivery, among others.

In experiments led by co-author Paul Ashby , a staff scientist in Berkeley Lab's Molecular Foundry and Materials Sciences Division, and Yu Chai, a former postdoctoral researcher in the Ashby group who is now an assistant professor at The City University of Hong Kong, the researchers used a special imaging technique called atomic force microscopy (AFM) to take the first-ever real-time movies of the NPSs crowding together and getting jammed at the oil-water interface, a critical step in locking a liquid into a specific shape.

The researchers' movies unveiled a portrait of the NPS interface with unprecedented detail, including the size of each NPS, whether the interface was composed of one or multiple layers, and how much time elapsed, down to the second, for each NPS to attach to and settle into the interface.

The spectacular AFM images also showed the angle at which an NPS "sits" at the interface - an unexpected result. "We were surprised by how rough the interfaces are," Ashby said. "We had always drawn illustrations of a uniform interface with nanoparticles attached at the same contact angle - but in our current study, we found there is actually a lot of variation."

Most nanoscale imaging tools can only investigate immobile samples that are either dry or frozen. Over the past couple of decades, Ashby has focused his research on developing unique AFM capabilities that allow the user to control the probe tip so it gently interacts with fast-moving samples, such as the NPSs of the current study, without touching the underlying liquid - a challenging feat.

"Imaging a liquid structure at the nanoscale, and watching the nanoparticles move around in liquid in real time using an AFM probe - that wouldn't be possible without Paul's extensive expertise," said co-author Thomas Russell , a visiting faculty scientist and professor of polymer science and engineering from the University of Massachusetts who leads the Adaptive Interfacial Assemblies Towards Structuring Liquids program in Berkeley Lab's Materials Sciences Division. "These kinds of capabilities aren't available anywhere else except at the Molecular Foundry."

The researchers next plan to study the effect of self-propelling particles in NPS liquid structures.