Culture

SARS-CoV-2 variants from mink evade inhibition by antibodies

image: Introduction of SARS-CoV-2 into farmed mink leads to the emergence of viral variants that partially evade antibody-mediated neutralization. A) SARS-CoV-2-infected workers introduced the virus into farmed mink populations, causing an epidemic spread of the virus in the animals. As a result, the virus mutated in mink and gave rise to a novel SARS-CoV-2 variant. This novel variant was subsequently transmitted back to workers, sparking transmission chains in the local community. B) SARS-CoV-2 from mink harbor one or more mutations in the viral spike protein, which is used by the virus to enter cells and constitutes the main target for neutralizing antibodies. These mutations enable the virus to partially evade from neutralization by antibodies from convalescent individuals and synthetic antibodies used for COVID-19 therapy.

Image: 
Markus Hoffmann

It has been known for about a year that minks can become infected with SARS-CoV-2. The virus had been transmitted from humans to farmed mink and mutated in infected animals. Mutations were acquired in the spike protein, which is crucial for the entry of the virus into host cells and represents the central point of attack for antibodies. These SARS-CoV-2 variants from mink were transmitted back to humans, raising concerns that minks could be a continuing source of infection of humans with SARS-CoV-2 variants with altered biological properties. Researchers at the German Primate Center (DPZ) - Leibniz Institute for Primate Research in Göttingen, Germany, have now shown that an antibody used for COVID-19 therapy is unable to effectively inhibit SARS-CoV-2 harboring a spike mutation acquired in minks. In addition, the mutation reduced the inhibition of the virus by antibodies produced in SARS-CoV-2 infected humans. These results show that SARS-CoV-2 can acquire mutations in minks that may reduce control of the virus by the human immune system (Cell Reports).

More than three million people have died worldwide from the pandemic spread of SARS coronavirus-2 and its associated disease COVID-19, according to the World Health Organization (WHO). Animal-to-human transmission of the virus is believed to be the origin of the pandemic, which began in Wuhan, China, in December 2019. In April 2020, mink in Dutch mink farms developed a respiratory disease due to infection with SARS-CoV-2, which was transmitted from infected farm workers to the animals. The virus mutated in mink and different virus variants emerged, which were transmitted back to farm workers and then also transmitted from human to human. This observation was also made in Denmark and millions of minks were killed to prevent the transmission of new viral variants to humans.

The spike protein in the envelope of SARS-CoV-2 is responsible for the entry of the virus into cells in which it replicates. Researchers led by Markus Hoffmann and Stefan Pöhlmann of the German Primate Center have studied mutations detected in the spike protein of SARS-CoV-2 from mink, including mutation Y453F. The researchers wanted to find out whether this mutation affects inhibition of the virus by antibodies that are used for COVID-19 therapy or are produced in COVID-19 patients.

"Our results show that one of two antibodies from an antibody cocktail used for COVID-19 therapy no longer efficiently inhibits the viral variant with the Y453F mutation. Furthermore, our study demonstrates that the Y453F mutation reduces inhibition of the virus by antibodies produced by COVID-19 patients. This means that people who were infected with SARS-CoV-2 may have reduced protection against mink variants of the virus", says Markus Hoffmann, first author of the study. In sum, SARS-CoV-2 can mutate in minks in a way that reduces immune control by antibodies. Whether this is also possible in other animals to which the virus can be transmitted by infected individuals is currently unclear. "In the meantime, the Y453F mutation has also occurred in humans, but not through infection with a mink variant. When the virus replicates for a long time in people who are immunocompromised, resistant variants can emerge. In this case, the resistance-mediating mutation was identical to the one observed in mink," says Stefan Pöhlmann.

Credit: 
Deutsches Primatenzentrum (DPZ)/German Primate Center

Traumatic brain injuries can increase risk of stroke for up to five years, finds study

Stroke risk for patients with traumatic brain injuries is at its highest in the four months following injury and remains significant for up to five years post-injury, finds a new systematic review led by a team at the University of Birmingham.

Traumatic brain injury (TBI) is a global health problem affecting over 60 million people a year worldwide. Incidences of TBI are rising due to a range of factors including increased falls in the elderly, military conflict, sports injuries and road traffic accidents. However, advances in critical care and imaging have led to a reduction in TBI-related mortality.

Previous studies have associated TBI with a long-term risk of neurological diseases including dementia, Parkinson's and epilepsy, and TBI has been proposed as an independent risk factor for stroke.

This latest review, which brings together 18 studies from four countries and publishes today (April 9) in the International Journal of Stroke, is the first of its kind to investigate post-injury stroke risk.

Funded by the National Institute for Health Research's Surgical Reconstruction and Microbiology Research Centre based at University Hospitals Birmingham NHS Foundation Trust, the review showed that TBI patients have an 86% increased risk of stroke compared to patients who have not experienced a TBI. Stroke risk may be at its highest in the first four months post-injury, but remains significant for up to five years, found the review.

Significantly, the findings suggest that TBI is a risk factor for stroke regardless of the severity or subtype of the injury. This is particularly noteworthy because 70% to 90% of TBI's are mild and suggests that TBI's should be considered a chronic condition even if it is mild and patients recover well.

Researchers also found that the use of anti-coagulants, such as VKA's and statins, could help to reduce stroke risk post-TBI, while the use of some classes of anti-depressants are associated with increased stroke risk post-TBI.

Lead author Dr Grace Turner, of the University of Birmingham's Institute of Applied Health Research, said: "Stroke is the second leading cause of death and third leading cause of disability worldwide, however, urgent treatment can prevent stroke related death and long-term disability.

"Our review found some evidence to suggest an association between reduced stroke risk post-TBI and the stroke prevention drugs VKAs and statins but, as previous studies have found, stroke prevention drugs are often stopped when an individual experiences a TBI.

She said more research is required to investigate the effectiveness of stroke prevention drugs post-TBI to help inform clinicians' prescribing and facilitate shared decision making.

Dr Turner added: "As our review has shown, TBI patients should be informed of the potential for increased stroke risk and with the risk of stroke at its highest in the first four months post-injury, this is a critical time period to educate patients and their care givers on stroke risk and symptoms.

"This initial four-month period should also be used by clinicians to administer stroke prevention medication and lifestyle advice to mitigate the excess risk of stroke associated with TBI."

Credit: 
University of Birmingham

Defects in a specific cell type may cause ulcerative colitis

There are many variants of "goblet cells" in the intestines and they seem to have different functions, according to a new study from the University of Gothenburg. The study indicates that defects in goblet cells of a particular type may be a factor contributing to ulcerative colitis, an inflammatory bowel disease.

The entire inside of our intestines is covered by a thin layer of mucus that protects the fragile mucous membrane (mucosa) from bacteria and other microorganisms. If the microorganisms repeatedly come into contact with the intestinal mucosa, inflammation and even cell changes may result. These increase the risk of intestinal cancer. In a healthy colon, the mucus layer is up to a millimeter thick. This layer, which undergoes complete renewal hourly, is formed from cells of a special type, known as goblet cells.

Many different goblet cells

In the present study, now published in the journal Science, the scientists separated goblet cells from other cells and investigated which proteins each individual goblet cell expresses. There proved to be many different subtypes of these cells, and goblet cells' functions turned out to vary more than researchers have previously realized.

"We believe this is important knowledge that may enable us to influence the protective function of the gut in the future. The system that maintains the protective intestinal mucus layer seems to be able to change its functions, and we could utilize this capacity by reprogramming the layer with various signals, for example by using new drugs", says Malin Johansson, Associate Professor at Sahlgrenska Academy, University of Gothenburg, who led the research behind the present study.

Connected with ulcerative colitis

The most impermeable part of the mucus layer is formed by glands in the gut. In particular, the research team studied one of the specific types of goblet cells, found on the outermost surface of the mucosa. These goblet cells provide another type of mucus, which contributes to the protection of the gut but allows certain nutrients to pass through.

"If the function of these specific cells is impaired, we see that unprotected cell surfaces arise. These lead to inflammation, both in studies on mice and in samples from patients with ulcerative colitis," Johansson says.

Appear to cause damage to mucosal protection

In the study, these specific goblet cells seemed to be repelled by the mucosa earlier than normal in patients with ulcerative colitis. Accordingly, the cells became fewer.

"To our surprise, we were able to observe this both in patients with active ulcerative colitis and in those who were temporarily asymptomatic. This indicates that premature rejection of the particular goblet cells we've been studying damages the mucus protection and that this is a contributing cause of inflammatory bowel disease. It could also be a partial explanation for these patients' elevated cancer risk," Johansson says.

There are some 30,000 people in Sweden with ulcerative colitis, which is a chronic but intermittent inflammatory bowel disease.

Credit: 
University of Gothenburg

Intellectual disability is rarely inherited -- risk for younger siblings is low

The prevalence of intellectual disabilities, which means difficulties with learning and understanding new things, is roughly 1-2% in the population. People with a severe intellectual disability need help from others in daily activities throughout their lives.

Such disabilities can be caused by genetic changes or external factors. According to estimates, roughly 2,500 genes underlie intellectual disability, of which approximately half remain unidentified.

In recent years, the diagnostics for intellectual disabilities have improved thanks to advancements in techniques that make it possible to sequence the entire genome. These techniques can also help to identify causes of intellectual disability not found in other medical examinations and tests. Exome sequencing, that is, the sequencing of the protein-coding regions of genes in the genome, enables the identification of new pathogenic gene variants as well. Identifying genes is a prerequisite for identifying disease mechanisms and developing treatments.

The study conducted at the University of Helsinki utilised exome sequencing to determine the potential genetic background of intellectual disability. The study participants included Finnish families with family members with delayed cognitive development for which no clear cause had been identified. The results were recently published in the Human Genetics journal.

It was found that in 64% of the study participants the cause of their developmental disorder was a known intellectual disability gene. The majority of these variants, 75%, was the result of random mutations taking place during foetal development (de novo), and variants not found in the parents' genome. An inherited mutation was identified in no more than a quarter of the pathogenic genes studied. More large-scale structural variants, which are usually not inherited, were found in only 8% of the families.

"Based on our findings, the risk of recurrence of intellectual disability in the next child of individual families is usually low," says Docent Irma Järvelä. According to Järvelä, this is a significant and relieving piece of information for many families.

She believes the use of exome sequencing as a primary method of examination in the diagnostics for intellectual disabilities is well justified. The technique makes it possible to investigate the cause of disability faster than before, which alleviates the uncertainty and concern felt by families, as well as generates savings in healthcare.

"The more familiar we are with the factors underlying intellectual disabilities and their hereditary nature, the better we are able to help families that encounter these serious disorders," Järvelä adds.

Human settlement history does not increase the prevalence of inherited diseases

The Finnish population has become known for its recessively inherited severe diseases caused by single gene defects known as founder variants, with some 40 of such diseases known so far.

The recently published study demonstrated that de novo variants created in early foetal development are the most common cause for intellectual disabilities also in the Finnish population. Known variants associated with recessive diseases were identified in only 5% of the families included in the study, a result in line with other European populations.

"In spite of the isolated nature of our population, Finns are not different from other European populations in terms of the inheritance of intellectual disabilities," Järvelä says.

A distant family connection going back 7 to 10 generations reduces the risk of establishing an recessively inherited disease even in small populations.

"In the light of contemporary gene research, the Finnish disease heritage appears an increasingly rare find. Related research in Finland is of a high medical standard," Järvelä emphasises.

In the recently published study, nine new candidate genes were identified, of which a handful were found to be recessive. In further research, one of these genes could turn out to be a previously unknown gene enriched in the Finnish population.

The study was conducted in cooperation with Finnish doctors involved in the treatment of people with intellectual disabilities and the Department of Medical Genetics at the University of Helsinki as well as Columbia University and the Baylor College of Medicine in the United States.

Credit: 
University of Helsinki

What does the study of domesticated birds tell us about the evolution of human language?

image: Researchers analysed the genomic, neurobiological and singing-type differences between the domesticated Bengalese finch (see image above) and its closest wild relative.

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UNIVERSITY OF BARCELONA

Language is one of the most remarkable abilities humans have. It allows us to express complex meanings and transmit knowledge from generation to generation. An important question in human biology is how this ability evolved, and researchers from the universities of Barcelona, Cologne and Tokyo have tackled this issue in a recent article, published in the journal Trends in Cognitive Sciences.

The article has among its authors experts from the Institute of Complex Systems of the UB (UBICS) Thomas O’Rourke and Pedro Tiago Martins, led by ICREA research professor Cedric Boeckx. According to this new study, the evolution of language would be related to another noteworthy feature of Homo sapiens: tolerance and cooperation towards each other.

The study draws on evidence from such diverse fields as archaeology, evolutionary genomics, neurobiology, animal behaviour and clinical research on neuropsychiatric disorders. The authors hypothesize that a reduction of reactive aggression, resulting from the evolution and process of self-domestication of our species, could have led to an increase in our language complexity. According to the authors, this development would be caused by a reduced impact on brain networks of stress hormones, neurotransmitters that activate in aggressive situations, and which would be crucial for how we learn to speak. To show this interaction, the researchers analysed the genomic, neurobiological and singing-type differences between the domesticated Bengalese finch and its closest wild relative.

Looking for keys of the human language evolution in birdsong

A central aspect of the authors’ approach in the study is that the aspects that make language special can be elucidated by comparing them to the communication systems of other animals. “For instance, take how children learn to speak and how birds learn to sing: unlike most animal communication systems, juvenile birdsong and the child speech only develop properly in presence of adult tutors. Without the vocal support from adults, the great range of sounds available to humans and songbirds does not develop properly”, the researchers note.

Moreover, although speech and birdsong evolved independently, the authors suggest both communication systems are associated with similar patterns in brain connectivity and are negatively affected by stress: “Birds that are regularly under stress during their development sing a more stereotypical song as adults, while children with chronic stress problems are more susceptible to developing repetitive tics, including vocalizations in the case of Tourette syndrome”.

In this context, Kazuo Okanoya, one of the authors of the study, has been studying the Bengalese finch for years. This domesticated songbird sings a more varied and complex song than its wild ancestor. The study points out that the same happens with other domesticated species. The Bengalese finch has a weakened stress response and is less aggressive than its wild counterpart. In fact, according to the authors, there is more and more “evidence of multiple domesticated species having altered vocal repertoires compared to their wild counterparts”.

The impact of domestication in stress and aggressiveness

For the researchers, these differences between domestic and wild animals are “a central piece in the puzzle of the evolution of human language”, since our species and domesticated species share particular physical changes related to their closest wild species. Modern humans have a flattened face, a rounded skull and reduced tooth size compared to our extinct archaic relatives, the Neanderthals. Domesticates have comparable changes to facial and cranial bone structures, often accompanied by the development of other traits such as skin depigmentation, floppy ears and curly tails. Finally, modern humans have marked reductions in measures of stress response and reactive aggression compared to other living apes. These similarities do not stop at physical traits since, according to researchers, the genomes of modern humans and multiple domesticated species show changes targeting the same genes.

In particular, a disproportionate number of these genes downregulate the activity of the glutamate neurotransmitter system, which drives the brain response to stressful experiences. Authors note that “glutamate, the brain’s main excitatory neurotransmitter, interacts with dopamine, in birdsong learning, aggressive behaviour, and the repetitive vocal tics of Tourette syndrome”.

Alterations in stress hormone balance in the striatum

In the study, authors show how the activity of glutamate tends to promote the release of dopamine in the striatum, an evolutionary old brain structure important for reward-based learning and motor output. “In adult songbirds, the increase in dopamine release in this striatal area is correlated with the learning of a more restricted song, which replaces experimental vocalizations typical of young birds”. “Regarding human beings and other mammals” —the authors add—, “dopamine release in the dorsal striatum promotes restrictive and repetitive motor outputs, such as vocalizations, while other more experimental and exploratory behaviours are supported by the dopaminergic activity of the ventral striatum”.

According to the study, many of the glutamatergic signaling genes that have changed in recent human evolution code for receptors that reduce the excitation of the dorsal striatum. Meanwhile, these receptors tend not to reduce activity, and even promote the dopamine release, in ventral striatal regions.

The authors say these alterations in the balance of stress hormones in the striatum were an important advance in the evolution of vocal learning in the lineage of modern humans. “These results suggest the glutamate system and its interactions with dopamine are involved in the process in which humans acquired their varied and flexible ability to speak. Selection against reactive aggression in our species would have altered the interaction of these neurotransmitters promoting the communicative skills of our species. These findings shed light on new ways for comparative biological research on the human language faculty” conclude researchers.

Credit: 
University of Barcelona

Sustainable chemical synthesis with platinum

image: The source of phenols in these experiments was lignin, which is involved in the tough structural components of rigid plant bodies such as trees. So woody biomass like this is the ideal raw material as it can be more sustainably sourced than petroleum.

Image: 
CC0 - Pixabay/ybernardi

Researchers used platinum and aluminum compounds to create a catalyst which enables certain chemical reactions to occur more efficiently than ever before. The catalyst could significantly reduce energy usage in various industrial and pharmaceutical processes. It also allows for a wider range of sustainable sources to feed the processes, which could reduce the demand for fossil fuels required by them.

There are many chemicals used in a wide range of industries, including pharmaceuticals, that you probably don't notice in everyday life; for example, benzene, toluene, xylene and ethylbenzene, to name a few. These are created at chemical production plants that use petroleum to feed the processes in question. But there is now a way to produce those chemicals in a more sustainable way.

Assistant Professor Xiongjie Jin and Professor Kyoko Nozaki from the Department of Chemistry and Biotechnology at the University of Tokyo and their team have created a new catalyst, a material that enables or speeds up a specific chemical reaction, that allows for more sustainable production of so-called aromatic hydrocarbons. At present the process typically requires temperatures of 200 degrees Celsius or more and pressures of 2 or more atmospheres. But with the team's new catalyst, the temperature can be brought down to between 100 degrees and 150 degrees Celsius, and the pressure to just 1 atmosphere, or ambient pressure. This could hugely reduce the energy cost of production.

"Our 'Pt catalyst' makes use of platinum nanoparticles and an aluminum metaphosphate substrate, which is rarely ever used in catalysts," said Jin. "Source molecules interacting with this catalyst at the right temperature and pressure break down into useful aromatic hydrocarbon compounds. This process is called hydrogenolysis. But the most exciting part for us is not just that the catalyst improves reaction efficiency, but that it opens up new options for the kinds of source materials that can now be used in these processes."

Currently, nonrenewable petroleum-based substances are used to create aromatic hydrocarbons, and this is not a sustainable scenario in the long run. The Pt catalyst allows the use of renewable woody biomass as source material, in particular a family of compounds known as lignins, which contain phenols, the basis of the reactions in question. Another benefit of the Pt catalyst is that it can be recycled and reused several times over. All these factors combined could lead to a vastly more sustainable way to produce aromatic hydrocarbons on an industrial scale.

"We hope our study contributes to the (United Nations) Sustainable Development Goals by making industrially important chemicals from renewable resources instead of petroleum, and at a lower energy cost," said Jin. "Our next steps will be to further increase the lifetime of the Pt catalyst and also to make the catalyst work directly on lignins, mitigating the need to break it down into phenols before the reactions can take place."

Credit: 
University of Tokyo

New properties of strontium titanate are significant for electronics research

image: EPR spectra of the (001)-oriented single-crystal samples having the shape of a bar and a plate of STO:Fe3+ at T = 300 K (a) and of a plate of STO:Mn4+ at T = 150 K (b). The orientations of the samples with respect to the magnetic field B are marked in the figure. Black lines are the measured spectra, the red ones are the fits and the blue lines show the simulated spectra of the non-perturbed cubic-symmetry centers (see text). Orientation dependence of the resonance fields for the Fe3+ centers in the STO:Fe (001)-plate (c) with the magnetic field rotated in the (001) and (100) crystallographic planes (rhombs and circles, respectively); its fit using the Hamiltonian (1) is shown by solid lines. Temperature dependences of the parameter corresponding to the axial component of the crystal field for a plate (squares) and a bar (circles) shaped samples (d); dotted lines are the guides for the eye.

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Kazan Federal University

While studying strontium titanate with electron paramagnetic resonance, a team from KFU's Center for Quantum Technology has found that the shape of a specimen of strontium titanate influences its internal symmetry. The research was co-conducted by the Ioffe Institute of Physics and Technology (Russia) and the Institute of Physics of the Czech Academy of Sciences.

At room temperature, SrTiO3 is a crystal with high cubic symmetry, that is, the lattice of strontium titanate, like bricks, is composed of unit cells, each of which is a regular cube. However, the researchers showed the picture is a bit more nuanced. In thin plates and columns measuring microns in width, the symmetry decreases to tetragonal (uniaxial), with a structure was not previously observed in SrTiO3. That is, each elementary cell turns into a parallelepiped.

"The results are of great scientific and practical importance. In many cases, the scale of breaking is not as important as its very presence. A decrease in symmetry opens up the possibility of phenomena that are forbidden in a cubic structure," said Roman Yusupov, Lead Research Associate of the Center for Quantum Technology.

He noted that strontium titanate is actively used in thin-film technologies, where the functional properties of materials are determined by layers that sometimes have a thickness of several atoms. They are crucial for electronic devices, such as processors, monitors, mobile screens, high-capacity batteries, and storage devices.

"Thin films are based on substrates -- typically thin (less than one millimeter in thickness) slabs of materials other than the film material. The properties of thin films are largely determined by the structure of the substrate. One of the widely used substrate materials is strontium titanate," explains Yusupov.

By changing the distortion magnitude of substrates, it's possible to change the characteristics of thin films deposited on them, and thus contribute to creating new devices, sensors, and detectors.

Credit: 
Kazan Federal University

Study shows education is not enough to overcome inequality

A recent study finds that social inequality persists, regardless of educational achievement - particularly for men.

"Education is not the equalizer that many people think it is," says Anna Manzoni, author of the study and an associate professor of sociology at North Carolina State University.

The study aimed to determine the extent to which a parent's social status gives an advantage to their children. The research used the educational achievements of parents as a proxy for social status, and looked at the earnings of adult children as a proxy for professional success.

To address the research question, Manzoni examined data from people who were interviewed as part of the National Survey of College Graduates between 2010 and 2017. Specifically, Manzoni focused on United States citizens between 35 and 67 years old who reported on their wages and parental education. The final sample size was 56,819 individuals: 32,337 men and 24,482 women.

The analysis found that if a son gets a degree similar to the degree that a parent had, the son will earn more money than if his parent did not achieve the same level of education.

For example, imagine that Son A becomes a doctor, and he had a parent who was also a doctor. Meanwhile, Son B also becomes a doctor, but his parents only had bachelor's degrees. The study found that, in general, Son A will earn more money than Son B, even though they have the same degree.

This effect also exists for daughters, but it is much weaker.

"The effect we see here essentially preserves social stratification for sons - less so for daughters," Manzoni says. "We like to think that if someone makes it to college, becomes a lawyer, becomes a doctor, they have 'made it.' But what we see is that even earning an advanced degree is unlikely to put you on the same professional footing as someone who earned the same degree but started higher on the social ladder.

"One take-away is that expanding access to education is valuable, but education alone is not enough to resolve our society's challenges in regard to inequality," Manzoni says.

"This work shows that social origin matters, but it's not clear what drives this structural inequality," Manzoni adds. "Is it social capital? Access to networks? Differing financial resources? Is parental background becoming more important as a larger percentage of the population is getting a college degree? Is the advantage at the beginning of a child's career? There is still a lot of room for additional research on this subject."

Credit: 
North Carolina State University

Army researchers create pioneering approach to real-time conversational AI

image: Army researchers create a novel approach that allows autonomous systems to flexibly interpret and respond to Soldier intent.

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(1st Lt. Angelo Mejia)

ADELPHI, Md. -- Spoken dialogue is the most natural way for people to interact with complex autonomous agents such as robots. Future Army operational environments will require technology that allows artificial intelligent agents to understand and carry out commands and interact with them as teammates.

Researchers from the U.S. Army Combat Capabilities Development Command, known as DEVCOM, Army Research Laboratory and the University of Southern California's Institute for Creative Technologies, a Department of Defense-sponsored University Affiliated Research Center, created an approach to flexibly interpret and respond to Soldier intent derived from spoken dialogue with autonomous systems.

This technology is currently the primary component for dialogue processing for the lab's Joint Understanding and Dialogue Interface, or JUDI, system, a prototype that enables bi-directional conversational interactions between Soldiers and autonomous systems.

"We employed a statistical classification technique for enabling conversational AI using state-of-the-art natural language understanding and dialogue management technologies," said Army researcher Dr. Felix Gervits. "The statistical language classifier enables autonomous systems to interpret the intent of a Soldier by recognizing the purpose of the communication and performing actions to realize the underlying intent."

For example, he said, if a robot receives a command to "turn 45 degrees and send a picture," it could interpret the instruction and carry out the task.

To achieve this, the researchers trained their classifier on a labeled data set of human-robot dialogue generated during a collaborative search-and-rescue task. The classifier learned a mapping of verbal commands to responses and actions, allowing it to apply this knowledge to new commands and respond appropriately.

Researchers developed algorithms to incorporate the classifier into a dialogue management system that included techniques for determining when to ask for help given incomplete information, Gervits said.

In terms of Army impact, the researchers said this technology can be applied to combat vehicles and autonomous systems to enable advanced real-time conversational capability for Soldier-agent teaming.

"By creating a natural speech interface to these complex autonomous systems, researchers can support hands-free operation to improve situational awareness and give our Soldiers the decisive edge," Gervits said.

According to Gervits, this research is significant and unique in that it enables back-and-forth dialogue between Soldiers and autonomous systems.

"Interacting with such conversational agents requires limited to no training for Soldiers since speech is a natural and intuitive interface for humans and there is no requirement to change what they could say," Gervits said. "A key benefit is that the system also excels at handling noisy speech, which includes pauses, fillers and disfluencies - all features that one would expect in a normal conversation with humans."

Since the classifier is trained ahead of time, the system can operate in real-time with no processing delay in the conversation, he said.

"This supports increased naturalness and flexibility in Soldier-agent dialogue, and can improve the effectiveness of these kinds of mixed-agent teams," Gervits said.

Compared to commercial deep-learning approaches, which require large, expensive data sets to train the system, this approach requires orders of magnitude fewer training examples, he said. It also has the advantage of being able to reduce deployment time and cold start capability for new environments.

Another difference is that commercial dialogue systems are typically trained in non-military domains, while his focus is on a search-and-rescue task specifically designed to mimic the style of Soldier-robot interaction that could occur in a future tactical environment.

Finally, the classification approach allows for better transparency and explainability of the system performance making it possible to analyze why the system produced a certain behavior. This is critical for military applications wherein ethical concerns demand greater transparency of autonomous systems, Gervits said.

The research was performed primarily a few years ago when Gervits was an intern at ICT. The subsequent manuscript was accepted to the International Workshop on Spoken Dialogue Systems in 2019 and presented at the conference. It was published in the conference proceedings in 2021.

Dr. David Traum, from the Natural Language Dialogue group at ICT, led the dialogue research, which included the statistical classifier. Dr. Matthew Marge from ARL led the Botlanguage project, a collaborative effort between ARL at the Adelphi Laboratory Center, ARL West and ICT.

The next steps for this research are threefold:

-To improve the system performance by supplementing the classifier with additional linguistic representations.

-Extending the approach to enable learning of new training examples through real-time dialogue. An example of this is a robot encountering something new in the environment and asking a Soldier what it is.

-Integrating additional interaction modalities such as gaze and gesture, in addition to speech, for more robust interaction in physical environments.

"With the tactical environment of the future likely to involve mixed Soldier-agent teams, I am optimistic that this technology will have a transformative effect on the future of the Army," Gervits said. "It is highly rewarding for me as a researcher to see such a tangible outcome for my efforts."

Credit: 
U.S. Army Research Laboratory

Ice cap study promises new prospects for accurate local climate projections

image: The antennas of the radar are situated at the rear end of the sleigh. They send impulses into the ice, which are reflected by different properties in the ice and return the impulse signals to the antennae. Data can be plotted as a radio-echogram, from which you can read out thickness of the ice, the rock under the ice and different layers of ice in the ice sheet. Radar measurements from flyovers work in much the same way as the sleigh radar. Each radar can be adapted to focus on different properties, such as the shift from ice to bedrock, ice layer, melt layer etc.

Image: 
Christian Panton

New, detailed study of the Renland Ice Cap offers the possibility of modelling other smaller ice caps and glaciers with significantly greater accuracy than hitherto. The study combined airborne radar data to determine the thickness of the ice cap with on-site measurements of the thickness of the ice cap and satellite data. Researchers from the Niels Bohr Institute - University of Copenhagen gathered the data from the ice cap in 2015, and this work has now come to fruition in the form of more exact predictions of local climate conditions.

The accuracy of the study allows for the construction of models for other smaller ice caps and glaciers, affording significantly improved local projections of the condition of glaciers locally, around the globe. The results have recently been published in Journal of Glaciology.

A combination of approaches results in greater accuracy

The initial, principal aim of the study, was to assess the thickness and volume of the Renland Ice Cap, and in the process, validate computer-modelled data against real data. Airborne radar, which measured the thickness of the ice, was compared with measurement results that were known in advance. In addition, researchers availed of satellite-based measurements of the ice velocity on the surface of the ice cap, again juxtaposed with various parameters entered into the computer model, e.g. "basal slide" - in other words, the velocity of movement at the bottom of the ice cap. The combined results provided researchers with an extremely detailed basis material for constructing a computer model that can be applied in other situations.

From Renland to the rest of the world

Iben Koldtoft, PhD student at the Physics of Ice, Climate and Earth section at the Niels Bohr Institute, and first author of the scientific article, explains: "We now have the most optimal parameters for this ice flow model, the Parallet Ice Sheet Model, for the Renland Ice Cap. But despite these being specific local measurements for Renland, we can use these modelling parameters to simulate the ice cap over an entire ice age cycle, for example, and compare the results with the Renland ice core we drilled in 2015. We can examine to what extent the ice cap has changed over time, or how quickly the ice will melt if the temperature rises by a few degrees in the future. Or put more concisely: We now know how the model can be "tuned" to match different climate scenarios. This ensures greater accuracy and a method that is also transferable to other smaller ice caps and glaciers".

"In fact, we can see that our scientific article initially received many views from Japan and Argentina. At first this was a bit surprising - why there, exactly? But it makes absolute sense. These are countries with smaller local ice sheets and glaciers, who are now excited to be able to project the future evolution of these", comments Iben Koldtoft.

Smaller scale provides greater visibility

The larger ice sheets in Greenland and Antarctica are of course the most important, when assessing temperature changes and the effects of melting on global climate. However, the smaller ice caps react faster and can be considered as "mini- environments", where it is possible to follow developments across a shorter timescale. In addition, it is easier to model the smaller scenarios more precisely, points out Iben Koldtoft.

"If we look at Svalbard, an archipelago that lies very far north, they experience climate change as having a far greater local effect than one sees in Greenland, for example. Over time, of course, all these changes will eventually affect the entire climate system, but we can observe it more clearly on a smaller scale".

The Renland ice core reveals more secrets

In 2015 a core was drilled on the Renland Ice Cap. In the intervening years, scientists have extracted data from the recovered ice core in the form of water isotopes, gases and chemical measurements. These are all proxies for temperature, precipitation accumulation, altitude changes and other climate conditions of east Greenland, where the Renland Ice Cap is located. This data can now be compared with the detailed study and with data from other locations in Greenland. As a result, the study contributes to the increasingly detailed picture of how the climate is changing. Iben Koldtoft emphasises the importance of combining the observational data with computer modelling, and that climate research in general is at a stage where the use of advanced computer simulations and the ability to "tune" them correctly, is now a vital competence. Although glaciers across the globe can be monitored with incredible accuracy by satellites today, there is a need to develop strong computer-based models, combining physics and mathematics, in order to calculate how glaciers will change in the climate of the future, and their effect on future increases in sea levels.

Credit: 
University of Copenhagen - Faculty of Science

Pandemic eviction bans found to protect entire communities from COVID-19 spread

A new study led by researchers at Johns Hopkins and the University of Pennsylvania uses computer modeling to suggest that eviction bans authorized during the COVID-19 pandemic reduced the infection rate and not only protected those who would have lost their housing but also entire communities from the spread of infections.

With widespread job loss in the U.S. during the pandemic, many state and local governments temporarily halted evictions last spring, and just as these protections were about to expire in September, the Centers for Disease Control and Prevention (CDC) declared a national eviction ban.

However, the order is only extended a few months at a time and is under constant challenge in the court system, including debates about whether such measures control infection transmission.

The research team aimed to study if eviction bans help control the spread of SARS-CoV-2, the virus that causes COVID-19, explains Alison Hill, Ph.D., an assistant professor of biomedical engineering at Johns Hopkins.

In a bid to document the potential impact, Hill and Michael Levy, Ph.D., of the University of Pennsylvania, teamed up with experts in housing policy from the University of Illinois Urbana-Champaign. Hill and Levy specialize in using mathematical models to study how infections spread.

A report on the research was published April 15 in Nature Communications.

In the new report, the investigators say they used simulations to predict the number of additional SARS-CoV-2 infections in major U.S. cities if evictions had been allowed to occur during the fall of last year.

They estimated, for example, that in a city of approximately 1 million residents with evictions occurring at a heightened rate of 1% of households per month, an additional 4% of the population could become infected with SARS-CoV-2, which corresponds to about 40,000 more cases. Even with a much lower eviction rate of 0.25% per month, which is similar to the pre-pandemic level in cities such as Atlanta, Detroit and Tucson, Arizona, estimates were for about 5,000 additional cases.

To make these predictions, the researchers first calibrated their math model to re-create the most common epidemic patterns seen in major U.S. cities in 2020. The model took into account changes in infection rates over time due to public health measures, and it was tailored to match reported COVID-19 cases and deaths. The researchers used the model to track the spread of infection in and out of households. Then, they ran another version of the model in which eviction bans were lifted, to estimate how the bans have affected transmission of the virus.

Hill and her colleagues found that without eviction bans, people who are evicted or who live in a household that hosts evictees have 1.5 to 2.5 times more risk of being infected with SARS-CoV-2 than if the eviction bans were in place.

"People who experience eviction often move in with other households, increasing the density of people living together," says Hill. "Households are known to be an important setting for SARS-CoV-2 infection, so this can increase transmission rates."

The researchers' computer simulations also found that without eviction bans, the risk of SARS-CoV-2 infection would rise for all residents of a city, not just those who are evicted.

Even when the researchers evaluated a different version of the model, in which a city is divided into neighborhoods of different socioeconomic status and evictions are restricted to certain districts, evictions still could cause increases in infections with the virus.

"Some opponents of eviction bans say that evictions only affect a narrow part of the population, but our simulations indicate that evictions not only put disadvantaged households at risk of infection, but entire communities as well," says Hill. "When it comes to a transmissible disease like COVID-19, no neighborhood is entirely isolated."

When the researchers used this data to examine how evictions would specifically impact Philadelphia residents, they found that people in all neighborhoods of the city would experience increased COVID-19 levels due to evictions.

Teaming up with researchers from Northeastern University who used de-identified information about how city residents travel throughout neighborhoods, the researchers estimated that, without eviction bans, there could have been approximately 5,000 more COVID-19 cases in Philadelphia if evictions occurred at pre-pandemic levels, and up to 50,000 additional cases if evictions were five times more frequent.

An early version of this research was cited in court cases challenging eviction bans in Philadelphia, and in the CDC's national eviction order (click here and here).

To alleviate infection risk and reduce economic burdens, the researchers say, governments should consider not only extended eviction bans but also financial assistance for both tenants and landlords, as well as resources for households to reduce transmission of the virus within the home.

Credit: 
Johns Hopkins Medicine

MIPT and Harvard researchers grow stem cells to cure glaucoma

image: Stem cells on the retinal surface by two weeks post-transplantation.

Image: 
<em>Molecular Therapy - Methods and Clinical Development</em>

A joint research carried out by MIPT scientists and Harvard researchers have presented retinal cells that can integrate into the retina. This is the first successful attempt to transplant ganglion cells (retinal neurons that are destroyed by glaucoma) derived from stem cells in a lab setting. Scientists tested the technology in mice and established that the cells successfully integrated and survived for a year. In the future, the researchers plan to create specialized cell banks, which will permit individual, tailored therapy for each patient.

The world's first successful attempt to grow and transplant retinal ganglion cells developed from stem cells was made by scientists from MIPT's genomic engineering laboratory in collaboration with researchers from Harvard Medical School. Retinal ganglion cells, commonly damaged in glaucoma, are responsible for the transmission of visual information. The scientists managed to not only grow neurons (retinal ganglion cells are considered specialized neurons), but also transplant them into the eyes of mice, achieving the correct ingrowth of artificial retinal tissue. Without treatment, glaucoma can lead to irreversible damage to the optic nerve and, as a result, the loss of part of the visual field. Progression of this disease can lead to complete blindness.

Retinal cells were grown using special organoids, with the tissue formed in a petri dish, according to Evgenii Kegeles, a junior researcher from MIPT's genomic engineering laboratory. These cells were subsequently transplanted into several groups of mice. The MIPT scientists were responsible for re-isolating and analyzing the transplanted cells.

"Our studies in mice have shed light on some of the basic questions surrounding retina cell replacement, i.e. can donor RGCs survive within diseased host retinas? Or are transplants only possible within young hosts?", noted Julia Oswald, the first author of the paper and a research fellow from the Schepens Eye Research Institute, Harvard Medical School affiliate. "Using mice in which we used microbeads to artificially elevate intraocular pressure and a model of chemically induced neurotoxicity, we could show that transplanted donor cells survive in disease-like microenvironments. In addition, we could demonstrate that cells survived independent of the donor's age and the location to which the cells were delivered within the retina."

According to the authors, these cells have successfully existed inside mouse retinas for 12 months, which is a significant period for the species. Scientists confirmed that they were able to receive signals from other neurons in the retina; however, the ability of the cells to transmit signals to the brain has yet to be assessed with absolute certainty.

"We are confident that the grown cells are embedded where necessary and have extended axons into the brain, but their full functionality is currently impossible to assess, due to the relatively low number of cells surviving the procedure. However, our study shows a first proof-of-concept for the re-isolation of donor cells post-transplant, to observe on a molecular level that cells did, indeed, form synapses, grow axons, and integrate into the retina. This technique will enable countless future studies into the cross talk between transplanted cells and the host microenvironment. This will allow us to find and employ molecular mechanisms which will help transplanted cells to function properly and, as a result, improve visual function when transplanted in the right quantity," explained Evgenii Kegeles.

Mouse retinal cells can be grown from stem cells in around 21 days. However, according to the scientists at MIPT, it will take longer for human cells -- from 50 to 100 days.

Even so, a person with glaucoma preparing for a transplant will most likely not require retinal tissue grown from their own autologous stem cells. Since the eye is an immune-privileged organ where rejection is rare, it is possible to create a cell bank for these patients; grown retinal cells from a universal donor or induced pluripotent stem cells would be stored there. This would mean that it would be possible to grow cells in advance and freeze them. When a patient with glaucoma requires help, the most suitable cells would be selected for transplantation.

"The Nobel Prize for induced pluripotent stem cells was awarded almost 10 years ago, in 2012," said Pavel Volchkov, head of the laboratory of genomic engineering. "The so-called hype, when literally all of the research teams involved in the process considered it their duty to explore the topic, has long faded away. Now is the time not just for words, but for real technologies based on iPS (induced pluripotent stem cells). And it is precisely this technology that this research on the transplantation of retinal ganglion cells is based on. This is an opportunity to demonstrate that stem cells can really be applied in practice, that, with their help, something can be corrected. Although this work has not yet been brought to clinical practice, it is only a few steps away from a real transplant for the purpose of treating glaucoma."

"It was indeed an enabling study in which we demonstrated that it is possible to make diverse retinal ganglion cell neurons in quantity sufficient for transplantation. Moreover, donor neurons' ability to integrate into the diseased retina and survive for over a year brings hope and excitement for cell therapy development," - added Petr Baranov, - the Principal Investigator from the Schepens Eye Research Institute, Harvard Medical School.

According to scientists, this technology is around 10 years from being ready for use in clinical practice.

Credit: 
Moscow Institute of Physics and Technology

Patients who are obese or overweight are at risk for a more severe course of COVID-19

COVID-19 patients who are overweight or obese are more likely to develop a more severe infection than patients of healthy weight, and they require oxygen and invasive mechanical ventilation more often. There is no increased risk of death . These conclusions, for which more than 7,000 patients were studied, appear from international research in eleven countries, including the Netherlands (Radboud university medical center).

The study, led by Australian researchers, examined over 7000 patients from eleven different countries who were admitted to 18 hospitals. Of this group, over a third (34.8%) were overweight and almost a third (30.8%) were obese. COVID-19 patients with obesity required oxygen more frequently and were 73% more likely to require invasive mechanical ventilation. Remarkably, no greater mortality was observed in these groups of patients than in patients of healthy weight. The international results have now been published in scientific journal Diabetes Care.

Immunologist Siroon Bekkering of Radboud university medical center, principal investigator of the Dutch part, explains that never before so many different data on obesity have been combined in one large study. "Several national and international observations already showed the important role of overweight and obesity in a more severe COVID-19 course. This study adds to those observations by combining data from several countries with the possibility to look at the risk factors separately. Regardless of other risk factors (such as heart disease or diabetes), we now see that too high a BMI can actually lead to a more severe course in corona infection."

One explanation for this is that overweight and obesity are characterized by chronic inflammation, which can perhaps lead to increased susceptibility to viruses. This is also the case with the flu virus. Also, obese people are more likely to suffer from shortness of breath, which may lead to an increased need for ventilation.

Different risk factors for severe COVID-19 infection

More risk factors emerge from the study. For example, this study, similar to other international studies, confirms that men are more likely to have a more severe course of COVID-19 infection. In addition, this study also shows that people older than 65 years of age needed supplemental oxygen more often and are at greater risk of death.

Cardiovascular disease and pre-existing respiratory disease may be associated with an increased risk of in-hospital death, but not with an increased risk of using oxygen and mechanical ventilation. For patients with diabetes, there was an increased risk of needing invasive respiratory support, but no additional increase in risk in those with both obesity and diabetes. There was no increased risk of death.

Credit: 
Radboud University Medical Center

Ocean currents modulate oxygen content at the equator

Due to global warming, not only the temperatures in the atmosphere and in the ocean are rising, but also winds and ocean currents as well as the oxygen distribution in the ocean are changing. For example, the oxygen content in the ocean has decreased globally by about 2% in the last 60 years, particularly strong in the tropical oceans. However, these regions are characterized by a complex system of ocean currents. At the equator, one of the strongest currents, the Equatorial Undercurrent (EUC), transports water masses eastwards across the Atlantic. The water transport by the EUC is more than 60 times larger than that of the Amazon river. For many years, scientists at GEOMAR have been investigating in cooperation with the international PIRATA programme fluctuations of this current with fixed observation platforms, so-called moorings. Based on the data obtained from these moorings, they were able to prove that the EUC has strengthened by more than 20% between 2008 and 2018. The intensification of this major ocean current is associated with increasing oxygen concentrations in the equatorial Atlantic and an increase in the oxygen-rich layer near the surface. Such a thickening of the surface oxygenated layer represents a habitat expansion for tropical pelagic fish. The results of the study have now been published in the international journal Nature Geoscience.

"At first, this statement sounds encouraging, but it does not describe the entire complexity of the system", says project leader and first author Prof. Dr. Peter Brandt from GEOMAR. "We found that the strengthening of the Equatorial Undercurrent is mainly caused by a strengthening of the trade winds in the western tropical North Atlantic", Peter Brandt explains further. The analysis of a 60-year data set has shown that the recent oxygen increase in the upper equatorial Atlantic is associated with a multidecadal variability characterised by low oxygen concentrations in the 1990s and early 2000s and high concentrations in the 1960s and 1970s. "In this respect, our results do not contradict the global trend, but indicate that the observed current intensification likely will switch back into a phase of weaker currents associated with enhanced oxygen reduction. It shows the need for long-term observations in order to be able to separate natural fluctuations of the climate system from trends such as oxygen depletion caused by climate warming", says Brandt.

The changes in oxygen supply in the tropics due to circulation fluctuations have an impact on marine ecosystems and ultimately on fisheries in these regions. "Habitat compression or expansion for tropical pelagic fish can lead to altered predator-prey relationships, but also make it particularly difficult to assess overfishing of economically relevant fish species, such as tuna", says Dr Rainer Kiko, co-author from the Laboratoire d'Océanographie de Villefranche at Sorbonne University, Paris.

The investigations are based partly on a ship expedition carried out along the equator at the end of 2019 with the German research vessel METEOR. This expedition included a physical, chemical, biogeochemical and biological measurement programme that supports the development of climate-based predictions for marine ecosystems as part of the EU-funded TRIATLAS project. While another expedition with RV METEOR along the equator had to be cancelled due to the COVID-19 pandemic, several long-term moorings in the tropical Atlantic - including the one at the equator - will now be recovered and redeployed during an additional expedition with RV SONNE in June-August 2021, of course under strict quarantine conditions.

Credit: 
Helmholtz Centre for Ocean Research Kiel (GEOMAR)

Researchers use laser paintbrush to create miniature masterpieces

image: The researchers used their new laser painting method to make a miniature version of Van Gogh's painting "The Starry Night."

Image: 
Yaroslava Andreeva

WASHINGTON -- Researchers are blurring the lines between science and art by showing how a laser can be used to create artistic masterpieces in a way that mirrors classical paints and brushes. The new technique not only creates paint-like strokes of color on metal but also offers a way to change or erase colors.

"We developed a way to use a laser to create localized color on a metallic canvas using a technique that heats the metal to the point where it evaporates," said research team leader Vadim Veiko from ITMO University in Russia. "With this approach, an artist can create miniature art that conveys complex meaning not only through shape and color but also through various laser-induced microstructures on the surface."

In Optica, The Optical Society's (OSA) journal for high impact research, Veiko and colleagues show that their new laser tools can be used to create unique colorful paintings, including a miniature version of Van Gogh's painting "The Starry Night."

"We hope that laser painting will attract the attention of modern artists and lead to the creation of a completely new type of art," said research team member Yaroslava Andreeva. "The approach can also be used for modern design and to create color markings on various products."

Painting with light

The new study builds on previous work in which the researchers investigated how to use lasers to create color on titanium and stainless steel. "We wanted to do more than offer a wide palette of stable colors," said Galina Odintsova, a member of the research team. "Thus, we worked to create a convenient tool for applying them more like an artist's brush."

For the new technique, the researchers heat the metal to a point where it starts to evaporate -- much higher than the melting temperatures used in previously developed approaches. When the metal cools, an extremely thin film of metal oxide forms. Light reflected from the metallic surface and the top of the oxide film interfere in a way that produces different colors depending on the thickness of the film.

"Increasing the laser heating range enough to create the evaporation process makes our color strokes reversible, rewritable, erasable and much more efficient," said Odintsova. "Our marking speed is more than 10 times faster than reported before."

Erasable color

The researchers used a nanosecond ytterbium fiber system equipped with a galvanometric scanner to create strokes that combine surface relief with optical effects, creating nine basic colors. A second pass of the laser at a faster scan rate can erase or change the color of an area. They showed that the surface color of erased areas was indistinguishable from a non-treated surface and that colors could be erased and rewritten several times without affecting the resulting color.

They demonstrated the new laser paintbrush by using it to create a 3X2-inch version of "Starry Night" in just 4 minutes. They also made original artwork to demonstrate color mixture and erasing. The researchers point out that pictures made using this laser painting approach are extremely resistant to harsh environments and chemicals and don't require any type of special storage.

The researchers would like to incorporate their new laser painting capabilities into a handheld tool that could be used much like a pen or paintbrush to create colorful pictures or drawings on metals or metallic foils. The approach could also be used to add nanostructured and hybrid materials or periodic surface gratings to achieve a variety of optical effects.

Credit: 
Optica