Culture

Species more likely to die out with rapid climate changes

The climate seems to be getting warmer. This could be bad news for species that depend on stable and abundant access to food at certain times of the year.

"If the changes happen too fast, species can become extinct," says Emily Simmonds, an associate professor at the Norwegian University of Science and Technology's (NTNU) Department of Biology.

She is the first author of an article in Ecology Letters that addresses how great tits can be affected if the supply of larvae changes in the spring.

Several bird species depend on the abundance of larvae while their young are small. If the larvae supply peaks earlier in the spring than normal, there may simply be too little food for the hatchlings.

The warming climate can bring about changes like this. An earlier spring causes trees to leaf out earlier, which in turn causes the larvae that feed on the plants to hatch out earlier.

"When the climate changes, the interactions between different species changes too," Simmonds says.

She and a team of researchers at the University of Oxford used population models to calculate the consequences of different climate scenarios. They wanted to see at what point the changes would happen too fast for the great tit to modify its behaviour quickly enough to keep up with the larvae.

Great tits have genetic variations and varying abilities to adapt to different conditions. This means that they can evolve in tandem with their prey up to a point.

An earlier larvae hatch can be advantageous for the great tits that also hatch their young earlier in the spring. This advantage can be transferred to the next generation of birds, which can in turn become early birds. And so on.

For this advantage to last, the great tits have to evolve fast enough and be flexible enough to keep up with the genetic variation in their prey.

"Given conditions with big greenhouse gas emissions, the great tits won't always be able to keep up with the changes in the larvae supply," says Simmonds.

In the worst case scenario, whole populations of great tits will simply disappear by the year 2100 because they aren't able to procure enough food for their young.

"This could happen even if the great tits are also modifying their behaviour faster in a rapidly changing environment. The larvae might be changing even faster than the great tits," Simmonds says.

The researchers found that populations of great tits would be guaranteed to become extinct by the year 2100 if the larvae appeared about 24 days earlier than the current norm in 2020. This also applies to populations that appear to be completely stable now.

"It could be that the apparent stability today is hiding a future collapse," says Simmonds.

The reason is that we might reach a kind of threshold where the great tits aren't keeping up. The rubber band gets stretched too far, you could say.

"The good news is that the populations will be able to survive scenarios with lower or medium warming trends," Simmonds says.

Credit: 
Norwegian University of Science and Technology

New technology allows cameras to capture colors invisible to the human eye

New research from Tel Aviv University will allow cameras to recognize colors that the human eye and even ordinary cameras are unable to perceive.

The technology makes it possible to image gases and substances such as hydrogen, carbon and sodium, each of which has a unique color in the infrared spectrum, as well as biological compounds that are found in nature but are "invisible" to the naked eye or ordinary cameras. It has groundbreaking applications in a variety of fields from computer gaming and photography as well as the disciplines of security, medicine and astronomy.

The research was conducted by Dr. Michael Mrejen, Yoni Erlich, Dr. Assaf Levanon and Prof. Haim Suchowski of TAU's Department of Physics of Condensed Material. The results of the study were published in the October 2020 issue of Laser & Photonics Reviews.

"The human eye picks up photons at wavelengths between 400 nanometers and 700 nanometers -- between the wavelengths of blue and red," explains Dr. Mrejen. "But that's only a tiny part of the electromagnetic spectrum, which also includes radio waves, microwaves, X-rays and more. Below 400 nanometers there is ultraviolet or UV radiation, and above 700 nanometers there is infrared radiation, which itself is divided into near-, mid- and far-infrared.

"In each of these parts of the electromagnetic spectrum, there is a great deal of information on materials encoded as 'colors' that has until now been hidden from view."

The researchers explain that colors in these parts of the spectrum are of great importance, since many materials have a unique signature expressed as a color, especially in the mid-infrared range. For example, cancer cells could be easily detected as they have a higher concentration of molecules of a certain type.

Existing infrared detection technologies are expensive and mostly unable to render those "colors." In medical imaging, experiments have been performed in which infrared images are converted into visible light to identify the cancer cells by the molecules. To date, this conversion required very sophisticated and expensive cameras, which were not necessarily accessible for general use.

But in their study, TAU researchers were able to develop cheap and efficient technology that could mount on a standard camera and allows, for the first time, the conversion of photons of light from the entire mid-infrared region to the visible region, at frequencies that the human eye and the standard camera can pick up.

"We humans can see between red and blue. If we could see in the infrared realm, we would see that elements like hydrogen, carbon and sodium have a unique color," explains Prof. Suchowski. "So an environmental monitoring satellite could 'see' a pollutant being emitted from a plant, or a spy satellite would see where explosives or uranium are being hidden. In addition, since every object emits heat in the infrared, all this information could be seen even at night."

After registering a patent for their invention, the researchers are developing the technology through a grant from the Innovation Authority's KAMIN project, and they have already met with a number of both Israel-based and international companies.

Credit: 
American Friends of Tel Aviv University

Story tips: Ice breaker data, bacterial breakdown, catching heat and finding order

image: The icebreaker R/V Polarstern carried more than 60 ARM instruments for the MOSAiC expedition.

Image: 
U.S. Dept. of Energy ARM User Facility

Climate - Ice breaker data

With the conclusion of an unprecedented yearlong expedition to the North Pole called MOSAiC, data from instruments installed on an Arctic ice floe are available to the scientific community to improve models that predict the environmental future of the planet.

Researchers at Oak Ridge National Laboratory were part of an international team that collected a treasure trove of data measuring precipitation, air particles, cloud patterns and the exchange of energy between the atmosphere and the sea ice. The data were captured by a suite of 63 instruments from the Department of Energy's Atmospheric Radiation Measurement User Facility. ORNL has processed these measurements and made massive amounts of observational data easily accessible and usable for climate modelers.

"We've never had this type of data for the northernmost reaches of the Arctic before," said Giri Prakash, director of the ARM Data Center at ORNL. "These data will be an invaluable resource for scientists to improve predictions of global environmental changes."

Media Contact: Kim Askey, 865.576.2841, askeyka@ornl.gov

Image: https://www.ornl.gov/sites/default/files/2020-11/49464987002_20dab0acb6_o.jpg

Caption: Researchers set up ARM instruments on the ice floe near the ship that served as home during the MOSAiC expedition. Credit: U.S. Dept. of Energy ARM User Facility

Image: https://www.ornl.gov/sites/default/files/2020-11/49464270498_a1ff680b23_o.jpg

Caption: Radiometer instruments collect data on the Arctic ice. Credit: U.S. Dept. of Energy ARM User Facility

Image: https://www.ornl.gov/sites/default/files/2020-11/50192950163_44318b4fe9_o.jpg

Caption: The icebreaker R/V Polarstern carried more than 60 ARM instruments for the MOSAiC expedition. Credit: U.S. Dept. of Energy ARM User Facility

Biology - Bacterial shield breakdown

An international research team discovered a mechanism that disease-causing bacteria use to anchor their protective outer membranes. Their findings could inform strategies to disrupt a microbe's cell structure, ultimately helping to combat pathogens that affect humans and plants.

Scientists from Oak Ridge National Laboratory used high-performance computing to create protein models that helped reveal how the outer membrane is tethered to the cell membrane in certain bacteria. These Gram-negative bacteria sandwich their cell walls between an outer and inner membrane, and the layers act as a shield that allows them to persist under harsh conditions.

ORNL's models informed further simulations and experiments by collaborators who observed these unusual linkages.

"Modeling and simulating membrane proteins help us understand complex cell structures," ORNL's Jerry Parks said. "These approaches are particularly important when relatively little is known about an organism, because it is challenging to study in the lab."

Media Contact: Kim Askey, 865.576.2841, askeyka@ornl.gov

Image: https://www.ornl.gov/sites/default/files/2020-11/Biology-gram-negative.jpg

Caption: ORNL assisted in investigating proteins called porins, one shown in red, which are found in the protective outer membrane of certain disease-causing bacteria and tether the membrane to the cell wall. Credit: Hyea (Sunny) Hwang/Georgia Tech and ORNL, U.S. Dept. of Energy

Batteries - Catching heat

Oak Ridge National Laboratory researchers proved that the heat transport ability of lithium-ion battery cathodes is much lower than previously determined, a finding that could help explain barriers to increasing energy storage capacity and boosting performance.

Research on lithium-ion batteries, which are used primarily in smart phones and laptops, has shown that lower heat transport is hampered, which leads to less energy density and poorer performance.

In the study, researchers used quantum mechanical calculations to predict the inherent heat transport capabilities of battery cathodes and the impacts of charging. Further evaluation looked at how strong vibrational forces among ions between the material's layers can influence heat.

"We found heat transport to be more inefficient than thought due to the non-harmonic vibrational forces among ions, worsening during charging," ORNL's Tianli Feng said. "Our results resolve long-standing issues regarding heat transport and provide guidance for how future high-density batteries can be designed."

Media Contact: Jennifer Burke, 865.414.6835, burkejj@ornl.gov

Image: https://www.ornl.gov/sites/default/files/2020-11/Batteries-Catching_heat.jpg

Caption: ORNL researchers determined lower heat exchange in lithium-ion batteries is caused by the strong non-harmonic forces among ions and weak interaction between layers, providing guidance for high-density battery design. Credit: Tianli Feng/ORNL, U.S. Dept. of Energy

Neutrons - Finding order in disorder

Researchers have revealed a new understanding of disordered ceramics - materials with nonuniform atomic arrangements used in a variety of energy-related applications including electronics, nuclear fuels and fuel cells.

Pauling's Rules is the standard model used to describe atomic arrangements in ordered materials. Neutron scattering experiments at Oak Ridge National Laboratory confirmed this approach can also be used to describe highly disordered materials.

Researchers demonstrated the model's ability to determine the distance between neighboring atoms and predict how the atoms move once disorder is introduced. The new knowledge overturns conventional wisdom that ions in disordered materials are mixed randomly, but instead arrange themselves in building blocks with a high degree of order.

"Disorder is the basis for many interesting properties and applications," said Maik Lang of the University of Tennessee and corresponding author of the Science Advances study. "A better understanding of how these materials behave could lead to realizing improved materials with more functionality."

Media Contact: Jeremy Rumsey, 865. 576.2038, rumseyjp@ornl.gov

Image: https://www.ornl.gov/sites/default/files/2020-11/Neutrons-disordered_ordered.png

Caption: UTK researchers used neutron probes at ORNL to confirm established fundamental chemical rules can also help understand and predict atomic movements and distortions in materials when disorder is introduced, as arrows show. Credit: Eric O'Quinn/UTK

Credit: 
DOE/Oak Ridge National Laboratory

Forthcoming COVID-19 preprints to be peer reviewed in Rapid Reviews

CAMBRIDGE, MA - November 4, 2020--Rapid Reviews: COVID-19 (RR:C19), an open-access overlay journal published by the MIT Press that accelerates peer review of COVID-19-related research preprints, is currently soliciting reviews of the following COVID-19 preprints. These preprints have been selected for review because they have the potential to enhance our understanding of SARS-CoV-2 or have been flagged as potentially misleading. Preprints with two finished reviews should be published within 10-14 days. Additional information or early access to these peer-reviews is available upon request.

Highlights from Rapid Reviews editorial team:

"Testing mobile air purifiers in a school classroom: Reducing the airborne transmission risk for SARS-CoV-2"

This preprint estimates that the use of air purifiers in school classrooms can reduce an inhaled dose of COVID-19 by a factor of six. Will be useful to parents and school districts planning how to safely reopen schools.
 

"Repurposed antiviral drugs for COVID-19; interim WHO SOLIDARITY trial results"

Remdesivir, Hydroxychloroquine, Lopinavir, and Interferon regimens have been touted as potential therapeutics for COVID-19 patients, but this preprint finds they have little to no effects on overall mortality, initiation of ventilation, or duration of hospital stay. This research has the potential to directly impact point of care decisions.
 

"Global projections of potential lives saved from COVID-19 through universal mask use" by Emmanuela Gakidou, et al.

This preprint shows that universal mask mandates could reduce deaths by 815,600 globally before the year's end. It adds to the growing science showing masks are an effective tool in fighting the spread of COVID-19.
 

"The relationship between neighborhood poverty and COVID-19 mortality within racial/ethnic groups (Cook County, Illinois)" by Justin M. Feldman, et al.

This large cross-sectional study explores how socioeconomics and race affect COVID-19 mortality. Its findings could lead to a more detailed understanding of the specific processes that result in health inequities.
 

"Less severe course of COVID-19 is associated with elevated levels of antibodies against seasonal human coronaviruses OC43 and HKU1 (HCoV OC43, HCoV HKU1)"

This research explores whether previous infections with seasonal coronaviruses protects against a severe COVID-19 disease course. This immunological cross-reactivity has important implications on vaccine strategies.
 

Physical Sciences/Engineering

"TRANSCOM/AMC commercial aircraft cabin aerosol dispersion tests" by David Silcott, et al.
"The effect of temperature and humidity on the stability of SARS-CoV-2 and other enveloped viruses" by Dylan H. Morris, et al.
"Multivalency transforms SARS-CoV-2 antibodies into broad and ultrapotent neutralizers" by Edurne Rujas, et al.
"Development, evaluation, and validation of machine learning models for COVID-19 detection based on routine blood tests" by Cabitza Federico, et al.
"Sniffing methanol in hand sanitizers" by Andreas T. Guntner, et al.

"A high-throughput microfluidic nano-immunoassay for detecting anti-SARS-CoV-2 antibodies in serum or ultra-low volume dried blood samples" by Zoe Swank, et al.
 

Biological/Chemical Sciences

"Early induction of SARS?CoV?2 specific T cells associates with rapid viral clearance and mild 2 disease in COVID?19 patients" by Anthony T. Tan, et al.
"Co-infection of influenza A virus enhances SARS-CoV-2 infectivity" by Lei Bai, et al.
"Preferential recognition and antagonism of SARS-CoV-2 spike glycoprotein binding to 3-O-sulfated heparan sulfate" by Vaibhav Tiwari, et al.
"Antigen-based testing but not real-time PCR correlates with SARS-CoV-2 virus culture" by Andrew Pekosz, et al.
"The effect of influenza vaccination on trained immunity: impact on COVID-19" by Priya A. Debisarun, et al.
"SARS-CoV-2 proteins and anti-COVID-19 drugs induce lytic reactivation of an oncogenic virus" by Jungang Chen, et al.

"Functional Landscape of SARS-CoV-2 Cellular Restriction" by Laura Martin-Sancho, et al.
 

Public Health

"Excess risk of COVID-19 to university populations resulting from in-person sporting events"
"COVID-19 and (un)desired fertility: The effect of stay-at-home orders on abortions in Mexico City" by Fernanda Marquez-Padilla, et al.
"Misinformation on COVID-19 origin and social distancing: A cross-sectional study"
"Economic precarity, social isolation, and suicidal ideation during the COVID-19 pandemic"
"Modelling testing and response strategies for COVID-19 outbreaks in remote Australian Aboriginal communities"
"Evaluating the sensitivity of SARS-CoV-2 infection rates on college campuses to wastewater surveillance"
"A cohort of SARS-CoV-2 infected asymptomatic and pre-symptomatic contacts from COVID-19 contact tracing in Hubei Province, China: short-term outcomes" by Peng Zhang, et al.
"Modelling the potential impact of mask use in schools and society on COVID-19 control in the UK" by J. Panovska-Griffiths, et al.
"Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreak"

"SARS-CoV-2 sequencing reveals rapid transmission from college student clusters resulting in morbidity and deaths in vulnerable populations" by Craig S. Richmond, et al.
 

Medical Sciences

"Enoxaparin is associated with lower rates of thrombosis, kidney injury, and mortality than Unfractionated Heparin in hospitalized COVID patients" by Colin Pawlowski, et al.
"Neuroinvasive potential of SARS-CoV-2 revealed in a human brain organoid model" by Eric Song, et al.
"Targeting androgen regulation of TMPRSS2 and ACE2 as a therapeutic strategy to combat COVID-19" Qu Deng, et al.
"Treatment with human umbilical cord-dervied mesenchymal stem cells for COVID-19 patients with lung damage: a randomised, double-blind, placebo-controlled phase 2 trial" by Lei Shi, et al.
"Risk of death during the 2020 UK COVID-19 epidemic among people with rare autoimmune diseases compared to the general population. Preliminary results from the RECORDER project" by Emily Peach, et al.
"Validation of a derived international patient severity phenotype to support COVID-19 analytics from electronic health record data"
"Dynamic dysregulation of IL-6 and genes functional in NETosis, complement and coagulation in severe COVID-19 illness"

"High and increasing prevalence of SARS-CoV-2 swab positivity during end September beginning October 2020: REACT-1 round 5 updated report"
 

RR:C19 is published by the MIT Press and the editorial offices are located at UC Berkeley, headed by editor-in-chief Stefano M. Bertozzi, Professor of Health Policy and Management and Dean Emeritus of the School of Public Health at University of California Berkeley. The journal is funded by a grant from the Patrick J. McGovern Foundation and hosted on PubPub, an open-source publishing platform from the Knowledge Futures Group. 

To learn more about this project and its editorial board, or to sign up for future news and alerts, visit rapidreviewscovid19.mitpress.mit.edu.

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About the MIT Press
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About the UC Berkeley School of Public Health
For 75 years and counting, the UC Berkeley SPH has been dedicated to making a transformative impact on the health of populations through its values of health as a right, strength through diversity, think forward, and impact first. To eliminate inequity and injustice that affects the health and dignity of all people, SPH is committed to radical public health collaborations that challenge conventional thinking, leverage technology, and build bridges between research, public policy, education, and action.

About the Patrick J. McGovern Foundation
The Patrick J. McGovern Foundation is dedicated to improving lives globally with technology, data and AI. The Foundation is the legacy of IDG founder Patrick J. McGovern, who believed in the potential for technology to democratize information, improve the human condition and advance social good.

About the Knowledge Futures Group
The Knowledge Futures Group, a nonprofit originally founded as a partnership between the MIT Press and MIT Media Lab, builds and sustains technology for the production, curation, and preservation of knowledge in service of the public good.

Credit: 
The MIT Press

Researchers use genomics to reconstitute yellow fever outbreak in São Paulo

Agência FAPESP – Yellow fever virus is normally confined to the Amazon region, but the virus circulated in the Southeast of Brazil between 2016 and 2018, causing the worst epidemic and epizootic outbreaks there for decades. The Ministry of Health confirmed 2,251 cases of yellow fever in humans and 1,567 cases in monkeys in Brazil between December 2016 and June 2019.

According to a study published in the journal PLOS Pathogens, the three epidemic/epizootic waves that occurred in this period in the state of São Paulo, the most populous in the Southeast region, were caused by different lineages of the virus. In the first wave (July 2016-January 2017), the virus entered the state from the north, probably coming from neighboring state Minas Gerais, and spread mainly in cities such as São José do Rio Preto and Ribeirão Preto. The second wave (February-June 2017) was more intense, washing over the area from the border with Minas Gerais at Poços de Caldas all the way to Campinas. The largest number of cases was notified in the third wave (July 2017-February 2018). After reaching São Paulo City, the virus spread south to the Ribeira Valley area, where it found densely populated cities with low vaccination coverage rates and became a major public health problem.

These findings, reported in the journal by an international group of researchers supported by FAPESP, were based on genomic analysis of 51 viral isolates extracted both from mosquitoes collected in the affected areas and from monkeys that died from the disease. The material was sent by the Center for Epidemiological Surveillance (CVE) – an agency of the São Paulo State Department of Health – to Adolfo Lutz Institute (IAL), the central laboratory for public health in São Paulo.

“Based on the geographical and temporal distribution of the cases in non-human primates, on phylogenetic analysis [studying the mutations in the viral genome that lead to the emergence of novel lineages] and on phylogeographical analysis [studying the processes that determined the geographical distribution of the different lineages], it was possible to pinpoint when the virus entered the state of São Paulo, how fast and which way it spread, and all facets of its circulation,” Renato de Souza, a researcher at IAL and one of the lead authors of the article, told Agência FAPESP.

This level of detail in the description of an epidemic was only possible thanks to the use of MinION genetic sequencing technology, Souza explained. The platform is portable, fast and cheap, permitting real-time monitoring of cases at the location where they are happening.

The strategy was first used in Brazil in 2016 to track the movement of zika virus in the Americas (read more at agencia.fapesp.br/25472). More recently it has helped researchers at the Brazil-UK Center for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) track the progress of COVID-19 in Brazil. The project is led by Ester Sabino, a researcher at the University of São Paulo, and Nuno Faria at the University of Oxford in the UK, and is supported by FAPESP (https://bv.fapesp.br/en/auxilios/103130), the UK Medical Research Council and the Newton Fund.

Accidental host

Yellow fever virus circulates permanently in the Amazon region and occasionally meets favorable conditions that let it escape. For this to happen, Souza explained, a population of the vector mosquito has to come into contact with a population of wild primates that is dense enough to maintain the chain of transmission for some time.

“This expansion isn’t permanent,” he said. “The virus eventually loses the capacity to circulate in the environment concerned and returns only if it’s reintroduced. Between 2016 and 2018, the circulation area expanded to an unprecedented extent. The conditions for the virus to spread were just right. It infected wild primates in Serra da Mantiqueira [forest area of the state of São Paulo] and reached an area near the large Zoological Park on the outskirts of São Paulo City. This may happen again in a few years, whenever there is sufficient growth of the populations of primates in these places.”

Epidemiologically speaking, there was an outbreak of sylvatic yellow fever in the period, Souza said. Although there were many cases among humans, transmission occurred solely outside the urban environment via arboreal mosquitoes such as Haemagogus and Sabethes.

“In this case, human exposure was accidental. Growing human penetration of natural environments and forests was one of the contributing factors,” he said, adding that if an urban transmission chain had been established via Aedes aegypti, the incidence of the disease would have been far greater, reaching the level seen in dengue outbreaks.

“The problem is that the sylvatic transmission structure is growing ever closer to urban areas, heightening the risk of introduction of the virus into the urban context,” he said.

Tracking the pathogen’s circulation in populations of monkeys has been considered an effective epidemiological surveillance strategy, as it facilitates early identification of high-risk areas and planning of control strategies such as vaccination campaigns.

“A surveillance strategy based solely on monitoring of cases in humans detects only 20% of those infected, which is the proportion of symptomatics, so that under-reporting will always be significant. Among monkeys, there are species in which 90% develop symptoms and die from the disease. Monitoring these animals identifies the disease as the virus is starting to spread and in time to implement combat programs,” Souza said.

The article “Genomic surveillance of yellow fever virus epizootic in São Paulo, Brazil, 2016-2018” can be read at: journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008699.

Journal

PLoS Pathogens

DOI

10.1371/journal.ppat.1008699

Credit: 
Fundação de Amparo à Pesquisa do Estado de São Paulo

Minor fluctuations in sound make it hard to identify in which concert hall music is played

image: Speaker orchestra

Image: 
Photo: Jukka Patynen

The volume and timbre of music have a significant impact on how people perceive the acoustics in a concert hall, according to two recent studies carried out by the research group of Aalto University Professor Tapio Lokki. Both have been published in the Journal of the Acoustical Society of America, one of the most prestigious journals in its field.

The first study demonstrated that, based on the music alone, it is difficult to distinguish which concert hall a piece of music is being played in. The test subjects listened to recordings of a single violin and of part of Beethoven's Seventh Symphony, all played in four different concert halls: the rectangular Concertgebouw in Amsterdam and Herkulessaal in Munich, the vineyard-shaped Berlin Philharmonic, and the fan-shaped Cologne Philharmonic. They first heard a sample from the reference location, after which they tried to identify the reference location from four music samples.

It was easier to identify the hall when the same music sample played in each concert halls. If the reference sample was from a slightly different part of the same piece of music as used in the control locations, it was harder to identify the hall.

'Even small differences in the music listened to made it very difficult to identify concert halls of similar size and architecture. Halls that were very different to each other were clearly more easily identified regardless of the music,' explains postdoctoral researcher Antti Kuusinen.

Another study showed that the acoustics of a concert hall are experienced differently depending on the volume at which the orchestra is playing. The concert halls used in the study were the Helsinki's Musiikkitalo, Munich Herkulessaal, Berlin Philharmonic and Berlin Konzerthaus.

The subjects listened to the orchestra playing at different volume levels, from the quietest piano pianoissimo to the strongest forte fortissimo, after which they placed the concert halls in order according to how loud and enveloping they experienced the music to be. The order of the concert halls changed in some cases related to the volume of the music.

'Traditionally, the acoustics of concert halls are studied by using objective measurements to calculate acoustic parameters, such as reverberation time, which is independent of the characteristics or dynamics of the music. Our research clearly shows that this is insufficient for understanding the acoustics in its entirety, because both the timbre of the sound and the listeners' perceptions shift as the volume changes,' Lokki explains.

Lokki's research group has also previously studied how the acoustics of concert halls affect the emotional reactions evoked by the music. The studies indicated that halls with acoustics that support large dynamic fluctuations evoke the strongest emotional experiences in listeners.

Credit: 
Aalto University

COVID-19 linked to worse stroke outcomes

People who experience strokes while infected with COVID-19 appear to be left with greater disability after the stroke, according a study led by UCL and UCLH researchers.

Having COVID-19 at stroke onset was also associated with more than double the mortality rate of other stroke patients, according to the findings published in the Journal of Neurology, Neurosurgery & Psychiatry.

The researchers found evidence that people of Asian descent might be more likely to experience COVID-19-associated ischaemic strokes (those caused by blockage of blood vessels supplying the brain) than those in other groups in the UK.

Lead researcher Dr Richard Perry (UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, UCLH) said: "By comparing characteristics and outcomes of strokes experienced by people with and without COVID-19, we found that there were differences between the groups, suggesting that COVID-19 exerts an influence over the presentation of stroke.

"Some of the differences relate to what other studies are uncovering about COVID-19, in that it might make blood stickier and more likely to clot."

The findings build on previous studies led by UCL researchers which have also suggested that some people with COVID-19 are experiencing neurological symptoms, and that the infection may increase the risk of stroke.

The researchers reviewed evidence from 86 people who had a stroke in England or Scotland and had COVID-19 at stroke onset, between March and July this year, and compared them to 1,384 stroke cases during the same period in people who did not have any evidence of COVID-19.

Evidence of infection was determined by a positive coronavirus test within four days of admission or suspected COVID-19 at the time of admission and confirmed on testing at any point during the subsequent 10 days.

The researchers found that ischaemic stroke patients who also had COVID-19 were only half as likely to leave hospital without any disability as those without COVID-19. The researchers do not yet have data on how long these excess disabilities might persist.

Ischaemic strokes in COVID-19 patients were around twice as likely to be caused by the blockage of more than one large blood vessel in the brain (18% vs 8%), which the researchers say suggests evidence of abnormal blood clotting. They also found that the COVID-19 associated strokes were more severe, with an average stroke severity (NIHSS) score of 8, compared to 5 in the control group.

Levels of D-dimers, a protein marker for the stickiness of blood, were also higher in COVID-19 related ischaemic stroke than in other ischaemic strokes. The new findings fit with other studies showing that people with COVID-19 appear to have sticky blood that is more liable to clot.

The researchers found differences by ethnicity, as people of Asian descent were overrepresented (by more than double) in the COVID-19 group than White or Black patients.

Dr Perry said: "Our study suggests that COVID-19 has had more impact on strokes in the Asian community than in other ethnic groups. We cannot say from our data whether this is because people of Asian descent are more likely to catch COVID-19, or whether Asian patients with COVID-19 are more likely to have ischaemic strokes, or both."

Co-author Professor David Werring (UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, UCLH) added: "Our findings suggest that in some people, COVID-19 may influence stroke risk through its effect on excessive blood clotting or inflammation, and may also influence the characteristics and outcome of the stroke, including greater severity with a higher chance of multiple large vessel blood clots.

"Our findings support testing people for COVID-19 if they come into hospital with a stroke, and further research is needed to determine whether treatments (such as the use of early full dose anticoagulation) should differ depending on this test result."

Credit: 
University College London

RUDN University physicist developed software solution to measure the black holes stability

image: Even if a black hole can be described with a mathematical model, it doesn't mean it exists in reality. Some theoretical models are unstable: though they can be used to run mathematical calculations, from the point of view of physics they make no sense. A physicist from RUDN University developed an approach to finding such instability regions.

Image: 
RUDN University

Even if a black hole can be described with a mathematical model, it doesn't mean it exists in reality. Some theoretical models are unstable: though they can be used to run mathematical calculations, from the point of view of physics they make no sense. A physicist from RUDN University developed an approach to finding such instability regions. The work was published in the Physics of the Dark Universe journal.

The existence of black holes was first predicted by Einstein's general theory of relativity. These objects have so strong gravitational pull that nothing, not even light, can escape them. Dense and massive, black holes deform space-time (a physical construct with three spatial and one temporal dimension). Many mathematical models used to describe black holes include corrections to account for such space-time curvatures. The main condition of existence for every black hole model is its stability in cases of minor spatial or temporal changes. Mathematically unstable black holes make no physical sense, as the objects they describe cannot exist in reality. A physicist from RUDN University suggested a method to identify black hole instability parameters in 4D space-time.

"For a model to be considered feasible, a black hole described by it has to remain stable in case of minor space-time fluctuations. One of the most promising approaches to developing alternative gravity theories includes adding corrections to Einstein's equation, including the fourth-order Gauss-Bonnet correction and the Lovelock correction that provides a higher level of generalization," said Roman Konoplya, a researcher at the Educational and Research Institute of Gravitation and Cosmology, RUDN University.

The physicist studied stability in the Einstein-Gauss-Bonnet theory in which a black hole is described by Einstein's equation with a fourth additional component. Previously, he had focused on a different mathematical description of a black hole, the so-called Lovelock theory, that describes a black hole as a sum of an infinite number of components. The instability region turned out to be closely associated with the values of the so-called coupling constants: numerical coefficients by which the corrections to Einstein's equation are multiplied.

According to the physicist, the Einstein-Gauss-Bonnet model does not provide for the existence of small black holes, because if coupling constants are relatively big compared to other parameters (such as the radius of a black hole), the model almost always turns out to be unstable. The stability region is much bigger if the coupling constant has a negative value. Based on these calculations, he and his team developed a program to calculate black hole stability based on any of its parameters.

"Our approach helps test black hole models for stability. We made the code publicly available so that any of our colleagues could use it to calculate instability regions for models with an unspecified set of parameters," added Roman Konoplya.

Credit: 
RUDN University

Nervous systems of insects inspire efficient future AI systems

Zoologists at the University of Cologne studied the nervous systems of insects to investigate principles of biological brain computation and possible implications for machine learning and artificial intelligence. Specifically, they analysed how insects learn to associate sensory information in their environment with a food reward, and how they can recall this information later in order to solve complex tasks such as the search for food. The results suggest that the transformation of sensory information into memories in the brain can inspire future machine learning and artificial intelligence applications to solving complex tasks. The study has been published in the journal PNAS.

Living organisms show remarkable abilities in coping with problems posed by complex and dynamic environments. They are able to generalize their experiences in order to rapidly adapt their behaviour when the environment changes. The zoologists investigated how the nervous system of the fruit fly controls its behaviour when searching for food. Using a computer model, they simulated and analysed the computations in the fruit fly's nervous system in response to scents emanated from the food source. 'We initially trained our model of the fly brain in exactly the same way as insects are trained in experiments. We presented a specific scent in the simulation together with a reward and a second scent without a reward. The model rapidly learns a robust representation of the rewarded scent after just a few scent presentations and is then able to find the source of this scent in a spatially complex and temporally dynamic environment,' said computer scientist Dr Hannes Rapp, who created the model as part of his doctoral thesis at the UoC's Institute of Zoology.

The model created is thus capable to generalize from its memory and to apply what it has learned previously in a completely new and complex odour molecule landscape, while learning required only a very small database of training samples. 'For our model, we exploit the special properties of biological information processing in nervous systems,' explained Professor Dr Martin Nawrot, senior author of the study. 'These are in particular a fast and parallel processing of sensory stimuli by means of brief nerve impulses as well as the formation of a distributed memory through the simultaneous modification of many synaptic contacts during the learning process.' The theoretical principles underlying this model can also be used for artificial intelligence and autonomous systems. They enable an artificial agent to learn much more efficiently and to apply what it has learned in a changing environment.

Credit: 
University of Cologne

Virus that causes COVID-19 puts a plug in cellular defenses

One of the novel coronavirus' most insidious tricks is that it can block the ability of cells to produce protective proteins without hindering its own ability to replicate.

Now, a multidisciplinary team of Yale researchers has discovered how SARS-CoV-2, the virus that causes COVID-19, accomplishes this trick by blocking production of cellular proteins, including immune molecules, and contributes to severe illness in its host.

"The virus essentially reprograms host cells, and by understanding this mechanism we can hopefully design new therapeutics,'' said Yong Xiong, professor of molecular biophysics and biochemistry and co-corresponding author of the research published in the journal Molecular Cell.

Previous studies had implicated a viral protein, nonstructural protein 1 or Nsp1, in the COVID-19 virus' ability to block cells' ability to produce new proteins. But exactly how NsP1 works in a cell was not known.

Using advanced genetic screening and cryogenic electron microscopy (cryo-EM), the Yale team was able to show that Nsp1 is one of SARS-CoV-2's most pathogenic viral proteins. In human lung cells, it can drastically alter host cell gene expression and essentially form a plug that prevents the ribosome, the cell's protein-making machinery, from receiving genetic instructions for new proteins encoded in messenger RNA.

"This is the entry channel for genetic material, and when it is blocked no protein can be made," Xiong explained. "We didn't understand this mechanism before, but now we know."

This process affects protein production in many parts of the body, and high levels of Nsp1 may help explain why some people fare poorly after infection by the virus, he said.

However, it remains unknown how the virus is still able to produce its own proteins, using the same ribosome, to replicate in the cell after it disables the cell's ability to make normal proteins, Xiong said.

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Yale University

Smokers switching exclusively to glo significantly reduce exposure to certain toxicants

New research by BAT has found that smokers who switched completely from smoking cigarettes to using BAT's flagship tobacco heating product (THP), glo, substantially reduced their exposure to certain cigarette smoke toxicants over three months.

For many of the toxicants measured, the levels found in participants were similar to those in people that stopped using tobacco completely.

This supports BAT's ambition to build A Better Tomorrow by reducing the health impact of its business, given respected public health agencies say that to be considered a modified risk tobacco product, switching completely should have a similar outcome for the smoker to quitting.

Scientists at BAT are conducting the UK's first ever year-long controlled study to see what impact switching from cigarettes to glo will have on general health as well as smoke-toxicant exposure.

Today's results find that smokers who switch from cigarettes to glo exclusively significantly reduce the levels of harmful toxicants they are exposed to, potentially reducing their risk of developing smoking-related diseases. Further results from this study will provide more evidence to help understand the impact of switching to glo and will be announced once the study has been completed.

Dr James Murphy, Group Head of Potentially Reduced-Risk Product Science, commented: "These initial results regarding glo are extremely encouraging - glo provides smokers who wish to continue using tobacco and nicotine products with a potentially reduced risk alternative to cigarettes. The results are another positive step for BAT as we continue our journey to reduce the health impact of our business by offering consumers a range of enjoyable and potentially reduced-risk products."

Credit: 
R&D at British American Tobacco

Soil carbon changes in transition areas suggest conservation for Amazon, scientists say

EUGENE, Ore. -- Nov. 5, 2020 -- Conservation efforts on the edges of the Amazon forest, especially in light of recent deforestation by human disturbance, could help the region weather the storm of climate change, researchers say.

That assessment comes from an analysis of vegetation changes and carbon isotope signatures in the soil at 83 sites. The project, led by University of Oregon doctoral student Jamie Wright, established a record of soil changes associated with both climate and human activity over the last 1,600 years based on radiocarbon dating.

The study was published online Oct. 30 ahead of print in Global Change Biology.

Woody vegetation expansion into savannas, the research team found, had continued amid increasing moisture levels regardless of human impacts until only recently, mostly from rapid deforestation in the last decade. Climate modeling previously has suggested that local water and carbon cycles, as well as global climate patterns, are at risk.

"The past, like most things, leaves a trace behind and with it a rich history left to be told," said Wright, a member of the UO's Soil Plant Atmosphere Lab headed by co-author Lucas Silva, a professor in the Environmental Studies Program.

The forest-savanna borderlands, known as the Amazon-Cerrado transition, experience broad climatic and ecological influences. The study helped address uncertainties of those influences in the tropical ecosystem.

"Through the use of soil science, specifically with carbon isotopes, we unearthed a history of forest expansion over several millennia. This region is at the epicenter of deforestation and socio-ecological transformations that cause and drive climate change," Wright said.

Previous studies had suggested that forest expansion was primarily driven by increased precipitation, but that work, Silva noted, did not fully consider the impacts of local influences, such as fire frequency and intensity or whether it was occurring because of climate dynamics in the region. Focusing on soil changes, he said, allowed for these factors to be examined.

"Carbon storage in woody savannas and forests plants at this large of scale can be a significant carbon sink," Wright said. "Increasing tree cover also can ameliorate adverse climatic change impacts, such as droughts, by influencing the hydrological cycle and generating rain clouds."

In total, 742 soil samples were taken from forests, savannas and transition zones across a large swath of north-central Brazil, between latitudes 4 to 16 degrees south and longitudes 46 to 56 degrees west -- an area where precipitation and distribution vary significantly.

The research team also measured the leaf index of the ecosystem's cover, mostly the forest canopy, to understand changes in carbon isotope signatures in the soil. Such changes reflect land usage. To determine changes over time, radiocarbon activity and isotopic ratios were profiled in 43 selected depths that represented the different sites.

While the research affirmed that forest expansion has occurred in most of the past 1,600 years, the researchers found a trend of decreasing woody vegetation in the study area's easternmost sites. The decline, they said, may reflect the prevalence of dry deciduous or semi-deciduous tree species in those areas.

The observed incremental expansion into savannas, they wrote, could have significant impacts on carbon-water relations, potentially affecting the balance between precipitation and evapotranspiration as seen in previous research. However, they noted, they did not see a clear effect of changes in vegetation on soil carbon stocks.

Future studies, they said, are needed to focus on the mechanisms that drive the permanence of carbon derived from woody vegetation expansion, especially because of recent documentation of hotter and longer dry seasons, as well as rising mortality rates of wet climate species.

The next phase of understanding, they said, will come from integrating plant, soil and atmospheric data to understand the influence of human activity on ecosystem-climate feedbacks as a path towards improving carbon sequestration and water conservation.

"Our data indicate a regional increase in tree cover prior to modern deforestation, which could help inform conservation and management for climate change mitigation," said Silva, who also is a professor of geography and member of the Institute of Ecology and Evolution. "We hope that our research will lead to a greater appreciation of ecological processes in the region and their importance for global climatic stability."

In addition to Silva and Wright, the study's co-authors are Barbara Bomfim, a former postdoctoral researcher in Silva's lab who is now at the Lawrence Berkeley National Laboratory, Corrine Wong of Boston College, and Ben Hur Marimon-Junior and Beatriz Marimon, both of the State University of Mato Grosso in Nova Xavantina, Brazil.

The research team is continuing to work closely with collaborators in the Amazon region in an effort to secure funding to launch a reforestation project, Silva said.

Credit: 
University of Oregon

Mystery molecule in bacteria is revealed to be a guard

image: Top row: E coli bacteria containing a retron break apart the membranes in the cell around 15 minutes after infection (center) Red reveals holes in membranes as cells die. (Right) 45 minutes post infection with a phage, many cells have died, but a few remain to restart growth. Bottom: bacteria lacking this retron look fine after 15 minutes, but 45 minutes later, the infected cells have died and the viral DNA has spilled out, on its way into the remaining few cells

Image: 
the Weizmann Institute of Science

Peculiar hybrid structures called retrons that are half RNA, half single-strand DNA are found in many species of bacteria. Since their discovery around 35 years ago, researchers have learned how to use retrons for producing single strands of DNA in the lab, but no one knew what their function was in the bacteria, despite much research into the matter. In a paper published today in Cell, a Weizmann Institute of Science team reports on solving the longstanding mystery: Retrons are immune system "guards" that ensure the survival of the bacterial colony when it is infected by viruses. In addition to uncovering a new strategy used by bacteria to protect themselves against viral infection -- one that is surprisingly similar to that employed by plant immune systems -- the research revealed many new retrons that may, in the future, add to the genome-editing toolkit.

The study, conducted in the lab of Prof. Rotem Sorek of the Institute's Molecular Genetics Department, was led by Adi Millman, Dr. Aude Bernheim and Avigail Stokar-Avihail in his lab. Sorek and his team did not set out to solve the retron mystery; they were seeking new elements of the bacterial immune system, specifically elements that help bacteria to fend off viral infection. Their search was made easier by their recent finding that bacteria's immune system genes tend to cluster together in the genome within so-called defense islands. When they uncovered the unique signature of retron within a bacterial defense island, the team decided to investigate further.

Their initial research showed that this retron was definitely involved in protecting bacteria against the viruses known as phages that specialize in infecting bacteria. As the researchers looked more closely at additional retrons located near known defense genes, they found that the retrons were always connected - physically and functionally - to one other gene. When either the accompanying gene or the retron was mutated, the bacteria were less successful in fighting off phage infection.

The researchers then set out to look for more such complexes in defense islands. Eventually, they identified some 5,000 retrons, many of them new, in different defense islands of numerous bacterial species.

To check if these retrons function, generally, as immune mechanisms, the researchers transplanted many retrons, one by one, into laboratory bacterial cells that were lacking retrons. As they suspected, in a great number of these cells they found retrons protecting the bacteria from phage infection.

How do retrons do this? Focusing back on one particular kind of retron and tracing its actions in the face of phage infection, the research team discovered that its function is to cause the infected cell to commit suicide. Cell suicide, once thought to belong solely to multicellular organisms, is a last-ditch means of aborting widespread infection - if the suicide mechanism works fast enough to kill the cell before the virus finishes making copies of itself and spreading out to other cells.

Further investigation showed that retrons do not sense the phage invasion itself, but rather keep watch on another part of the immune system known as RecBCD, which is one of the bacterium's first lines of defense. If it realizes that the phage has tampered with the cell's RecBCD, the retron activates its program through the second, linked genes to kill the infected cell and protect the rest of the colony.

"It's a clever strategy, and we found it works in a similar way to a guard mechanism employed in plant cells," says Sorek. "Just like viruses that infect plants, phages come equipped with a variety of inhibitors to block assorted parts of the cell immune response. The retron, like a guard mechanism known to exist in plants, does not need to be able to identify all possible inhibitors, just to have a handle on the functioning of one particular immune complex. Infected plant cells apply this 'abortive infection' method, killing off a small region of a leaf or root, in an effort to save the plant itself. Since most bacteria live in colonies, this same strategy can promote the survival of the group, even at the expense of individual members."

Retrons are so useful to biotechnology because they begin with a piece of RNA, which is the template for the synthesis of the DNA strand. This template in the retron sequence can be swapped out for any desired DNA sequence and used, sometimes in conjunction with another tool borrowed from the bacterial immune toolkit - CRISPR - to manipulate genes in various ways. Sorek and his team believe that within the diverse list of retrons they identified may be hiding more than a few that could provide better templates for specific gene editing needs.

Credit: 
Weizmann Institute of Science

ACA results in fewer low-income uninsured, but non-urgent ER visits haven't changed

Since the Affordable Care Act's (ACA) Medicaid expansion program went into effect 10 years ago, the U.S. has seen a larger reduction in the number of uninsured low-income, rural residents, compared to their urban contemporaries.

But the likelihood of repeated visits to emergency rooms for non-urgent reasons has not decreased.

That's what Washington State University's Bidisha Mandal discovered in a new paper published in the journal Applied Economic Perspectives and Policy.

"Using emergency departments for non-urgent care is often a sign that people don't have convenient access to doctors," said Mandal, a professor in WSU's School of Economic Sciences. "With more people having insurance under the ACA, demand has increased for doctors. Supply seems to have gone up in cities, but not in rural areas."

Non-urgent visits put an additional strain on emergency rooms, and cost more for patients as well, she said.

One potential reason that non-urgent emergency room visits haven't decreased with more insurance is that Medicaid reimbursements for doctors are lower than other insurances. Physicians don't have a monetary incentive to increase the number of low-income patients they see.

"I was surprised to see that low-income rural residents actually had more insurance gains than urban residents," Mandal said. "But providers just don't have enough incentive to accept new Medicaid patients."

Low-income people benefited from the ACA's Medicaid expansion, and the Supreme Court ruling that made the expansion optional for states allowed researchers to compare outcomes between states that accepted or rejected the expansion, Mandal said.

She also found that the number of annual checkups has increased for low-income people in rural areas. But those additional visits haven't led to fewer non-urgent ER visits.

Mandel hopes policymakers looking to improve the ACA will read papers like hers to see and fix weaknesses in the law.

"There are definite gaps in the ACA, and I hope this paper helps fill some of them," Mandal said. "Having access to proper medical care is really important for our entire population."

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Washington State University

SARS-CoV-2 uses 'genome origami' to infect and replicate inside host cells

Scientists at the University of Cambridge, in collaboration with Justus-Liebig University, Germany, have uncovered how the genome of SARS-CoV-2 - the coronavirus that causes COVID-19 - uses genome origami to infect and replicate successfully inside host cells. This could inform the development of effective drugs that target specific parts of the virus genome, in the fight against COVID-19.

SARS-CoV-2 is one of many coronaviruses. All share the characteristic of having the largest single-stranded RNA genome in nature. This genome contains all the genetic code the virus needs to produce proteins, evade the immune system and replicate inside the human body. Much of that information is contained in the 3D structure adopted by this RNA genome when it infects cells.

The researchers say most current work to find drugs and vaccines for COVID-19 is focused on targeting the proteins of the virus. Because the shape of the RNA molecule is critical to its function, targeting the RNA directly with drugs to disrupt its structure would block the lifecycle and stop the virus replicating.

In a study published today in the journal Molecular Cell, the team uncovered the entire structure of the SARS-CoV-2 genome inside the host cell, revealing a network of RNA-RNA interactions spanning very long sections of the genome. Different functional parts along the genome need to work together despite the great distance between them, and the new structural data shows how this is accomplished to enable the coronavirus life cycle and cause disease.

"The RNA genome of coronaviruses is about three times bigger than an average viral RNA genome - it's huge," said lead author Dr Omer Ziv at the University of Cambridge's Wellcome Trust/Cancer Research UK Gurdon Institute.

He added: "Researchers previously proposed that long-distance interactions along coronavirus genomes are critical for their replication and for producing the viral proteins, but until recently we didn't have the right tools to map these interactions in full. Now that we understand this network of connectivity, we can start designing ways to target it effectively with therapeutics."

In all cells the genome holds the code for the production of specific proteins, which are made when a molecular machine called a ribosome runs along the RNA reading the code until a 'stop sign' tells it to terminate. In coronaviruses, there is a special spot where the ribosome only stops 50% of the times in front of the stop sign. In the other 50% of cases, a unique RNA shape makes the ribosome jump over the stop sign and produce additional viral proteins. By mapping this RNA structure and the long-range interactions involved, the new research uncovers the strategies by which coronaviruses produce their proteins to manipulate our cells.

"We show that interactions occur between sections of the SARS-CoV-2 RNA that are very long distances apart, and we can monitor these interactions as they occur during early SARS-CoV-2 replication," said Dr Lyudmila Shalamova, a co-lead investigator at Justus-Liebig University, Germany.

Dr Jon Price, a postdoctoral associate at the Gurdon Institute and co-lead of this study, has developed a free, open-access interactive website hosting the entire RNA structure of SARS-CoV-2. This will enable researchers world-wide to use the new data in the development of drugs to target specific regions of the virus's RNA genome.

The genome of most human viruses is made of RNA rather than DNA. Ziv developed methods to investigate such long-range interactions across viral RNA genomes inside the host cells, in work to understand the Zika virus genome. This has proved a valuable methodological basis for understanding SARS-CoV-2.

Credit: 
University of Cambridge