Culture

A new study examining how people with severe and profound intellectual disabilities resist activities while in care recommends that institutions improve training to help carers better understand non-verbal cues, as well as offer greater flexibility to allow individual preferences to take priority over institutional schedules.

The research, published in the journal Sociology of Health and Illness, investigated how people with limited language ability expressed their wishes and preferences, and how their support workers responded. It was carried out at a residential home and a day care centre in the UK.

The study, by Dr Clare Nicholson of St Mary's University, Twickenham, and Dr Mick Finlay and Dr Steven Stagg of Anglia Ruskin University (ARU), involved taking notes and filming everyday interactions such as feeding, drinking, art and music activities, and physiotherapy, over the course of a year.

The research found that the service users signalled in very subtle ways, usually non-verbally, when they did not want to do something. For people with severe disabilities, how well their care workers recognise and respond to these subtle behaviours is crucial to their autonomy and empowerment.

Behaviour which appeared to signal resistance to activities included pretending to be asleep, dropping tools such as paint brushes, turning the head or the gaze away from the care worker, pushing objects away, dragging feet along the ground to slow movement in a wheelchair, and making loud vocalisations.

When these behaviours were not responded to by care workers, who instead continued with the activity, the person would sometimes escalate their resistance to behaviour involving self-injury, such as thrashing their body around in a wheelchair, striking their own face, and digging their fingernails into their hands.

In addition to encouraging care workers to adopt greater flexibility around which activities take place and when, the authors believe further training using real life examples, such as those outlined in the study, could help staff better understand some of the common signs of resistance.

Co-author Dr Mick Finlay, Reader in Social Psychology at Anglia Ruskin University (ARU), said: "Our research shows that people with severe intellectual disabilities can and do make responsible decisions regarding their wellbeing and wishes, and are able to indicate when they want to remove themselves from situations which make them distressed, bored or unhappy.

"However, for a person to act in a self-determined manner, they need to be able to communicate with others. Communication for people with severe intellectual disabilities is often non-verbal and can be ambiguous, and we found that this can present a challenge for their carers.

"We found that staff often continued to promote or even complete activities on behalf of the people they support, despite signs of resistance. This could be because the carer failed to pick up on the non-verbal cues. Or it could be because of a desire to maximise participation in activities or stick to a schedule.

"Institutional timetables need to be flexible enough to respect the everyday rights and choices of people with severe intellectual disabilities, and support staff need to have the ability to depart from fixed institutional agendas where appropriate, particularly when it would not cause detriment to the people in their care."

University of California, Irvine, biologists have discovered that plants influence how their bacterial and fungal neighbors react to climate change. This finding contributes crucial new information to a hot topic in environmental science: in what manner will climate change alter the diversity of both plants and microbiomes on the landscape? The paper appears in Elementa: Sciences of the Anthropocene.

The research took place at the Loma Ridge Global Change Experiment, a decade-long study in which scientists simulate the impacts of climate change on neighboring grasslands and coastal scrublands in Southern California. Experimental treatments there include nitrogen addition, a common result of local fossil fuel burning, and simulated drought imposed by covering patches of land with waterproof roofs during rainstorms.

In the project's early years, researchers focused on answering climate questions involving plants only. A research team led by Jennifer Martiny, professor of ecology & evolutionary biology and co-director of the UCI Microbiome Initiative, decided to examine whether the vegetation itself influences how climate change affects the bacteria and fungi in the ground. Soil microbes decompose dead plants, regulating the amount of carbon dioxide exchanged with the atmosphere.

The scientists sequenced microbial DNA in the grassland and scrubland, finding that the types and number of bacteria and fungi differed between them. Next, the team compared how the microbes reacted to nitrogen fertilizer and drought by monitoring the microbial DNA in plant litter, primarily dropped leaves and stems, over a three-year period.

"We thought diminished water might cause the scrubland microbial community to become more similar to that of the grasslands because there is evidence that scrublands start to grow increased grasses under drought conditions," said Sarai Finks, the paper's first author and UCI graduate student. "However, it didn't happen. The two microbial communities remained distinct."

The team also discovered that while simulated drought affected both bacteria and fungi in grassland and scrubland, there were some unexpected differences. Nitrogen addition only affected the bacteria and its impact was far less than that of drought.

"Researchers have looked at this kind of interaction previously, but not on the scale we have done here. We were able to investigate two different kinds of plant communities right next to each other," Finks said, adding that the team hopes their findings will be helpful to other scientists investigating microbial communities. "Microbes are crucial to the carbon cycle and we need to learn what changes in microbial diversity mean for the environment."

The researchers' paper was the latest to be published from scientific data collected before the Silverado wildfire struck the Loma Ridge Global Change Experiment in October 2020. "Scientists are now looking into researching post-fire interactions between plants and the microbial communities at the site," Finks said.

The human brain regions responsible for speech and communication keep our world running by allowing us to do things like talk with friends, shout for help in an emergency and present information in meetings.

However, scientific understanding of just how these parts of the brain work is limited. Consequently, knowledge of how to improve challenges such as speech impediments or language acquisition is limited as well.

Using an ultra-lightweight, wireless implant, a University of Arizona team is researching songbirds - one of the few species that share humans' ability to learn new vocalizations - to improve scientific understanding of human speech. A paper about their work was published today in the journal Nature Communications.

"Using new methods of antenna design and optimized electronics, we were able to shrink the devices dramatically compared to existing versions, to about a third of the size of a dime and as thin as a sheet of paper," said lead author Jokubas Ausra, a biomedical engineering doctoral student in the Gutruf Lab, where the devices were created.

There are several ways the device can be used to study the link between brain behavior and vocalization. It can monitor the bird for slight temperature changes that indicate when a bird is most likely to sing. Using a technique called optogenetics, researchers can modulate neuron groups in the brain regions used for birdsong. In this study, the team found that remotely controlling specific neurons during birdsong using their unique device caused the song to change pitch.

"We are excited to expand the toolbox of neuroscientists and hope to enable many exciting studies that decipher the working principles of the brain," said senior author Philipp Gutruf, assistant professor of biomedical engineering and Craig M. Berge Fellow in the UArizona College of Engineering.

The Gutruf Lab has developed other wireless lightweight devices used to monitor brain activity in rodents, but birds' ability to move in 3D space represents an added challenge. This tiny device allows the birds to move without restriction - a breakthrough enabled by careful management of the energy sent wirelessly to the implant.

"Because of the small size and light weight, the birds can move freely and live permanently with the implant without affecting their behavior or health, which opens up many possibilities to study the basis for vocal communication," said co-senior author Julie Miller, an assistant professor of neuroscience and speech, language and hearing sciences at UArizona.

The team's next goal is to expand device capabilities to also record neuron activity. This could allow researchers to visualize brain activity during song learning and performance to gain a deeper understanding of the underlying brain mechanisms.

Osaka, Japan - Streptococcus pyogenes is one of the most important bacterial causes of human skin infections. If S. pyogenes invades deep into the tissue, it can cause life-threatening illnesses, such as sepsis and toxic shock. With its limited supply of carbohydrates, the skin is generally an effective barrier against infection and not a good surface for the survival of S. pyogenes. To survive successfully and invade deep into the tissue, bacteria must be able to find a source of nutrients and also evade the skin's immune defenses.

Now, an international team led by Osaka University, Japan, in collaboration with Keio University, Japan, and University of California San Diego, USA, has discovered a way this disease organism obtains nutrition from the skin surface. This knowledge could lead to new therapeutic approaches to tackle infections. The team recently published the work in Cell Reports.

It was already known that some bacteria break down arginine (an amino acid - one of the building blocks of proteins) via a biochemical pathway named the arginine deaminase (ADI) pathway. The team confirmed that S. pyogenes can survive using arginine even when starved of glucose. When they deleted the bacterial gene (named arcA) encoding the first enzyme in the ADI pathway, the S. pyogenes lost that ability and also became less toxic towards human skin cells grown in culture.

When arginine is supplied, the ADI pathway of S. pyogenes is activated but there are also widespread changes in gene expression. Some genes are down-regulated but large numbers of genes are up-regulated, including genes associated with virulence of S. pyogenes, such as those that produce bacterial toxins.

Using mouse skin as a model system for human skin, the team showed for the first time that S. pyogenes can use arginine to survive on the skin surface. S. pyogenes lacking the arcA gene survived poorly and were less virulent on mouse skin, confirming the importance of this pathway in the disease process. In contrast, in blood (containing plentiful glucose), the altered S. pyogenes appeared no different to normal S. pyogenes since the ADI pathway was not needed.

"We showed that arginine from stratum corneum-derived filaggrin was a key substrate for the ADI pathway of S. pyogenes," says lead researcher Dr. Yujiro Hirose. "In mice that do not produce filaggrin, less arginine is available and the S. pyogenes bacteria do not utilize ADI pathway to cause the skin lesion."

"This represents a significant step forward in understanding how S. pyogenes survives on the skin," explains Dr. Hirose. "We expect our study will lead to novel treatment strategies: if we can block arginine metabolism in S. pyogenes it should restrict the pathogen's survival and virulence."

Scientists from Tomsk Polytechnic University jointly with Russian colleagues and researchers from Technical University of Denmark the first time have experimentally proved the existence of a two-dimensional (2D) curved flux of plasmonic quasiparticles, a plasmonic hook. A flat 2D hook is smaller than a 3D hook and possesses new properties, due to them, the researchers consider it as the most promising transmitter in high-speed microoptical circuits. The research findings are published in Applied Physics Letters (IF: 3,597; Q1) academic journal.

Electrons transmit information in existing calculation devices. The scientists suppose if electrons are replaced by photons, light quanta, it will be possible to transmit the data literally at the speed of light. In order that microoptical circuits and optical computers would become ordinary devices and become mass-produced, it is required to find a way to compress light to the nanoscale.

"We are searching for new types of curved wave fluxes, which can solve this task. Previously, we simulated and experimentally proved the existence of photonic and acoustic hooks and now we have proved the existence of a plasmonic hook. Nowadays, it is the most promising method to transmit a signal. The plasmonic wavelength is shorter than a 3D wavelength in free space and the area of radiation localization is in nanoscale. It is a crucial indicator for miniaturization," Igor Minin, Professor of the TPU Division for Electronic Engineering, a supervisor of the research work, says.

The authors of the article obtained a flat plasmonic hook using a simple and cheap focusing element. The flat plasmonic hook is an asymmetric dielectric particle sized 4-5 μm and about 0.25 μm thick. According to the scientists, the participle shape can be various, in this case, it was a microcube with a docked prism. This particle was placed on the 0.1 μm thick gold film, on the other side of the film, the diffraction grating was deposited.

During the experiments, the laser ray was directed at the diffraction grating. Plasmon resonance occurred next to the surface of the diffraction grafting under sunlight that is the sunlight was converted into plasmonic waves. These waves passed through the asymmetric dielectric particle focused in a 2D curved ray.

"We obtained a 2D curved ray due to a special shape of a dielectric particle. One of the mechanisms of sub-wave structured focusing is based on the phenomenon of a plasmonic nanojet that we managed to experimentally fix for the first time earlier. When we shift free 3D space to plasmon polaritons, in other words, 2D space, the quantum nature of matter reveals. It allows implementing implicitly new opportunities to control the interaction between matter and light, for instance, to implement biosensing methods based on the detection of micro- and nanoparticles, biomolecules in the near field. Of course, it is too early to speak about the application of results, it is a task for future research. Therefore, any research and experiments to transmit signals based on optical principles are still in the practice of fundamental research. Scientists of various fields will have to overcome many challenges to create, for instance, a productive optical computer or even efficient microcircuits. To overcome these challenges, 10-15 years might be spent," Igor Minin, TPU Professor, initiator of the research work, says.

Some 8,300 million metric tons of plastics have been manufactured since production exploded in the 1950s, with more than 75 percent ending up as waste and 15 million metric tons reaching oceans every year. Plastic waste fragments into increasingly smaller but environmentally persistent "microplastics," with potentially harmful effects on the health of people, wildlife and ecosystems. A new collection, "Confronting Plastic Pollution to Protect Environmental and Public Health," is publishing on March 30th, 2021 in the open access journal PLOS Biology that addresses critical scientific challenges in understanding the impacts of microplastics.

The collection features three evidence-based commentaries from ecotoxicology and environmental health experts that address gaps in understanding and flag research priorities for improving methods to detect, evaluate, and mitigate threats associated with this emerging contaminant. The guest editor of the collection is Judith Enck, former EPA regional administrator, president of the nonprofit Beyond Plastics and visiting professor at Bennington College's Center for the Advancement of Public Action.

Plastic production increased from 2 million metric tons a year in 1950 to 380 million metric tons by 2015 and is expected to double by 2050. The plastic pollution crisis will worsen, experts say, as petrochemical companies shift from fossil fuels to fracking, which produces the plastic feedstock ethane.

The commentaries explores pressing challenges in three areas: the difficulty of developing health protective policies for emerging contaminants, the migration of toxic and undisclosed plastic additives into food and understanding how microplastics, a form of carbon themselves, impact carbon cycling in soils.

In the Essay, "Addressing the environmental and health impacts of microplastics requires open collaboration between diverse sectors," ecotoxicologist Scott Coffin and colleagues use California as a case study to suggest strategies to design research, policies and regulations for a contaminant scientists are just starting to understand, drawing on parallels with a similar class of emerging contaminants (per- and polyfluoroalkyl substances).

In her Essay, "Tackling the toxics in plastics packaging," environmental toxicologist Jane Muncke focuses on a major driver of the global plastic pollution crisis: single-use food packaging. Efforts to reduce plastic waste through recycling ignore evidence that chemicals in plastic migrate into food, she argues, making harmful chemicals an unintentional part of the human diet.

In their Essay, "Microplastic effects on carbon cycling processes in soils," plant ecologist Matthias Rillig and colleagues explore how microplastics appear to be interfering with the very fabric of the soil environment itself and call for a "major concerted effort" to understand the pervasive effects of these ubiquitous particles on the function of soils and terrestrial ecosystems.

New observations with the European Southern Observatory's Very Large Telescope (ESO's VLT) indicate that the rogue comet 2I/Borisov, which is only the second and most recently detected interstellar visitor to our Solar System, is one of the most pristine ever observed. Astronomers suspect that the comet most likely never passed close to a star, making it an undisturbed relic of the cloud of gas and dust it formed from.

2I/Borisov was discovered by amateur astronomer Gennady Borisov in August 2019 and was confirmed to have come from beyond the Solar System a few weeks later. "2I/Borisov could represent the first truly pristine comet ever observed," says Stefano Bagnulo of the Armagh Observatory and Planetarium, Northern Ireland, UK, who led the new study published today in Nature Communications. The team believes that the comet had never passed close to any star before it flew by the Sun in 2019.

Bagnulo and his colleagues used the FORS2 instrument on ESO's VLT, located in northern Chile, to study 2I/Borisov in detail using a technique called polarimetry [1]. Since this technique is regularly used to study comets and other small bodies of our Solar System, this allowed the team to compare the interstellar visitor with our local comets.

The team found that 2I/Borisov has polarimetric properties distinct from those of Solar System comets, with the exception of Hale-Bopp. Comet Hale-Bopp received much public interest in the late 1990s as a result of being easily visible to the naked eye, and also because it was one of the most pristine comets astronomers had ever seen. Prior to its most recent passage, Hale-Bopp is thought to have passed by our Sun only once and had therefore barely been affected by solar wind and radiation. This means it was pristine, having a composition very similar to that of the cloud of gas and dust it -- and the rest of the Solar System -- formed from some 4.5 billion years ago.

By analysing the polarisation together with the colour of the comet to gather clues on its composition, the team concluded that 2I/Borisov is in fact even more pristine than Hale-Bopp. This means it carries untarnished signatures of the cloud of gas and dust it formed from.

"The fact that the two comets are remarkably similar suggests that the environment in which 2I/Borisov originated is not so different in composition from the environment in the early Solar System," says Alberto Cellino, a co-author of the study, from the Astrophysical Observatory of Torino, National Institute for Astrophysics (INAF), Italy.

Olivier Hainaut, an astronomer at ESO in Germany who studies comets and other near-Earth objects but was not involved in this new study, agrees. "The main result -- that 2I/Borisov is not like any other comet except Hale-Bopp -- is very strong," he says, adding that "it is very plausible they formed in very similar conditions."

"The arrival of 2I/Borisov from interstellar space represented the first opportunity to study the composition of a comet from another planetary system and check if the material that comes from this comet is somehow different from our native variety," explains Ludmilla Kolokolova, of the University of Maryland in the US, who was involved in the Nature Communications research.

Bagnulo hopes astronomers will have another, even better, opportunity to study a rogue comet in detail before the end of the decade. "ESA is planning to launch Comet Interceptor in 2029, which will have the capability of reaching another visiting interstellar object, if one on a suitable trajectory is discovered," he says, referring to an upcoming mission by the European Space Agency.

An origin story hidden in the dust

Even without a space mission, astronomers can use Earth's many telescopes to gain insight into the different properties of rogue comets like 2I/Borisov. "Imagine how lucky we were that a comet from a system light-years away simply took a trip to our doorstep by chance," says Bin Yang, an astronomer at ESO in Chile, who also took advantage of 2I/Borisov's passage through our Solar System to study this mysterious comet. Her team's results are published in Nature Astronomy.

Yang and her team used data from the Atacama Large Millimeter/submillimeter Array (ALMA), in which ESO is a partner, as well as from ESO's VLT, to study 2I/Borisov's dust grains to gather clues about the comet's birth and conditions in its home system.

They discovered that 2I/Borisov's coma -- an envelope of dust surrounding the main body of the comet -- contains compact pebbles, grains about one millimetre in size or larger. In addition, they found that the relative amounts of carbon monoxide and water in the comet changed drastically as it neared the Sun. The team, which also includes Olivier Hainaut, says this indicates that the comet is made up of materials that formed in different places in its planetary system.

The observations by Yang and her team suggest that matter in 2I/Borisov's planetary home was mixed from near its star to further out, perhaps because of the existence of giant planets, whose strong gravity stirs material in the system. Astronomers believe that a similar process occurred early in the life of our Solar System.

While 2I/Borisov was the first rogue comet to pass by the Sun, it was not the first interstellar visitor. The first interstellar object to have been observed passing by our Solar System was ?Oumuamua, another object studied with ESO's VLT back in 2017. Originally classified as a comet, ?Oumuamua was later reclassified as an asteroid as it lacked a coma.

Notes

[1] Polarimetry is a technique to measure the polarisation of light. Light becomes polarised, for example, when it goes through certain filters, like the lenses of polarised sunglasses or cometary material. By studying the properties of sunlight polarised by a comet's dust, researchers can gain insights into the physics and chemistry of comets.

More information

This research highlighted in the first part of this release was presented in the paper "Unusual polarimetric properties for interstellar comet 2I/Borisov" to appear in Nature Communications (doi: [10.1038/s41467-021-22000-x] - https://www.nature.com/articles/s41467-021-22000-x ). The second part of the release highlights the study "Compact pebbles and the evolution of volatiles in the interstellar comet 2I/Borisov" to appear in Nature Astronomy (doi: [10.1038/s41550-021-01336-w] - https://www.nature.com/articles/s41550-021-01336-w ).

The team who conducted the first study is composed of S. Bagnulo (Armagh Observatory & Planetarium, UK [Armagh]), A. Cellino (INAF - Osservatorio Astrofisico di Torino, Italy), L. Kolokolova (Department of Astronomy, University of Maryland, US), R. Nežič (Armagh; Mullard Space Science Laboratory, University College London, UK; Centre for Planetary Science, University College London/Birkbeck, UK), T. Santana-Ros (Departamento de Fisica, Ingeniería de Sistemas y Teoría de la Señal, Universidad de Alicante, Spain; Institut de Ciencies del Cosmos, Universitat de Barcelona, Spain), G. Borisov (Armagh; Institute of Astronomy and National Astronomical Observatory, Bulgarian Academy of Sciences, Bulgaria), A. A. Christou (Armagh), Ph. Bendjoya (Université Côte d'Azur, Observatoire de la Côte d'Azur, CNRS, Laboratoire Lagrange, Nice, France), and M. Devogele (Arecibo Observatory, University of Central Florida, US).

The team who conducted the second study is composed of Bin Yang (European Southern Observatory, Santiago, Chile [ESO Chile]), Aigen Li (Department of Physics and Astronomy, University of Missouri, Columbia, USA), Martin A. Cordiner (Astrochemistry Laboratory, NASA Goddard Space Flight Centre, USA and Department of Physics, Catholic University of America, Washington, DC, USA), Chin-Shin Chang (Joint ALMA Observatory, Santiago, Chile [JAO]), Olivier R. Hainaut (European Southern Observatory, Garching, Germany), Jonathan P. Williams (Institute for Astronomy, University of Hawai'i, Honolulu, USA [IfA Hawai'i]), Karen J. Meech (IfA Hawai'i), Jacqueline V. Keane (IfA Hawai'i), and Eric Villard (JAO and ESO Chile).

ESO is the foremost intergovernmental astronomy organisation in Europe and the world's most productive ground-based astronomical observatory by far. It has 16 Member States: Austria, Belgium, the Czech Republic, Denmark, France, Finland, Germany, Ireland, Italy, the Netherlands, Poland, Portugal, Spain, Sweden, Switzerland and the United Kingdom, along with the host state of Chile and with Australia as a Strategic Partner. ESO carries out an ambitious programme focused on the design, construction and operation of powerful ground-based observing facilities enabling astronomers to make important scientific discoveries. ESO also plays a leading role in promoting and organising cooperation in astronomical research. ESO operates three unique world-class observing sites in Chile: La Silla, Paranal and Chajnantor. At Paranal, ESO operates the Very Large Telescope and its world-leading Very Large Telescope Interferometer as well as two survey telescopes, VISTA working in the infrared and the visible-light VLT Survey Telescope. Also at Paranal ESO will host and operate the Cherenkov Telescope Array South, the world's largest and most sensitive gamma-ray observatory. ESO is also a major partner in two facilities on Chajnantor, APEX and ALMA, the largest astronomical project in existence. And on Cerro Armazones, close to Paranal, ESO is building the 39-metre Extremely Large Telescope, the ELT, which will become "the world's biggest eye on the sky".

The Atacama Large Millimeter/submillimeter Array (ALMA), an international astronomy facility, is a partnership of ESO, the U.S. National Science Foundation (NSF) and the National Institutes of Natural Sciences (NINS) of Japan in cooperation with the Republic of Chile. ALMA is funded by ESO on behalf of its Member States, by NSF in cooperation with the National Research Council of Canada (NRC) and the Ministry of Science and Technology (MOST) and by NINS in cooperation with the Academia Sinica (AS) in Taiwan and the Korea Astronomy and Space Science Institute (KASI). ALMA construction and operations are led by ESO on behalf of its Member States; by the National Radio Astronomy Observatory (NRAO), managed by Associated Universities, Inc. (AUI), on behalf of North America; and by the National Astronomical Observatory of Japan (NAOJ) on behalf of East Asia. The Joint ALMA Observatory (JAO) provides the unified leadership and management of the construction, commissioning and operation of ALMA.

UNIVERSITY PARK, Pa. -- A reproducibility crisis is ongoing in scientific research, where many studies may be difficult or impossible to replicate and thereby validate, especially when the study involves a very large sample size. For example, to evaluate the validity of a high-throughput genetic study's findings scientists must be able to replicate the study and achieve the same results. Now researchers at Penn State and the University of Minnesota have developed a statistical tool that can accurately estimate the replicability of a study, thus eliminating the need to duplicate the work and effectively mitigating the reproducibility crisis.

The team used its new method, which they describe in a paper publishing today (March 30) in Nature Communications, to confirm the findings of a 2019 study on the genetic factors that contribute to smoking and drinking addiction but noted that it also can be applied to other genome-wide association studies -- or studies that investigate the genetic underpinnings for diseases.

"While we applied the method to study smoking and drinking addiction-related outcomes, it could benefit other similar large-scale consortia studies, including current studies on the host genetic contribution to COVID-19 symptoms," said Dajiang Liu, associate professor of public health sciences and biochemistry and molecular biology, Penn State.

According to Liu, to detect patterns in genome-wide association studies it is important to obtain data from a large number of individuals. Scientists often acquire these data by combining many existing similarly designed studies, which is what Liu and his colleagues did for the 2019 smoking and drinking addiction study that ultimately comprised 1.2 million individuals.

"We worked really hard to collect all of the patient samples that we could manage," said Liu, noting that the data came from biobanks, epidemiology studies and direct-to-consumer genetic testing companies, such as 23andMe. However, he added, since the team used all of the available studies in its analysis, there were none leftover to use as comparisons for validation. "Our statistical method allows researchers to assess the replicability of genetic association signals without a replication dataset," he said. "It helps to maximize the power of genetic studies as no samples need to be reserved for replication; instead, all samples can be used for discoveries."

The team's method, which they call MAMBA (Meta-Analysis Model-Based Assessment of replicability), evaluates the strength and consistency of the associations between atypical bits of DNA, called single nucleotide polymorphisms (SNPs), and disease traits such as addiction. Specifically, MAMBA calculates the probability that if an experiment can be repeated with a different set of individuals, the relationships between the SNPs and those individuals' traits would be the same or similar as in the first experiment.

Qunhua Li, associate professor of statistics, Penn State, explained that MAMBA assigns a higher probability of replicability (PPR) for each SNP if the SNP is significantly associated with the trait being evaluated and if its estimated effect sizes are consistent across multiple studies.

"For example," said Li, "if the majority of participants who are addicted to smoking have a certain SNP that differs from non-addicted people, and if this SNP shows up across people in multiple smaller studies, then MAMBA will give it a higher PPR, which suggests that the SNP is probably important in addiction."

The researchers demonstrated the value of their method by applying it to Liu's 2019 study on smoking and drinking addiction. Among the 556 common and low-frequency SNP association signals, the team identified 529 with PPR greater than 99%. In an extended analysis of around 4,300 rare SNPs, the researchers identified 2,807 SNPs with PPR greater than 99%.

"Interestingly, we found that certain genes that are known to be responsible for lipid metabolism also influence smoking addiction," said Bibo Jiang, assistant professor of public health sciences, Penn State, noting that the phenomenon is known as pleiotropy -- when a gene influences two seemingly irrelevant traits. "If we want to design medications that target those genes to help people stop smoking, we should be mindful of any underlying conditions related to lipid metabolism, such as high cholesterol, that they may have."

Liu noted that the method can be applied to genome-wide association studies focused on a wide variety of traits. "I think in the next decade or so, an essential focus of biology will be to interpret and make sense of those genome-wide association study discoveries and whether we can translate some of them into medications to facilitate personalized medicine," he said. "We are excited to be able to offer this statistical approach as a service to the research community."

IIASA researchers have used Sentinel 1 satellite imagery from the European Space Agency to produce a map of the extent and year of detection of oil palm plantations in Indonesia, Malaysia, and Thailand that will help policymakers and other stakeholders understand trends in oil palm expansion while also providing an accurate map for landscape-level planning.

The world's appetite for palm oil seems to know no bounds. We use it in everything from beauty products and food, to industrial processes and biofuels to fulfill our energy needs. This ever growing demand has caused oil palm production to more than double in the last two decades, a development which has in turn deeply impacted natural forest ecosystems and biodiversity, while also significantly contributing to climate change by releasing carbon from converted forests and peatlands into the atmosphere. Today, almost 90% of the world's oil palm production takes place in Southeast Asia. While oil palm is known to be the most efficient oil producing plant globally, yields vary dynamically with plantation stand age, management practices, and location. To understand trends in oil palm plantation expansion and for landscape-level planning, accurate maps are needed. To this end, IIASA researchers have provided a detailed map of oil palm extent in 2017 using *Sentinel 1 satellite imagery from the European Space Agency in a new paper published in Nature Scientific Data.

"We specifically wanted to determine the extent and age of oil palm plantations across Southeast Asia and see if we could use technologies such as Google Earth Engine and data mining algorithms to produce an accurate map of oil palm extent from Sentinel 1 radar data, which could potentially be operationalized into a near-real time oil palm detection system. In addition, we wanted to explore the possibility of using time series analysis to go backwards in time and determine the age at which the plantation can first be detected (i.e., when trees are around 2 to 3 years in age)," explains lead author Olga Danylo, a researcher with the IIASA Novel Data Ecosystems for Sustainability Research Group.

While oil palm extent has been mapped before, this paper uses Sentinel 1 satellite data in combination with other data sets to map extent, along with time series from the Landsat archive to derive the year of plantation detection (which is a proxy for productive age of the plantations). This additional information is valuable for examining questions related to oil palm expansion over the last two decades, as well as the ability to calculate yields from the age information. (Yields increase during the plant's youth phase in the first seven years, reach a plateau during the prime age of 7-15 years, and then slowly start to decline before palms are replaced at the age of 25-30 years.) Therefore, knowing the exact extent and age of plantations across a landscape is crucial for landscape-level planning to allow for both sustainable oil palm production and forest conservation.

The paper's key output is a 30 m resolution map of Southeast Asia that indicates if oil palm is present and the year of detection of the plantation - a brand new feature that allows for a better understanding of oil palm expansion in Southeast Asia. The oil palm extent map has an overall accuracy of 83%, which is comparable to other products. The largest area of oil palm can be found in Sumatra and Kalimantan, with expansions in all major regions since the year 2000. The maps shows that the largest relative expansions over the last decade have taken place in Kalimantan, insular Malaysia, and Thailand, but interestingly, the net oil palm plantation area, excluding milling facilities, roads, and other related infrastructure, might be significantly smaller than previously thought.

According to the researchers, the new map could furthermore support the calculation of estimates of greenhouse gas emissions and removals for specific regions, provide a means whereby official statistics can be independently verified, and could also be used in analyses related to determining the economic trade-offs in different types of land use. In addition, the oil palm map in combination with spatial information about estate boundaries could help to identify specific actors and their adherence to environmental legislation and compliance with sustainability standards.

"Buying certified palm oil (RSPO) is a means of avoiding tropical deforestation. Our map can inform which sites are eligible for RSPO certification and it can help policymakers such as the EU commission to make more accurate and directed policies in relation to palm oil by for instance excluding palm oil from certain (recently deforested) areas from biofuels in the EU," concludes coauthor Johannes Pirker, a guest researcher with the Agriculture, Forestry, and Ecosystem Services Research Group at IIASA

The data set used in this paper is publicly accessible for download from the IIASA DARE repository.

* The Sentinel-1 mission comprises a constellation of two polar-orbiting satellites, operating day and night performing C-band synthetic aperture radar imaging, enabling them to acquire imagery regardless of the weather. Sentinel 1 satellite imagery is particularly valuable in tropical countries which are covered by clouds nearly all year.

RESTON, Va. - Greater sage-grouse populations have declined significantly over the last six decades, with an 80% rangewide decline since 1965 and a nearly 40% decline since 2002, according to a new report by the U.S. Geological Survey. Although the overall trend clearly shows continued population declines over the entire range of the species, rates of change do vary regionally.

The report represents the most comprehensive analysis of greater sage-grouse population trends ever produced and lays out a monitoring framework to assess those trends moving forward. The study can also be used to evaluate the effectiveness of greater sage-grouse conservation efforts and analyze factors that contribute to habitat loss and population change -- all critical information for resource managers.

"Every day, the USGS brings diverse stakeholders the compelling science they need to make strategic, on-the-ground policy and management decisions," said David Applegate, associate director exercising the delegated authority of the USGS director. "With this framework in place, resource managers can more nimbly respond to population declines with actions such as redistributing monitoring efforts or prioritizing where management intervention may be needed."

USGS scientists and colleagues developed the framework to estimate greater sage-grouse population trends in the 11 western states where the species lives - California, Colorado, Idaho, Montana, Nevada, North Dakota, Oregon, South Dakota, Utah, Washington and Wyoming. The greater sage-grouse is a vulnerable species and an indicator of the overall health of the iconic sagebrush ecosystem.

The research found that in recent decades the rate of greater sage-grouse decline increased in western portions of the species' range, particularly in the Great Basin, while the declines have been less severe in eastern areas. Western Wyoming was the only region to show relatively stable sage-grouse populations recently. Taken as a whole, the greater sage-grouse population now is less than a quarter of what it was more than 50 years ago.

To complete the framework, USGS and Colorado State University researchers collaborated with the Western Association of Fish and Wildlife Agencies, individual state wildlife agencies and the Bureau of Land Management. Together, they compiled information and created a rangewide database of greater sage-grouse breeding grounds. Researchers used that information to assess past and current sage-grouse population trends in different parts of the species' range.

In addition to the database and population-trend assessment, researchers also developed a "Targeted Annual Warning System" to alert biologists and managers when local greater sage-grouse populations begin to decline or have diverged from regional trends. The research identified the most at-risk breeding grounds, with the greatest risk seen at the periphery of the species' range. The report shows that there is only a 50% chance that most breeding grounds, called leks, will be productive in about 60 years from now if current conditions persist. USGS scientists will continue to analyze information to determine the factors driving changes in breeding areas and populations, including the influence of habitat loss and degradation.

"The framework we developed will help biologists and managers make timely decisions based on annual monitoring information," said Peter Coates, USGS scientist and lead author of the report. "This will allow them to address local issues before they have significant impacts on the population."

What The Study Did: Researchers investigated COVID-19 vaccine intentions among racially and ethnically diverse samples of health workers and the general population in the San Francisco Bay area.

Authors: Kevin Grumbach, M.D., of the San Francisco General Hospital and University of California, San Francisco, is the corresponding author.

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/

(doi:10.1001/jamainternmed.2021.1445)

Editor's Note: The article includes conflict of interest and funding/support disclosures. Please see the article for additional information, including other authors, author contributions and affiliations, conflict of interest and financial disclosures, and funding and support.

Working with fruit flies, scientists at Johns Hopkins Medicine say they have identified a new molecular pathway that helps steer moving cells in specific directions. The set of interconnected proteins and enzymes in the pathway act as steering and rudder components that drive cells toward an "intended" rather than random destination, they say.

In a report on the work, published March 2 in Cell Reports, these same molecular pathways, say the scientists, may drive cancer cells to metastasize or travel to distant areas of the body and may also be important for understanding how cells assemble and migrate in an embryo to form organs and other structures.

The team of scientists was led by Deborah Andrew, Ph.D., professor of cell biology and associate director for faculty development for the Institute for Basic Biomedical Sciences at the Johns Hopkins University School of Medicine.

Andrew and her colleagues began this research while studying a gene called Tre1 and its role in the development of salivary glands in fruit flies. The tools to study the effects of turning the gene on and off weren't ideal, she says. So, two of the team members, Caitlin Hanlon, Ph.D., of Quinnipiac University and JiHoon Kim, Ph.D., of Johns Hopkins, generated fruit flies that lack the protein-coding portion of the Tre1 gene. The pair also put a fluorescent tag on the Tre1 protein to learn where it localized during key steps in development.

In experiments with fruit fly embryos carrying an intact Tre1 gene, cells that produce future generations of the organism, called germ cells, migrate correctly to the sex organ, known as the gonad.

"Without the Tre1 gene, however, most of the germ cells failed to meet up with other nongerm cells, or somatic cells, of the gonad," says Andrew. "Correct navigation of germ cells is important to ensure that future generations of the organism will happen."

This is not the first time that scientists noted Tre1's importance in germ cell navigation. Two research teams from Indiana University and the Massachusetts Institute of Technology had previously made the link. However, says Andrew, questions remained about what happens inside germ cells to get cells to the right place once Tre1 activates.

It was already known that the Tre1 gene encodes a protein that spans the cell membrane multiple times and pokes out onto the cell's surface. It's a member of a large family of proteins called G protein-coupled receptors, which enable cells to communicate and respond to signals from other cells and light and odor cues. Nearly 35% of FDA approved medicines target G protein-coupled receptors, says Andrew.

To more precisely track the molecular events downstream of Tre1, Kim, a research associate and postdoctoral fellow at the Johns Hopkins University School of Medicine, used tissue cultures of fruit fly cells to find the location of fluorescently tagged molecules that are potentially triggered by the activated Tre1 protein. In the tissue cultures and germ cells of living flies, Kim uncovered the downstream genetic pathway.

He found that Tre1 functions as the cell's helmsman, controlling steering of the cell. Tre1 activates the cell's steering and rudder components by spurring on a cascade of proteins and enzymes, including a phospho-inositol kinase, PI(4,5)P2, dPIP5K, dWIP and WASp.

At the end of the molecular cascade, a chain of actin proteins forms in a protrusion at the cell's leading edge to exert mechanical forces for movement.

The scientists also searched for the upstream signal that activates Tre1. They used a genetically engineered protein made by researchers at the University of California, San Francisco to track the location of a signaling protein called Hedgehog, which has previously been linked to germ cell migration, although its role in this process has been disputed.

In germ cells, Hedgehog signaling increases the membrane levels of a protein called Smoothened, which is found in the cells' leading edge protrusion where Tre1 is also found.

The scientists plan to continue studying the pathways surrounding Tre1 and connections between the proteins and enzymes involved in the pathway.

"A deeper understanding of how moving cells navigate and spread has the potential to provide more targets for interrupting the spread of cancer cells," says Andrew.

Researchers at KU Leuven (Belgium) have succeeded for the first time in measuring brain waves directly via a cochlear implant. These brainwaves indicate in an objective way how good or bad a person's hearing is. The research results are important for the further development of smart hearing aids.

A cochlear implant enables people with severe hearing loss to hear again. An audiologist adjusts the device based on the user's input, but this is not always easy. Think of children who are born deaf or elderly people with dementia. They have more difficulty assessing and communicating how well they hear the sounds, resulting in an implant that is not optimally tuned to their situation.

A possible solution is to adjust the implant based on brain waves, which contain information about how the person processes the sounds that they hear. This kind of objective measurement can be made with an electroencephalogram (EEG), whereby electrodes are placed on the head. However, it would be more efficient if the implant itself could record the brain waves to measure hearing quality.

Experimental implant

Research by KU Leuven and manufacturer Cochlear on a few human test subjects has shown for the first time that this is possible. "We used an experimental implant that works exactly the same way as a normal implant, but with easier access to the electronics," says postdoctoral researcher Ben Somers from the Experimental Oto-rhino-laryngology unit.

"A cochlear implant contains electrodes that stimulate the auditory nerve. This is how sound signals are transmitted to the brain. In our research, we have succeeded in using these implanted electrodes to record the brain waves that arise in response to sound. That is a first. An additional advantage is that by carefully choosing the right measuring electrodes, we can measure larger brain responses than the classical EEG with electrodes on the head."

Self-tuning device

An implant that can register brain waves and measure hearing quality on its own has various advantages, adds co-author Professor Tom Francart. "Firstly, we get an objective measurement that does not depend on the user's input. In addition, you could measure a person's hearing in everyday life and monitor it better. So, in the long run, the user would no longer have to undergo testing at the hospital. An audiologist could consult the data remotely and adjust the implant where necessary."

"In the future, it should even be possible for the hearing implant to adjust itself autonomously based on the recorded brain waves. We have a long way to go before that, but this study is a necessary first step. Based on our findings, manufacturers can now move forward with developing smart hearing devices that improve the quality of life of the people that use them. Besides audiological applications, there are numerous other possibilities that come with measuring brain waves. Think of monitoring sleep, attention span or epilepsy, but also, for example, so-called brain computer interfaces that allow you to control other devices with brainwaves."

Replacing regular common salt consumed by hypertensive patients in rural areas with a salt substitute can have a significant impact in terms of lowering their blood pressure, a new study by The George Institute for Global Health has revealed.

Researchers found that substituting a small part of the sodium in salt with potassium without altering the taste led to a substantial reduction in systolic blood pressure in these patients, supporting salt substitution as an effective, low-cost intervention for lowering blood pressure in rural India.

The study entitled "Effects of reduced-sodium added-potassium salt substitute on blood pressure in rural Indian hypertensive patients: a randomized, double-blind, controlled trial" provides the first-of-its-kind evidence from rural India on the effectiveness of a salt substitute and has been published in the American Journal of Clinical Nutrition.

Excess salt intake causes high blood pressure, a leading risk for cardiovascular disease. Almost all adult populations worldwide consume more than the recommended level of salt including those living in rural India, where average salt intake is nearly double the World Health Organization (WHO) recommendations of less than 5 g/day (2 g/day sodium).

"A large proportion of dietary salt in India comes from salt added to food cooked at home, but whether reduced-sodium salt substitutes can help to lower blood pressure had not been tested thus far," said Dr Jie Yu, Research Fellow, Cardiovascular Program, The George Institute and lead author of the study. "Our study is the first to show that salt substitutes could make a real difference in these communities."

"The study was conducted in the Siddipet region of Telangana State, and 502 participants with hypertension from 7 villages were enrolled," She added, "Participants were randomized to receive either regular salt (100% sodium chloride) or the salt substitute (70% sodium chloride/30% potassium chloride blend) and advised to replace all home salt use with the substitute."

The primary outcome was the change in systolic blood pressure from baseline to 3 months in the salt substitute group compared to the regular salt groups. Secondary outcomes included the change in diastolic blood pressure, 24-hour urinary biomarkers, and self-reported use and satisfaction with the study salts provided.

"At 3 months, the salt substitute intervention significantly decreased average systolic blood pressure by about 4.6 units, an effect comparable to some commonly prescribed anti-hypertensive medications," said Sudhir Raj Thout, Research Fellow, The George Institute India, the study co-author who led the study's field operations.

"There was also a significant increase in the amount of potassium consumed in the salt substitute group. Participants reported that they used the study salt nearly every day of the week and rated the taste of the study salts similarly, indicating that the reduced-sodium salt substitutes are acceptable for home cooking for our study participants." he added.

The findings have policy implications. "Our data suggest that using reduced-sodium, added-potassium salt substitute to replace regular salt for home cooking will likely be an effective and scalable intervention for blood pressure control in rural India," said Jason Wu, Associate Professor and Scientia Fellow at The George Institute, and supervisor of the study.

"As none of the participants were aware of the existence of reduced-sodium salt at the beginning of the study, this suggests policymakers should consider supporting increased access to, and education about the use of such salt substitutes for hypertensive patients in India."

Tsukuba, Japan - Although the heart beats autonomously, its function can be regulated by the brain in response to, for instance, stressful events. In a new study, researchers from the University of Tsukuba discovered a novel mechanism by which a specific part of the brain, the lateral habenula (LHb), regulates the cardiovascular system.

The cardiovascular system, specifically the heart and blood vessels, have a certain autonomy that allows them to function independently from the brain. In order for the individual to adapt to new, potentially threatening situations, the brain does have some regulatory power over the cardiovascular system. This is achieved by controlling the autonomic nervous system, which consists of the sympathetic and parasympathetic system. While the former has a stimulating effect on the cardiovascular system, including increasing the heart rate and blood pressure, the latter causes the opposite.

"From an evolutionary standpoint, the brain has had in incredibly important function in protecting the individual from predators," says lead author of the study Professor Tadachika Koganezawa. "But even in the absence of predators, our bodies react to stressful situations. In this study, we wanted to determine how the brain regulated the cardiovascular system via the autonomic nervous system."

To achieve their goal, the researchers focused on the LHb. Located deep within the brain, the LHb has been known to control behavioral responses to stressful events, and as such to elicit strong cardiovascular responses. However, the way in which it does so has remained unclear. To address this question, the researchers electrically stimulated the LHb in rats by inserting an electrode through the skull. Stimulation of the LHb resulted in bradycardia (low heart rate) and increased mean arterial pressure (MAP), which is a clinically useful parameter for assessing overall blood pressure.

To determine how the LHb interplays with the autonomic nervous system to regulate the cardiovascular system, the researchers then turned off the parasympathetic system by means of cutting the main parasympathetic nerve, the vagal nerve, or using a drug to antagonize it. While this suppressed the LHb's effect on the heart rate, it did not change the MAP. Antagonizing the sympathetic system did the opposite--it decreased the MAP but did not change the heart rate.

To understand the mechanism by which the LHb elicits these cardiovascular responses, the researchers focused on the neurotransmitter serotonin, which plays an important role in the brain in modulating mood, cognition, and memory, among other functions. While blocking all serotonin receptors significantly reduced the LHb's effect on both the MAP and heart rate, the researchers found that specific subtypes of serotonin receptors were particularly involved in the process.

"These are striking results that show how the lateral habenula controls the cardiovascular system. Our results demonstrate the mechanism of a neural circuit that plays an important role in stress-induced behavioral responses," says author of the study Professor Masayuki Matsumoto.