Culture

They call it artificial intelligence -- not because the intelligence is somehow fake. It's real intelligence, but it's still made by humans. That means AI -- a power tool that can add speed, efficiency, insight and accuracy to a researcher's work -- has many limitations.

It's only as good as the methods and data it has been given. On its own, it doesn't know if information is missing, how much weight to give differing kinds of information or whether the data it draws on is incorrect or corrupted. It can't deal precisely with uncertainty or random events -- unless it learns how. Relying exclusively on data, as machine-learning models usually do, it does not leverage the knowledge experts have accumulated over years and physical models underpinning physical and chemical phenomena. It has been hard to teach the computer to organize and integrate information from widely different sources.

Now researchers at the University of Delaware and the University of Massachusetts-Amherst have published details of a new approach to artificial intelligence that builds uncertainty, error, physical laws, expert knowledge and missing data into its calculations and leads ultimately to much more trustworthy models. The new method provides guarantees typically lacking from AI models, showing how valuable -- or not -- the model can be for achieving the desired result.

Joshua Lansford, a doctoral student in UD's Department of Chemical and Biomolecular Engineering, and Prof. Dion Vlachos, director of UD's Catalysis Center for Energy Innovation, are co-authors on the paper published Oct. 14 in the journal Science Advances. Also contributing were Jinchao Feng and Markos Katsoulakis of the Department of Mathematics and Statistics at the University of Massachusetts-Amherst.

The new mathematical framework could produce greater efficiency, precision and innovation for computer models used in many fields of research. Such models provide powerful ways to analyze data, study materials and complex interactions and tweak variables in virtual ways instead of in the lab.

"Traditionally in physical modelings, we build a model first using only our physical intuition and expert knowledge about the system," Lansford said. "Then after that, we measure uncertainty in predictions due to error in underlying variables, often relying on brute-force methods, where we sample, then run the model and see what happens."

Effective, accurate models save time and resources and point researchers to more efficient methods, new materials, greater precision and innovative approaches they might not otherwise consider.

The paper describes how the new mathematical framework works in a chemical reaction known as the oxygen reduction reaction, but it is applicable to many kinds of modeling, Lansford said.

"The chemistries and materials we need to make things faster or even make them possible -- like fuel cells -- are highly complex," he said. "We need precision.... And if you want to make a more active catalyst, you need to have bounds on your prediction error. By intelligently deciding where to put your efforts, you can tighten the area to explore.

"Uncertainty is accounted for in the design of our model," Lansford said. "Now it is no longer a deterministic model. It is a probabilistic one."

With these new mathematical developments in place, the model itself identifies what data are needed to reduce model error, he said. Then a higher level of theory can be used to produce more accurate data or more data can be generated, leading to even smaller error boundaries on the predictions and shrinking the area to explore.

"Those calculations are time-consuming to generate, so we're often dealing with small datasets -- 10-15 data points. That's where the need comes in to apportion error."

That's still not a money-back guarantee that using a specific substance or approach will deliver precisely the product desired. But it is much closer to a guarantee than you could get before.

This new method of model design could greatly enhance work in renewable energy, battery technology, climate change mitigation, drug discovery, astronomy, economics, physics, chemistry and biology, to name just a few examples.

Artificial intelligence doesn't mean human expertise is no longer needed. Quite the opposite.

The expert knowledge that emerges from the laboratory and the rigors of scientific inquiry is essential, foundational material for any computational model.

New Orleans, LA - A review of heat-not-burn (HNB) tobacco products from the laboratory of Dr. Jason Gardner, Professor of Physiology at LSU Health New Orleans School of Medicine, reports an association with elevated blood pressure, increased heart rate, cell death, and circulatory dysfunction shown by early studies. Additionally, chemicals found in the vapor produced by HNB devices have previously been shown to impair lung function, put users at risk of heart attack and stroke, cause cancers, increase circulating low-density lipoprotein ("bad cholesterol") and more. The review is published in the American Journal of Physiology-Heart and Circulatory Physiology, available online here.

Cigarette smoking continues to decline globally, but vaping is becoming more popular, especially among youth and young adults. Recent cases of vaping-associated lung injury may lead consumers to try new methods of nicotine consumption. Heat-not-burn products are newcomers to the U.S. market. They produce nicotine-containing vapor by heating tobacco at low temperatures. This is in contrast to cigarettes that use high temperatures to burn tobacco and produce smoke or e-cigarettes that heat e-liquid, which contains nicotine but not tobacco, to produce vapor.

Due to the novelty of these products, little research has been conducted on HNB devices. The Gardner lab compiled findings from dozens of human, animal, and cell culture studies to determine associated inhalants and potential health effects, with an emphasis on the heart, arteries, and veins. Findings suggest that HNB devices produce fewer pollutants than cigarettes, but it is unclear if these reductions are reflected in health outcomes of users.

"While relatively new to the U.S., heat-not-burn products have become popular in other countries including Japan, Italy, and Korea," notes lead author Nicholas Fried, an MD/PhD student in Dr. Gardner's laboratory. "These products are often touted as a replacement for cigarettes, but the evidence does not necessarily support that. Almost all Korean users of heat-not-burn products are also current cigarette smokers; nearly half of Italian users had never even smoked a cigarette. These trends worryingly suggest that heat-not-burn may be a compliment or gateway to cigarette smoking, rather than a 'healthy' replacement. More troubling, nearly 2% of high school students in the U.S. are already using HNB tobacco products, and surveys show that 25% of students are susceptible to trying them. There is potential for these devices to become a significant public health issue."

Dr. Gardner adds, "Heat-not-burn devices are marketed as a safer alternative to cigarettes for existing smokers. However, as we have learned from vaping and e-cigarettes, these products are very likely to be used by minors and never-smokers due to marketing, flavor options, and lack of social stigma that is found with traditional cigarettes."

The authors conclude, "Use of these products can lead to nicotine addiction and additional clinical, basic science, and epidemiological studies are needed to better understand the health effects of HNB products. This knowledge will assist consumers, physicians, lawmakers, and regulatory bodies in making informed decisions about these products."

COLUMBUS, Ohio - Knowing you have developed antibodies against the SARS-CoV-2 virus after recovering from COVID-19 doesn't tell you everything about your immunity. The levels and even types of antibodies can differ among patients, and those differences can influence whether a person is protected against being reinfected.

Scientists at The Ohio State University have developed a new lab testing procedure for the detection of antibodies against SARS-CoV-2 that gives results more quickly than existing assays and specifically identifies so-called "neutralizing" antibodies - those that protect by blocking infection of cells.

"With many assays currently in use, we can detect antibodies, but that doesn't tell us if they're neutralizing antibodies. We only know the level of antibodies someone has," said Shan-Lu Liu, professor in the Ohio State College of Veterinary Medicine's Department of Veterinary Biosciences and the senior author of a new journal article describing the assay.

"Some antibodies might be protective, some might not be protective, and some might even enhance infection - we know with this type of coronavirus and some other viruses, some antibodies can even do harm," he said. "Our assay examines whether antibodies are potentially protective, which means they prevent a patient from reinfection and block viral replication. That's the outcome of infection that we want people to have."

In analyses of blood samples from several different populations that had tested positive for COVID-19, the researchers found with this new assay that, overall, ICU patients had produced the highest concentration of neutralizing antibodies, and convalescent plasma donors and health care workers had the lowest antibody levels.

"So the more severe the disease, the higher the antibody levels produced. And what this tells us is there is a wide spectrum of different antibody levels after infection," said Liu, also an investigator in the Center for Retrovirus Research and co-director of the Viruses and Emerging Pathogens Program in Ohio State's Infectious Diseases Institute. "We're in a pandemic now, but eventually we'll be able to see not just how many people were infected, but also the outcome. Our assay could be used to tell whether antibodies have been developed in individuals who have had contacts with SARS-CoV-2."

The research is published online in the journal JCI Insight.

Liu and colleagues developed what is called a "pseudotype" virus neutralizing antibody assay, in which an HIV vector and core is coated with the SARS-CoV-2 spike protein to detect antibodies against the coronavirus. The team applied a new approach by selecting a different form of light-producing enzyme that can be detected conveniently in culture media containing the virus-infected cells. That choice saved several steps, and time, in the detection process without losing accuracy and sensitivity to the target virus.

Co-first authors Cong Zeng, a postdoctoral researcher, and Jack Evans, a student in the molecular, cellular and developmental biology graduate program, completed the majority of the work to develop the assay.

With the new analytical tool in hand, scientists in the College of Veterinary Medicine collaborated with Gerard Lozanski and others in the College of Medicine to analyze 221 patient blood samples to validate the effectiveness of the assay and verify that the detection test could be scaled up for widespread screening.

The samples were derived from 104 hospitalized COVID-19 patients, 49 of whom were in intensive care; 42 health care professionals who had tested positive for COVID-19; 38 convalescent plasma donors (recovered patients who donated plasma for potential therapeutic use in very sick COVID-19 patients); and 37 control samples from patients who had been hospitalized with respiratory conditions before September 2019.

Results showed that, in general, hospitalized patients - and ICU patients in particular - had the highest concentrations, or titers, of neutralizing antibodies in their systems. However, over 14% of those who had been hospitalized had no or very low levels of antibodies.

Of the health care professionals, 40% were negative for neutralizing antibodies and 36% had low concentrations. And more than half of the convalescent blood donors had concentrations of antibodies that were too low to qualify them as donors for treatment of COVID-19 patients, Liu said.

The assay detected no SARS-CoV-2 antibodies in the samples from people who had been sick with other types of respiratory diseases.

The test accuracy was further validated by verifying in a lab setting that the antibodies detected in the COVID-19 patient blood samples did in fact neutralize the authentic SARS-CoV-2 virus.

It won't be long before the assay is put to a larger test. The effectiveness, sensitivity and specificity of the assay were important factors in Ohio State's successful application for a $10 million National Cancer Institute grant awarded last month for studies of the long-term impact of COVID-19 on first responders, health care workers and the general population. Two of the co-authors on the JCI Insights paper will be co-principal investigators of the first-responders study: Eugene Oltz, chair of microbial infection and immunity in the College of Medicine, and Linda Saif, Distinguished University Professor in the College of Veterinary Medicine's Department of Veterinary Preventive Medicine and the Food Animal Health Research Program in the College of Food, Agricultural and Environmental Sciences.

"We will use this assay to conduct a serological study of first responders in Columbus, among others," Liu said.

Additional applications could include screening for protective qualities in lab-manufactured monoclonal antibodies designed for therapeutic purposes and neutralizing antibody production in vaccine candidates.

Patent applications have been filed covering the assay and its use in a variety of applications. Inventors named on the applications are Liu, Zeng, Evans, and co-authors Panke Qu and Yi Min Zheng.

"We are pleased to have developed a neutralization assay which provides a sensitive, specific and simple method for determining the neutralizing antibody titers in patient serum or plasma with results being achieved in 24 hours - without requiring access to a biosafety level-3 facility," Liu said.

"We'd like to make it widely available as quickly as possible because we think it's a rapid and simple system compared to other systems."

Situated at the threshold of the South Asian monsoon, the Thar Desert is an important region for understanding how past environmental change impacted patterns of human migration and adaptation to new habitats (Figure 1). Recent research highlighting the role of the Thar Desert in human prehistory has indicated that humans spread eastwards into the region starting from 114 thousand years ago during a phase of enhanced monsoonal rainfall, when the desert was transformed into lush grasslands. However, more recent phases of sand dune activity have obscured these ancient landscapes inhabited by earlier human populations.

In a new study published in Quaternary Science Reviews, researchers from The Max Planck Institute for the Science of Human History (MPI-SHH), Anna University, and the Indian Institute of Science, Education and Research (IISER) Kolkata document evidence for river activity in the central Thar Desert. This evidence indicates a river flowed with phases of activity dating to approx. 172, 140, 95 and 78 thousand years ago, nearby to Bikaner, which is over 200 km away from the nearest modern river. These findings predate evidence for activity in modern river courses across the Thar Desert as well as dried up course of the Ghaggar-Hakra River. The presence of a river running through the central Thar Desert would have offered a life-line to Palaeolithic populations, and potentially an important corridor for migrations.

Lost Rivers of the Thar Desert

Located at the threshold of monsoonal Asia, the Thar Desert marks the eastern extent of the desert belt that stretches westwards across Arabia and the Sahara. While this desert belt is typically thought of as inhospitable to early humans, it is becoming increasingly clear that during humid phases in the past human populations have prospered in these landscapes. This is perhaps best known in western South Asia from studying the Indus Civilisation (also known as the Harappan Civilisation) which flourished at the margins of the Thar Desert along the course of the now-seasonal Ghaggar-Hakra River between 3200-1500 BCE, and is thought to have inspired the mythological Saraswati River mentioned in the Rig Veda.

Yet the potential importance of 'lost' rivers for earlier inhabitants of the Thar Desert have been overlooked. "The Thar Desert has a rich prehistory, and we've been uncovering a wide range of evidence showing how Stone Age populations not only survived but thrived in these semi-arid landscapes," says Jimbob Blinkhorn of MPISHH. "We know how important rivers can be to living in this region, but we have little detail on what river systems were like during key periods of prehistory".

Studies of satellite imagery have shown a dense network of river channels crossing the Thar Desert. "These studies can indicate where rivers and streams have flown in the past, but they can't tell us when" explains Prof Hema Achyuthan of Anna University, Chennai. "To demonstrate how old such channels are, we had to find evidence on the ground for river activity in the middle of the desert".

Nal Quarry

A deep deposit of river sands and gravels was studied by the team, which had been exposed by quarrying activity near the village of Nal, just outside of Bikaner. By studying the different deposits, the researchers were able to document different phases of river activity. "We immediately saw evidence for a substantial and very active river system from the bottom of the fluvial deposits, which gradually decreased in power through time" explained Achyuthan. "Standing in the middle of the desert, the question we had to answer was 'How old was this river?'".

The researchers used a method called luminescence dating to understand when quartz grains in the river sands were buried. The results indicated that the strongest river activity at Nal occurred at approx. 172 and 140 thousand years ago, at a time when the monsoon was much weaker than today in the region. River activity continued at the site between 95 to 78 thousand years ago, after which only limited evidence for the presence of a river at the site, with evidence for a brief reactivation of the channel 26 thousand years ago.

A life-line in the desert

The age of this river flowing in the middle of the desert is of particular interest. The river was flowing at its strongest during a phase of weak monsoonal activity in the region, and may have been a life-line to human populations enabling them to inhabit the Thar Desert. The timeframe over which this river was active also overlaps with significant changes in human behaviour in the region, which have been linked with the earliest expansions of Homo sapiens from Africa into India. "This river flowed at a critical timeframe for understanding human evolution in the Thar Desert, across South Asia and beyond" says Blinkhorn, adding "This suggests landscape in which the earliest members of our own species, Homo sapiens, first encountered the monsoons and crossed the Thar Desert may have been very different to the landscape we can see today".

The next phase of research is to demonstrate where the river flowed from. Studies of satellite images have suggested a potential connection with a Himalayan source, such as the Sutlej. "We can't demonstrate where the river flowed from at present" says Blinkhorn, adding "but the Indira Ghandi Canal, sourced from the Sutlej River, gives us some insight into what happens when a river flows through the centre of the Thar Desert - plants and wildlife flourish, providing ideal conditions for early human populations."

October 19, 2020

JUPITER, FL--Human cells are encased by a membrane coated with diverse sugar molecules known as glycans. These glycans play many roles in health and disease, making them important to understand. Due to their unique properties, however, scientists have had limited tools to study them and their interactions in the body.

New research from the lab of biochemist Mia Huang, PhD, an assistant professor at Scripps Research in Jupiter, Florida, presents a strategy for capturing elusive interactions among glycans and their protein activators in live human cells. Huang and her colleagues applied the technique to improve understanding of liver disease and immune activation.

Writing in the journal the Proceedings of the National Academies of Sciences on Friday, Huang and colleagues focus on a glycan-binding protein called galectin-3. Collaborating with the lab of Scripps Research chemist Chris Parker, PhD, the team was able to catalog galectin-3's array of receptors by combining two strategies: proximity labelling and quantitative proteomics.

In the process, they discovered hundreds of galectin-3 interactors in live liver stellate cells and immune cells.

"These interactions escape traditional query because of their weak affinity and dynamic binding events," Huang says. "Our findings will empower our ability to approach, and hopefully treat, diseases based on glycosylation-mediated events, especially liver fibrosis and autoimmune disorders."

Finding the hook

Cells communicate with each other through the release of molecular signals. These signals, such as galectin-3, can activate the inflammatory response following viral infection, or generate a buildup of scar tissue following injury, for example.

At the biochemical level, for this to happen, a glycan-binding protein must attach to its membrane receptor like a fisherman's line hook wading through thick kelp to find its catch. Characterizing which hooks fit which glycoproteins is a necessary step to addressing the root causes of many illnesses, Huang says.

A graduate student in Huang's lab, Eugene Joeh, devised a chemical fishing expedition to search for galectin-3. Joeh, a student in Scripps Research's Skaggs Graduate School of Chemical and Biological Sciences, suggested tethering an enzyme called APEX2, chosen for its relatively small size and ability to stay active both inside and outside the cell, to the galectin-3 molecules. He then allowed the paired molecules to freely diffuse onto cells. Next, he added the chemicals biotin phenol and hydrogen peroxide to create highly reactive tags that label the binding complexes so that they could be more easily identified and characterized. He was helped by a participant in the institute's high school internship program, Kenan Fellow Jonathan Hung, a student at Suncoast High School at the time of his internship, now a freshman at Johns Hopkins University.

Liver fibrosis and beyond

The liver plays many roles. It processes nutrients and medicines absorbed through digestion. It clears toxins, breaks down alcohol, and stores or releases fats and sugars during times of plenty or scarcity. It makes bile to help digest fats. Over time, injury to the liver from conditions such as alcoholism, autoimmune disease, drug abuse, or viral hepatitis, can lead to a condition called liver fibrosis. This can cause chronic high blood pressure, cirrhosis or even liver failure.

The events that lead to this unhealthy cascade involve an interaction between liver-based immune white blood cells called macrophages and fat-storing liver cells called stellate cells. The cascade begins when liver macrophages activate liver stellate cells through the release of galectin-3. The docking of galectin-3 to its sugary glycoprotein receptors triggers the stellate cell to ooze collagen and make other changes.

This signal, galectin-3, isn't only a force to consider in liver fibrosis. It also plays an important role in other cells--especially those in the immune system that help defend against infections, cancer and poisons, Huang says.

"It is noteworthy that several of these proteins are important in both the innate and adaptive immune responses," Huang says.

The discovery of so many galectin-3 receptors raises many new questions, she adds. The work continues.

"This has given us a priority list of proteins that will be the subject of further work on the regulation of immunity and the activation of liver stellate cells," she says.

HERSHEY, Pa. -- Certain oral antiseptics and mouthwashes may have the ability to inactivate human coronaviruses, according to a Penn State College of Medicine research study. The results indicate that some of these products might be useful for reducing the viral load, or amount of virus, in the mouth after infection and may help to reduce the spread of SARS-CoV-2, the coronavirus that causes COVID-19.

Craig Meyers, distinguished professor of microbiology and immunology and obstetrics and gynecology, led a group of physicians and scientists who tested several oral and nasopharyngeal rinses in a laboratory setting for their ability to inactivate human coronaviruses, which are similar in structure to SARS-CoV-2. The products evaluated include a 1% solution of baby shampoo, a neti pot, peroxide sore-mouth cleansers, and mouthwashes.

The researchers found that several of the nasal and oral rinses had a strong ability to neutralize human coronavirus, which suggests that these products may have the potential to reduce the amount of virus spread by people who are COVID-19-positive.

"While we wait for a vaccine to be developed, methods to reduce transmission are needed," Meyers said. "The products we tested are readily available and often already part of people's daily routines."

Meyers and colleagues used a test to replicate the interaction of the virus in the nasal and oral cavities with the rinses and mouthwashes. Nasal and oral cavities are major points of entry and transmission for human coronaviruses. They treated solutions containing a strain of human coronavirus, which served as a readily available and genetically similar alternative for SARS-CoV-2, with the baby shampoo solutions, various peroxide antiseptic rinses and various brands of mouthwash. They allowed the solutions to interact with the virus for 30 seconds, one minute and two minutes, before diluting the solutions to prevent further virus inactivation. According to Meyers, the outer envelopes of the human coronavirus tested and SARS-CoV-2 are genetically similar so the research team hypothesizes that a similar amount of SARS-CoV-2 may be inactivated upon exposure to the solution.

To measure how much virus was inactivated, the researchers placed the diluted solutions in contact with cultured human cells. They counted how many cells remained alive after a few days of exposure to the viral solution and used that number to calculate the amount of human coronavirus that was inactivated as a result of exposure to the mouthwash or oral rinse that was tested. The results were published in the Journal of Medical Virology.

The 1% baby shampoo solution, which is often used by head and neck doctors to rinse the sinuses, inactivated greater than 99.9% of human coronavirus after a two-minute contact time. Several of the mouthwash and gargle products also were effective at inactivating the infectious virus. Many inactivated greater than 99.9% of virus after only 30 seconds of contact time and some inactivated 99.99% of the virus after 30 seconds.

According to Meyers, the results with mouthwashes are promising and add to the findings of a study showing that certain types of oral rinses could inactivate SARS-CoV-2 in similar experimental conditions. In addition to evaluating the solutions at longer contact times, they studied over-the-counter products and nasal rinses that were not evaluated in the other study. Meyers said the next step to expand upon these results is to design and conduct clinical trials that evaluate whether products like mouthwashes can effectively reduce viral load in COVID-19-positive patients.

"People who test positive for COVID-19 and return home to quarantine may possibly transmit the virus to those they live with," said Meyers, a researcher at Penn State Cancer Institute. "Certain professions including dentists and other health care workers are at a constant risk of exposure. Clinical trials are needed to determine if these products can reduce the amount of virus COVID-positive patients or those with high-risk occupations may spread while talking, coughing or sneezing. Even if the use of these solutions could reduce transmission by 50%, it would have a major impact."

Future studies may include a continued investigation of products that inactive human coronaviruses and what specific ingredients in the solutions tested inactivate the virus.

INDIANAPOLIS -- Transfers from the nursing home to the emergency department (ED) or the hospital can have negative longer-term impact on the health of older adults. A new study from Regenstrief Institute and Indiana University School of Medicine looked at which residents were most likely to be admitted to the hospital after a trip to the ED with the hope of identifying areas to improve care and reduce unnecessary transfers.

The study team analyzed hundreds of transfers from the nursing facility to the ED and found the factors most associated with discharge back to the facility were:

Falls, trauma or fracture

Bleeding (non-gastrointestinal)

Pain

Residents who had the following characteristics were more likely to be admitted to the hospital following an ED visit:

Cognitive impairment

Respiratory difficulties

"Transfers of care can be very difficult on the patient. Our goal in analyzing this data is to identify new opportunities to improve care, whether it's preventing transfers to the emergency department or finding ways to avoid hospital admissions," said Kathleen Unroe, M.D., MHA, first author of the paper, Regenstrief research scientist and associate professor of medicine at IU School of Medicine. "This information helps us understand what ailments could potentially be treated in the nursing home, avoiding a potentially risky transfer of care."

About one quarter of nursing facility residents will experience a transfer to the hospital over the course of a year. There is a significant likelihood of reduced functioning and overall negative impact on their health after discharge from the hospital.

Analyzing the data for hospital admission

The research team looked at 867 long-stay nursing home facility residents enrolled in the OPTIMISTIC project. OPTIMISTIC (Optimizing Patient Transfers, Impacting Medical quality, Improving Symptoms -- Transforming Institutional Care) was a demonstration project funded by the Centers for Medicare and Medicaid that successfully reduced potentially avoidable hospitalizations of people in nursing homes.

"Through OPTIMISTIC, we've determined that we can reduce avoidable hospitalizations. The next step is to gain a more nuanced understanding of transfers," said Susan Hickman, PhD, senior author on the paper and director of Indiana University Center for Aging Research at Regenstrief Institute. "This helps us find opportunities for improvement from both the facility perspective and the emergency department perspective."

Researchers say these results suggest one area for exploration may include targeted resources and protocols focused on treatment for falls or symptom management within nursing homes. Another potential area of improvement is the creation of strategies to ensure that providers in the ED have more information when they are assessing the residents, as well as an understanding of the care capabilities of the nursing home to increase the number of discharges back to the facility and avoid hospitalizations.

Life on Earth has a long, but also an extremely turbulent history. On more than one occasion, the majority of all species became extinct and an already highly developed biodiversity shrank to a minimum again, changing the course of evolution each time. The most extensive mass extinction took place about 252 million years ago. It marked the end of the Permian Epoch and the beginning of the Triassic Epoch. About three quarters of all land life and about 95 percent of life in the ocean disappeared within a few thousands of years only.

Gigantic volcanic activities in today's Siberia and the release of large amounts of methane from the sea floor have been long debated as potential triggers of the Permian-Triassic extinction. But the exact cause and the sequence of events that led to the mass extinction remained highly controversial. Now, scientists from Germany, Italy and Canada, in the framework of the EU-funded project BASE-LiNE Earth led by Prof. Dr. Anton Eisenhauer from GEOMAR Helmholtz Centre for Ocean Research Kiel in cooperation with the Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences, have for the first time been able to conclusively reconstruct the entire cascade of events at that time using cutting-edge analytical techniques and innovative geochemical modelling. The study has been published today in the international journal Nature Geoscience.

For their study, the BASE-LiNE Earth team used a previously often neglected environmental archive: the shells of fossil brachiopods. "These are clam-like organisms that have existed on Earth for more than 500 million years. We were able to use well-preserved brachiopod fossils from the Southern Alps for our analyses. These shells were deposited at the bottom of the shallow shelf seas of the Tethys Ocean 252 million years ago and recorded the environmental conditions shortly before and at the beginning of extinction", explains Dr. Hana Jurikova. She is first author of the study, which she conducted as part of the BASE-LiNE Earth project and her doctoral thesis at GEOMAR.

By measuring different isotopes of the element boron in the fossil shells, the team was able to trace the development of the pH values in the ocean 252 million years ago. Since seawater pH is tightly coupled to the CO2 concentration in the atmosphere, the reconstruction of the latter was also possible. For the analyses, the team used high-precision isotope analyses at GEOMAR as well as high-resolution microanalyses on the state-of-the-art large-geometry secondary ion mass spectrometer (SIMS) at GFZ.

"With this technique, we can not only reconstruct the evolution of the atmospheric CO2 concentrations, but also clearly trace it back to volcanic activity. The dissolution of methane hydrates, which had been suggested as a potential further cause, is highly unlikely based on our data", explains Dr. Marcus Gutjahr from GEOMAR, co-author of the study.

As a next step, the team fed their data from the boron and additional carbon isotope-based investigations into a computer-based geochemical model that simulated the Earth's processes at that time. Results showed that warming and ocean acidification associated with the immense volcanic CO2 injection to the atmosphere was already fatal and led to the extinction of marine calcifying organisms right at the onset of the extinction. However, the CO2 release also brought further consequences; with increased global temperatures caused by the greenhouse effect, chemical weathering on land also increased.

Over thousands of years, increasing amounts of nutrients reached the oceans via rivers and coasts, which then became over-fertilized. The result was a large-scale oxygen depletion and the alteration of entire elemental cycles. "This domino-like collapse of the inter-connected life-sustaining cycles and processes ultimately led to the observed catastrophic extent of mass extinction at the Permian-Triassic boundary," summarizes Dr. Jurikova.

The study was conducted within the framework of the EU-funded ITN project BASE-LiNE Earth, in which the use of brachiopods as an environmental archive was systematically studied for the first time, and relevant analytical methods were improved and newly developed. "Without these new techniques it would be difficult to reconstruct environmental processes more than 250 million years ago in the same level of detail as we have done now", emphasizes Prof. Dr. Anton Eisenhauer from GEOMAR, the former BASE-LiNE Earth project coordinator and co-author of the new study, "in addition, the new methods can be applied for other scientific applications".

The social and economic impacts of COVID-19 have battered small- and medium-sized enterprises, putting millions of jobs in the U.S. at risk. And a year rife with natural disasters has not done many struggling businesses any favors.

To learn about the strategies and experiences of businesses managing this double threat, researchers at the National Institute of Standards and Technology (NIST), in collaboration with the National Oceanic and Atmospheric Administration (NOAA), surveyed small- and medium-sized enterprises across the country. In a new report of survey results, nearly a quarter of businesses felt natural disaster preparations helped them address COVID-19. They tended to find preparations of broad applicability during natural disasters, such as telework readiness, more useful than hazard-specific measures. The survey also identified areas of hardship for businesses, including uncertainty and a lack of guidance and resources.

"The survey results can help by drawing attention to how small- and medium-sized businesses are thriving or suffering and showing where natural disaster planning and preparation helped," said Ariela Zycherman, NOAA social scientist and co-author of the report. "The results will also help us identify places where there are needs and opportunities to build social and economic resilience to multiple types of disasters."

The NIST and NOAA researchers conducted the survey from July 8 to Aug. 8, reaching businesses with fewer than 10 to more than 100 employees from a wide array of industries, including construction, manufacturing and retail. With help from other entities, such as the Minority Business Development Agency and the Small Business Administration, the authors promoted the survey via email, newsletter and social media, obtaining more than 1,300 responses.

In the survey, the team asked businesses about challenges presented by COVID-19 and measures taken to manage them. The researchers also inquired about experiences with sudden, high-impact disasters, such as hurricanes, earthquakes and wildfires, as well as longer-lasting, slower-onset events, including droughts and winter storms.

Twenty-nine percent of respondents said they had experienced natural disasters since March 13, when the federal government declared the pandemic a national emergency. The researchers expect this figure would be much higher had the survey been distributed later, however, as events such as the wildfires along the West Coast surged after the survey closed.

Some 24% of survey respondents said experience preparing for natural disasters in the past helped them during the COVID-19 pandemic. Through the survey's open-ended responses, the researchers were able to glean insights into which types of preparation businesses found most beneficial.

Practices with broad applicability shone through over those specific to one kind of disaster. Two notable examples from the responses were having rainy-day funds for when income streams dry up and the ability to operate a business remotely, said Jennifer Helgeson, a NIST research economist and lead author of the report.

One respondent wrote, "We have dealt with many weather emergencies in the past as well [as] a bad flu pandemic, all of which prepared us for something like COVID-19, especially as it relates to teleworking. Our employees have been used to teleworking during emergencies."

Many businesses have not made a smooth transition, however. Smaller operations that rely on in-person customers, such as in the service industry, face a particularly grave threat in COVID-19, which has eaten away at customer bases for lengths of time these businesses were not prepared for.

The outlook for many of the surveyed businesses is currently worrisome, as 72% are concerned about heading into another distressing scenario on top of the pandemic. Almost a third of these businesses are wary of natural disasters specifically. A strong sense of uncertainty also looms over numerous businesses -- a sense that may be compounded by a lack of resources, a situation reported by 37% of respondents.

The researchers found that businesses are commonly struggling to obtain guidance on prioritizing their actions amid the strains of the pandemic, personal protective equipment, and training on how to receive support from financial institutions and lending personnel.

A large portion of businesses anticipate that they are in for the long haul before returning to pre-COVID operating capacity. While 39% said they believe recovery will take less than 18 months, 23% estimate the process will go on for longer. And nearly a fifth of respondents indicated full recovery as an unlikely outcome, no matter the time frame, with many indicating they are now considering early retirement.

The researchers plan to complement the data from this initial report by distributing another survey in the winter to both previously contacted and new businesses. With a second wave, the team plans to collect information about how businesses operating in a pandemic respond to events expected in the near future, including winter storms and the flu season, Helgeson said. Further study might also identify where and how businesses are currently receiving aid.

"I do think there will be more of a focus on understanding if there are certain attributes of the business, whether it be employee size or ownership demographics, that can correlate loosely with the kinds of support they've received or the places they're asking for support," Helgeson said. "Is it more about friends and family or is it more about small-business loans? And how might this change if they experience a natural disaster during the pandemic?"

For agencies and institutions committed to supporting small- and medium-sized enterprises for resilience planning and adaptation, the data from this and any subsequent reports could enhance strategies to reach vulnerable populations and deliver some certainty during a deeply uncertain time.

More than a third of people (34%) in Turkey and one sixth of people (17%) in the UK are 'hesitant' about a COVID-19 vaccine, according to a study by UCL and Dokuz Eylul University in Turkey.

The research, published in the journal Psychological Medicine, asked over 5,000 participants in Turkey and the UK about their willingness to vaccinate for a potential COVID-19 vaccine and beliefs on the origin of the novel coronavirus. The findings show concerning levels of COVID-19 vaccine hesitancy.

Lead author, Dr Gul Deniz Salali, an evolutionary anthropologist at UCL, said: "From an evolutionary point of view, natural selection should favour a bias towards making the least costly decision when there is uncertainty. This is why when people face a choice between taking a specific action or doing nothing, they sometimes prefer to do nothing. This cognitive bias, called the omission bias, may kick in when people make vaccination decisions."

The researchers examined the factors that are associated with acceptance of a COVID-19 vaccine. One of the key factors that explained the probability of vaccine acceptance was a person's belief on the origin of the novel coronavirus.

Odds of vaccine acceptance were 26% higher in Turkey and 63% higher in the UK if a person believed in the natural origin, compared to those who were not sure about the virus origin. In Turkey, participants who believed in the artificial origin of the virus (i.e. SARS-Cov-2 was human-made) were 54% more likely to be vaccine-hesitant.

The research is led by Dr Salali and conducted in collaboration with a social psychology doctoral researcher, Mete Sefa Uysal at Dokuz Eylul University in Turkey.

The study reported several other behavioural and demographic factors that influenced vaccination and origin beliefs. Participants who had higher levels of pandemic related anxieties, such as being more worried about catching or passing on the virus, were more likely to accept COVID-19 vaccination. Compared to women, men in Turkey were more likely to accept a COVID-19 vaccine and believe in the natural origin of the virus.

Dr Salali said "From an evolutionary perspective, emotions can be seen as detectors helping us to avoid death or promote reproduction, especially under uncertainty. The positive correlation between COVID-19 related anxiety and vaccine acceptance can be rooted in the adaptive function of anxiety in decreasing mortality risk."

"Because women are more likely to take healthcare decisions for their children, they may also be more likely to seek out information about vaccines and be exposed to online anti-vaccination content. Moreover, women score higher on disgust sensitivity which is associated with vaccine hesitancy."

Much research effort is focused on developing an effective vaccine for combatting COVID-19. Vaccine development itself, however, will not be enough given that a sufficient amount of people will need to be vaccinated for widespread immunity. The study findings point at a concerning level of COVID-19 vaccine hesitancy, especially in Turkey, and suggest that wider communication of the scientific consensus on the origin of the novel coronavirus with the public may help future campaigns targeting COVID-19 vaccine hesitancy.

A new study, led by the doctors who regularly treat gunshot victims, examined the way the media covers shootings and found that news reports place a disproportionate emphasis on fatal and multiple shootings, while also focusing on uncommon victims, such as women. The researchers fear that the gap between what is covered - and what goes uncovered - in the news could be painting an unrealistic picture of gun violence, which might affect the way the public perceives it. The study was published today in the journal Preventive Medicine.

"As a trauma surgeon, and someone who feels very connected to my patients, I take notice of gun violence coverage in the news--most often the lack thereof. I am particularly saddened when I find there was no media reporting on the shootings that have caused injury and death to my patients, which is most often the case," said the study's lead author, Elinore Kaufman, MD, an assistant professor of Surgery in Traumatology in the Perelman School of Medicine at the University of Pennsylvania. "While I was not surprised to see data on under-reporting in the media, I was startled to see how much it varied related to victim characteristics."

Kaufman and her fellow researchers drew on police reports and information kept by the Gun Violence Archive, a non-profit research group, to monitor media reporting during 2017 inthree different cities: Philadelphia, Cincinnati, and Rochester, NY. Of the 1,801 victims of intentional shootings (outside of self-inflicted shootings), the researchers saw that almost exactly half, 900, were covered in the news.

Of these victims, roughly 83 percent were Black, but just 49 percent of them made the news. Moreover, if the victim was a man, he was about 40 percent less likely to be covered on the news than a woman.

Disparities in news coverage continued when the deadliness of the shootings was examined. Although 16 percent of the victims from the analyzed shootings died, these fatal shootings accounted for 83 percent of the cases covered by the news.

"A vast majority of the victims of gun violence survive, but I don't think the public knows much about people whose lives have been disrupted in so many ways by their injuries, and who need all our support to recover," Kaufman said. "I like to think that more public awareness of the impact of gun violence on survivors would lead to broader support for the services and programs that they need."

Statistics have shown that one in four Americans perceive mass shootings to be the greatest gun violence threat facing their communities, but the study showed that shootings with multiple victims occurred just 22 percent of the time. However, mass shootings were almost six times as likely to make the news.

"This skews our focus toward things like active shooter drills in schools, and away from the kind of community investment that we need to prevent the forms of gun violence that are so much more common," Kaufman said.

There were some differences on the city level data that the study uncovered. Philadelphia had the most shooting victims in 2017 with 1,216 (compared to 407 in Cincinnati and 178 in Rochester), but those victims were also covered the least: only 46 percent of the time (compared to 55 percent in Cincinnati and 65 percent in Rochester).

"I think the news media in any given market has limited space for reporting on violence, and so in areas where violence is common, there's going to be a lot of underreporting. The opposite could be true as well: In areas with little violence, the reporting may be disproportionate," she explained.

While the study focused on the numbers and percentages associated with media reporting on gun violence, Kaufman and her fellow researchers believe that it is just the beginning of the story. Public perception and support are key to making public health policy changes, and media reporting clearly has an influence on them. As such, changing the content of the reports appears key.

That might especially be important as newsrooms are hit by budget cuts and downsizing. With a smaller pool of reporters to cover incidents, shifting the focus of coverage to more truly represent the realities of gun violence could solve issues the study found.

"We understand that reporting community gun violence is an interminable obligation, especially for contracting newsrooms," said senior author Jim McMillan, the director of the Philadelphia Center for Gun Violence Reporting, a project of the Initiative for Better Gun Violence Reporting. "But instead of trying to double down on incident coverage, we recommend that journalists collaborate with other stakeholders to advance best reporting practices such as focusing on evidence-based solutions to the crisis."

So while every instance may not make the news due to the realities of modern newsrooms, such shifts in focus could go a long way toward solving perception issues.

"Many of these reports that we counted were one- or two-liners that tell very little about the humans whose lives are impacted by these shootings," Kaufman said. "We hope to soon study how widely reporters are able to engage more deeply and substantively with the subject, and perhaps even measure the impact of different kinds of stories on readers and watchers of the news."

Abu Dhabi, UAE - October 17, 2020: Large swaths of single-celled eukaryotes, non-bacterial single-cell organisms like microalgae, fungi or mold, can control microbiomes (a collection of tiny microbes, mostly bacteria) by secreting unusual small molecules around their cells, maintaining host survival and ecological success, according to a new study by NYU Abu Dhabi (NYUAD) Assistant Professor of Biology Shady Amin.

Research in the past decade has shown that most eukaryotes need microbiomes to survive. While we understand how large eukaryotes, like humans, corals and plants, control their microbiomes, scientists do not know how single-celled eukaryotes, like microalgae, do so.

In humans, microbiomes can influence digestion, physical features, weight, susceptibility to disease, and even mental health. In corals, microbiomes sustain corals and enable them to withstand environmental change. In trees, microbiomes provide essential nutrients that enable forests and agricultural crops to grow. In microalgae, these microbiomes provide vitamins and other nutrients that keep microalgae alive.

In the paper, Diatom Modulation of Select Bacteria Through Use of Two Unique Secondary Metabolites, published in the Proceedings of the National Academy of Sciences of the USA (PNAS), researchers from NYUAD and other institutions, found that single-celled eukaryotes can control the behavior and growth of microbiomes by promoting beneficial microbes while preventing bad (parasitic) microbes from coming close, enabling scientists to understand how organisms like microalgae control bacteria around them.

The findings will enable scientists to predict how climate change will impact fisheries and atmospheric gas composition because single-celled eukaryotes in the oceans are responsible for a significant fraction of oxygen production on Earth and support the marine food web, including the fish and corals. The findings will also help expand scientists' understanding of evolution since single-celled eukaryotes constitute a significant fraction of life on earth.

"The discovery that a cryptic chemical language enables some single-celled eukaryotes to manipulate bacterial behavior is significant since most eukaryotes on Earth are single-celled and many are essential for our survival, " said Amin.

The Polish-Israeli team from the Faculty of Physics of the University of Warsaw and the Weizmann Institute of Science has made another significant achievement in fluorescent microscopy. In the pages of the Optica journal the team presented a new method of microscopy which, in theory, has no resolution limit. In practice, the team managed to demonstrate a fourfold improvement over the diffraction limit.

The continued development of biological sciences and medicine requires the ability to examine smaller and smaller objects. Scientists need to see into the structure of, and the mutual relationships between, for example, proteins in cells. At the same time, the samples being observed should not differ from the structures naturally occurring in biological organisms, which rules out the use of aggressive procedures and reagents. Although it revolutionised the natural sciences, the classical optical microscope is clearly insufficient today. Due to the wavelike nature of light, an optical microscope does not allow imaging structures smaller than about 250 nanometres. As a result, objects closer to each other than half the wavelength of light (which is about 250 nm for green light) cannot be discerned. This phenomenon, known as the diffraction limit, one of the main obstacles in observing the tiniest biological structures, scientists have long attempted to overcome. Electron microscopes provide orders of magnitude better resolution but only allow the examination of inanimate objects, which must be placed in a vacuum and bombarded by an electron beam. For this reason, electron microscopy cannot be used for studying living organisms and the natural processes occurring in them. This is where fluorescence microscopy steps in, hence the rapid development of super-resolution fluorescence microscopy as a field of physical sciences and the two Nobel Prizes already awarded for related research - in 2008 and 2014.

Nowadays several techniques of fluorescence microscopy are available, and some of them have become widespread in biological imaging. Some methods, such as PALM, STORM or STED microscopy, are characterised by an ultra-high resolution and allow discerning objects located just a dozen or so nanometres from each other. However, these techniques require long exposure times and a complex procedure of biological specimen preparation. Other techniques, such as SIM or ISM microscopy, are easy to use, but offer a very limited resolution improvement, allowing to identify structures only half the size of the diffraction limit.

Aleksandra Sroda, Adrian Makowski and Dr. Radek Lapkiewicz from the Quantum Optics Lab at the Faculty of Physics of the University of Warsaw, in cooperation with Dr. Ron Tenne, Uri Rossman, Gur Lubin and Prof. Dan Oron from the Weizmann Institute of Science in Israel, have introduced a new technique of super-resolution microscopy, called Super-resolution optical fluctuation image scanning microscopy (SOFISM). In SOFISM, the naturally occurring fluctuations in emission intensity of fluorescent markers are used to further enhance the spatial resolution of an image scanning microscope (ISM). ISM, an emerging super-resolution method, has already been implemented in commercial products and proven valuable for the bio-imaging community. Largely, since it achieves a modest improvement in lateral resolution (x2), with very few changes to the optical setup and without the common handicap of long exposure times. Thus, it enables a natural extension of the capabilities of a standard confocal microscope. ISM uses a confocal microscope in which a single detector is replaced with a detector array. In SOFISM correlations of intensities detected by multiple detectors are computed. In principle, the measurement of the n-th order correlation can lead to a factor of 2n resolution improvement with respect to the diffraction limit. In practice, the resolution achievable for higher-order correlations is limited by the signal-to-noise ratio of the measurements.

"SOFISM is a compromise between ease of use and resolution. We believe that our method will fill the niche between the complex, difficult-to-use techniques providing very high resolution and the easy-to-use lower-resolution methods. SOFISM does not have a theoretical resolution limit, and in our article, we demonstrate results which are four times better than the diffraction limit. We also show that the SOFISM method has a high potential in the imaging of three-dimensional biological structures," said Dr. Radek Lapkiewicz.

Crucially, SOFISM is, in its technical aspects, highly accessible, as it only requires introducing a small modification to the widely-used confocal microscope - replacing its photomultiplier tube with a SPAD array detector. In addition, it is necessary to slightly increase the measurement time and change the data processing procedure. "Until recently, SPAD array detectors were expensive and their specifications were not sufficient for correlation-based microscopy. This situation has recently changed. The new SPAD detectors introduced last year removed both the technological and price-related barriers. This makes us think that fluorescence microscopy techniques such as SOFISM might, in a few years' time, become widely used in the field of microscopic examination," stressed Dr. Lapkiewicz.

Twenty years after the release of the human genome, the genetic "blueprint" of human life, an international research team, including the University of British Columbia's Chris Overall, has now mapped the first draft sequence of the human proteome.

Their work was published Oct. 16 in Nature Communications and announced today by the Human Proteome Organization (HUPO). Overall is the only Canadian scientist involved in the Nature Communications paper.

"Today marks a significant milestone in our overall understanding of human life," says Overall, a professor in the faculty of dentistry and a member of the Centre for Blood Research at UBC. "Whereas the human genome provides a complete 'blueprint' of human genes, the human proteome identifies the individual building blocks of life encoded by this blueprint: proteins. "Proteins interact to shape everything from life-threatening diseases to cellular structure in our bodies."

With 90 per cent of the proteins in the human body now mapped, Overall says scientists have a deeper understanding of how individual proteins interact to influence human health, providing insights into disease prevention and individualized medicine.

Their work may have implications for scientists studying potential treatments for COVID-19.

"In COVID-19, for instance, there are two proteomes involved, that of the SARS-CoV-2 virus and that of the infected cells, both of which likely interact with, modify, and change the function of the other," says Overall. "Understanding this relationship can shed light on why some cells and individuals are more resilient to COVID-19 and others more vulnerable, providing essential functional information about the human body that genomics alone cannot answer."

As many human diseases result from changes in the composition or functions of proteins, mapping the proteome strengthens the foundation for disease diagnosis, prediction of outcomes, treatment, and precision medicine.

"Humans share 99.9 per cent of their DNA between individuals, yet deficiencies in the proteome 'parts' stemming from inherited genetic mutations can lead to genetic diseases, or defective or inadequate immune and cellular responses to environmental, nutritional and infection stressors," says Overall. "Knowing which proteins are key to protection from disease, and the deficiencies in expression or activity that are hallmarks of disease, can inform individualized medicine and the development of new therapies."

Science, technology, engineering and mathematics (STEM) fields lack diversity. It is an issue that a group of University of Minnesota-led biology education researchers is aiming to address through a targeted effort to bring diverse perspectives to the foreground.

Their report published in CBE--Life Sciences Education lays out gaps in the biology education field and proposes leveraging an existing research coordination network called Equity and Diversity in Undergraduate STEM (EDU-STEM) to tackle them.

The vast majority of biology education research is completed at leading public research universities, known as R1 institutions, where the student populations tend to be majority middle- and upper-class white students. Research conducted in these settings informs teaching strategies and content that is leveraged in classrooms with more diverse demographics, including tribal universities and colleges, community colleges, minority-serving institutions, and historically Black colleges and universities. These institutions serve a much larger portion of historically underrepresented groups than R1 institutions.

"As it stands now, biology education research does not capture student experiences across diverse institutions," said Seth Thompson, the director of outreach in the College of Biological Sciences (CBS) and a lead author on the report.

EDU-STEM consists of education researchers from across STEM disciplines who focus on addressing gaps in introductory courses. The network first launched in 2017 and is co-led by CBS Associate Professor Sehoya Cotner and Cissy Ballen, a former postdoc in the Cotner Lab and now a faculty member at Auburn University. Although the network currently consists of biology educational researchers, the group hopes to expand and include education researchers in other STEM disciplines.

EDU-STEM is seeking additional collaborators to join the network. Instructors from tribal universities and colleges, community colleges, minority-serving institutions, and historically Black colleges and universities are encouraged to join.

"Student experiences are very different across institutions and thus the effect of educational interventions can be wildly different," said Thompson. "The majority of recommendations highlight student experiences from predominantly white R1 institutions. This collaborative network seeks to change that."