It’s possible that I shall make an ass of myself. But in that case one can always get out of it with a little dialectic. I have, of course, so worded my proposition as to be right either way (K.Marx, Letter to F.Engels on the Indian Mutiny)
Saturday, July 17, 2021
Study identifies monoclonal antibodies that may neutralize many norovirus variants
IMAGE: JAMES CROWE JR., MD, DIRECTOR OF THE VANDERBILT VACCINE CENTER view more
CREDIT: VANDERBILT UNIVERSITY MEDICAL CENTER
Researchers at Vanderbilt University Medical Center (VUMC) and the Baylor College of Medicine in Houston, Texas, have taken a big step toward developing targeted treatments and vaccines against a family of viruses that attacks the gastrointestinal tract.
Each year in the United States circulating strains of the human norovirus are responsible for approximately 20 million cases of acute gastroenteritis. Hallmark symptoms include severe abdominal cramping, diarrhea and vomiting.
Several vaccine candidates are in clinical trials, but it is unclear how effective they will be, given the periodic emergence of novel norovirus variants. Developing broadly effective vaccines will require an understanding of the genetic diversity of the virus and the mechanisms by which the immune system can neutralize it.
Reporting this week in the journal Nature Communications, the researchers isolated a panel of human monoclonal antibodies from subjects with a history of acute gastroenteritis that are cross-reactive and which neutralize a broad range of norovirus variants in laboratory tests.
They describe a conserved, antigenic site on the norovirus that could be used to reformulate vaccine candidates so that they are broadly effective against circulating viral strains. The monoclonal antibodies also could be used to treat or prevent norovirus infection directly or as diagnostic reagents, they added.
Leading the research were the paper's corresponding authors, James Crowe Jr., MD, director of the Vanderbilt Vaccine Center, and B.V. Venkataram Prasad, PhD, the Alvin Romansky Chair in Biochemistry, in collaboration with Mary Estes, PhD, the Cullen Chair and professor of virology at Baylor College of Medicine.
First authors of the paper were Gabriela Alvarado, PhD, formerly of the Crowe lab, now at the National Institute of Allergy and Infectious Diseases, and Wilhelm Salmen, a graduate student in the Prasad lab.
"We were surprised to find naturally occurring antibodies that recognized so many different noroviruses," said Crowe, the Ann Scott Carell Chair and professor of Pediatrics and Pathology, Microbiology & Immunology at VUMC.
"Previously, many experts thought that this would not be possible because of the extreme sequence diversity in the various groups and types of noroviruses in circulation," he said. "The human immune system continues to surprise us in its capacity to recognize diverse virus variants."
"One of the fascinating aspects of this study was the unexpected finding of where the human antibody attacks the virus for neutralization," Prasad said.
"It is exciting to now have human monoclonal antibodies that neutralize many norovirus variants," added Estes.
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Also contributing to the work were Khalil Ettayebi and Liya Hu, PhD, Baylor College of Medicine, and Banumathi Sankaran, PhD, from the Lawrence Berkeley National Laboratory in Berkeley, California.
The research was supported in part by the National Institutes of Health and the Welch Foundation of Houston, Texas.
RUDN University biologists prove the anticancer potential of macrophages
IMAGE: RUDN UNIVERSITY BIOLOGISTS DISCOVERED THE WAY HOW MACROPHAGES (THE CELLS OF THE "FIRST LINE " IMMUNE RESPONSE) RESPOND TO INFLAMMATION AND IDENTIFIED HOW THE IMMUNE RESPONSE DEPENDS ON THEIR ORIGIN. IT... view more
CREDIT: RUDN UNVIERSITY
RUDN University biologists discovered the way how macrophages (the cells of the "first line" immune response) respond to inflammation and identified how the immune response depends on their origin. It turned out that when exposed to an inflammatory stimulus, two opposing mechanisms are activated in macrophages simultaneously -- inducing and inhibiting inflammation. These data can potentially be useful in the treatment of cancer, as targeted activation of macrophages will strengthen the immune response of the organism in the fight against a tumor. The results were published in the journal Biomedicine & Pharmacotherapy.
Macrophages are the cells responsible for phagocytosis -- they capture bacteria, the dead cells remains and other foreign particles. This is the first line of defense of immune system. Most macrophages are formed from blood monocytes, which in turn differ in the level of two proteins on their surface: CD14 and CD16. Until now, it was not known how macrophages derived from the two most polar types of monocytes -- called CD14+monocytes and CD16+monocytes-respond to inflammation. RUDN University biologists have identified these differences.
"Surprisingly, among the published data, there is practically no information about the activation of macrophages obtained from CD14+monocytes and CD16+monocytes. There have only been several published works devoted to the pro-inflammatory polarization of human macrophages with varying monocytic origin. Most data derived from mouse models. We decided to fill this gap and discover how macrophages obtained from CD14+ and CD16+monocytes are activated", said Polina Vishnyakova, PhD, researcher at Medical Biotechnology Laboratory at RUDN University.
The receptors on the surface of macrophages react, for example, to lipopolysaccharides (LPS) -- the main component of bacterial membranes. RUDN University biologists used blood samples from six healthy women aged 26 to 34 years and isolated CD14+monocytes and CD16+monocytes from the blood using magnetic separation. Then the monocytes were "turned" into macrophages - by cultivation with special differentiation factors. Macrophages obtained from different types of monocytes were subjected to LPS and analyzed using flow cytometry, secretome, transcriptomic and proteomic analysis.
The results demonstrated that, firstly, the traditional division of macrophages into pro-inflammatory and anti-inflammatory is not quite correct -- they switch their functions depending on the surrounding conditions. RUDN University biologists also found out that macrophages derived from CD14+monocytes are more prone to a pro-inflammatory response. Flow cytometry showed that these macrophages synthesize more CD86 protein, which is responsible for the activation of T-lymphocytes -- other cells of the immune response. At the same time, secretome analysis showed that macrophages derived from CD14+monocytes secrete more pro-inflammatory and anti-inflammatory cytokine molecules.
These results can be used in the future for the treatment of oncological diseases. The fact is that pro-inflammatory macrophages are able to fight tumors. Picking the most suitable monocytes of the patient (CD14 or CD16), turning them into pro-inflammatory macrophages and transplanting them back to the tumor, one can stimulate the organism's fight against cancer cells.
"The key issue is the choice of monocyte subset for further therapeutic application of macrophages. Thus, macrophages obtained from different populations of human monocytes are potentially relevant for cell therapy in case of malignant oncological diseases", said Polina Vishnyakova, PhD, researcher at Medical Biotechnology Laboratory at RUDN University.
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New discoveries and insights into the glass transition
IMAGE: DSC TRACES OF THE LA(CE)NIAL SYSTEM, THE ARROWS INDICATE THE CALORIMETRIC GLASS-TRANSITION TEMPERATURE (TG) (LEFT). THE TEMPERATURE DEPENDENCE OF THE LOSS MODULUS OF THE LA(CE)NIAL SYSTEM NORMALIZED BY THE MAXIMUM... view more
CREDIT: KATO LABORATORY, IMR, TOHOKU UNIVERSITY
A collaborative group from Tohoku University and Johns Hopkins University have provided valuable insights into the glass transition.
When a liquid is cooled rapidly, it gains viscosity and eventually becomes a rigid solid glass. The point at which it does so is known as the glass transition.
But the exact physics behind the glass transition, and the nature of glass in general, still pose many questions for scientists.
Metallic Glasses (MGs) are highly sought after since they combine the flexibility of plastic with the strength of steel. They are amorphous materials with a disordered atomic structure and exhibit unique and divergent thermodynamic and dynamic characteristics, especially when approaching the glass-transition temperature.
The glass transition in MGs is usually determined by calorimetric and dynamical measurements. The calorimetric glass transition detects the temperature at which specific heat has an abrupt jump, whereas dynamical transition looks at the diverse relaxation responses that emerge with increasing temperature forms.
Generally, the calorimetric glass-transition temperature follows the same trend as the dynamic α-relaxation temperature.
However, the collaborative group discovered that high configuration entropy significantly influences the glass transition of MGs and leads to the decoupling between calorimetric and dynamical glass transitions of high entropy metallic glasses.
The results of their research were published in the journal Nature Communication on June 22, 2021.
Their study presents a new glass-forming system that uses high configurational entropy, named high entropy metallic glasses (HEMGs).
The group featured Specially Appointed Professor Jing Jiang and Professor Hidemi Kato from the Institute for Materials Research at Tohoku University and Professor Mingwei Chen from Johns Hopkins University.
"We are excited about this discovery and believe this work furthers our understanding of the fundamental mechanism behind the glass transition," said members of the research group.
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Individual protected areas in Amazonia differ greatly in how effectively they help to fight deforestation and carbon emissions
IMAGE: INDIVIDUAL PROTECTED AREAS SHOWED SUBSTANTIAL VARIATION IN THEIR IMPACT, I.E. ESTIMATED AMOUNT OF PREVENTED DEFORESTATION. THE AVERAGE IMPACT OVER ALL AREAS, AND ALSO WITHIN EACH PROTECTION CATEGORY, WAS POSITIVE. view more
CREDIT: TEEMU KOSKIMÄKI ET AL.
While tropical forests remain threatened and their future is uncertain, the importance of understanding how well individual protected areas avoid deforestation increases. Researchers from the University of Turku and University of Helsinki, Finland, have investigated this question in a newly published study that focuses on the State of Acre in Brazilian Amazonia.
Tropical forests are unique environments that have huge species diversity and also act as important reservoirs of organic carbon, thereby counteracting climate change. However, their area is diminishing due to deforestation, which gives reason to worry both about the survival of their biodiversity and about the increasing carbon emissions. To help to optimise conservation efforts, it is important to understand how well conservation areas succeed in safeguarding tropical forests.
A group of researchers from the Amazon Research Team of the University of Turku and from the University of Helsinki have now compared deforestation rates between protected and environmentally similar non-protected areas in the Acre state of Amazonian Brazil.
- We found that most protected areas have been effective against deforestation and the associated carbon emissions. In total, we estimated that each year the network of protected areas in Acre helps to avoid the same amount of carbon emissions that is produced by more than 120,000 Europeans, explains the lead author of the study, Doctoral Candidate Teemu Koskimäki.
Carrying out this kind of analyses is based on massive amounts of data and requires sophisticated analytical methods. The computer software needed to do this was developed by Postdoctoral Researcher Johanna Eklund and colleagues in an earlier project.
- To quantify the effect of protection, we had to take into account many other variables to find and match protected and non-protected areas that are similar in terms of deforestation threat. For example, the closer an area is to a big city and the easier it is to reach, the more deforestation pressure it faces whether it is protected or not, explains Eklund.
CAPTION
One of the main threats to Amazonian biodiversity is beef production for export. The biomass (and therefore carbon content) of the intact forest is many times larger than the biomass of the pasture and cattle together. Therefore, forest conversion releases significant amounts of carbon dioxide into the atmosphere.
CREDIT
Hanna Tuomiston
Identifying Differences Helps to Plan Future Conservation Actions
Interestingly, the researchers discovered significant variation among the protected areas.
- Some of the protected areas were very effective, whereas others seemed to suffer from even more severe deforestation than similar non-protected forests. Recognising these differences and their causes could make the management of protected areas more efficient and help to allocate resources to areas where they are most needed, Koskimäki says.
In the case of indigenous lands, the primary objective is to safeguard space for the local traditional peoples to live in rather than to protect nature. Nevertheless, these areas were found to be at least as effective in preventing deforestation as other categories of protected area. It seems that indigenous peoples have not been called guardians of the forest without good reason.
- We are now starting a new project to assess how climate change is affecting biodiversity and the livelihoods of indigenous communities in central Amazonia. This is done in collaboration with the local people. They are worried, because the seasonal patterns of rains and river floods seem to be changing and becoming less predictable, says Professor Hanna Tuomisto.
In the future, it would be interesting to clarify what the components of a successful protected area are in order to identify and spread the good practices. The results of this new study could be used to identify potential study subjects for future on-the-ground research at the local level. Such research could also focus on other factors that contribute to conservation success than prevention of deforestation, such as how well protected areas prevent selective logging or unsustainable levels of hunting.
The research article has been published in the journal Environmental Conservation.
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Bats are kings of small talk in the air
Echoes contain redundant information to help with high-speed navigation
IMAGE: UC RESEARCHERS FOUND THAT THE ECHOES OF BATS COULD BE COMPRESSED DIGITALLY BY 90% WITHOUT LOSING MUCH INFORMATION, SUGGESTING THEIR CALLS ARE NOT VERY COMPLEX. view more
CREDIT: MICHAEL MILLER
Bat conversations might be light on substance, according to researchers from the University of Cincinnati.
Echoes from bats are so simple that a sound file of their calls can be compressed 90% without losing much information, according to a study published in the journal PLOS Computational Biology.
The study demonstrates how bats have evolved to rely on redundancy in their navigational "language" to help them stay oriented in their complex three-dimensional world.
"If you can make decisions with little information, everything becomes simpler. That's nice because you don't need a lot of complex neural machinery to process and store that information," study co-author Dieter Vanderelst said.
UC researchers suspected that the calls of bats contain redundant information and that bats might use efficient encoding strategies to extract the most relevant information from their echoes. Many natural stimuli encountered by animals have a lot of redundancy. Efficient neural encoding retains essential information while reducing this redundancy.
To test their hypothesis, they built their own "bat on a stick," a tripod-mounted device that emits a pulse of sound sweeping from 30 to 70 kilohertz, a frequency range used by many bats. By comparison, human speech typically ranges from 125 to 300 hertz (or 0.125 to 0.3 kHz).
More than 1,000 echoes were captured in distinct indoor and outdoor environments such as in a barn, in different-sized rooms, among bushes and tree branches and in a garden.
Researchers converted the recorded echoes to a graph of the sound, called a cochleogram. Then they subjected these graphs to 25 filters -- essentially compressing the data. They trained a neural network, a computer system modeled on the human brain, to determine if the filtered graphs still contained enough information to complete a number of sonar-based tasks known to be performed by bats.
They found that the neural network correctly identified the location of the echoes even when the cochleogram was stripped of as much as 90% of its data.
"What that tells us is you can compress that data and still do what you need to do. It also means if you're a bat, you can do this efficiently," said Vanderelst, an assistant professor in UC's College of Arts and Sciences and in the College of Engineering and Applied Science.
Vanderelst said researchers often can infer what bats are doing just by listening to their calls.
"Even if you don't see the bat, you can tell with a high degree of certainty what a bat is doing," he said. "If it calls more frequently, it's looking for something. If the calls are spread out, it's cruising or studying something far away."
CAPTION
Researchers found that echoes from bats could be digitally compressed by 90% without losing much information.
CREDIT
Margaret Weiner/UC Creative
Bats produce their ultrasonic calls with a larynx much like ours. But what a voice box. It can contract 200 times a second, making it the fastest known muscle in all mammals.
The nighttime forest can be deafening to people because of its chorus of frogs and drone of insects. But Vanderelst said the ultrasonic frequency by comparison is pretty quiet, allowing bats to hear their own chittering calls that bounce off tree branches and other obstacles during echolocation.
While bats use different chirps for navigating than for communicating with each other, Vanderelst said they're all pretty simple. But human language has lots of built-in redundancy as well, Vanderelst said.
Fr xmpl, cn y rd ths sntnc wth mssng vwls?
"Take out a lot of letters in a sentence and it's still readable," Vanderelst said.
UC graduate Adarsh Chitradurga Achutha, Vanderelst's student, was the study's lead author. Co-authors include Vanderelst's mentor Herbert Peremans at the University of Antwerp, Belgium, and bat expert Uwe Firzlaff with the University of Munich, Germany.
The way bats perceive the world is fascinating both from biological and engineering perspectives, Vanderelst said.
"It's like a riddle, looking at something that shouldn't be able to do what it does. So the question is how?" he said. "It's given me an appreciation for the elegant efficiency underlying this system."
CAPTION
University of Cincinnati assistant professor Dieter Vanderelst uses cues from nature to inform his engineering research.
CREDIT
Joseph Fuqua II/UC Creative
First 3D simulation of rat's complete whisker system acts as a tactile 'camera'
Model gives rare insight into how rats use whiskers to actively sense their natural environments
NORTHWESTERN UNIVERSITY
VIDEO: WITH ITS 60 ANATOMICALLY CORRECT WHISKERS, A SIMULATED RAT ACTIVELY USES ITS WHISKERS TO EXPLORE THE EDGE OF A DRAIN PIPE. view more
CREDIT: NORTHWESTERN UNIVERSITY
Northwestern University engineers have developed the first full, three-dimensional (3D), dynamic simulation of a rat's complete whisker system, offering rare, realistic insight into how rats obtain tactile information.
Called WHISKiT, the new model incorporates 60 individual whiskers, which are each anatomically, spatially and geometrically correct. The technology could help researchers predict how whiskers activate different sensory cells to influence which signals are sent to the brain as well as provide new insights into the mysterious nature of human touch.
The research was published last week in the Proceedings of the National Academy of Sciences.
With just a brush of their whiskers, rats can extract detailed information from their environments, including an object's distance, orientation, shape and texture. This keen ability makes the rat's sensory system ideal for studying the relationship between mechanics (the moving whisker) and sensory input (touch signals sent to the brain).
But while the rat whisker system is a widely used simplified model system in sensory neuroscience, it's challenging to study an animal's nervous system as it moves to interact with its natural environment.
"We cannot measure the signals at the base of a real rat's whisker using current technology because, as soon as you embed a sensor, it interferes with the signals themselves," said Northwestern's Mitra Hartmann, the study's senior author. "The only way we can really capture a rat actively sensing its environment under natural conditions is to simulate it."
With potential to overcome these challenges, simulations have become an increasingly important component of neuroscience. By developing WHISKiT, the study authors now have the first complete model of tactile input to a moving sensory system, which shows how rats actively "whisk" and passively sense their complex 3D environments.
"Because none of the individual whiskers works in isolation, WHISKiT is crucial to understanding how the brain processes incoming tactile sensory information," said Nadina Zweifel, the paper's first author. "It's equivalent to a tactile 'camera' that can capture the mechanical signals an animal may acquire while using the whiskers to interact with the environment. That way, we believe that our tool considerably widens the range of possibilities for computational and experimental studies in the future."
Hartmann is a professor of biomedical and mechanical engineering at Northwestern's McCormick School of Engineering, where she is a member of the Center for Robotics and Biosystems and the Northwestern University Interdepartmental Neuroscience program. Zweifel is a Ph.D. candidate in Hartmann's laboratory.
To develop the new WHISKiT model, the Northwestern team combined more than a decade's worth of experimental data from Hartmann's lab. Because every whisker is slightly different, her group previously calculated the proper geometry (including arc, base diameter and slope) for individual whiskers. After validating models for individual whiskers, the researchers combined the whiskers into a full array.
The resulting model considers the geometry, spatial arrangement and movement of all 60 whiskers (30 on each side) on a rat's face. Each whisker is embedded in a follicle, where the mechanical signals are generated at the base.
WHISKiT also incorporates new data collected from 3D scans that Zweifel captured of rats' natural environments, including in urban alleys, around dumpsters and at drain pipes, across the cities of Chicago and Evanston. The model simulates rats in these natural environments ("whisking" around a drain pipe, for example) as well as in laboratory settings. The researchers found that each typical, exploratory scenario generates a unique pattern of data.
"The tactile signals associated with exploring a complicated drain pipe or dumpster are very different from those associated with exploring a blank wall," Hartmann explained.
The researchers next plan to use the simulation to address several long-standing questions, including how rats can use touch to distinguish between stationary and moving objects and how active whisking compares to passive sensing.
CAPTION
Researchers incorporated 3D scans from rats' natural environments, including this photo of a drain pipe, into their WHISKiT simulation.
CREDIT
Northwestern University
The study, "A dynamical model for generating synthetic data to quantify active tactile sensing behavior in the rat," was authored by Hartmann, Zweifel, Nicholas Bush, Ian Abraham and Todd Murphey.
US corn and soybean maladapted to climate variations, study shows
UNIVERSITY OF ILLINOIS COLLEGE OF AGRICULTURAL, CONSUMER AND ENVIRONMENTAL SCIENCES
IMAGE: MADHU KHANNA AND CHENGZHENG YU, DEPARTMENT OF AGRICULTURAL AND CONSUMER ECONOMICS, UNIVERSITY OF ILLINOIS, STUDIED CORN AND SOYBEAN ADAPTATION TO CLIMATE VARIATIONS IN THE U.S. view more
CREDIT: LAURA MABRY, COLLEGE OF ACES, UNIVERSITY OF ILLINOIS.
URBANA, Ill. - U.S. corn and soybean varieties have become increasingly heat and drought resistant as agricultural production adapts to a changing climate. But the focus on developing crops for extreme conditions has negatively affected performance under normal weather patterns, a University of Illinois study shows.
"Since the 1950s, advances in breeding and management practices have made corn and soybean more resilient to extreme heat and drought. However, there is a cost for it. Crop productivity with respect to the normal temperature and precipitation is getting lower," says Chengzheng Yu, doctoral student in the Department of Agricultural and Consumer Economics (ACE) at the University of Illinois and lead author on the new paper, published in Scientific Reports.
Climate projections indicate a mix of extreme and normal weather patterns in the next 50 years, so crops must perform well under a variety of conditions, explains study co-author Madhu Khanna, ACES distinguished professor of environmental economics in ACE.
"It is not enough to just focus on extreme weather conditions. We can't look at the impacts of climate change in a piecemeal fashion and develop varieties only to cope with certain aspects of it," Khanna states.
Yu, Khanna, and co-author Ruiqing Miao, Auburn University, studied corn and soybean yield from 1951 to 2017 in the eastern part of the U.S., an area where crops can grow without irrigation. Crop yield increased significantly during this period due to a wide range of technological and breeding improvements. But when the researchers isolated the effect of climate-related adaptations, they found significant negative impacts on yield.
While heat and drought tolerance increased yield by 33% for corn and 20% for soybean over this period, the gain was offset by reduced productivity under normal conditions. Overall, maladaptation due to climate-related factors reduced corn and soybean yield by 8% and 67%, respectively, the researchers found.
"There's been this trade-off; crops become better adapted to extreme weather, but less adapted to normal conditions," Khanna says. "Overall, crop yields went up by 100% to 200% over the past decades. We break this down into the components that happened because of climate-related changes, and components that happened irrespective of climate change. And we find the impact of climate-related adaptation has been negative," she explains.
The researchers also projected net effects of climate change adaptation on crop yields by 2050 under a range of warming scenarios. In the most extreme scenarios, weather-adapted variations will perform better. But under less extreme scenarios varieties that perform well in normal climate would be more productive.
Khanna and Yu conclude that crop breeders should focus on developing crop varieties for diverse weather patterns. Flexibility is important for agricultural producers to be well prepared for future conditions.
"There will be a very significant reduction in crop yield for both corn and soybean over the next 50 years under some extreme warming scenarios, even though the crops are supposedly adapted to extreme conditions. There's overall maladaptation, because the crops are not fully adapted to every possible combination of extreme and normal conditions. And the overall impact is going to be very negative," Khanna says. "We need to drastically change how we're adapting our crops so that they're better prepared for the mix of conditions we are likely to encounter in the following years."
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The Department of Agricultural and Consumer Economics is in the College of Agricultural, Consumer and Environmental Sciences, University of Illinois.
The paper, "Maladaptation of U.S. corn and soybeans to a changing climate," is published in Nature Scientific Reports. [https://doi.org/10.1038/s41598-021-91192-5]. Authors are Chengzheng Yu, Ruiqing Miao, and Madhu Khanna.
Funding for this research was provided by a USDA National Institute of Food and Agriculture Hatch grant.
BERNIE SANDERS STATE
Invention: The Storywrangler
Vermont scientists create tool to explore billions of social media messages, potentially predict political and financial turmoil
IMAGE: UVM SCIENTISTS HAVE INVENTED A NEW TOOL: THE STORYWRANGLER. IT VISUALIZES THE USE OF BILLIONS OF WORDS, HASHTAGS AND EMOJI POSTED ON TWITTER. IN THIS EXAMPLE FROM THE TOOL'S ONLINE... view more
CREDIT: UVM
For thousands of years, people looked into the night sky with their naked eyes -- and told stories about the few visible stars. Then we invented telescopes. In 1840, the philosopher Thomas Carlyle claimed that "the history of the world is but the biography of great men." Then we started posting on Twitter.
Now scientists have invented an instrument to peer deeply into the billions and billions of posts made on Twitter since 2008 -- and have begun to uncover the vast galaxy of stories that they contain.
"We call it the Storywrangler," says Thayer Alshaabi, a doctoral student at the University of Vermont who co-led the new research. "It's like a telescope to look -- in real time -- at all this data that people share on social media. We hope people will use it themselves, in the same way you might look up at the stars and ask your own questions."
The new tool can give an unprecedented, minute-by-minute view of popularity, from rising political movements to box office flops; from the staggering success of K-pop to signals of emerging new diseases.
The story of the Storywrangler -- a curation and analysis of over 150 billion tweets--and some of its key findings were published on July 16 in the journal Science Advances.
EXPRESSIONS OF THE MANY
The team of eight scientists who invented Storywrangler -- from the University of Vermont, Charles River Analytics, and MassMutual Data Science -- gather about ten percent of all the tweets made every day, around the globe. For each day, they break these tweets into single bits, as well as pairs and triplets, generating frequencies from more than a trillion words, hashtags, handles, symbols and emoji, like "Super Bowl," "Black Lives Matter," "gravitational waves," "#metoo," "coronavirus," and "keto diet."
"This is the first visualization tool that allows you to look at one-, two-, and three-word phrases, across 150 different languages, from the inception of Twitter to the present," says Jane Adams, a co-author on the new study who recently finished a three-year position as a data-visualization artist-in-residence at UVM's Complex Systems Center.
The online tool, powered by UVM's supercomputer at the Vermont Advanced Computing Core, provides a powerful lens for viewing and analyzing the rise and fall of words, ideas, and stories each day among people around the world. "It's important because it shows major discourses as they're happening," Adams says. "It's quantifying collective attention." Though Twitter does not represent the whole of humanity, it is used by a very large and diverse group of people, which means that it "encodes popularity and spreading," the scientists write, giving a novel view of discourse not just of famous people, like political figures and celebrities, but also the daily "expressions of the many," the team notes.
In one striking test of the vast dataset on the Storywrangler, the team showed that it could be used to potentially predict political and financial turmoil. They examined the percent change in the use of the words "rebellion" and "crackdown" in various regions of the world. They found that the rise and fall of these terms was significantly associated with change in a well-established index of geopolitical risk for those same places.
WHAT'S HAPPENING?
The global story now being written on social media brings billions of voices -- commenting and sharing, complaining and attacking -- and, in all cases, recording -- about world wars, weird cats, political movements, new music, what's for dinner, deadly diseases, favorite soccer stars, religious hopes and dirty jokes.
"The Storywrangler gives us a data-driven way to index what regular people are talking about in everyday conversations, not just what reporters or authors have chosen; it's not just the educated or the wealthy or cultural elites," says applied mathematician Chris Danforth, a professor at the University of Vermont who co-led the creation of the StoryWrangler with his colleague Peter Dodds. Together, they run UVM's Computational Story Lab.
"This is part of the evolution of science," says Dodds, an expert on complex systems and professor in UVM's Department of Computer Science. "This tool can enable new approaches in journalism, powerful ways to look at natural language processing, and the development of computational history."
How much a few powerful people shape the course of events has been debated for centuries. But, certainly, if we knew what every peasant, soldier, shopkeeper, nurse, and teenager was saying during the French Revolution, we'd have a richly different set of stories about the rise and reign of Napoleon. "Here's the deep question," says Dodds, "what happened? Like, what actually happened?"
GLOBAL SENSOR
The UVM team, with support from the National Science Foundation, is using Twitter to demonstrate how chatter on distributed social media can act as a kind of global sensor system -- of what happened, how people reacted, and what might come next. But other social media streams, from Reddit to 4chan to Weibo, could, in theory, also be used to feed Storywrangler or similar devices: tracing the reaction to major news events and natural disasters; following the fame and fate of political leaders and sports stars; and opening a view of casual conversation that can provide insights into dynamics ranging from racism to employment, emerging health threats to new memes.
In the new Science Advances study, the team presents a sample from the Storywrangler's online viewer, with three global events highlighted: the death of Iranian general Qasem Soleimani; the beginning of the COVID-19 pandemic; and the Black Lives Matter protests following the murder of George Floyd by Minneapolis police. The Storywrangler dataset records a sudden spike of tweets and retweets using the term "Soleimani" on January 3, 2020, when the United States assassinated the general; the strong rise of "coronavirus" and the virus emoji over the spring of 2020 as the disease spread; and a burst of use of the hashtag "#BlackLivesMatter" on and after May 25, 2020, the day George Floyd was murdered.
"There's a hashtag that's being invented while I'm talking right now," says UVM's Chris Danforth. "We didn't know to look for that yesterday, but it will show up in the data and become part of the story."
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CTHULHU STUDIES
3D printed replicas reveal swimming capabilities of ancient cephalopods
Experiments in water tanks, including a U pool, suggest the ancient animals lived a vertical marine lifestyle
IMAGE: RECONSTRUCTION OF THE ORTHOCONE AMMONITE, BACULITES COMPRESSUS. view more
CREDIT: DAVID PETERMAN
University of Utah paleontologists David Peterman and Kathleen Ritterbush know that it's one thing to use math and physics to understand how ancient marine creatures moved through the water. It's another thing to actually put replicas of those creatures into the water and see for themselves. They're among the scientists who are, through a range of methods including digital models and 3-D printed replicas, "de-fossilizing" animals of the past to learn how they lived.
Peterman, Ritterbush and their colleagues took 3-D printed reconstructions of fossil cephalopods to actual water tanks (including a University of Utah swimming pool) to see how their shell structure may have been tied to their movement and lifestyle. Their research is published in PeerJ and in an upcoming memorial volume to the late paleontologist William Cobban. They found that cephalopods with straight shells called orthocones likely lived a vertical life, jetting up and down to catch food and evade predators. Others with spiral shells, called torticones, added a gentle spin to their vertical motions.
"Thanks to these novel techniques," says Peterman, a postdoctoral scholar in the Department of Geology and Geophysics, "we can trudge into a largely unexplored frontier in paleobiology. Through detailed modeling, these techniques help paint a clearer picture of the capabilities of these ecologically significant animals while they were alive."
The researchers are veterans of this style of "virtual paleontology," having worked with digital ammonoid models and 3-D printed versions to test hypotheses about their evolution and lifestyles. Most ammonoids have coiled shells, like today's chambered nautilus, and darted around the ocean in all directions.
But in their researcher published in PeerJ, Peterman and Ritterbush, assistant professor of Geology & Geophysics, explored a different shell shape--the straight-shelled orthocone. Straight shells evolved several times in different lineages throughout the fossil record, suggesting they had some adaptive value.
"This is important because orthocones span a huge chunk of time and are represented by hundreds of genera [plural of genus]," Peterman says, and many reconstructions and dioramas show orthocones as horizontal swimmers like squid. "They were major components of marine ecosystems, yet we know very little about their swimming capabilities."
So he and Ritterbush took 3-D scans of fossils of Baculites compressus, an orthocone species that lived during the Cretaceous, and designed four different digital models, each with different physical properties. Find an orthocone digital model here.
How did they know how to weight the structures of the models? "Math," Peterman says. They adjusted the centers of mass and counterweights within the models, representing the balances of soft tissue and air-filled voids that the orthocone would likely have maintained in its life. "The resultant model is balanced the same as the living animal, allowing very detailed analyses of their movement," he says.
The resultant 3-D printed models were nearly two feet long. With the help of Emma Janusz and Mark Weiss at the U's George S. Eccles Student Life Center, the researchers set up a camera rig in a 7-foot-deep part of the Crimson Lagoon pool and released the models underwater to see how they naturally moved.
The results showed clearly that the most efficient method of movement was vertical, since moving side to side created a lot of drag. "I was surprised by how stable they are," Peterman says. "Any amount of rotation away from their vertical orientation is met with a strong restoring moment so many species of living orthocones were likely unable to modify their own orientations. Furthermore, the source of jet thrust is situated so low that, during lateral movement, much energy would be lost due to rocking."
The results also showed that orthocones may have been capable of high velocities among shelled cephalopods. That could have come in handy in evading predators. Looking at the results of the pool experiments and calculating the time needed to escape modern predators (as stand-ins for the orthocones' long-extinct predators), they found that orthocones may have been able to jet upward fast enough to evade animals similar to crocodiles or whales. They may not have been as lucky against fast swimmers like sharks, however.
So most species of orthocones couldn't have lived a horizonal-swimming lifestyle. "Instead," Peterman says, "species without counterweights in their shells assumed a vertical life habit, either feeding near the seafloor or vertically migrating in the water column. While orthocones were not as athletic or active as modern squid, they could have maintained the ability to thwart predators with upward dodges."
CAPTION
David Peterman in the AMMLab (Ammonoid Motility Modeling Laboratory) holding a 3-D-printed reconstruction of the planispiral ammonite, Paracoroniceras lyra.
CREDIT
David Peterman
Peterman and Ritterbush, along with recent graduate Nicholas Hebdon and Ryan Shell from the Cincinnati Museum Center, also ran a similar set of experiments with torticones, smaller cephalopods with a corkscrew-shaped shell. The results will be published in the American Association of Petroleum Geologists and Wyoming Geological Association Special Volume - Insights into the Cretaceous: Building on the Legacy of William A. Cobban (1916-2015). Although the torticones also likely preferred vertical movement, their shape caused a different result in the water, Peterman says."While orthocones were masters of vertical movement, torticones were masters of rotation."
Many mollusks today have similar helical shells, and some researchers previously assumed that torticones may have had a similar lifestyle, crawling along the seafloor. "However," Peterman says, "the hydrostatic models demonstrate that the chambered shells of torticone ammonoids had the capacity for neutral buoyancy, which would have liberated them from the seafloor. These ammonoids experience different forms of movement only possible in a free-swimming lifestyle."
In experiments conducted in a 50-gallon water tank (no swimming pool needed for the 6-inch-long torticone models that are available digitally here) the team found that the torticones naturally and efficiently rotated in the water just due to the shape of the shell, gently spinning face-first when descending and spinning the opposite direction when ascending. Also, they found, the placement of the torticones' source of thrust relative to their center of mass would have improved the efficiency of active rotation.
Rotating while descending, Peterman says, may have helped the torticones feed, allowing them to graze on small planktonic organisms.
"I was surprised at how easily torticones could rotate," Peterman says. "Even small thrusts such as breathing [gill ventilation] could have produced rotation of 20 degrees per second."
Both orthocones and torticones, because of their repeated appearance throughout the fossil record, not only show that cephalopods found some advantage to a straight or helical shell, as opposed to their nautilus-shaped coiled shell, but that an uncoiled shell might have evolved in times of "ecological saturation," when the ecological niches of coiled cephalopods were full.
Peterman says this work calls for a revision of how we envision the ancient ocean.
"These experiments," he says, "transform our understanding of ancient ecosystems. Rather than crawling along the seafloor like snails, or swiftly swimming like modern squid, these animals were assuming rather unique lifestyles. These experiments refine our understanding of these animals by painting a picture of ancient seascapes dotted with pirouetting helical cephalopods and vertically-oriented orthocones."
CAPTION
Motion tracking analysis of a 3D-printed torticone model.
