Aurelia Butler

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  • 175 Shares109 Views

    in Computers Math

    Turning big data into better breeds and varieties: Can AI help feed the planet?

    Artificial intelligence could hold the key to feeding 10 billion people by 2050 in the face of climate change and rapidly evolving pests and pathogens according to researchers at The University of Queensland.
    Professor Lee Hickey from UQ’s Queensland Alliance for Agriculture and Food Innovation said AI offered opportunities to accelerate the development of high performing plants and animals for better farm sustainability and profitability.
    “Breeders are collecting billions of data points, but the big challenge is how we turn this colossal amount of data into knowledge to support smarter decisions in the breeding process,” Professor Hickey said.
    “AI can help to identify which plants and animals we use for crossing or carry forward to the next generation.”
    Professor Ben Hayes, the co-inventor of genomic prediction, said the QAAFI team had identified four applications for AI in crop and livestock breeding.
    “The first one is deciding what to breed — it might sound simple, but this decision is becoming more complex,” Professor Hayes said.
    “In an increasingly challenging environment, consumer acceptance will be more important, so AI is a good way to pull together the preferences of millions of people. More

  • 113 Shares149 Views

    in Computers Math

    A new weapon in the war on robocall scams

    The latest weapon in the war on robocalls is an automated system that analyzes the content of these unsolicited bulk calls to shed light on both the scope of the problem and the type of scams being perpetuated by robocalls. The tool, called SnorCall, is designed to help regulators, phone carriers and other stakeholders better understand and monitor robocall trends — and take action against related criminal activity.
    “Although telephone service providers, regulators and researchers have access to call metadata — such as the number being called and the length of the call — they do not have tools to investigate what is being said on robocalls at the vast scale required,” says Brad Reaves, corresponding author of a paper on the work and an assistant professor of computer science at North Carolina State University.
    “For one thing, providers don’t want to listen in on calls — it raises significant privacy concerns. But robocalls are a huge problem, and are often used to conduct criminal fraud. To better understand the scope of this problem, and gain insights into these scams, we need to know what is being said on these robocalls.
    “We’ve developed a tool that allows us to the characterize the content of robocalls,” Reaves says. “And we’ve done it without violating privacy concerns; in collaboration with a telecommunications company called Bandwidth, we operate more than 60,000 phone numbers that are used solely by us to monitor unsolicited robocalls. We did not use any phone numbers of actual customers.”
    The new tool, SnorCall, essentially records all robocalls received on the monitored phone lines. It bundles together robocalls that use the same audio, reducing the number of robocalls whose content needs to be analyzed by around an order of magnitude. These recorded robocalls are then transcribed and analyzed by a machine learning framework called Snorkel that can be used to characterize each call.
    “SnorCall essentially uses labels to identify what each robocall is about,” Reaves says. “Does it mention a specific company or government program? Does it request specific personal information? If so, what kind? Does it request money? If so, how much? This is all fed into a database that we can use to identify trends or behaviors.”
    As a proof of concept, the researchers used SnorCall to assess 232,723 robocalls collected over 23 months on the more than 60,000 phone lines dedicated to the study. More

  • 150 Shares99 Views

    in Heart

    The fastest-evolving moss in the world may not adapt to climate change

    The world’s oldest moss has seen three mass extinctions — but may not survive climate change.

    The genus Takakia has the highest number of fast-evolving genes of any moss, researchers report August 9 in Cell. A decade-long study of Takakia in the Himalayas shows that the moss is well-adapted to its high-altitude home, with resistance to extreme cold and intense ultraviolet light. But no matter how fast it can tweak its genes, the scientists found, rapidly rising temperatures in the region were associated with a decrease in the moss’s range — a faster decrease than any of the mosses around it.

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    Takakia consists of just two species of moss. While they can be found individually in the United States and Japan, both species occur together only on the Tibetan Plateau in the Himalayas. The two are unlike any other plant in the world. The evolutionary shoot containing Takakia branched off the other bryophytes — mosses, liverworts and hornworts — around 390 million years ago.

    “The evolutionary position of Takakia in plants is like that of platypus in mammals,” says Yikun He, a plant geneticist at the Capital Normal University in Beijing. Just as the platypus has a lot of strange, not-quite-mammal traits — like egg-laying and a beak — Takakia has a bunch of features that make it not quite like other plants, such as featherlike leaves and a lack of pores for controlling the flow of oxygen and carbon dioxide.

    “It looks very different from other mosses,” says Ralf Reski, a plant biotechnologist at the University of Freiburg in Germany. “For a long time, it was unclear if it was a moss.”

    The tiny, lobed leaves on this Takakia moss haven’t changed their looks since the Jurassic Period, which ended about 145 million years ago.Xuedong Li

    To learn more about mysterious Takakia, Reski, He and their colleagues set up a long-term study in the Tibetan Plateau, more than 4,000 meters above sea level.

    Over 11 years, the researchers collected samples, analyzed genomes, collected data on the surrounding ecosystem and compared modern specimens with fossils from 165 million years ago. The team also had to evacuate several students due to altitude sickness. The field sites were accessible only in August and September, and even then, “the climate is unpredictable, and one day may experience spring, summer, autumn and winter,” He says.

    Humans might have had a tough time, but the moss was comfortable in its high-altitude home. That’s due in part to its genes. While Takakia sports a genome whose length is average for a bryophyte — just over 27,400 genes — it has the largest known number of fast-evolving genes of any moss, liverwort or hornwort, the researchers found.

    Takakia needed that speed when the Himalayas began to rise 65 million years ago. As the mountains stretched toward the sky, the mosses on them were exposed to lower temperatures and higher amounts of ultraviolet light. They had to adapt. And adapt Takakia did.

    The new study showed the moss’s ability to withstand solar radiation. When the researchers exposed Takakia to a high amount of UV light, it was unharmed, while comparison mosses began to die within 72 hours. The hardy moss produces “high amounts of metabolites like flavonoids and polyunsaturated fatty acids to protect against radiation,” Reski says. It also sports genes to enable more efficient DNA repair — essential protection against harmful rays.

    Takakia also adapted to the extreme cold. It can go dormant for eight months of the year while under snow, and gets all of its growth and reproduction done, He says, “in the precious three-to-four-month light window period.”

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    All of these features evolved from about 50 million years ago to the present, the study showed, without ever changing the moss’s physical appearance compared with fossils of Takakia from about 165 million years ago.

    But this relatively speedy evolution doesn’t seem to be fast enough to help the moss adapt to climate change (SN: 3/10/22).

    During the 11 years of the study, Reski, He and their colleagues documented an average increase in temperature of about four-tenths of a degree Celsius in the region. Meanwhile, the coverage of Takakia in their sample population decreased by about 1.6 percent per year — faster than four other local mosses.

    The researchers predict that by the end of the 21st century, suitable conditions for Takakia will be limited to only 1,000 to 1,500 square kilometers around the world. By that time, the researchers suspect, the world’s oldest moss could be extinct.

    Others are more optimistic about the fate of this tough little moss. There are populations in other places, says evolutionary biologist S. Blair Hedges. So while the Tibetan Plateau may eventually be Takakia-free, he hopes the moss can make it elsewhere.

    What’s more, “it’s fantastic to see all these different things known about a single [genus], from the fossil record all the way up to the complete genome,” says Hedges, of Temple University in Philadelphia.

    In the meantime, He, Reski and their colleagues are cultivating Takakia populations and transplanting them to other regions in Tibet in the hopes of giving old moss a new lease on life. “Takakia saw the dinosaurs come and go. It saw us humans coming,” Reski says. “Now we can learn something about resilience and extinction from this tiny moss.” More

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    Extreme ocean heat off Florida has ebbed. But for marine life, the danger remains

    In late July, a fierce ocean heat wave ratcheted up temperatures in Florida’s coastal waters to unprecedented highs. One buoy bobbing in shallow, turbid Manatee Bay logged a measurement of 38.3˚ Celsius (101˚ Fahrenheit). That may be the highest temperature ever recorded in the ocean. A week later, that surge in ocean heat had ebbed. But South Florida’s denizens are still in hot water.

    The concern is not just that the Manatee Bay buoy recorded shockingly high, hot tub–level temperatures — actually, “close to the limit of hot tub temperatures” — for several days in a row, says Benjamin Kirtman, a climate scientist at the University of Miami’s Rosenstiel School of Marine, Atmospheric and Earth Science.

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    And it’s not just that June and July’s brutally hot water temperatures in the North Atlantic Ocean are linked to shockingly hot temperatures on land. This summer, Miami’s heat index, a measure of air temperature and humidity, soared to a record-breaking streak of nearly two months, reaching a daily heat index of 38° C (100° F).

    It’s not even that such ocean heat waves are becoming the new normal, as swells of heat more and more frequently crest atop the baseline warming of the global ocean due to climate change (SN: 2/1/22). Florida’s waters may have hit a record high, but July saw widespread ocean heat waves around the world, from the North Atlantic Ocean to the eastern equatorial Pacific to the Southern Indian Ocean.

    “The global oceans have warmed up so much … we’re seeing a ratcheting up that’s unprecedented in the modern instrument record, and maybe in the last 125,000 years,” Kirtman says. “It’s really quite remarkable.”

    ‘Way outside of the bounds of anything these corals have experienced’

    In Florida, the temperatures of the coastal waters have returned to a normal summertime range for now. But the danger remains acute for many ocean dwellers, from corals to fish, says Andrew Baker, a coral biologist also at the University of Miami’s Rosenstiel School.

    Murky Manatee Bay, swirling with sediment, isn’t home to corals — but the water temperatures in the reefs around the Florida Keys were still “incredibly hot,” perhaps reaching up to 36° C (96° F), Baker says.

    As the sweltering sea temperatures peaked in July, the Coral Restoration Foundation, a nonprofit marine conservation organization based in Key Largo, Fla., found 100 percent coral mortality at one site, Sombrero Reef off Key West. There, heat had caused the corals to bleach.

    Corals may survive a few days of very high temperatures but too long spent in extremely hot water can kill them. That accumulated heat stress is measured by coral scientists in “degree heating weeks,” or DHW, a measure of both the intensity and duration of the heat the corals experienced over the previous 12 weeks. Significant coral bleaching begins to occur at 4˚ C–weeks; at 8˚ C–weeks, corals experience severe, widespread bleaching and significant mortality is expected. The accumulated heat stress on the corals at Sombrero Reef in the Florida Keys (shown) generally peaks in August and September (gray lines). But the mounting heat stress on the corals in 2023 (red line) is unprecedented in records going back to 1985.

    Bleaching occurs when corals’ symbiotic algae, the main source of their food, flee, leaving the corals colorless and essentially starving. Corals can recover from bleaching, but if the events are too severe or too frequent, they can kill entire reefs. U.S. National Oceanic and Atmospheric Administration records show that the heat burden on corals globally has been rising since the 1980s (SN: 1/4/18).

    Even with the return to typical summertime water temperatures off Florida’s coasts, the impacts of July’s heat wave on the region’s corals will linger. That’s because corals have a limit to how much accumulated heat they can tolerate before bleaching. And with this heat wave, the corals have already received far too much heat far too early in the summer, researchers say.

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    NOAA records from sites across the Florida Keys each tell the same worrisome story — that what’s happened in 2023 so far is “way outside of the bounds of anything these corals have experienced,” Baker says. And the corals still must contend with two more months of expected, but still very hot, water in August and September.

    Meanwhile, scientists are racing to save corals growing at nurseries in the Keys, bringing them to onshore laboratories away from the overheated coastal waters. The cultivated corals are part of a decade-long effort to protect the two most important reef species in the region, staghorn and elkhorn coral, from the ever-looming threat of bleaching.

    Members of the Coral Restoration Foundation retrieved these young staghorn corals from an ocean nursery to guarantee their survival after water temperatures rose to as high as 36° Celsius (96° Fahrenheit).Carolyn Cole / Los Angeles Times via Getty Images

    The fledgling finger- to hand-sized corals are cultivated in coastal waters atop bits of PVC tubing, and are ultimately destined to be planted in reefs. As the water temperatures rose, researchers hurried to collect the cultivated corals ahead of their expected spawning in early August. Scientists feared the “heat stress is just too much for these baby corals,” and that they might not spawn at all, Baker says. Happily, some of the rescued staghorn corals, now ensconced in the laboratory, did manage to spawn on August 3, releasing clouds of eggs and sperm into the water. Whether the sperm will fertilize the eggs remains uncertain, but Baker and colleagues are cautiously optimistic.

    It’s not just corals in trouble

    The overheated water is also bad news for everything from sponges to sea grasses to fish. “There are a lot of studies that show that species experiencing ocean heat waves are migrating [to cooler waters],” says Regina Rodrigues, a physical oceanographer at the Federal University of Santa Catarina in Brazil (SN: 8/10/20). But in tropical regions like the Caribbean and the Gulf of Mexico, where cooler waters are prohibitively far away, “that community doesn’t have anywhere to go.”

    That lack of access to an escape route to cooler waters is why the region’s cold-blooded ocean species, including fish, may be even more vulnerable to warming than their counterparts on land. On average, ocean ectotherms spend more time near the upper limits for body temperature than land ectotherms, as marine ecologist Malin Pinsky of Rutgers University in New Brunswick, N.J., and colleagues reported in 2019.

    Then there’s the anoxia. As water heats up, it releases oxygen, like bubbles escaping a pot boiling on the stove, leaving less oxygen available for sea life. Such heat-amped anoxic waters have been linked to increased sea grass die-offs as well as fish kills. In June, for example, thousands of fish killed by a low-oxygen event washed up on the Texas Gulf Coast just south of Houston.

    Florida’s sea grasses have been in free fall for years, with thousands of hectares of marine sea grass beds wiped out by anoxia as well as nutrient pollution, which can lead to harmful algal blooms that block out the light for underwater plants. The loss of those sea grass ecosystems has been deadly for manatees and other creatures that rely on the grasses for food.

    ‘It’s just bonkers hot’

    What’s driving the brutal ocean temperatures is still uncertain — but human-caused climate change is undeniably at its core, researchers say. “Ninety-three percent of the excess heat in the atmosphere is being absorbed by the ocean,” Rodrigues says. That’s raised the average temperature of ocean waters, “and once the mean temperature is raised, the extremes are easier to achieve.”

    Other factors are also likely playing a role, including this year’s onset of the global climate pattern known as the El Niño-Southern Oscillation (SN: 7/13/23). The El Niño phase of that climate pattern tends to increase the global average temperature, and this year’s El Niño is bidding to be “a strong one,” Kirtman says.

    “Certainly, one of the questions that’s come up is how much [of the heat] is internal natural variability, and how much a ratcheting up of climate change,” he says.

    Local extremes — such as the temporary hot tub in Manatee Bay — may also be influenced by factors such as the shallowness of the water and murkier, less-reflective waters absorbing more heat. 

    But, Kirtman says, the global oceans have warmed up so much that El Niño or sediment-laden waters alone can’t possibly explain what’s going on. “This is so crazy, so bonkers. It’s just bonkers hot.” More

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    Disclosing ‘true normal price’ recommended to protect consumers from deceptive pricing

    Fifty years ago, the Federal Trade Commission (FTC) stopped enforcing deceptive pricing regulations, assuming that competition would keep retailers honest.
    Since then, competition has increased significantly — yet the practice of posting false, inflated comparison prices alongside sale prices has continued unchecked.
    Think of an advertisement from a furniture store that touts a $599 sale price for a couch as an $800 savings from a promoted regular price of $1,399. The problem is that the store may have never offered the couch for sale at the higher price.
    This practice, called “fictitious pricing,” is ubiquitous in the retail trade. One recent investigation tracked the prices of 25 major retailers and found that “most stores’ sale prices … are bogus discounts” because the listed regular price is seldom, if ever, the price charged for the products.
    “Competition and the Regulation of Fictitious Pricing” is forthcoming in the Journal of Marketing from Joe Urbany, professor of marketing at the University of Notre Dame’s Mendoza College of Business, along with Rick Staelin from Duke University and Donald Ngwe, a senior researcher at Microsoft.
    The paper critically evaluates two assumptions underlying the FTC’s decision to halt deceptive pricing prosecution.
    The first is that inflated reference prices are largely ignored by consumers, who focus primarily on the sale prices, leading to price competition that pushes selling prices lower and renders reference prices harmless. More

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    People’s everyday pleasures may improve cognitive arousal and performance

    Listening to music and drinking coffee are the sorts of everyday pleasures that can impact a person’s brain activity in ways that improve cognitive performance, including in tasks requiring concentration and memory.
    That’s a finding of a new NYU Tandon School of Engineering study involving MINDWATCH, a groundbreaking brain-monitoring technology.
    Developed over the past six years by NYU Tandon’s Biomedical Engineering Associate Professor Rose Faghih, MINDWATCH is an algorithm that analyzes a person’s brain activity from data collected via any wearable device that can monitor electrodermal activity (EDA). This activity reflects changes in electrical conductance triggered by emotional stress, linked to sweat responses.
    In this recent MINDWATCH study, published in Nature Scientific Reports, subjects wearing skin-monitoring wristbands and brain monitoring headbands completed cognitive tests while listening to music, drinking coffee and sniffing perfumes reflecting their individual preferences. They also completed those tests without any of those stimulants.
    The MINDWATCH algorithm revealed that music and coffee measurably altered subjects’ brain arousal, essentially putting them in a physiological “state of mind” that could modulate their performance in the working memory tasks they were performing.
    Specifically, MINDWATCH determined the stimulants triggered increased “beta band” brain wave activity, a state associated with peak cognitive performance. Perfume had a modest positive effect as well, suggesting the need for further study.
    “The pandemic has impacted the mental well-being of many people across the globe and now more than ever, there is a need to seamlessly monitor the negative impact of everyday stressors on one’s cognitive function,” said Faghih. “Right now MINDWATCH is still under development, but our eventual goal is that it will contribute to technology that could allow any person to monitor his or her own brain cognitive arousal in real time, detecting moments of acute stress or cognitive disengagement, for example. At those times, MINDWATCH could ‘nudge’ a person towards simple and safe interventions — perhaps listening to music — so they could get themselves into a brain state in which they feel better and perform job or school tasks more successfully.”
    The specific cognitive test used in this study — a working memory task, called the n-back test — involves presenting a sequence of stimuli (in this case, images or sounds) one by one and asking the subject to indicate whether the current stimulus matches the one presented “n” items back in the sequence. This study employed a 1-back test — the participant responded “yes” when the current stimulus is the same as the one presented one item back — and a more challenging 3-back test, asking the same for three items back. More

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    Researchers use SPAD detector to achieve 3D quantum ghost imaging

    Researchers have reported the first 3D measurements acquired with quantum ghost imaging. The new technique enables 3D imaging on a single photon level, yielding the lowest photon dose possible for any measurement.
    “3D imaging with single photons could be used for various biomedical applications, such as eye care diagnostics,” said researcher Carsten Pitsch from the Fraunhofer Institute of Optronics, System Technologies and Image Exploitation and Karlsruhe Institute of Technology, both in Germany. “It can be applied to image materials and tissues that are sensitive to light or drugs that become toxic when exposed to light without any risk of damage.”
    In the Optica Publishing Group journal Applied Optics, the researchers describe their new approach, which incorporates new single photon avalanche diode (SPAD) array detectors. They apply the new imaging scheme, which they call asynchronous detection, to perform 3D imaging with quantum ghost imaging.
    “Asynchronous detection might also be useful for military or security applications since it could be used to observe without being detected while also reducing the effects of over-illumination, turbulence and scattering,” said Pitsch. “We also want to investigate its use in hyperspectral imaging, which could allow multiple spectral regions to be recorded simultaneously while using a very low photon dose. This could be very useful for biological analysis.”
    Adding a third dimension
    Quantum ghost imaging creates images using entangled photon-pairs in which only one member of the photon pair interacts with the object. The detection time for each photon is then used to identify entangled pairs, which allows an image to be reconstructed. This approach not only allows imaging at extremely low light levels but also means that the objects being imaged do not have to interact with the photons used for imaging.
    Previous setups for quantum ghost imaging were not capable of 3D imaging because they relied on intensified charge-coupled device (ICCD) cameras. Although these cameras have good spatial resolution, they are time-gated and don’t allow the independent temporal detection of single photons. More

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    The ‘unknome’: A database of human genes we know almost nothing about

    Researchers from the United Kingdom hope that a new, publicly available database they have created will shrink, not grow, over time. That’s because it is a compendium of the thousands of understudied proteins encoded by genes in the human genome, whose existence is known but whose functions are mostly not. The database, dubbed the “unknome,” is the work of Matthew Freeman of the Dunn School of Pathology, University of Oxford, England, and Sean Munro of MRC Laboratory of Molecular Biology in Cambridge, England, and colleagues, and is described in the open access journal PLOS Biology. Their own investigations of a subset of proteins in the database reveal that a majority contribute to important cellular functions, including development and resilience to stress.
    The sequencing of the human genome has made it clear that it encodes thousands of likely protein sequences whose identities and functions are still unknown. There are multiple reasons for this, including the tendency to focus scarce research dollars on already-known targets, and the lack of tools, including antibodies, to interrogate cells about the function of these proteins. But the risks of ignoring these proteins are significant, the authors argue, since it is likely that some, perhaps many, play important roles in critical cell processes, and may both provide insight and targets for therapeutic intervention.
    To promote more rapid exploration of such proteins, the authors created the unknome database (www.unknome.org), that assigns to every protein a “knownness” score, reflecting the information in the scientific literature about function, conservation across species, subcellular compartmentalization, and other elements. Based on this system, there are many thousands of proteins whose knownness is near-zero. Proteins from model organisms are included, along with those from the human genome. The database is open to all and is customizable, allowing the user to provide their own weights to different elements, thereby generating their own set of knownness scores to prioritize their own research.
    To test the utility of the database, the authors chose 260 genes in humans for which there were comparable genes in flies, and which had knownness scores of 1 or less in both species, indicating that almost nothing was known about them. For many of them, a complete knockout of the gene was incompatible with life in the fly; partial knockdowns or tissue-specific knockdowns led to the discovery that a large fraction contributed to essential functions influencing fertility, development, tissue growth, protein quality control, or stress resistance.
    The results suggest that, despite decades of detailed study, there are thousands of fly genes that remain to be understood at even the most basic level, and the same is clearly true for the human genome. “These uncharacterized genes have not deserved their neglect,” Munro said. “Our database provides a powerful, versatile and efficient platform to identify and select important genes of unknown function for analysis, thereby accelerating the closure of the gap in biological knowledge that the unknome represents.”
    Munro adds, “The role of thousands of human proteins remains unclear and yet research tends to focus on those that are already well understood. To help address this we created an Unknome database that ranks proteins based on how little is known about them, and then performed functional screens on a selection of these mystery proteins to demonstrate how ignorance can drive biological discovery.” More