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Scooped by Dr. Stefan Gruenwald
October 26, 2023 5:00 PM
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Hacking the Human Body - The Human Protein Atlas

Hacking the Human Body - The Human Protein Atlas | Amazing Science | Scoop.it
 

In the past decade, we have seen an increasing number of large-scale bioimage initiatives. These efforts have generated a rich source of histology images, covering a plethora of organs and tissues in the human body, which should ultimately come together to form a reference map of the human body.

Combining massive amounts of imaging data requires harmonization and consensus image analysis pipelines, including segmentation algorithms that perform well on images from diverse sources. This led researchers from the Human Protein Atlas (HPA) and the Human Biomolecular Atlas (HuBMAP) to co-host a community-driven machine learning challenge, called "Hacking the Human Body", on the Kaggle platform. The challenge setup and the results were recently presented in Nature Communications.

The competition engaged 1175 teams, bringing together people with various expertise and from 78 countries, who not only competed, but also collaborated and interacted extensively. The challenge focused on segmentation of Functional Tissue Units (FTUs) in five different organs using tissue images from both the HPA and HuBMAP. An FTU is defined as the smallest anatomical structure that performs a unique physiologic function in an organ, such as alveoli in the lung or glomeruli in the kidney. As their structure and composition are often subjected to alterations in human diseases, robust segmentation of FTUs is an important step towards image segmentation tasks in medical settings. The code from the winning models will be productized and deployed in the HuBMAP, but all data and code is also publicly available at GitHub and Zenodo.

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Scooped by Dr. Stefan Gruenwald
October 25, 2023 3:14 PM
Scoop.it!

Former State Secretary Henry Kissinger Says AI Could Replace Humans In Next 5 Years

Former State Secretary Henry Kissinger Says AI Could Replace Humans In Next 5 Years | Amazing Science | Scoop.it

Henry Kissinger described artificial intelligence as the "biggest challenge of our times," predicting that humanity could be replaced by machines in the next five years.

 

As per a report published on Insider, Kissinger, in an interview with Mathias Döpfner, CEO of Axel Springer, stated that AI is the “biggest challenge of our times.” The conversation was aired by Welt TV, a subsidiary of Die Welt newspaper.

 

AI’s potential has been a significant discussion point since the launch of OpenAI’s ChatGPT in November 2022. Experts have pointed out that white-collar jobs, especially in sectors such as technology, media, law, and customer service, are in danger of being replaced by AI.

 

Since the release of OpenAI's ChatGPT in November 2022, the potential of AI has loomed large, threatening to replace humans in some jobs, particularly white-collar ones, Insider previously reported. Jobs in technology, media, law, market research analysis, education, trade, graphic design, accounting, and customer service are among those most at risk of being replaced by AI, experts previously told Insider.

 

Kissinger, who is 100, said he was concerned AI could become so powerful in the long run that it leads to the sci-fi-esque outcome of humans serving machines — not the other way around. "I think it can be avoided, but only by understanding the essence of this intelligence, which will also be able to generate its own point of view," he said.

 

Kissinger co-wrote a book on artificial intelligence, "The Age of AI and Our Human Future," in which he, along with former Google CEO Eric Schmitt and computer scientist Daniel Huttenlocher, explored how AI may change our relationships with knowledge, politics, and society.

 
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Rescooped by Dr. Stefan Gruenwald from Virology News
October 20, 2023 6:04 PM
Scoop.it!

Rate of climate-induced extinction is 'shocking'

Rate of climate-induced extinction is 'shocking' | Amazing Science | Scoop.it
 
A study of a lizard species in Arizona revealed that nearly 70 years' worth of climate-related extinction occurred in just seven years.

 

Researchers surveyed populations of the Yarrow’s spiny lizard in 18 mountain ranges in southeastern Arizona and analyzed the rate of climate-related extinction over time. “The magnitude of extinction we found over the past seven years was similar to that seen in other studies that spanned almost 70 years,” says John J. Wiens, a professor in the ecology and evolutionary biology department at the University of Arizona and senior author of the study in Ecology Letters.

 

The Yarrow’s spiny lizard native to the southwestern US and western Mexico can be spotted in oak and pine forests in 18 of Arizona’s Sky Islands mountain ranges. Wiens and his group did initial surveys of the Yarrow’s spiny lizard in these mountain ranges in 2014 and 2015.

 

In 2021 and 2022, Wiens, along with Kim Holzmann, his former master’s student and the new study’s lead author, and Ramona Walls, a part-time researcher at the University of Arizona’s BIO5 institute, resurveyed to investigate if there had been any changes in the lizard populations since then.

 

They found that about half of the lizard populations at lower elevations had disappeared. This is because temperatures are warmer at lower elevations, Wiens says, and the lizards at lower elevations were presumably not able to tolerate the increasing heat. This loss of low-elevation populations is a signature pattern of climate change, he says. “The rate of extinction in such a short time period was shocking,” Wiens says.

 

After comparing the findings to historical records from the same mountain ranges, Wiens’ group found that the average extinction rate of the lizard populations at low elevations had tripled over the past seven years, relative to the preceding 42 years. Although previous studies have predicted that climate-related extinctions will increase with the rising pace of global warming, Wiens says he hasn’t seen any showing that this acceleration of extinction has already happened.

 

Also, a distinct 3-million-year-old lineage of the Yarrow’s spiny lizard from the Mule Mountains, near Bisbee, may be completely extinct by 2025, Wiens says. “The low-elevation populations in the Mules were fine in 2014. Now the only ones that we have found left were within about 300 feet of the top of the mountain in 2022, and they appear to have been losing about 170 feet per year,” he says.

 

However, not all low-elevation populations went extinct between the surveys, Wiens says. For example, two populations that occurred at very low elevations survived. Before they disappeared, the research group had collected genomic data from most of those populations in 2014 and 2015. They found that those populations that were less genetically variable and were exposed to greater climate change effects were the ones that tended to go extinct. This suggests that the populations with less genetic variation had less ability to adapt to climate change.


Via Ed Rybicki
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Could AI find alien life faster than humans, and would it tell us?

Could AI find alien life faster than humans, and would it tell us? | Amazing Science | Scoop.it
 

Turn a radio telescope to the stars in the sky, and it's instantly deafened. From pulsars to radio galaxies, and ionospheric disturbances in the atmosphere to radio-frequency interference (RFI) from our own technology, the sky is a cacophony of radio noise. And somewhere, among all that, may lie a needle in a haystack: a signal from another world.

 

For over 60 years scientists have been scanning the skies in the search for extraterrestrial life but have yet to find any aliens. When you consider the sheer volume of search space — all those stars, all those radio frequencies — versus our limited searches so far, then it's little wonder we've not found ET yet. It's a daunting task, especially for a human. Thankfully, we've got some non-human intelligence to join the search.

 

The use of artificial intelligence (AI) is reaching critical mass, in our everyday lives and in science, so it is no surprise that it's now being employed in Search for Extraterrestrial Intelligence (SETI). AI is already helping astronomers make incredible discoveries. Here's how. We're not talking about Skynet, or the machines from The Matrix movies, or even Star Trek: The Next Generation's Data. The AI that is so in vogue at present is based on machine-learning algorithms designed to do very specific jobs, even if it's just to talk to you on ChatGPT.

 

To explain how AI is assisting in SETI, astronomer and SETI researcher Eamonn Kerins of the University of Manchester compares it to the needle in a haystack problem. "You basically treat the data as though it's the hay," Kerins told Space.com Space.com. "Then you're asking the machine-learning algorithm to tell you if there is anything in the data that isn't hay, and that hopefully is the needle in the haystack — unless there's other stuff in the haystack too."

 

That other stuff is usually RFI, but the machine-learning algorithm is trained to recognize all the types of RFI we already know about. Those signals — the familiar patterns of mobile phones, local radio transmitters, electronics and so on — are the hay. The training involves "injecting signals into the data and then the algorithm learns to look for signals that are like that," Steve Croft, an astronomer with the Breakthrough Listen SETI project at the University of California, Berkeley, told Space.com The algorithm learns to spot the patterns of these familiar signals and disregard them. Should it spot something in the data that it hasn't been trained on, then it flags this up as something interesting that requires a human to follow up on.

 

"There have been attempts recently at sifting through some of the Breakthrough Listen data with a machine-learning algorithm," said Kerins. "The data had already been combed through quite carefully previously by more conventional means, but yet the algorithm was still able to pick out new signals after being trained on the stuff that we know about."

 

This project was led by Croft and an undergraduate student, Peter Ma of the University of Toronto, who wrote the algorithm and put it to work analyzing data from 820 stars observed by the 100-meter radio telescope at Green Bank Observatory in West Virginia. The data, totaling 489 hours' worth of observations, contained millions of radio signals, almost all of which were human-made interference. The algorithm checked every single one of them and found eight signals that did not match anything it had been trained on and which had been missed by earlier analyses of the data.

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October 20, 2023 5:44 PM
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We should find extraterrestrial life within 60 light-years if Earth is average

We should find extraterrestrial life within 60 light-years if Earth is average | Amazing Science | Scoop.it

In 1960, while preparing for the first meeting on the Search for Extraterrestrial Intelligence (SETI), legendary astronomer and SETI pioneer Dr. Frank Drake unveiled his probabilistic equation for estimating the number of possible civilizations in our galaxy—aka The Drake Equation. A key parameter in this equation was ne, the number of planets in our galaxy capable of supporting life—aka "habitable." At the time, astronomers were not yet certain other stars had systems of planets. But thanks to missions like Kepler, 5,523 exoplanets have been confirmed, and another 9,867 await confirmation.

 

Based on this data, astronomers have produced various estimates for the number of habitable planets in our galaxy—at least 100 billion, according to one estimate. In a recent study posted to the arXiv preprint server, Professor Piero Madau introduced a mathematical framework for calculating the population of habitable planets within 100 parsecs (326 light-years) of our sun.

 

Assuming Earth and the solar system are representative of the norm, Madau calculated that this volume of space could contain as much as 11,000 Earth-sized terrestrial (aka rocky) exoplanets that orbit within their stars' habitable zones (HZs).

 

Prof. Madau is a professor of astronomy and astrophysics at the University of California, Santa Cruz (UCSC). Central to his study is the Copernican Principle, named for famed Polish astronomer Nicolaus Copernicus, inventor of the heliocentric model. Also known as the Cosmological Principle (or Mediocrity Principle), the principle states that neither humans nor Earth are in a privileged position to observe the universe. In short, what we see when we look upon the solar system and out into the cosmos is representative of the whole.

 

For his study, Madau considered how time-dependent factors have played a vital role in the emergence of life in our universe. This includes the star formation history of our galaxy, the enrichment of the interstellar medium (ISM) by heavy elements (forged in the interior of the first population of stars), the formation of planets, and the distribution of water and organic molecules between planets.

 

As Madau explained to Universe Today, the central role of time and age are not explicitly stressed in the Drake Equation:

 
  • "The Drake equation amounts to a useful pedagogical summary of the factors (probabilities) that may affect the likelihood of detecting life-bearing worlds—and eventually technologically advanced extraterrestrial civilizations—around us today. But that likelihood and those factors depend, among other quantities, on the star formation and chemical enrichment history of the local Galactic disk, as well as on the timeline of the emergence of simple microbial and eventually complex life."
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Scooped by Dr. Stefan Gruenwald
October 20, 2023 5:34 PM
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Revolutionizing radar: Integrated THz emitter for precise rotating target detection

Revolutionizing radar: Integrated THz emitter for precise rotating target detection | Amazing Science | Scoop.it

You may not realize it, but the Doppler effect is everywhere in our lives, from tracking the speed of cars with radar to locating satellites in the sky. It's all about how waves change their frequency when a source (like a radar signal) and a detector are in motion relative to each other. However, traditional radar systems hit a roadblock when trying to detect objects moving at right angles to their radar signals. This limitation has driven researchers to explore an entirely new approach.

 

 

Imagine a radar system that doesn't just rely on linear waves but instead uses spiraling electromagnetic waves with orbital angular momentum (OAM). These special "vortex" waves have a helical twist and introduce a signature rotational Doppler effect when they encounter a spinning object.

 

To improve identification and detection of these rotational Doppler effects, researchers from University of Shanghai for Science and Technology (USST) have harnessed terahertz (THz) waves by developing an integrated THz vortex beam emitter, as reported in Advanced Photonics.

 

According to USST Professor Yiming Zhu, corresponding author for the article, "To the best of our knowledge, this study represents the first demonstration of an integrated THz vortex beam emitter specifically designed for the detection of rotating targets."

 

Terahertz waves are uniquely suited for high-resolution radar imaging. In terms of frequency, they reside between microwaves and infrared waves, and have a unique ability to penetrate various materials while carrying minimal risk of damage. Yet while THz waves show great promise, they face their own set of challenges, such as low efficiency and instability issues.

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Scooped by Dr. Stefan Gruenwald
October 19, 2023 2:49 PM
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Tiny Texas fish among 21 species that recently went extinct

Tiny Texas fish among 21 species that recently went extinct | Amazing Science | Scoop.it

The U.S. Fish and Wildlife Service on Monday finalized a rule removing 21 species from the list of threatened and endangered species under the Endangered Species Act because of extinction, including a tiny fish found only in Texas.

 

The San Marcos gambusia hasn’t been seen since 1983. The tiny species of fish was once found in only a half-mile stretch of the San Marcos River.

 

It joins a list of species that includes eight types of honeycreepers from Hawaii, the bridled white-eye and the little Mariana fruit bat from Guam, and nine southeastern mussels found mostly in the South.

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Rescooped by Dr. Stefan Gruenwald from Virus World
October 18, 2023 1:47 PM
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Viral Persistence and Serotonin Reduction Can Cause Long COVID Symptoms

Viral Persistence and Serotonin Reduction Can Cause Long COVID Symptoms | Amazing Science | Scoop.it

A new Penn Medicine study finds components of the SARS-CoV-2 virus remain in the gut of some long COVID patients, causing persistent inflammation, vagus nerve dysfunction, and neurological symptoms. Patients with long COVID—the long-term symptoms like brain fog, fatigue, or memory loss in the months or years following COVID-19—can exhibit a reduction in circulating levels of the neurotransmitter serotonin, according to new research published in Cell. The study, led by researchers from the Perelman School of Medicine, sheds new light on the mechanisms of how persistent inflammation after contracting the SARS-CoV-2 virus can cause long-term neurological symptoms. “Many aspects of the basic biology underlying long COVID have remained unclear. As a result, we are lacking effective tools for the diagnosis and treatment of the disease,” says senior author Maayan Levy, an assistant professor of microbiology at Penn Medicine. “Our findings may not only help to untangle some of the mechanisms that contribute to long COVID, but also provide us with biomarkers that can help clinicians diagnose patients and objectively measure their response to individual treatments.”

 

In a collaboration between Penn’s departments of MicrobiologyPathology and Laboratory Medicine, and Physical Medicine and Rehabilitations’ Post COVID Assessment and Recovery Clinic, researchers evaluated the effects of long COVID in blood and stool samples from various clinical studies and in small animal models. The researchers found that when tryptophan absorption is reduced by persistent viral inflammation, serotonin is depleted, leading to disrupted vagus nerve signaling, which in turn can cause several of the symptoms associated with long COVID, such as memory loss. “Clinicians treating patients with long COVID have been relying on personal reports from those patients to determine if their symptoms are improving. Now, our research shows that there are biomarkers we may be able to use to match patients to treatments or clinical trials that address the specific causes of their long COVID symptoms, and more effectively assess their progress,” says co-senior author, Sara Cherry, a professor of pathology and laboratory medicine. The authors took this insight one step further, to identify if replenishing tryptophan or serotonin in patients who exhibit deficiencies could treat long COVID symptoms. They demonstrated that serotonin levels could be restored, and memory impairment reversed, through treatment with serotonin precursors or selective serotonin reuptake inhibitors.

 

Read more at Penn Medicine News.

 

Study published in Cell (Oct. 16, 2023):

https://doi.org/10.1016/j.cell.2023.09.013 


Via Juan Lama
Issam Hasni's curator insight, December 7, 2023 12:13 PM
Long covid symptoms related to serotonine reduction
Rescooped by Dr. Stefan Gruenwald from Virus World
October 17, 2023 4:23 PM
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Targeting a Coronavirus Ion Channel (E) could Result in Novel Covid-19 Drugs

Targeting a Coronavirus Ion Channel (E) could Result in Novel Covid-19 Drugs | Amazing Science | Scoop.it

The genome of the SARS-CoV-2 virus encodes 29 proteins, one of which is an ion channel called E. This channel, which transports protons and calcium ions, induces infected cells to launch an inflammatory response that damages tissues and contributes to the symptoms of Covid-19. MIT chemists have now discovered the structure of the “open” state of this channel, which allows ions to flow through. This structure, combined with the “closed” state structure that was reported by the same lab in 2020, could help scientists figure out what triggers the channel to open and close. These structures could also guide researchers in developing antiviral drugs that block the channel and help prevent inflammation. “The E channel is an antiviral drug target. If you can stop the channel from sending calcium into the cytoplasm, then you have a way to reduce the cytotoxic effects of the virus,” says Mei Hong, an MIT professor of chemistry and the senior author of the study. MIT postdoc Joao Medeiros-Silva is the lead author of the study, which appears today in Science Advances. MIT postdocs Aurelio Dregni and Pu Duan and graduate student Noah Somberg are also authors of the paper.

 

Open and closed

 

Hong has extensive experience in studying the structures of proteins that are embedded in cell membranes, so when the Covid-19 pandemic began in 2020, she turned her attention to the coronavirus E channel. When SARS-CoV-2 infects cells, the E channel embeds itself inside the membrane that surrounds a cellular organelle called the ER-Golgi intermediate compartment (ERGIC). The ERGIC interior has a high concentration of protons and calcium ions, which the E channel transports out of ERGIC and into the cell cytoplasm. That influx of protons and calcium leads to the formation of multiprotein complexes called inflammasomes, which induce inflammation. To study membrane-embedded proteins such as ion channels, Hong has developed techniques that use nuclear magnetic resonance (NMR) spectroscopy to reveal the atomic-level structures of those proteins. In previous work, her lab used these techniques to discover the structure of an influenza protein known as the M2 proton channel, which, like the coronavirus E protein, consists of a bundle of several helical proteins. Early in the pandemic, Hong’s lab used NMR to analyze the structure of the coronavirus E channel at neutral pH. The resulting structure, reported in 2020, consisted of five helices tightly bundled together in what appeared to be the closed state of the channel. “By 2020, we had matured all the NMR technologies to solve the structure of this kind of alpha-helical bundles in the membrane, so we were able to solve the closed E structure in about six months,” Hong says.

 

Once they established the closed structure, the researchers set out to determine the structure of the open state of the channel. To induce the channel to take the open conformation, the researchers exposed it to a more acidic environment, along with higher calcium ion levels. They found that under these conditions, the top opening of the channel (the part that would extend into the ERGIC) became wider and coated with water molecules. That coating of water makes the channel more inviting for ions to enter. That pore opening also contains amino acids with hydrophilic side chains that dangle from the channel and help to attract positively charged ions. The researchers also found that while the closed channel has a very narrow opening at the top and a broader opening at the bottom, the open state is the opposite: broader at the top and narrower at the bottom. The opening at the bottom also contains hydrophilic amino acids that help draw ions through a narrow “hydrophobic gate” in the middle of the channel, allowing the ions to eventually exit into the cytoplasm. Near the hydrophobic gate, the researchers also discovered a tight “belt,” which consists of three copies of phenylalanine, an amino acid with an aromatic side chain. Depending on how these phenylalanines are arranged, the side chains can either extend into the channel to block it or swing open to allow ions to pass through. “We think the side chain conformation of these three regularly spaced phenylalanine residues plays an important role in regulating the closed and open state,” Hong says.

 

Viral targeting

 

Previous research has shown that when SARS-CoV-2 viruses are mutated so that they don’t produce the E channel, the viruses generate much less inflammation and cause less damage to host cells. Working with collaborators at the University of California at San Francisco, Hong is now developing molecules that could bind to the E channel and prevent ions from traveling through it, in hopes of generating antiviral drugs that would reduce the inflammation produced by SARS-CoV-2. Her lab is also planning to investigate how mutations in subsequent variants of SARS-CoV-2 might affect the structure and function of the E channel. In the Omicron variant, one of the hydrophilic, or polar, amino acids found in the pore opening is mutated to a hydrophobic amino acid called isoleucine. “The E variant in Omicron is something we want to study next,” Hong says. “We can make a mutant and see how disruption of that polar network changes the structural and dynamical aspect of this protein.”

 

The research was funded by the National Institutes of Health and the MIT School of Science Sloan Fund.

 

REsearc published in Science Advances (Oct. 13, 2023):

https://doi.org/10.1126/sciadv.adi9007 

 

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NASA’s Bennu Asteroid Sample Contains Abundant Carbon and Water

NASA’s Bennu Asteroid Sample Contains Abundant Carbon and Water | Amazing Science | Scoop.it
 
 

Initial studies of the 4.5-billion-year-old asteroid Bennu sample collected in space and brought to Earth by NASA show evidence of high-carbon content and water, which together could indicate the building blocks of life on Earth may be found in the rock. NASA made the news Wednesday from its Johnson Space Center in Houston where leadership and scientists showed off the asteroid material for the first time since it landed in September.

 

This finding was part of a preliminary assessment of NASA’s OSIRIS-REx (Origins, Spectral Interpretation, Resource Identification and Security – Regolith Explorer) science team. “The OSIRIS-REx sample is the biggest carbon-rich asteroid sample ever delivered to Earth and will help scientists investigate the origins of life on our own planet for generations to come,” said NASA Administrator Bill Nelson. “Almost everything we do at NASA seeks to answer questions about who we are and where we come from. NASA missions like OSIRIS-REx will improve our understanding of asteroids that could threaten Earth while giving us a glimpse into what lies beyond. The sample has made it back to Earth, but there is still so much science to come – science like we’ve never seen before.”  

 

Although more work is needed to understand the nature of the carbon compounds found, the initial discovery bodes well for future analyses of the asteroid sample. The secrets held within the rocks and dust from the asteroid will be studied for decades to come, offering insights into how our solar system was formed, how the precursor materials to life may have been seeded on Earth, and what precautions need to be taken to avoid asteroid collisions with our home planet.

 

Bonus sample material

The goal of the OSIRIS-REx sample collection was 60 grams of asteroid material. Curation experts at NASA Johnson, working in new clean rooms built especially for the mission, have spent 10 days so far carefully disassembling the sample return hardware to obtain a glimpse at the bulk sample within. When the science canister lid was first opened, scientists discovered bonus asteroid material covering the outside of the collector head, canister lid, and base. There was so much extra material it slowed down the careful process of collecting and containing the primary sample.

“Our labs were ready for whatever Bennu had in store for us,” said Vanessa Wyche, director, NASA Johnson.

 

“We’ve had scientists and engineers working side-by-side for years to develop specialized gloveboxes and tools to keep the asteroid material pristine and to curate the samples so researchers now and decades from now can study this precious gift from the cosmos.”

 

Within the first two weeks, scientists performed “quick-look” analyses of that initial material, collecting images from a scanning electron microscope, infrared measurements, X-ray diffraction, and chemical element analysis. X-ray computed tomography was also used to produce a 3D computer model of one of the particles, highlighting its diverse interior. This early glimpse provided the evidence of abundant carbon and water in the sample.

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Singularity: The Dark Side of AI (100% AI-Generated Non-Fiction Film)

 

Singularity: The Dark Side of AI (100% AI Generated Non-Fiction Film)

 

In a world increasingly shaped by artificial intelligence, humanity stands at a crossroads. As AI technology advances rapidly, we must consider both its benefits and dangers. In this video, we will explore the negative aspects of AI, discussing the potential risks and serious consequences of its uncontrolled use. We will explore the hidden dangers and face the uncomfortable truths about our world that is becoming more and more reliant on AI.

 

Created by Maksim Shmeljov using several neural networks:

  • Text: Chat GPT and Google Bard
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  • Animation: Pika Labs and Runway Gen-2
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It was springtime on the Northern hemisphere when the dinosaurs died, ancient fish fossils suggest

It was springtime on the Northern hemisphere when the dinosaurs died, ancient fish fossils suggest | Amazing Science | Scoop.it
 

On a spring day 66 million years ago, paddlefish and sturgeon swam in a river that meandered through a flourishing landscape populated by mighty dinosaurs and small mammals at North America's southwestern corner. Death came from outer space that day.

 

Scientists examined well-preserved fish fossils to get a deeper understanding of one of the worst days in the history of life on Earth and shedding light on the global calamity triggered by an asteroid 7.5 miles (12 km) wide striking Mexico's Yucatan Peninsula. The ensuing mass extinction erased about three-quarters of Earth's species, including the dinosaurs at the end of the Cretaceous Period, paving the way for mammals - eventually humans - to become dominant on the planet.

 

The researchers determined that it was springtime at the fossil site called the Tanis deposit - and throughout the Northern hemisphere, including the spot where the asteroid hit - based on sophisticated examinations of bones from three paddlefishes and three sturgeons that died within about 30 minutes of the impact that occurred 2,200 miles (3500 km) away.

 

They found evidence that a hail of glass pelted the site, finding small spherules - molten material blasted by the impact into space that crystallized before falling back to Earth - embedded in fish gills. The Tanis fossils also indicated that a huge standing wave of water swept through after the impact, burying the local denizens alive. Among the dinosaurs living in the Tanis area was apex predator Tyrannosaurus rex.

 

"Every living thing in Tanis on that day saw nothing coming and was killed almost instantaneously," said Melanie During, a paleontology doctoral student at Uppsala University in Sweden and lead author of the research published in the journal Nature. During compared the fossils deposited at Tanis to "a car crash frozen in place."

 

Multiple lines of evidence pointed to a springtime impact. Annual growth rings in certain fish bones - resembling those in tree trunks - showed increased growth levels associated with springtime after reduced growth in leaner winter months. Chemical evidence from one of the paddlefishes indicated that food availability was increasing as it does in springtime, but not at peak summer levels.

 

Springtime marks a time of growth and reproduction for many organisms. "This season is crucial for the survival of species," said study co-author Sophie Sanchez, an Uppsala University senior lecturer in paleohistology. In the southern hemisphere, it was autumn at the time, Sanchez noted, a season when many creatures prepare for the deprivations of winter. Dinosaurs - aside from their bird descendants - went extinct, as did major marine groups, including the carnivorous reptiles that dominated the seas. Among the survivors were paddlefishes and sturgeons, which survive to this day.

 

The Tanis fossils helped the researchers better understand the events following the impact, which left a crater about 110 miles (180 km) wide at a Yucatan site called Chicxulub. The asteroid rocked the continental plate, generated earthquakes, sparked extensive wildfires, unleashed a massive shockwave in the air and seismic waves on the ground, and spawned massive standing waves called seiche waves - perhaps hundreds of yards tall - in water bodies. These waves, carrying immense amounts of sediment and debris, inundated the Tanis site within approximately 15 to 30 minutes after the impact, burying alive all the inhabitants, including the fish whose fossils were studied.

 

The peril did not end that day. A cloud of dust enrobed Earth, precipitating a climate catastrophe akin to a "nuclear winter" that blocked sunlight for perhaps years, condemning countless species to oblivion. "Although most of the extinction unfolded during the aftermath of the impact, which lasted much longer, zero hour - the exact timing of the impact - determined the course of the mass extinction," said study co-author Jeroen van der Lubbe, a geochemist and paleoclimatologist at Vrije Universiteit Amsterdam in the Netherlands.

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Adobe Firefly’s generative AI models can now create vector graphics in Adobe Illustrator

Adobe Firefly’s generative AI models can now create vector graphics in Adobe Illustrator | Amazing Science | Scoop.it
 

Adobe Illustrator is a widely used vector graphics tool for graphic artists and it’s about to join the generative AI era with the launch of the Firefly Vector Model at Adobe’s MAX conference today. Adobe describes the new model as “the world’s first generative AI model focused on producing vector graphics.” Like Firefly for creating images and photos, Firefly for Illustrator will be able to create entire vector graphics from scratch. And like the other Firefly models, the vector model, too, was trained on data from Adobe Stock.

 

In its beta, Illustrator will now let you create entire scenes through a text prompt. What’s nifty here is that those scenes can consist of multiple objects. So this isn’t just a jumble of vectors that make up the overall graphic but Illustrator will automatically generate these different objects and you can manipulate them individually to your heart’s content, just like any other group or layer in Illustrator.

 

Alexandru Costin, Adobe’s VP for generative AI and Sensei, told me the company used tens of millions of vector images in Adobe Stock to train Firefly to enable this new capability. Costin described the process as “a journey” and since there hasn’t been as much work done on using generative AI to create vector drawings compared to the work on creating other images, this surely took a bit more work on the team’s part. He noted that the team focused on creating a model that could generate these images with the fewest possible points, too.

 

Another new feature that’s coming to Illustrator is called Mockup, which allows Illustrator users to take any 3D scene and then take any vector art and apply it to that 3D scene. That could be a design for a drink can, for example, or a mockup of a new logo on a t-shirt. “Mockup is really exciting to show your customers the art in context so they understand what they’re buying when they contract you as a freelancer,” Costin explained. Also new is Retype, which converts static text in images to editable text — and it’ll find matching fonts, too — and Illustrator is now available on the web, too!

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Determination of the Total Mass, Number, and Distribution of Immune Cells in the Human Body

Determination of the Total Mass, Number, and Distribution of Immune Cells in the Human Body | Amazing Science | Scoop.it
 
A team of scientists characterized the human body’s immune cells distribution and provided its total weight. The findings demonstrate that an average individual’s immune system consists of approximately 1.8 trillion cells and weighing around 1.2 kg. Lymphocytes make up 40% of the total number of immune cells and 15% of their mass. Similarly, neutrophils account for comparable proportions. Notably, macrophages constitute 10% of immune cells but contribute nearly 50% of the total cellular mass due to their larger size. This knowledge gives an integrative quantitative view of the immune system and facilitates the development of models.
 
The immune system is a complex network of cells with critical functions in health and disease. However, a comprehensive census of the cells comprising the immune system is still lacking.
This new work now estimated the abundance of the primary immune cell types throughout all tissues in the human body. The researchers conducted a literature survey and integrated data from multiplexed imaging and methylome-based deconvolution. They also considered cellular mass to determine the distribution of immune cells in terms of both number and total mass.
 
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How the Current Bird Flu Strain Evolved To Be So Deadly

How the Current Bird Flu Strain Evolved To Be So Deadly | Amazing Science | Scoop.it
 

Genetic changes to avian influenza viruses have led to spread among many wild species, creating an uncontrollable global outbreak. Researchers studying the evolution of the bird flu virus over the past 18 years have shown how the strain currently circulating worldwide, an extremely deadly form of the H5N1 subtype, has become increasingly infectious to wild birds. The strain emerged in Europe in 2020, and has spread to an unprecedented number of countries. The study, published in Nature on the 18th October 2023 looked at changes to the virus’s genome over time and used data on reported outbreaks to track how it spread. In 2020, the rate of spread among wild birds was three times faster than that in farmed poultry, because of mutations that allowed the virus to adapt to diverse species. “What was once very clearly a poultry pathogen has now become an animal-health issue much more broadly,” says Andy Ramey, a wildlife geneticist at the US Geological Survey Alaska Science Center in Anchorage. “That has implications for wildlife and domestic poultry as well as us humans that rely upon these resources.”

Persistent outbreaks

H5N1, classified as a highly pathogenic avian influenza (HPAI) virus because of its high death toll in poultry, was first detected in birds in China in 1996. Outbreaks are usually seasonal, synchronizing with bird migration in Northern Hemisphere autumn. But since November 2021, they have become persistent. In 2022, the virus killed millions of birds across five continents and seeded outbreaks among farmed mink and various marine mammals. To study changes in the virus’s behaviour, the authors examined data reported to the Food and Agricultural Organization of the United Nations and the World Organisation for Animal Health between 2005 and 2022, and analysed more than 10,000 viral genomes. Their work reveals that in mid-2020, a new H5N1 strain evolved from an earlier variety, called H5N8, which first emerged in poultry in Egypt between 2016 and 2017 and caused global flare-ups throughout 2020 and 2021 (see ‘Bird flu outbreaks’). The new H5N1 virus mutated through interactions with non-deadly varieties of bird flu, called low-pathogenic avian influenza (LPAI) viruses, that had been circulating among wild birds in Europe since 2019. It developed two subtypes in 2021 and 2022. One spread across the northern coastal regions of central Europe and was eventually carried to North America by birds migrating across the Atlantic Ocean. The other was carried around the Mediterranean Sea and into Africa. Many bird flu outbreaks begin in poultry, but spillover into wild birds has spread the disease into larger areas, creating a global challenge that is difficult to manage, the study found. “Once it’s adapted to wild birds, we have no mechanism to control the virus. And I think that’s the biggest impact that has changed now,” says co-author Vijaykrishna Dhanasekaran, an evolutionary biologist and virologist at the University of Hong Kong. Louise Moncla, an evolutionary virologist at the University of Pennsylvania in Philadelphia, agrees. “Regardless of how much outbreak response you do in poultry, if it’s coming in from wild birds repeatedly, this is going to be really hard to manage.” “This is really something that most of the world at this point has skin in the game,” adds Ramey.

Mixing viruses

LPAI viruses often circulate freely in poultry and wild birds. Previous infection with these non-deadly strains is thought to encourage population immunity in wild birds. “You can think of it as an imperfect vaccine, that doesn’t stop infection, but it helps mitigate the effects of disease,” says Ramey. But “there’s probably two sides of the coin here”, he adds. HPAI viruses can mutate through interactions with LPAI ones. In both, the genome is split into eight segments that can be mixed and matched. “When two viruses co-infect the same cell, they could swap their genes when the virus is getting packaged,” says Dhanasekaran. Because of this, LPAI viruses — especially a strain called H9N2 — play a major part in the evolution of H5N1, he adds. But they are not well monitored. “Eradication or elimination strategies that target these low pathogenic viruses would be a huge step forward in terms of controlling avian influenza itself,” says Dhanasekaran.

 

Research Cited published in Nature (Oct. 18, 2023):

 https://doi.org/10.1038/s41586-023-06631-2 


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A new innovative view of all objects in the universe

A new innovative view of all objects in the universe | Amazing Science | Scoop.it
 
The most comprehensive view of the history of the universe ever created has been produced by researchers at The Australian National University (ANU). The study also offers new ideas about how our universe may have started.

 

Lead author Honorary Associate Professor Charley Lineweaver from ANU said he set out wanting to understand where all the objects in the universe came from. "When the universe began 13.8 billion years ago in a hot big bang, there were no objects like protons, atoms, people, planets, stars or galaxies. Now the universe is full of such objects," he said. "The relatively simple answer to where they came from is that, as the universe cooled, all of these objects condensed out of a hot background."

 

To show this process in the simplest possible way, the researchers made two plots. The first shows temperature and density of the universe as it expanded and cooled. The second plots the mass and size of all objects in the universe. The result is the most comprehensive chart ever created of all the objects in the universe. The study is published in the latest issue of the American Journal of Physics.

 

Co-author and former ANU research student Vihan Patel said the project raised some important questions. "Parts of this plot are 'forbidden'—where objects cannot be denser than black holes, or are so small, quantum mechanics blurs the very nature of what it really means to be a singular object." Patel said. The researchers say the boundaries of the plots and what lies beyond them are also a major mystery.

 

"At the smaller end, the place where quantum mechanics and general relativity meet is the smallest possible object—an instanton. This plot suggests the universe may have started as an instanton, which has a specific size and mass, rather than a singularity, which is a hypothetical point of infinite density and temperature," Patel said. "On the larger end, the plot suggests that if there were nothing—a complete vacuum—beyond the observable universe, our universe would be a large, low density black hole. This is a little scary, but we have good reason to believe that's not the case."

 

Reference: Charles H. Lineweaver et al, All objects and some questions, American Journal of Physics (2023). DOI: 10.1119/5.0150209

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Astronomers Find a Newly-Forming Quadruple-Star System

Astronomers Find a Newly-Forming Quadruple-Star System | Amazing Science | Scoop.it
 
Scientists have observed a rare quadruple star system in formation, revealing new insights into how multi-star systems form.

 

In a surprising find, the international ALMA Survey of Orion Planck Galactic Cold Clumps (ALMASOP) team recently observed a young quadruple star system within a star-forming region in the Orion constellation. The discovery was made during a high-resolution survey of 72 dense cores in the Orion Giant Molecular Clouds (GMCs) using the Atacama Large Millimeter/submillimeter Array (ALMA) in Chile. These observations provide a compelling explanation for the origins and formation mechanisms of binary and multiple-star systems.

 

It’s a well-known fact among astronomers and astrophysicists that roughly half of the stars in the Milky Way reside in binary systems. Knowing how multiple star systems form is essential to understanding galactic evolution, planetary formation, and the emergence of life. The most widely accepted theory regarding star formation (the Nebular Hypothesis) states that stars form in the densest regions of molecular clouds (aka. “dense core”). While this theory accounts for individual star systems very well, the mechanisms that drive the formation of multi-star systems are not yet well understood.

 

It is currently thought that multiple star systems form via the fragmentation of cloud cores during their early evolution, but observations are historically lacking. To investigate this mystery, the ALMASOP team examined 72 young and cold cores in the GMCs in the Orion constellation for thermal emissions corresponding to a wavelength of 1.3 mm – in the extremely high frequency (EHF) range. When observing a dense cold core in Orion B GMC about 1,500 light-years from Earth (designated G206.93-16.61E2), they observed a system of four stellar objects. These consisted of two protostars and two gas concentrations that are likely to undergo gravitational collapse in the near future. They further observed that the largest separation between the four objects in the system was about 1,000 Astronomical Units (AUs), over 33 times the distance between the Sun and Neptune (30 AUs). This stands in contrast to the last time a quadruple system was observed in 2015 by another international team using ALMA. In that case, the discovery team observed a young protostar and three gravitationally-bound dense gas clouds that would form new stars in ~40,000 years.

 
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October 20, 2023 5:40 PM
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Gene therapy for children paralyzed by rare mutations

Gene therapy for children paralyzed by rare mutations | Amazing Science | Scoop.it
 
Scientists looked at 50 families who come from the Netherlands, the United Kingdom, the United States and China. Each family has a child who is paralyzed from a mutation in a single gene named Contactin-Associated Protein 1 (Cntnap1). The children are locked inside their bodies, unable to move. The families feed them and change them, and someone monitors them 24/7.

 

Thousands of miles away in South Texas, Manzoor Bhat, MS, Ph.D., and his team at The University of Texas Health Science Center at San Antonio are making discoveries that point to a gene therapy for these profoundly affected children. The journal Cell Reports published the findings. Co-authors of the study are Cheng Chang, Lacey Sell and Qian Shi, Ph.D.

 

"We obtained genetic information from the families and created mouse models that recapitulated the human mutations and the human disease. Our mice developed phenotypes, or weaknesses, like the children," said Bhat, vice dean for research in the health science center's Joe R. and Teresa Lozano Long School of Medicine.

 

Transgenic animals are animals that have had a foreign gene inserted into their genome. The Bhat lab developed transgenic mice that have both a normal copy of the Cntnap1 gene and a mutated copy that reflects the mutations observed in the children.

"We can control when the normal gene is turned on," Bhat said. "And it turns out that we can use the normal gene to rescue the mice from their neurological deficits."

 

In a series of experiments, the researchers turned on the normal gene at birth, five days after birth, two weeks after, one month after and three months after birth. The earlier the team turned it on, the quicker the mice got better and the more complete the rescue was.

 

"The longer we wait, the worse the mice will do," Bhat said. "This is because the Cntnap1 gene makes a protein that drives nerve impulse conduction. If we wait a month or two, then the nerve function is already weak, muscles become weak and the mice cannot maintain motor coordination."

 

Mice were placed on a beam to measure their movement. After the normal copy of the gene is turned on, and with time, the mice start passing the beam with ease. This is because the normal gene is producing protein that improves nerve signal conduction.

Path to gene therapy

The next phase of the research is to inject a virus that makes the Cntnap1 protein into the Cntnap1 mutant mice. If preclinical studies give good indications, then a step down the road would be to go for gene therapy for children. "The mouse models we created are the first mouse models of this disease and the first rescue of the disease," Bhat said. "We are now getting ready for future gene therapy."

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October 20, 2023 5:32 PM
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A fully automated process: First supernova detected, confirmed, classified and shared by AI

A fully automated process: First supernova detected, confirmed, classified and shared by AI | Amazing Science | Scoop.it
 

Developed by an international collaboration led by Northwestern University, the new system automates the entire search for new supernovae across the night sky—effectively removing humans from the process. Not only does this rapidly accelerate the process of analyzing and classifying new supernova candidates, it also bypasses human error.

 

The team alerted the astronomical community to the launch and success of the new tool, called the Bright Transient Survey Bot (BTSbot), this week. In the past six years, humans have spent an estimated total of 2,200 hours visually inspecting and classifying supernova candidates. With the new tool now officially online, researchers can redirect this precious time toward other responsibilities in order to accelerate the pace of discovery.

 

"For the first time ever, a series of robots and AI algorithms has observed, then identified, then communicated with another telescope to finally confirm the discovery of a supernova," said Northwestern's Adam Miller, who led the work. "This represents an important step forward as further refinement of models will allow the robots to isolate specific subtypes of stellar explosions. Ultimately, removing humans from the loop provides more time for the research team to analyze their observations and develop new hypotheses to explain the origin of the cosmic explosions that we observe. We achieved the world's first fully automatic detection, identification and classification of a supernova," added Northwestern's Nabeel Rehemtulla, who co-led the technology development with Miller.

 

"This significantly streamlines large studies of supernovae, helping us better understand the life cycles of stars and the origin of elements supernovae create, like carbon, iron and gold." Miller is an assistant professor of physics and astronomy at Northwestern's Weinberg College of Arts and Sciences and a member of the Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA). Rehemtulla is an astronomy graduate student in Miller's research group.

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October 18, 2023 3:01 PM
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Study elucidates evolution of mosquitoes and their hosts

Study elucidates evolution of mosquitoes and their hosts | Amazing Science | Scoop.it
 

Researchers at North Carolina State University and global collaborators have mapped the mosquito's tree of life, a major step toward understanding important traits, such as how the insects choose their hosts, feed on blood and spread disease. The findings will help researchers make better predictions to model disease transmission and understand what makes some mosquitoes better disease carriers than others.

 

The research suggests that mosquito evolution over the past 200 million years mirrors the Earth's history of shifting land masses and changing host organisms, says Dr. Brian Wiegmann, William Neal Reynolds Professor of Entomology at NC State and corresponding author of a paper describing the mosquito family tree, published in Nature Communications.

 

"This ongoing project builds a big-data resource that mines the academic literature with published observations of the sources of blood mosquitoes drink, from animals as diverse as fish to humans," Wiegmann said. "It focuses explicitly on data collection to infer aspects of mosquito biology in a contextualized way. That means linking up the family, or phylogenetic, tree with the narrative of life on Earth: geologic history, climate history and organism history."

 

While the researchers pored over the academic literature to capture as much published information about mosquitoes as possible, new genomic sequencing techniques also allowed them to take decades-old mosquitoes—some held in place by pins inside insect collections—and capture a great deal of information on their genetic similarities from just fragments of their genetic blueprints, or genomes.

 

"A lot of research goes into the important mosquitoes and there's not much known about the incredible mosquito diversity across the globe," Wiegmann said. "We now have the tools to sample genetic information more rapidly and very thoroughly. And so the time was right to take a big stab at putting the disease vectors and the well-known mosquitoes into the context they evolved in."

 

Piecing the genetic and published information together gave the researchers a few notable findings and these can be evaluated against current patterns and distributions. Mosquitoes are an ancient group—around 217 million years old—that probably originated in South America before it was South America, on one big land mass called Gondwana that hadn't yet split apart. "Major events like continental drift certainly influenced the diversification of mosquitoes," Wiegmann said.

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October 18, 2023 1:46 PM
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Lab-Grown Skin Organoids Help Scientists Understand Monkeypox Infection Better

Lab-Grown Skin Organoids Help Scientists Understand Monkeypox Infection Better | Amazing Science | Scoop.it
 

Skin organoids offer a powerful platform for drug discovery in the ongoing fight against the virus formerly known as monkeypox. A new model system for studying mpox virus infections in the laboratory is providing valuable insights into the virus's mechanisms of attack on skin cells, offering a potential catalyst in the quest to discover innovative drugs to combat this emerging pathogen. An international research team that included KAUST scientists has demonstrated that lab-grown human skin — stem cell-derived 3D structures called organoids — can effectively facilitate the active replication of mpox virus, the virus formerly known as monkeypox virus, that spread rapidly during a major outbreak in 2022.

 

"Researchers can now use this model to study how the mpox virus causes disease and to test new therapeutics," says Intikhab Alam, a bioinformatician who contributed to the study along with his colleague Roberto Incitti, both from KAUST.

 

People infected with the mpox virus typically develop rashes and skin lesions, often leading to scarring and disfigurement — and the lab-grown skin organoids now help show why. KAUST's Alam and Incitti collaborated with Qiuwei Abdullah Pan and his team from the Erasmus MC-University Medical Center in Rotterdam to report that the virus takes up residence inside keratinocytes, the predominant cell type in the skin's outer layer. There, the virus undergoes its four steps of assembly, a process that the researchers could observe under high-power microscopes.

 

Gene expression analyses conducted by the researchers revealed that numerous viral genes become activated in the days following infection. This activation, in turn, appears to induce changes in host cells, leading to alterations in the activity of multiple human genes associated with immunity and cell death. These genetic alterations likely compromise the skin's protective barrier, resulting in the characteristic lesions observed in infected people. The observed effects could be reversed through use of an antiviral drug called tecovirimat.

 

In the infected organoids, this drug proved highly effective in halting virus replication and thwarting the subversion of host cells. The findings validate the mpox-inhibiting potential of tecovirimat, a drug approved to treat infections with the related smallpox virus. They also underscore the potential of the organoid system as a versatile platform with which to screen for novel substances with similar properties. Notably, the impact of mpox extends beyond skin-related issues. In severe cases, the virus can wreak havoc on internal organs. The same KAUST-affiliated research team previously developed a kidney organoid system designed to study mpox infections in renal tissues. Other groups have investigated mpox dynamics within colon and brain organoids. Collectively, the efforts in organoid models — which the KAUST researchers and their collaborators are now extending to other viral infection systems as well — should "help to combat the current mpox outbreak and enhance pandemic preparedness for the future," Incitti says.

 

Studies published in Nature Microbiology (Oct. 13, 2023):

https://doi.org/10.1038/s41564-023-01489-6 


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Scooped by Dr. Stefan Gruenwald
October 17, 2023 4:16 PM
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Morphogenetic Metasurfaces: Emergence of Self-Organized Anisotropic Patterns

Morphogenetic Metasurfaces: Emergence of Self-Organized Anisotropic Patterns | Amazing Science | Scoop.it
 

The reaction-diffusion principle imagined by Alan Turing in an attempt to explain the structuring of living organisms is leveraged in this recent work for the procedural synthesis of radiating metasurfaces. The adaptation of this morphogenesis technique ensures the growth of anisotropic cellular patterns automatically arranged to satisfy local electromagnetic constraints, facilitating the radiation of waves controlled in frequency, space, and polarization.

 

Experimental validations of this method are presented, designing morphogenetic metasurfaces radiating far-field circularly polarized beams and generating a polarization-multiplexed hologram in the radiative near-field zone. The exploitation of morphogenesis-inspired models proves particularly well suited for solving generative design problems, converting global physical constraints into local interactions of simulated chemical reactants ensuring the emergence of self-organizing meta-atoms.

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Scooped by Dr. Stefan Gruenwald
October 13, 2023 2:02 AM
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Antimatter in Free Fall Downwards: Observation of the Effect of Gravity on the Motion of Antimatter

Antimatter in Free Fall Downwards: Observation of the Effect of Gravity on the Motion of Antimatter | Amazing Science | Scoop.it
 
 

ALPHA-g determines that antimatter falls downwards as expected. It took longer than anticipated, but now we have the result. Observation of the effect of gravity on the motion of antimatter: Antimatter falls down with (0.75 ± 0.13 (statistical + systematic) ± 0.16 (simulation)) g, compatible with the expected 1 g and ruling out -1 g.

Einstein’s general theory of relativity from 19151 remains the most successful description of gravitation. From the 1919 solar eclipse2 to the observation of gravitational waves3, the theory has passed many crucial experimental tests. However, the evolving concepts of dark matter and dark energy illustrate that there is much to be learned about the gravitating content of the universe.

 

Singularities in the general theory of relativity and the lack of a quantum theory of gravity suggest that our picture is incomplete. It is thus prudent to explore gravity in exotic physical systems. Antimatter was unknown to Einstein in 1915.

 

Dirac’s theory4 appeared in 1928; the positron was observed5 in 1932. There has since been much speculation about gravity and antimatter. The theoretical consensus is that any laboratory mass must be attracted6 by the Earth, although some authors have considered the cosmological consequences if antimatter should be repelled by matter7,8,9,10. In the general theory of relativity, the weak equivalence principle (WEP) requires that all masses react identically to gravity, independent of their internal structure.

 

Scientists now show that antihydrogen atoms, released from magnetic confinement in the ALPHA-g apparatus, behave in a way consistent with gravitational attraction to the Earth. Repulsive ‘antigravity’ is ruled out in this case. This experiment paves the way for precision studies of the magnitude of the gravitational acceleration between anti-atoms and the Earth to test the WEP.

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October 12, 2023 7:48 PM
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Alan Schoen geometry: Triply-periodic minimal surfaces (TPMS) and the gyroid

Alan Schoen geometry: Triply-periodic minimal surfaces (TPMS) and the gyroid | Amazing Science | Scoop.it
 

The gyroid was discovered in 1970 by NASA scientist Alan Schoen. He calculated the angle of association and gave a convincing demonstration of pictures of intricate plastic models, but did not provide a proof of embeddedness. Schoen noted that the gyroid contains neither straight lines nor planar symmetries. Karcher gave a different, more contemporary treatment of the surface in 1989 using conjugate surface construction. In 1996 Große-Brauckmann and Wohlgemuth proved that it is embedded, and in 1997 Große-Brauckmann provided CMC (constant mean curvature) variants of the gyroid and made further numerical investigations about the volume fractions of the minimal and CMC gyroids.

 

The gyroid separates space into two oppositely congruent labyrinths of passages. The gyroid has space group I4132 (no. 214). Channels run through the gyroid labyrinths in the (100) and (111) directions; passages emerge at 70.5 degree angles to any given channel as it is traversed, the direction at which they do so gyrating down the channel, giving rise to the name "gyroid". One way to visualize the surface is to picture the "square catenoids" of the P surface (formed by two squares in parallel planes, with a nearly circular waist); rotation about the edges of the square generate the P surface. In the associate family, these square catenoids "open up" (similar to the way the catenoid "opens up" to a helicoid) to form gyrating ribbons, then finally become the Schwarz D surface. For one value of the associate family parameter the gyrating ribbons lie in precisely the locations required to have an embedded surface.

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October 12, 2023 7:04 PM
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Scientists develop AI tool that predicts virus mutations which can evade the immune system

Scientists develop AI tool that predicts virus mutations which can evade the immune system | Amazing Science | Scoop.it
 

EVEscape uses evolutionary and biological information to predict how a virus could change to escape the immune system.

 

The COVID-19 pandemic seemed like a never-ending parade of SARS-CoV-2 variants, each equipped with new ways to evade the immune system, leaving the world bracing for what would come next. But what if there were a way to make predictions about new viral variants before they actually emerge?

 

A new artificial intelligence tool named EVEscape, developed by researchers at Harvard Medical School and the University of Oxford, can do just that. The tool has two elements: A model of evolutionary sequences that predicts changes that can occur to a virus, and detailed biological and structural information about the virus. Together, they allow EVEscape to make predictions about the variants most likely to occur as the virus evolves.

 

In a recent study published in Nature, the researchers show that had it been deployed at the start of the COVID-19 pandemic, EVEscape would have predicted the most frequent mutations and identified the most concerning variants for SARS-CoV-2. The tool also made accurate predictions about other viruses, including HIV and influenza. The researchers are now using EVEscape to look ahead at SARS-CoV-2 and predict future variants of concern; every two weeks, they release a ranking of new variants. Eventually, this information could help scientists develop more effective vaccines and therapies. The team is also broadening the work to include more viruses.

 

“We wanted to know if we can anticipate the variation in viruses and forecast new variants — because if we can, that’s going to be extremely important for designing vaccines and therapies,” said senior author Debora Marks, professor of systems biology in the Blavatnik Institute at HMS.

From EVE to EVEscape

The researchers first developed EVE, short for evolutionary model of variant effect, in a different context: gene mutations that cause human diseases. The core of EVE is a generative model that learns to predict the functionality of proteins based on large-scale evolutionary data across species.

 

In a previous study, EVE allowed researchers to discern disease-causing from benign mutations in genes implicated in various conditions, including cancers and heart rhythm disorders.

 

“Viruses are flexible — it’s almost like they’ve evolved to evolve.”

explains Debora Marks, Blavatnik Institute at Harvard Medical School. “You can use these generative models to learn amazing things from evolutionary information — the data have hidden secrets that you can reveal,” Marks said.

 

As the COVID-19 pandemic hit and progressed, the world was caught off guard by SARS-CoV-2’s impressive ability to evolve. The virus kept morphing, changing its structure in ways subtle and substantial to slip past vaccines and therapies designed to defeat it. “We underestimate the ability of things to mutate when they’re under pressure and have a large population in which to do so,” Marks said. “Viruses are flexible — it’s almost like they’ve evolved to evolve.”

 

Watching the pandemic unfold, Marks and her team saw an opportunity to help: They rebuilt EVE into a new tool called EVEscape for the purpose of predicting viral variants. They took the generative model from EVE — which can predict mutations in viral proteins that won’t interfere with the virus’s function — and added biological and structural details about the virus, including information about regions most easily targeted by the immune system.

 

“We’re taking biological information about how the immune system works and layering it on our learnings from the broader evolutionary history of the virus,” explained co-lead author Nicole Thadani, a former research fellow in the Marks lab.

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