Hexbyte Glen Cove Dismayed by oil spill, some in Huntington Beach say it’s time to end offshore drilling

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Credit: CC0 Public Domain

A large yellow bulldozer pushed a mound of sand toward the mouth of the Huntington Beach Channel, creating a barrier that would hopefully slow the amount of oil that was floating up to the nearby wetlands.

Farther up, in the underpass, cleaning crews on two boats replaced the booms that had absorbed the oil.

On one end, two men placed the long, white booms on the water, tying them together. On the other end, two other men picked up the spent, blackened barriers as if they were picking up a large python and placed it in a large see-through bag.

Rolling up on his skateboard with his wife riding her bicycle behind, Sumio Uchida, 67, came to watch the aftermath of this past weekend’s massive oil .

He looked at the dozer and the warning signs about swimming in the ocean.

“This is sad.”

His wife, Gloria Uchida, nodded and added, “Very sad.”

The couple, longtime residents of Huntington Beach, were angry. The spill has left many residents questioning the oil industry off its shore and officials calling for a ban on drilling off the coast.

“This is why offshore oil drilling needs to stop,” Sumio Uchida said. “This happened in 1990.”

Uchida was referring to Feb. 7, 1990, when the oil tanker American Trader ran over its anchor in shallow water off Huntington Beach, ripping a hole in its hull and spilling nearly 417,000 gallons of crude that fouled popular beaches along the Orange County coast. The oil killed fish and about 3,400 birds.

Uchida now was witness to another ecological disaster.

“Many of my neighbors are upset,” he said before shaking his head. “Oil companies.”

Uchida questioned how long it would take to recover from this spill. He worried not just about the wildlife that had been affected but also for his coastal town, which had already suffered economically from the pandemic and now had to deal with the oil spill.

He worried that events such as surfing and volleyball competitions that brought revenue to the city may not happen again. He worried the organizers would choose to go elsewhere.

Sitting on her bicycle, staring out at the crashing waves, Gloria Uchida said she too worried about that, but all anyone could do now was volunteer and help clean up.

“I may do that.”

The spill, first reported Saturday morning but perhaps detected the night before, originated from a pipeline running from the Port of Long Beach to an offshore oil platform known as Elly. The failure caused as much as 144,000 gallons of oil to gush into the Catalina Channel.

In the days that followed, the spill has left crude along stretches of sand in Newport Beach, Laguna Beach and Huntington Beach, killing fish and birds and threatening sensitive marine habitats.

“The ecological and economic damage from this oil spill has the potential to reverberate for generations,” state Sen. Dave Min (D-Irvine) said this week. At a news conference Tuesday, Min called the spill “either a case of negligence or inaction.”

“The legislation after the Santa Barbara damage [from the Refugio spill in 2015] was meant to prevent this,” he said. “It really speaks to the need to get rid of these .”

Gov. Gavin Newsom said during a news conference at Bolsa Chica State Beach on Tuesday afternoon that it’s “time once and for all to disabuse ourselves that [oil drilling] has to be part of our future.”

“This is part of our past, and we can moralize and talk about the good old days, we can talk about how important these rigs had been to the prosperity of this country in the , but at the end of the day, this is about the stale air of normalcy versus the fresh air of progress,” he said.

©2021 Los Angeles Times. Distributed by Tribune Content Agency, LLC.

Dismayed by oil spill, some in Huntington Beach say it’s time to end offshore drilling (2021, October 6)

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Hexbyte Glen Cove Smoggier skies, lower scores? A Brazilian study examines the effects of air pollution on students’ cognitive performance

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Credit: CC0 Public Domain

A new study published in the Journal of the Association of Environmental and Resource Economists looks at the causal relationship between outdoor air pollution levels on nationwide university entry examination day and students’ cognitive performance in Brazil.

In “The Effects of Air Pollution on Students’ Cognitive Performance: Evidence from Brazilian University Entrance Tests,” authors Juliana Carneiro, Matthew A. Cole, and Eric Strobl use Brazilian data on concentrations of ozone (O3) and particulate matter (PM10) and a data set of students’ scores to examine the impact of air pollution on academic performance in national examinations. The air pollution data focuses on Rio de Janeiro and São Paulo—Brazil’s most industrialized states—using air pollution and weather monitoring station data to build a unique data panel from 2015–17.

The authors constructed individual-level panel data for the two days of exams across three years and applied student fixed effects to address potential endogeneity concerns. “In addition,” they note, “We take advantage of plausibly exogenous spatial and temporal variation in PM10 across municipalities in the states of Rio de Janeiro and São Paulo and utilize an instrumental variable approach based on .”

The findings suggest that an increase of 10 micrograms per cubic meter (mg/m3) of PM10 on the day of the examination decreases students’ scores by 6.1 points (8% SD). “Even when including a more flexible measure of our treatment that is utilizing a dummy variable to account for the days in which PM10 exceeded the WHO’s acceptable threshold, our findings still point to negative effects of air pollution on cognitive performance during examinations,” they note. Placebo tests, sensitivity checks, and falsifications tests reinforced the main findings: evidence of a link between air pollution and exam performance.

Consistent with previous studies, the authors also find evidence that the effect of air pollution on exam performance appears to affect males more adversely than females. “Our results also suggest that poorer students may be more susceptible to air than wealthier exam takers,” they write, adding, “Our findings provide plausible evidence to suggest that may be hindered by poor air quality, but unequally so.”

More information:
Juliana Carneiro et al, The Effects of Air Pollution on Students’ Cognitive Performance: Evidence from Brazilian University Entrance Tests, Journal of the Association of Environmental and Resource Economists (2021). DOI: 10.1086/714671

Smoggier skies, lower scores? A Brazilian study examines the effects of air pollution on students’ cognitive performance (2021, October 6)
retrieved 7 October 2021
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Hexbyte Glen Cove Exceptional learning capacities revealed in some gifted dogs

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Whiskey is one of the talented dogs who participate in experiments at Eötvös Loránd University. Credit: Helge O. Savela

Does your dog understand you? All dogs are smart but some are uniquely gifted at learning words. According to a new study, just published in Royal Society Open Science, these gifted dogs can learn up to 12 new toy names in one week. Not only that, but they can also remember the new toy names for at least two months. The dogs presented their exceptional skills as part of the Genius Dog Challenge, a series of live broadcasted experiments, which went viral over social media.

“We know that can easily learn words that are linked to actions, such as ‘sit’ or ‘down’. But very few dogs can learn names of objects” explains Shany Dror, leading researcher, from the Family Dog Project, Eötvös Loránd University. “For more than two years we searched around the world for dogs that had learnt the names of their toys, and we managed to find 6.”

The dogs: Max (Hungary), Gaia (Brazil), Nalani (Holland), Squall (USA), Whisky (Norway), and Rico (Spain), all qualified to participate in the challenge by proving to know the names of more than 28 toys, with some knowing more than 100.

“These gifted dogs can learn new names of toys in a remarkable speed” says Dr. Claudia Fugazza, head of the research team. “In our previous study we found that they could learn a new toy name after hearing it only 4 times. But, with such short exposure, they did not form a long-term memory of it.”

In this new study, the researchers wanted to push the limits of the dogs’ talent, so they challenged the owners to teach their dogs the names of first 6 and then 12 new toys in only one week. The researchers were amazed by the dogs’ performance. “It turned out that, for these talented dogs, this was not much of a challenge. They easily learned between 11 to 12 toys,” discloses Shany Dror. The researchers also tested the dogs one, and two months after they had learned the names of the new toys and found that they still remembered those.

The study not only reveals that some gifted dogs can learn new words in an astonishing rate but also standardizes a new way of conducting science.

The researchers explained that they collected data during COVID-19 lockdowns, which meant that they needed to take the laboratory to the owner’s home. To do this, they asked the owners to set up two and connect to a livestream, which meant that they could fully monitor the dogs’ and the owners’ behavior. “Once we realized we can remotely test the dogs, we decided to bring the experiment to the homes of people all around the world by broadcasting the tests live on YouTube” says Shany Dror.

All of the dogs in this research are Border Collies, is this the smartest dog breed?

“Originally Border Collies were breed to work as herding dogs, so most of them are very sensitive and responsive to the behavior of their owners. However, although the ability to learn names of toys appears to be more common among Border Collies, in a recently published study we found that even among this breed it is very rare” emphasizes Shany Dror. “Moreover, this talent is not unique to this breed. We are constantly searching for more gifted dogs. Thanks to the Genius Dog Challenge we have managed until now to find also dogs from other breeds including a German Shepherd, a Pekingese, a Mini Australian Shepherd and a few dogs of mixed breeds.” Previous research has documented this talent also in Yorkshire Terriers.

Why study gifted dogs?

“Dogs are good models for studying as they evolved and develop in the ” explains Prof. Adam Miklósi, head of the Department of Ethology at Eötvös Loránd University and coauthor of the study. “With these talented dogs we have a unique opportunity to study how another species understands the human language and how learning words influences the way we think about the world.”

“Moreover, gifted dogs are especially interesting because they show that also among other species there are individuals that are uniquely talented. With the help of these dogs, we hope to better understand the factors that contribute to the development of talent.”

The skill to learn object names is very rare and dogs with this capacity are important for research. By studying these dogs, we can not only better understand dogs, but also better understand ourselves. So, the researchers encourage dog owners that believe their dogs know multiple toy names to contact them through the Genius Dog Challenge.

More information:
Acquisition and long-term memory of object names in a sample of Gifted Word Learner dogs, Royal Society Open Science (2021). royalsocietypublishing.org/doi/10.1098/rsos.210976

Provided by
Eötvös Loránd University

Exceptional learning capacities revealed in some gifted dogs (2021, October 5)
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Hexbyte Glen Cove Researchers describe new tardigrade fossil found in 16 million year old Domincan amber

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Artistic reconstruction of Paradoryphoribius chronocaribbeus gen. et sp. nov. in mosses. Credit: Original art created by Holly Sullivan

Tardigrades, also known as water bears, are a diverse group of charismatic microscopic invertebrates that are best known for their ability to survive extreme conditions. A famous example was a 2007 trip to space where tardigrades were exposed to the space vacuum and harmful ionizing solar radiation, and still managed to survive and reproduce after returning to Earth. Tardigrades are found in all the continents of the world and in different environments including marine, freshwater, and terrestrial.

Tardigrades have survived all five Phanerozoic Great Mass Extinction events, yet the earliest modern-looking tardigrades are only known from the Cretaceous, approximately 80 million years ago. Despite their long evolutionary history and global distribution, the fossil record is exceedingly sparse. Due to their microscopic size and non-biomineralizing body, the chance of tardigrades to become fossilized is small.

In a paper published October 6 in Proceedings of the Royal Society B researchers describe a new modern-looking tardigrade fossil that represents a new genus and new species. The study used confocal laser microscopy to obtain higher resolution images of important anatomical characteristics that aid in phylogenetic analyses to establish the taxonomic placement of the fossil.

The new fossil Paradoryphoribius chronocaribbeus is only the third tardigrade amber fossil to be fully described and formally named to date. The other two fully described modern-looking tardigrade fossils are Milnesium swolenskyi and Beorn leggi, both known from Cretaceous-age amber in North America. Paradoryphoribius is the first fossil to be found embedded in Miocene (approximately 16 million years ago) Dominican amber and the first fossil representative of the tardigrade superfamily Isohypsibioidea.

Co-author Phillip Barden, New Jersey Institute of Technology, introduced the fossil to lead author Marc A. Mapalo, Ph.D. Candidate, and senior author Professor Javier Ortega-Hernández, both in the Department of Organismic and Evolutionary Biology, Harvard University. Barden’s lab discovered the fossil and teamed with Ortega-Hernández and Mapalo to analyse the fossil in detail. Mapalo, who specializes in tardigrades, took the lead in analyzing the fossil using confocal microscopes located in the Harvard Center for Biological Imaging.

“The difficulty of working with this amber specimen is that it’s far too small for dissecting microscopes, we needed a special microscope to fully see the fossil,” Mapalo said. Generally the light transmitted by dissecting microscopes works well to reveal the morphology of larger inclusions such as insects and spiders in amber. Paradoryphoribius, however, has a total body length of only 559 micro meters, or slightly over half a millimeter. At such a small scale a dissecting microscope can only reveal the external morphology of the fossil.

Left) Lateral view of Paradoryphoribius chronocaribbeus gen. et sp. nov. viewed with transmitted light under streomicroscope (top) and with autofluorescence under confocal laser microscope (bottom). Right) Ventral view of Paradoryphoribius chronocaribbeus gen. et sp. nov. viewed with transmitted light under streomicroscope (top) and with autofluorescence under confocal laser microscope (bottom). Credit: Marc A. Mapalo

Fortunately, Tardigrade’s cuticle is made of chitin, a fibrous glucose substance that is a primary component of cell walls in fungi and the exoskeletons of arthropods. Chitin is fluorescent and easily excited by lasers making it possible to fully visualize the tardigrade fossil using confocal laser microscopy. The use of confocal laser microscopy instead of transmitted light to study the fossil created degrees of fluorescence allowing a more clear view of the internal morphology. With this method Mapalo was able to fully visualize two very important characters of the fossil, the claws and the buccal apparatus, or the foregut of the animal which is also made of cuticle.

“Even though externally it looked like a modern tardigrade, with confocal laser microscopy we could see it had this unique foregut organization that warranted for us to erect a within this extant group of tardigrade superfamilies,” said Mapalo. “Paradoryphoribius is the only genus that has this specific unique character arrangement in the superfamily Isohypsibioidea.”

“Tardigrade fossils are rare,” said Ortega-Hernández. “With our new study, the full tally includes only four specimens, from which only three are formally described and named, including Paradoryphoribius. This paper basically encompasses a third of the tardigrade fossil record known to date. Furthermore, Paradoryphoribius offers the only data on a tardigrade buccal apparatus in their entire fossil record.”

The authors note there is a strong preservation bias for tardigrade fossils in amber due to their and habitat preferences. Thus, amber deposits provide the most reliable source for finding new tardigrade fossils, even though that does not mean finding them is an easy task. The discovery of a tardigrade fossil in Dominican amber suggests that other frequently sampled sites, such as Burmese and Baltic amber deposits, could also harbor tardigrade fossils. Historically there is a bias towards larger inclusions in amber as inclusions as small as tardigrades are hard to see and require extremely good observational skills, as well as some specialist knowledge.

“Scientists know where tardigrades broadly fit in the tree of life, that they are related to arthropods, and that they have a deep origin during the Cambrian Explosion. The problem is that we have this extremely lonely phylum with only three named fossils. Most of the fossils from this phylum are found in amber but, because they’re small, even if they are preserved it may be really difficult to see them,” Ortega-Hernández said.

Mapalo agreed, “If you look at the external morphology of tardigrades, you might assume that there are no changes that occurred within the body of tardigrades. However, using confocal laser microscopy to visualize the internal morphology, we saw characters that are not observed in extent species but are observed in the fossils. This helps us understand what changes in the body occurred across millions of years. Furthermore, this suggests that even if tardigrades may be the same externally, some changes are occurring internally.”

Mapalo and Ortega-Hernández continue to employ confocal laser microscopy technology to study other tardigrades in amber in their hopes to expand the tardigrade fossil record.

More information:
A tardigrade in Dominican amber, Proceedings of the Royal Society B (2021). rspb.royalsocietypublishing.or … .1098/rspb.2021.1760

Researchers describe new tardigrade fossil found in 16 million year old Domincan amber (2021, October 5)
retrieved 6 October 2021
from https://phys.org/news/2021-10-tardigrade-fossil-million-year-domincan.html

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Hexbyte Glen Cove Process leading to supernova explosions and cosmic radio bursts unearthed at PPPL

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Physicist Kenan Qu with figures from his paper. Credit: Photo of Qu by Elle Starkman/PPPL Office of Communications. Collage by Kiran Sudarsanan.

A promising method for producing and observing on Earth a process important to black holes, supernova explosions and other extreme cosmic events has been proposed by scientists at Princeton University’s Department of Astrophysical Sciences, SLAC National Acceleraor Laboratory, and the U.S. Department of Energy’s (DOE) Princeton Plasma Physics Laboratory (PPPL). The process, called quantum electrodynamic (QED) cascades, can lead to supernovas—exploding stars—and fast radio bursts that equal in milliseconds the energy the sun puts out in three days.

First demonstration

The researchers produced the first theoretical demonstration that colliding a laboratory laser with a dense electron beam can produce high-density QED cascades. “We show that what was thought to be impossible is in fact possible,” said Kenan Qu, lead author of a paper in Physical Review Letters (PRL) that describes the breakthrough demonstration. “That in turn suggests how previously unobserved collective effects can be probed with existing state-of-the-art laser and electron beam technologies.”

The process unfolds in a straightforward manner. Colliding a strong laser pulse with a high energy electron beam splits a vacuum into high-density electron-positron pairs that begin to interact with one another. This interaction creates what are called collective plasma effects that influence how the pairs respond collectively to electrical or magnetic fields.

Plasma, the hot, charged state of matter composed of free electrons and atomic nuclei, makes up 99 percent of the visible universe. Plasma fuels fusion reactions that power the sun and stars, a process that PPPL and scientists around the world are seeking to develop on Earth. Plasma processes throughout the universe are strongly influenced by electromagnetic fields.

The PRL paper focuses on the electromagnetic strength of the laser and the energy of the electron beam that the theory brings together to create QED cascades. “We seek to simulate the conditions that create electron-positron pairs with sufficient density that they produce measurable collective effects and see how to unambiguously verify these effects,” Qu said.

The tasks called for uncovering the signature of successful plasma creation through a QED process. Researchers found the signature in the shift of a moderately intense laser to a higher frequency caused by the proposal to send the laser against an electron beam. “That finding solves the joint problem of producing the QED plasma regime most easily and observing it most easily,” Qu said. “The amount of the shift varies depending on the density of the plasma and the energy of the pairs.”

Beyond current capabilities

Theory previously showed that sufficiently strong lasers or electric or magnetic fields could create QED pairs. But the required magnitudes are so high as to be beyond current laboratory capabilities.

However, “It turns out that current technology in lasers and relativistic beams [that travel near the speed of light], if co-located, is sufficient to access and observe this regime,” said physicist Nat Fisch, professor of astrophysical sciences and associate director for academic affairs at PPPL, and a co-author of the PRL paper and principal investigator of the project. “A key point is to use the laser to slow down the pairs so that their mass decreases, thereby boosting their contribution to the plasma frequency and making the collective effects greater,” Fisch said. “Co-locating current technologies is vastly cheaper than building super-intense lasers,” he said.

This work was funded by grants from the National Nuclear Security Administration and the Air Force Office of Scientific Research. Researchers now are gearing up to test the theoretical findings at SLAC at Stanford University, where a moderately strong is being developed and the source of electrons beams is already there. Physicist Sebastian Meuren, a co-author of the paper and a former post-doctoral visitor at PPPL who now is at SLAC, is centrally involved in this effort.

“Like most fundamental physics this research is to satisfy our curiosity about the universe,” Qu said. “For the general community, one big impact is that we can save billions of dollars of tax revenue if the theory can be validated.”

More information:
Kenan Qu et al, Signature of Collective Plasma Effects in Beam-Driven QED Cascades, Physical Review Letters (2021). DOI: 10.1103/PhysRevLett.127.095001

Process leading to supernova explosions and cosmic radio bursts unearthed at PPPL (2021, October 5)

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Hexbyte Glen Cove Team measures the breakup of a single chemical bond thumbnail

Hexbyte Glen Cove Team measures the breakup of a single chemical bond

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Researchers measured the mechanical forces applied to break a bond between carbon monoxide and iron phthalocyanine, which appears as a symmetrical cross in scanning probe microscope images taken before and after the bond rupture. Credit: Pengcheng Chen et al.

The team used a high-resolution atomic force microscope (AFM) operating in a controlled environment at Princeton’s Imaging and Analysis Center. The AFM probe, whose tip ends in a single copper atom, was moved gradually closer to the iron-carbon bond until it was ruptured. The researchers measured the mechanical forces applied at the moment of breakage, which was visible in an image captured by the microscope. A team from Princeton University, the University of Texas-Austin and ExxonMobil reported the results in a paper published Sept. 24 in Nature Communications.

“It’s an incredible image—being able to actually see a single small molecule on a surface with another one bonded to it is amazing,” said coauthor Craig Arnold, the Susan Dod Brown Professor of Mechanical and Aerospace Engineering and director of the Princeton Institute for the Science and Technology of Materials (PRISM).

“The fact that we could characterize that particular , both by pulling on it and pushing on it, allows us to understand a lot more about the nature of these kinds of bonds—their strength, how they interact—and this has all sorts of implications, particularly for catalysis, where you have a molecule on a surface and then something interacts with it and causes it to break apart,” said Arnold.

Nan Yao, a principal investigator of the study and the director of Princeton’s Imaging and Analysis Center, noted that the experiments also revealed insights into how bond breaking affects a catalyst’s interactions with the surface on which it’s adsorbed. Improving the design of chemical catalysts has relevance for biochemistry, materials science and energy technologies, added Yao, who is also a professor of the practice and senior research scholar in PRISM.

In the experiments, the carbon atom was part of a carbon monoxide molecule and the iron atom was from iron phthalocyanine, a common pigment and chemical catalyst. Iron phthalocyanine is structured like a symmetrical cross, with a single iron atom at the center of a complex of nitrogen- and carbon-based connected rings. The iron atom interacts with the carbon of carbon monoxide, and the iron and carbon share a pair of electrons in a type of covalent bond known as a dative bond.

Yao and his colleagues used the atomic-scale probe tip of the AFM instrument to break the iron-carbon bond by precisely controlling the distance between the tip and the bonded molecules, down to increments of 5 picometers (5 billionths of a millimeter). The breakage occurred when the tip was 30 picometers above the molecules—a distance that corresponds to about one-sixth the width of a carbon atom. At this height, half of the iron phthalocyanine molecule became blurrier in the AFM image, indicating the rupture point of the chemical bond.

The researchers used a type of AFM known as non-contact, in which the microscope’s tip does not directly contact the molecules being studied, but instead uses changes in the frequency of fine-scale vibrations to construct an image of the molecules’ surface.

By measuring these frequency shifts, the researchers were also able to calculate the force needed to break the bond. A standard copper probe tip broke the iron-carbon bond with an attractive force of 150 piconewtons. With another carbon monoxide molecule attached to the tip, the bond was broken by a repulsive force of 220 piconewtons. To delve into the basis for these differences, the team used quantum simulation methods to model changes in the densities of electrons during .

The work takes advantage of AFM technology first advanced in 2009 to visualize single chemical bonds. The controlled breaking of a chemical bond using an AFM system has been more challenging than similar studies on bond formation.

“It is a great challenge to improve our understanding of how chemical reactions can be carried out by atom manipulation, that is, with a tip of a scanning probe microscope,” said Leo Gross, who leads the Atom and Molecule Manipulation research group at IBM Research in Zurich, and was the lead author of the 2009 study that first resolved the chemical structure of a molecule by AFM.

By breaking a particular bond with different tips that use two different mechanisms, the new study contributes to “improving our understanding and control of bond cleavage by atom manipulation. It adds to our toolbox for chemistry by atom manipulation and represents a step forward toward fabricating designed molecules of increasing complexity,” added Gross, who was not involved in the study.

The experiments are acutely sensitive to external vibrations and other confounding factors. The Imaging and Analysis Center’s specialized AFM instrument is housed in a high-vacuum environment, and the materials are cooled to a temperature of 4 Kelvin, just a few degrees above absolute zero, using liquid helium. These controlled conditions yield precise measurements by ensuring that the ‘ energy states and interactions are affected only by the experimental manipulations.

“You need a very good, clean system because this reaction could be very complicated—with so many involved, you might not know which bond you break at such a small scale,” said Yao. “The design of this system simplified the whole process and clarified the unknown” in breaking a chemical bond, he said.

The study’s lead authors were Pengcheng Chen, an associate research scholar at PRISM, and Dingxin Fan, a Ph.D. student at the University of Texas-Austin. In addition to Yao, other corresponding authors were Yunlong Zhang of ExxonMobil Research and Engineering Company in Annandale, New Jersey, and James R. Chelikowsky, a professor at UT Austin. Besides Arnold, other Princeton coauthors were Annabella Selloni, the David B. Jones Professor of Chemistry, and Emily Carter, the Gerhard R. Andlinger ’52 Professor in Energy and the Environment. Other coauthors from ExxonMobil were David Dankworth and Steven Rucker.

More information:
Breaking a dative bond with mechanical forces, Nature Communications (2021). DOI: 10.1038/s41467-021-25932-6 , www.nature.com/articles/s41467-021-25932-6


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Hexbyte Glen Cove Our DNA is becoming the world's tiniest hard drive thumbnail

Hexbyte Glen Cove Our DNA is becoming the world’s tiniest hard drive

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3D-model of DNA. Credit: Michael Ströck/Wikimedia/ GNU Free Documentation License

Our genetic code is millions of times more efficient at storing data than existing solutions, which are costly and use immense amounts of energy and space. In fact, we could get rid of hard drives and store all the digital data on the planet within a couple hundred pounds of DNA.

Using DNA as a high-density data storage medium holds the potential to forge breakthroughs in biosensing and biorecording technology and next-generation digital storage, but researchers haven’t been able to overcome inefficiencies that would allow the technology to scale.

Now, researchers at Northwestern University propose a new method for recording information to DNA that takes minutes, rather than hours or days, to complete. The team used a novel enzymatic system to synthesize DNA that records rapidly changing environmental signals directly into DNA sequences, a method the paper’s senior author said could change the way scientists study and record neurons inside the brain.

The research, “Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis,” was published Thursday (Sept. 30) in the Journal of the American Chemical Society.

The paper’s senior author, Northwestern engineering professor Keith E.J. Tyo, said his lab was interested in leveraging DNA’s natural abilities to create a new solution for storing data.

“Nature is good at copying DNA, but we really wanted to be able to write DNA from scratch,” Tyo said. “The ex vivo (outside the body) way to do this involves a slow, chemical synthesis. Our method is much cheaper to write information because the enzyme that synthesizes the DNA can be directly manipulated. State-of-the-art intracellular recordings are even slower because they require the mechanical steps of protein expression in response to signals, as opposed to our enzymes which are all expressed ahead of time and can continuously store information.”

Tyo, a professor in chemical and biological engineering in the McCormick School of Engineering, is a member of the Center for Synthetic Biology, and studies microbes and their mechanisms for sensing environmental changes and responding to them quickly.

Bypassing protein expression

Existing methods to record intracellular molecular and digital data to DNA rely on multipart processes that add new data to existing sequences of DNA. To produce an accurate recording, researchers must stimulate and repress expression of specific proteins, which can take over 10 hours to complete.

The Tyo lab hypothesized they could use a new method that they called Time-sensitive Untemplated Recording using Tdt for Local Environmental Signals, or TURTLES, to synthesize completely new DNA instead of copying a template of it, making a faster and higher resolution recording.

As the DNA polymerase continues to add bases, data is recorded into the on a scale of minutes as changes in the environment impact the composition of the DNA it synthesizes. The environmental changes, such as changes in the concentration of metals, are recorded by the polymerase, acting as a “molecular ticker tape” and indicating to scientists the time of an environmental change. Using biosensors to record changes into DNA represents a major step in proving TURTLES’ viability for use inside cells, and could give researchers the ability to use recorded DNA to learn about how neurons communicate with each other.

“This is a really exciting proof of concept for methods that could one day lets us study the interactions between millions of cells simultaneously,” said Namita Bhan, co-first author and a postdoctoral researcher in the Tyo lab. “I don’t think there’s any previously reported direct enzyme modulation recording system.”

From brain cells to polluted water

With more potential for scalability and accuracy, TURTLES could offer the basis for tools that catapult brain research forward. According to Alec Callisto, also a co-first author and graduate student in the Tyo lab, researchers can only study a tiny fraction of a brain’s neurons with today’s technology, and even then, there are limits on what they know they do. By placing recorders inside all the in the brain, scientists could map responses to stimuli with single-cell resolution across many (million) neurons.

“If you look at how current technology scales over time, it could be decades before we can even record an entire cockroach brain simultaneously with existing technologies—let alone the tens of billions of neurons in human brains,” Callisto said. “So that’s something we’d really like to accelerate.”

Outside the body, the TURTLES system also could be used for a variety of solutions to address the explosive growth in data storage needs (up to 175 zettabytes by 2025).

It’s particularly good for long term archival data applications such as storing closed-circuit security footage, which the team refers to as data that you “write once and read never,” but need to have accessible in the event an incident occurs. With technology developed by engineers, hard drives and disk drives that hold years of beloved camera memories also could be replaced by bits of DNA.

Outside of , the “ticker tape” function could be used as a biosensor to monitor environmental contaminants, like the heavy metal concentration in drinking water.

While the lab focuses on moving beyond a proof of concept in both digital and cellular recording, the team expressed hope that more engineers would take interest in the concept and be able to use it to record signals important to their research.

“We’re still building out the genomic infrastructure and cellular techniques we need for robust intracellular recording,” Tyo said. “This is a step along the way to getting to our long-term goal.”

More information:
Namita Bhan et al, Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis, Journal of the American Chemical Society (2021)

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Hexbyte Glen Cove A look back into record-breaking 2020 mei-yu rainfall and flooding throughout China thumbnail

Hexbyte Glen Cove A look back into record-breaking 2020 mei-yu rainfall and flooding throughout China

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Credit: CC0 Public Domain

During summer 2020, heavy precipitation affected a significant portion of China and East and South Asia. The Yangtze River basin bore the brunt of extensive flooding, which caused loss of lives, considerable property damage and prompted millions of people to move to higher ground. To better understand why annual “mei-yu” conditions began earlier and ended later than normal, Dr. Ambrogio Volonté and his team from the University of Reading focused on specific atmospheric dynamics throughout China’s Yangtze River region that contributed to such an unusual season. They have just published their research and findings in in Advances in Atmospheric Sciences.

“The amount of rainfall in June and July 2020 in the basin was higher than in the previous 20 years, and anomalously high in most sub-basins, with similar results applying to river discharge,” said Dr. Mark Muetzelfeldt, a main contributor in Volonté’s study.

Results show that the East Asian Summer Monsoon front played a dominant role bringing frequent persistent precipitation to the Yangtze River basin. Typically, the front progresses farther north during . However, in 2020, the front stalled south of its usual position, leading to a longer mei-yu season with several multi-day rain events throughout most of the river valley.

Researchers analyzed two 5-day episodes during this extended mei-yu season. Warm monsoonal and cool continental air masses frequently converged over the region, as suggested by the unusual frontal position. Upper air circulation also played a role, with pattern variations affecting the air moving toward the front at lower levels. This caused the two heavy rain events to develop with different intensity and in different locations along the river valley.

The full study provides more in-depth statistics resulting from the historic 2020 mei-yu rainfall. Researchers also showcase several analysis tools that they developed specifically to study similar high-precipitation seasonal events.

More information:
Ambrogio Volonté et al, Magnitude, Scale, and Dynamics of the 2020 Mei-yu Rains and Floods over China, Advances in Atmospheric Sciences (2021). DOI: 10.1007/s00376-021-1085-z

A look back into record-breaking 2020 mei-yu rainfall and flooding throughout China (2021, October 4)
retrieved 5 October 2021
from https://phys.org/news/2021-10-record-breaking-mei-yu-rainfall-china.html

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Hexbyte Glen Cove Europe-Japan space mission captures images of Mercury thumbnail

Hexbyte Glen Cove Europe-Japan space mission captures images of Mercury

Hexbyte Glen Cove

A view of Mercury captured on Friday by the joint European-Japanese BepiColombo spacecraft.

The European-Japanese BepiColombo spacecraft has sent back its first images of Mercury, the nearest planet to the Sun, the European Space Agency said Saturday.

The images were obtained almost three years after the unmanned mission vessel was launched aboard an Ariane 5 Rocket.

The cameras attached the BepiColombo provided black-and-white images, the ESA said in a statement.

But as the arrived on the night side of the planet, conditions were “not ideal” for taking images at its to the planet, an altitude of 199 kilometres (124 miles), so the closest was from about 1,000 km.

The region shown is part of Mercury’s , including large craters and an area flooded by lava billions of years ago.

“The flyby was flawless from the spacecraft point of view, and it’s incredible to finally see our target planet,” said Elsa Montagnon, Spacecraft Operations Manager for the mission.

The BepiColombo mission will study all aspects of this mysterious inner planet from its core to , and exosphere, “to better understand the origin and evolution of a planet close to its “, said the agency.

Mercury is also the only rocky planet orbiting the Sun beside our own to have a magnetic field.

Magnetic fields are generated by a liquid core but given its size, Mercury’s should have grown cold and solid by now, as Mars did.

This anomaly might be due to some feature of the core’s composition, something BepiColombo’s instruments will measure with much greater precision than has been possible so far.

On its surface, Mercury is a planet of extremes, vacillating between hot days of about 430 degrees Celsius (more than 800 degrees Fahrenheit) to super-frosty nights of minus 180C (minus 290F).

Those days and nights last nearly three Earth months each.

Earlier missions have detected evidence of ice in the deepest recesses of the planet’s polar craters.

Scientists speculate that this may have accumulated from comets crashing onto Mercury’s surface.

BepiColombo is due to make five more flybys of Mercury during a complex trajectory that will also see the satellite fly past Venus and Earth.

It could not be sent directly to Mercury, as the Sun’s pull is so strong that a huge braking manoeuvre would be needed to place the satellite successfully, requiring too much fuel for a spacecraft of this size. The mission will last for around another five years.

The gravity exerted by the Earth and Venus—known as gravitational assist—allows it to slow down ‘naturally’ during its journey.

© 2021 AFP

Europe-Japan space mission captures images of Mercury (2021, October 3)
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Hexbyte Glen Cove Is your machine learning training set biased? How to develop new drugs based on merged datasets thumbnail

Hexbyte Glen Cove Is your machine learning training set biased? How to develop new drugs based on merged datasets

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The authors combined proprietary (GSK) and published (CCDC) datasets to better train machine learning (ML) models for drug discovery. Credit: Alex Moldovan.

Polymorphs are molecules that have different molecular packing arrangements despite identical chemical compositions. In a recent paper, researchers at GlaxoSmithKline (GSK) and the Cambridge Crystallographic Data Centre (CCDC) combined their proprietary (GSK) and published (CCDC) datasets to better train machine learning (ML) models to predict stable polymorphs to use in new drug candidates.

What are the key differences between the CCDC and GSK datasets?

CCDC curates and maintains the Cambridge Structural Database (CSD). For the past century, scientists all over the world have contributed published, experimental crystal structures to the CSD, which now has over 1.1 million structures. The paper’s authors used a drug subset from the CSD combined with structures from GSK. The GSK structures were collected at different stages of the pharmaceutical pipeline and are not limited to marketed products. Co-author Dr. Jason Cole, senior research fellow on CCDC’s research and development team, explained why structures gathered at different stages of the drug discovery pipeline are so important.

“In early-stage drug discovery, a crystal can help to rationalize conformational effects, for example, or characterize the chemistry of a new chemical entity where other techniques have led to ambiguity,” Cole said. “Later in the process, when a new chemical entity is studied as a candidate molecule, crystal structures are critical as they inform form selection and can later aid in overcoming formulation and tabletting issues.”

This information can help researchers prioritize their efforts—saving time and potentially lives down the road.

“By understanding a range of crystal structures, scientists can also assess the risk of a given form being long-term unstable,” Cole said. “A full characterization of the structural landscape leads to confidence in taking a form forward.”

How do ML models in pharmaceutical science benefit from multiple datasets?

Industrial data sets reflect more than just science; they reflect cultural choices within a given organization.

“You will only find co-crystals if you look for co-crystals,” Cole said, as an example. “Most companies prefer to formulate a free, or unbound, drug. One can assume that the types of structures in an industrial set reflect conscious decisions to search for forms of given types, whereas fewer bounds are placed on the researchers who contribute to the CSD.”

ML models benefit from two key things: data volume and data specificity. That’s why coupling the volume and variety of data in the CSD with proprietary data sets is so helpful.

“Large amounts of data lead to more confident predictions,” Cole said. “Data that are most directly relevant to the problem lead to more accurate predictions. In the predictions that use CCDC software, we select a subset of the most relevant entries that is large enough to give confidence. The GSK set is bound to have highly relevant compounds to other compounds in their commercial portfolio. So the model-building software can use these.”

Industrial researchers working with highly relevant data can run into issues when they don’t have enough to generate confident models.

“Consider that CSD software typically picks around two thousand structures from the 1.1 million in the CSD,” Cole said. “The industrial set is tiny by comparison, but you could pick, say, 40 or 50 highly relevant structures. You’d have insufficient data to build a good model with that alone, but the added compounds from the CSD supplement the data set. In essence, by including the GSK and CSD sets we get the best of both worlds: all the highly relevant industrial structures and a set of quite relevant CSD structures together to build a high-quality model.”

Why do polymorphs present a risk to the pharmaceutical industry?

The different packing arrangements mean that one polymorph might be more suited for therapeutic delivery, while another form of the same compound might not. Researchers use databases to make knowledge-based predictions about whether a potential new drug is comprised of a good, stable form that manufacturers can make, store, and deliver in a therapeutic manner. The authors at GSK and CCDC completed a robust analysis of the small molecule crystal structures containing X-ray diffraction results from GSK and its heritage companies for the past 40 years. They then combined those results with a drug subset of structures from CCDC’s CSD, which contains over 1.1 million small-molecule organic and metal-organic crystal structures from researchers all over the world.

More information:
Leen N. Kalash et al, First global analysis of the GSK database of small molecule crystal structures, CrystEngComm (2021). DOI: 10.1039/D1CE00665G

Provided by
CCDC – Cambridge Crystallographic Data Centre


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