Brain-Imaging Studies Hampered by Small Data Sets, Study Finds

For two decades, researchers have used brain-imaging technology to try to identify how the structure and function of a person’s brain connects to a range of mental-health ailments, from anxiety and depression to suicidal tendencies. But a new paper, published Wednesday in Nature, calls into question whether much of this research is actually yielding valid findings. The New York Times reports: Many such studies, the paper’s authors found, tend to include fewer than two dozen participants, far shy of the number needed to generate reliable results. “You need thousands of individuals,” said Scott Marek, a psychiatric researcher at the Washington University School of Medicine in St. Louis and an author of the paper. He described the finding as a “gut punch” for the typical studies that use imaging to try to better understand mental health.

Studies that use magnetic-resonance imaging technology commonly temper their conclusions with a cautionary statement noting the small sample size. But enlisting participants can be time-consuming and expensive, ranging from $600 to $2,000 an hour, said Dr. Nico Dosenbach, a neurologist at Washington University School of Medicine and another author on the paper. The median number of subjects in mental-health-related studies that use brain imaging is around 23, he added. But the Nature paper demonstrates that the data drawn from just two dozen subjects is generally insufficient to be reliable and can in fact yield ‘massively inflated’ findings,” Dr. Dosenbach said. The findings from the Nature paper can “absolutely” be applied to other fields beyond mental health, said Marek. “My hunch this is much more about population science than it is about any one of those fields,” he said.

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Protein Tweak Makes CRISPR Gene Editing 4,000 Times Less Error-Prone

Researchers at the University of Texas at Austin have identified a previously unknown structure of the protein that’s responsible for making edits to the wrong sections of DNA. After some tweaking, they were able to reduce the likelihood of off-target mutations by 4,000 times. New Atlas reports: CRISPR tools use certain proteins, most often Cas9, to make precise edits to specific DNA sequences in living cells. This can involve cutting out problematic genes, such as those that cause disease, and/or slotting in beneficial ones. The problem is that sometimes the tool can make changes to the wrong parts, potentially triggering a range of other health issues. And in the new study, the UT researchers discovered how some of these errors can happen. Usually, the Cas9 protein is hunting for a specific sequence of 20 letters in the DNA code, but if it finds one where 18 out of 20 match its target, it might make its edit anyway. To find out why this occurs, the team used cryo-electron microscopy to observe what Cas9 is doing when it interacts with a mismatched sequence.

To their surprise, they discovered a strange finger-like structure that had never been observed before. This finger reached out and stabilized the DNA sequence so the protein could still make its edit. Having uncovered this mechanism, the team tweaked this finger so that it no longer stabilized the DNA, instead pushing away from it. That prevents Cas9 from editing that sequence, making the tool 4,000 times less likely to produce off-target mutations. The team calls the new protein SuperFi-Cas9. The research was published in the journal Nature.

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Scientists Demonstrate Self-Awareness In Fish

Researchers from the Graduate School of Science, Osaka City University, have provided evidence to suggest that fish have the capacity for MSR, a behavioral test to determine whether an animal possesses the ability of visual self-recognition. As Phys.Org explains, an animal’s capacity for MSR is determined when they “touch or scrape a mark placed on their body in a location that can only be indirectly viewed in a mirror.” From the report: Professor [Masanori Kohda] says, “Previously, using a brown marking on the throat area of [cleaner fish Labroides dimidiatus], we had shown three out of four cleaner fish to scrape their throats several times after swimming in front of a mirror, a number on par with similar studies done on other animals like elephants, dolphins, and magpies.” However, one of the criticisms laid against this result was sample size and the need for repeated studies showing positive results. Teaming up with researchers from the Max Planck Institute of Animal Behavior in Germany and the University of Neuchatel in Switzerland, this study increased the sample size to 18 cleaner fish, with a 94% positive result of 17 of them demonstrating the same behavior from the previous study.
[…]
Prof. Kohda says, “Our previous study demonstrated MSR in L. dimidiatus; however, studies with other animals have shown that simply moving a mirror reignites aggressive behavior, suggesting the animal has only learned a spatial contingency, not MSR.” To address this, the team transferred mirror-trained cleaner fish to a tank with a mirror on one side of the tank and then three days later to a tank with a mirror on the other side, and saw the fish show no aggression toward their mirror image in both tanks. Also, to ensure the L. dimidiatus that passed the mark test truly are recognizing themselves, they placed mirror-trained fish in adjacent tanks that were separated by transparent glass. After two to three days, when fish largely reduced their aggressive behavior towards each other, they were marked the standard way the following night. None of the fish scraped their throat during the 120 mins of exposure to each other the following morning. This new experiment was recently published in PLOS Biology.

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Kombucha Cultures Make Excellent Sustainable Water Filters, Study Finds

Long-time Slashdot reader shoor shares a report from Ars Technica: The refreshing kombucha tea that’s all the rage these days among certain global demographics might also hold the key to affordable, environmentally sustainable living membranes for water filtration, according to a recent paper published in the American Chemical Society journal ACS ES&T Water. Experiments by researchers at Montana Technological University (MTU) and Arizona State University (ASU) showed that membranes grown from kombucha cultures were better at preventing the formation of biofilms — a significant challenge in water filtration — than current commercial membranes.

Co-author Katherine Zodrow, an environmental engineer at MTU, led an earlier 2020 study demonstrating the feasibility of making sustainable living filtration membranes (LFMs) out of a bacterial cellulose network and the native microorganisms of a kombucha SCOBY (symbiotic culture of bacteria and yeast) culture. Zodrow and her new collaborators made their membranes for this latest round of experiments the same way: by placing a SCOBY in a growth solution of sugar, black tea, and distilled white vinegar dissolved in deionized water. The researchers then placed the mixture in a temperature-controlled room for 10-12 days until a thick membrane formed on the mixture’s surface. The grown membranes were stored in deionized water and used in experiments within eight days. The 20 liters of raw water samples for the experiments were taken from the three drinking water treatment plants in Butte, Montana: Basin Creek Reservoir, Moulton Reservoir, and Big Hole River. The water samples were then pretreated in accordance with standard practices at each plant.

Both the LFMs and polymer-based filters, the researchers discovered, became clogged over time, causing them to flow and filter more slowly. The LFMs used in the experiments, however, showed between 19 and 40 percent better performance than their commercial counterparts on that score. The SCOBY-based LFMs were also more resistant to befouling. While biofilms eventually formed, fewer microorganisms were found in those films. Zodrow et al. sequenced the DNA of any bacteria and fungi in the SCOBY-based membrane and found that 97 percent of the bacteria present belonged to the genus Acetobacter. This is not surprising, since it’s also the dominant bacteria in kombucha, but it may explain why the LFMs performed so well with regard to biofilms. As the name implies, a defining characteristic of this genus is the ability to oxidize organic carbon sources like sucrose, glucose, and ethanol into acetic acid, which is known for its antimicrobial properties. Acetobacter has also been shown to reduce or even remove biofilms, in keeping with the results of Zodrow et al.’s experiments.

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Large Ocean Fossil Discovered in Nevada Could Hold Key To Aquatic Evolution

An 8-foot-long skull discovered in the Augusta Mountains of Nevada is the largest fossil ever found from its time. The research team believes that the remarkable discovery could provide insight into how modern whales developed, and how to preserve their presence in our oceans. From a report: The fossil — a newly discovered species of ichthyosaur, a type of large aquatic reptile — dates to about 246 million years ago. The newly-named cymbospondylus youngorum is, according to the research team, the largest animal found from that time period, both in the sea and on land. It currently holds the title of the first giant animal to ever inhabit Earth. The well-preserved skull was excavated along with part of the creature’s backbone, shoulder and forefin. At more than 55 feet long, the ichthyosaur was estimated to be the size of a large sperm whale, according to the study released Thursday by the American Association for the Advancement of Science and the Natural History Museums of Los Angeles County. The ichthyosaur has an elongated snout and conical teeth, leading researchers to believe it ate squid and fish. It also could have hunted smaller marine reptiles and younger members of its species.

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Florida Manatees Facing Starvation to Be Fed in Trial Program

Wildlife officials in Florida are preparing to feed manatees in the wild, an unprecedented response to the animals’ mass starvation caused by the loss of seagrasses they normally eat. From a report: So far this year, 1,056 manatees have died in Florida, nearly double the average for the same period of the past five years, according to state data. While the record tally includes those killed by watercraft and other causes, malnourishment is the main reason propelling the increase, researchers say. The state’s total manatee population numbered at least 5,733 in 2019, the most recent year in which officials conducted a count. The U.S. Fish and Wildlife Service declared an “unusual mortality event” along Florida’s Atlantic coast this year — a designation indicating a significant die-off that demands an immediate response. The problem can worsen in the winter when the animals congregate in warmer waters that have become devoid of food, researchers say.

“The status of manatees going into this winter is so poor that without this supplemental feeding to help get them through, we’re going to have hundreds and hundreds of [them] dying,” said Patrick Rose, executive director of the advocacy group Save the Manatee Club. Seagrasses are disappearing because of deteriorating water quality caused by improperly treated sewage, leaking septic tanks and runoff containing fertilizer used for lawns and agriculture, researchers say. It’s part of a broader threat to other marine species, they say, and to Florida’s economy, which relies heavily on visitors drawn to the state’s coastline.

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Forget Dogs: These Rats Could Be the Future of Search and Rescue

Researcher Argues Data Paints ‘Big Red Flashing Arrow’ Toward Wuhan Market as Covid-19 Origin

CNN reports on researcher Michael Worobey, “who specializes in tracing the genetic evolution of viruses,” who has now found “considerable evidence that the virus arose in an animal, and did not start circulating until the end of 2019.”

One case especially stood out — that of a 41-year-old accountant who allegedly got sick on December 8, 2019 and who had no connection to the market. The case has been cited as evidence the pandemic must not have started at the market.

Worobey found records that showed the man didn’t become ill with Covid-19 until later in December and that his December 8 problem was related to his teeth.

“This is corroborated by hospital records and a scientific paper that reports his COVID-19 onset date as 16 December and date of hospitalization as 22 December,” Worobey wrote in a commentary in the journal Science. That would make a seafood vendor who worked at the market and who got sick December 11, 2019, the earliest documented case, Worobey said.

Other research helped Worobey come up with a map of the earliest cases that clusters them all around the market. “That so many of the more than 100 COVID-19 cases from December with no identified epidemiologic link to Huanan Market nonetheless lived in its direct vicinity is notable and provides compelling evidence that community transmission started at the market,” he wrote. “It tells us that there’s a big red flashing arrow pointing at Huanan Market as the most likely place that the pandemic started,” Worobey told CNN. “The virus didn’t come from some other part of Wuhan and then get to Huanan market. The evidence speaks really quite strongly to the virus starting at the market and then leaking into the neighborhoods around the market….”

The journal Science subjected Worobey’s research to outside scrutiny before publishing it.

Interestingly, Science also published a letter in May in which Worobey had joined 17 other scientists to urge the investigation of both the “natural origin” and “lab leak” theories. But now while he still believes the Chinese government should’ve investigated the lab leak theory, “holy smokes — is there a lot of evidence against it, and in favor of natural origin,” Worobey tells CNN. And he’s now telling the Los Angeles Times that his new research “takes the lab-leak idea almost completely off the table…. So many of the early cases were tied to this one Home Depot-sized building in a city of 11 million people, when there are thousands of other places where it would be more likely for early cases to be linked to if the virus had not started there.”

Or, as he explained his research to the Washington Post, “It becomes almost impossible to explain that pattern if that epidemic didn’t start there.”

A virologist at Texas A&M University who was one of the coronavirus experts giving SARS-CoV-2 its name called Worobey’s research “detailed and compelling,” while a virologist at Tulane University also tells the Post the new research “shows beyond a shadow of a doubt that in fact the Huanan market was the epicenter of the outbreak.”

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