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Research Report

Gesturing with your hands can make your words more memorable, new research suggests

Daily Mail - Science & tech

Searching for a way to make your point? Then look no further than your hands. Gestures such as slicing the air or waving can make what we are saying more memorable, according to scientists. It may explain politicians' annoying habit of making chopping motions to emphasise words in their speeches – and why people in some countries such as Italy tend to gesticulate when they speak. The research shows gestures can affect the sounds people hear, for example making vowels seem longer.

Salvaging the school year depends on quickly vaccinating teachers, lower infection rates

Los Angeles Times

Saving the Los Angeles school year has become a race against the clock -- as campuses are unlikely to reopen until teachers are vaccinated against COVID-19 and infection rates decline at least three-fold, officials said Monday. The urgency to salvage the semester in L.A. and throughout the state was underscored by new research showing the depth of student learning loss and by frustrated parents who organized statewide to pressure officials to bring back in-person instruction. A rapid series of developments Monday -- involving the governor, L.A. Unified School District, the teachers union and the county health department -- foreshadowed the uncertainties that will play out in the high-stakes weeks ahead for millions of California students. "We're never going to get back if teachers can't get vaccinated," said Assemblyman Patrick O'Donnell (D-Long Beach), who chairs the state's Assembly Education Committee and has two high schoolers learning from home. He expressed frustration that educators are not being prioritized by the L.A. County Health Department even as teachers in Long Beach are scheduled for vaccines this week. Although Long Beach is part of L.A. County, it operates its own independent health agency.

Competition among human females likely contributed to concealed ovulation

Daily Mail - Science & tech

Competition for mates between prehistoric human women may have contributed to'concealed ovulation' – a lack of any notable physical clues that a woman is fertile, experts say. Using computational models, US researchers found evidence that concealed ovulation in humans – which is unusual in the animal kingdom – evolved to allow women to hide their fertility status from other females. This would have helped avoid female conflict, perhaps driven by aggression towards potential rivals for male mates. Previously, scientists have thought women evolved to conceal ovulation from males to encourage them to help with looking after children. The new research shows that the origin of concealed ovulation might have actually have been much more female-oriented than previously thought. 'The study of human evolution has tended to look at things from a male perspective,' said senior study author Athena Aktipis, associate professor of psychology at Arizona State University in the US.

New Algorithms Could Reduce Racial Disparities in Health Care


Researchers trying to improve healthcare with artificial intelligence usually subject their algorithms to a form of machine med school. Software learns from doctors by digesting thousands or millions of x-rays or other data labeled by expert humans until it can accurately flag suspect moles or lungs showing signs of Covid-19 by itself. A study published this month took a different approach--training algorithms to read knee x-rays for arthritis by using patients as the AI arbiters of truth instead of doctors. The results revealed radiologists may have literal blind spots when it comes to reading Black patients' x-rays. The algorithms trained on patients' reports did a better job than doctors at accounting for the pain experienced by Black patients, apparently by discovering patterns of disease in the images that humans usually overlook.

Comparison of Read Mapping and Variant Calling Tools for the Analysis of Plant NGS Data


High-throughput sequencing technologies have rapidly developed during the past years and have become an essential tool in plant sciences. However, the analysis of genomic data remains challenging and relies mostly on the performance of automatic pipelines. Frequently applied pipelines involve the alignment of sequence reads against a reference sequence and the identification of sequence variants. Since most benchmarking studies of bioinformatics tools for this purpose have been conducted on human datasets, there is a lack of benchmarking studies in plant sciences. In this study, we evaluated the performance of 50 different variant calling pipelines, including five read mappers and ten variant callers, on six real plant datasets of the model organism Arabidopsis thaliana. Sets of variants were evaluated based on various parameters including sensitivity and specificity. We found that all investigated tools are suitable for analysis of NGS data in plant research. When looking at different performance metrics, BWA-MEM and Novoalign were the best mappers and GATK returned the best results in the variant calling step.

Growing up in bilingual home 'provides lasting cognitive benefits'

Daily Mail - Science & tech

Growing up in a bilingual home can provide unexpected cognitive benefits later in life – especially if exposed to two or more languages from birth. UK experts found that adults who were exposed earlier to two languages in their lives were the highest performers in cognitive tests. 'Early bilinguals' – those who learn a second language as an infant or young child – have cognitive advantages over those who learn a second language later, suggesting the earlier we're exposed to two languages, the better for our brains. In the experiments, early bilinguals were found to be quicker at shifting attention and detecting visual changes compared to adults who learnt their second language later in life (late bilinguals). Both early and late bilinguals performed better than those people who spent their early lives in single-language homes.

Global temperatures in 2020 tied record highs


Housebound by a pandemic, humanity slowed its emissions of greenhouse gases in 2020. But Earth paid little heed: Temperatures last year tied the modern record, climate scientists reported last week. Overall, the planet was about 1.25°C warmer than in preindustrial times, a trend that puts climate targets in jeopardy, according to jointly reported assessments from NASA, Berkeley Earth, the U.K. Met Office, and the National Oceanic and Atmospheric Administration. The annual update of global surface temperatures—an average of readings from thousands of weather stations and ocean probes—shows 2020 essentially tied records set in 2016. But the years were nothing alike. Temperatures in 2016 were boosted by a strong El Niño, a weather pattern that warms the globe by blocking the rise of cold deep waters in the eastern Pacific Ocean. Last year, however, the Pacific entered La Niña, which has a cooling effect. That La Niña didn't provide more relief is an unwelcome surprise, says Nerilie Abram, a climate scientist at Australian National University. “It makes me worried about how quickly the global warming trend is growing.” The past 6 years are the six warmest on record, but the warming of the atmosphere is unsteady because of its chaotic nature. The ocean, which absorbs more than 90% of the heat from global warming, displays a steadier trend, and here, too, 2020 was a record year. The upper levels of the ocean contained 20 zettajoules (1021 joules) more heat than in 2019, and the rise was double the typical annual increase, scientists reported last week in Advances in Atmospheric Sciences . The subtropical Atlantic Ocean was particularly hot, fueling a record outbreak of hurricanes, says Lijing Cheng, a climate scientist at the Chinese Academy of Sciences's Institute of Atmospheric Physics who led the work. This heat, monitored down to 2000 meters by a fleet of 4000 robotic probes, is spreading deeper into the ocean while also migrating toward the poles. An extreme heat wave struck the northern Pacific, killing marine life. For the first time, warm Atlantic waters were seen penetrating into the Arctic Ocean, melting sea ice from below and reducing its extent nearly to a record low ( Science , 28 August 2020, p. [1043][1]). The warming ocean and melting ice sheets are raising sea levels by 4.8 millimeters per year, and the rate is accelerating ( Science , 20 November 2020, p. [901][2]). On land, 2020 was even more relentless, with temperatures rising 1.96°C above preindustrial levels, a clear record, Berkeley Earth reported. It was the warmest year ever in Asia and Europe and tied for the warmest in South America. Russia was particularly hot, breaking its previous record by 1.2°C, while swaths of Siberia were 7°C warmer than in preindustrial times, leading to large-scale fires and thawing permafrost that caused buildings to founder and set off oil spills ( Science , 7 August 2020, p. [612][3]). “Siberia was crazy,” says Zeke Hausfather, a climate scientist at the Breakthrough Institute and co-author of the Berkeley Earth analysis. “That heat would effectively be impossible without the warming we've seen.” In Australia, record-setting heat and drought fueled catastrophic bushfires at the start of 2020. Fires torched nearly one-quarter of southeastern Australia's forests and destroyed 3000 homes. Climate change was to blame for the country's “Black Summer,” Abram and co-authors concluded in a study published this month in Communications Earth & Environment . Meanwhile, in the United States, unprecedented heat came to the desert Southwest, which is already warming faster than the rest of the country. Phoenix wilted under its hottest summer ever, averaging 36°C. Arizona's Maricopa county, home to Phoenix, is a leader in addressing heat exposure, yet its heat deaths have hit a new record each year since 2016. In 2020, the number approached 300, a jump of some 50% over the previous year, says David Hondula, a climatologist who studies heat mortality at Arizona State University, Tempe. “It was just off the charts in terms of heat.” ![Figure][4] Turning up the heatCREDITS: (GRAPHIC) N. DESAI/ SCIENCE ; (DATA) MET OFFICE; NASA; BERKELEY EARTH; NOAA Although the global economic slowdown of the COVID-19 pandemic cut carbon dioxide (CO2) emissions by some 7%, atmospheric CO2 is long-lived, and warming from previous emissions is preordained. In any case, the drop in emissions is unlikely to last. Later this year, in May, before photosynthesis in the Northern Hemisphere draws down CO2, the U.K. Met Office predicts that levels of atmospheric CO2 will pass 417 parts per million for several weeks, 50% higher than preindustrial levels. Only dramatic action by the world's countries, far beyond existing efforts, can begin to halt this build up, Cheng says. Should the current rate of warming continue, the world will breach the targets set in the Paris climate agreement—limiting warming to 1.5°C or 2°C—by 2035 and 2065, respectively. But Hausfather says it's quite possible that warming, which has largely held steady for the past few decades at 0.19°C per decade, will actually speed up. The rate of warming over the past 14 years is well above the long-term trend. The debate now, he says, is whether that is an omen of an even darker future. [1]: [2]: [3]: [4]: pending:yes

Separation anxiety


Phase separation, an idea about how cells organize their contents and functions into dropletlike compartments, has divided biologists. For 7 years as president of the Howard Hughes Medical Institute, Robert Tjian helped steer hundreds of millions of dollars to scientists probing provocative ideas that might transform biology and biomedicine. So the biochemist was intrigued a couple of years ago when his graduate student David McSwiggen uncovered data likely to fuel excitement about a process called phase separation, already one of the hottest concepts in cell biology. Phase separation advocates hold that proteins and other molecules self-organize into denser structures inside cells, like oil drops forming in water. That spontaneous sorting, proponents assert, serves as a previously unrecognized mechanism for arranging the cell's contents and mustering the molecules necessary to trigger key cellular events. McSwiggen had found hints that phase separation helps herpesviruses replicate inside infected cells, adding to claims that the process plays a role in functions as diverse as switching on genes, anchoring the cytoskeleton, and repairing damaged DNA. “It's pretty clear this process is at play throughout the cell,” says biophysicist Clifford Brangwynne of Princeton University. The pharmaceutical industry is as excited as some academic researchers, given studies linking phase separation to cancer, amyotrophic lateral sclerosis (ALS), diabetes, and other diseases. Dewpoint Therapeutics, a startup pursuing medical treatments targeting cellular droplets, recently signed development deals worth more than $400 million with pharma giants Merck and Bayer. And three other companies looking to exploit the process opened their doors late last year. Reflecting that enthusiasm, Science picked phase separation as a runner-up in its 2018 Breakthrough of the Year issue. Tjian says he was agnostic at first about the importance of the process. But after McSwiggen's findings inspired him and colleagues to look more closely at the range of claims, the researchers began to have doubts. Tjian and a camp of similarly skeptical biologists now argue that the evidence that liquidlike condensates arise naturally in cells is largely qualitative and obtained with techniques that yield equivocal results—in short, they believe much of the research is shoddy. Moreover, the contention that those intracellular droplets perform important roles “has gone from hypothetical to established dogma with no data,” says Tjian, who stepped down as president of Howard Hughes in 2016 and now co-directs a lab at the University of California (UC), Berkeley. “That to me is so perverse and destructive to the scientific discovery process.” Although proponents of phase separation bridle at some of those criticisms, many scientists agree that the research requires a jolt of rigor. “I don't think the whole field is bunk,” says biophysicist Stephanie Weber of McGill University. “But we do need to be more careful” in identifying instances of phase separation in cells and ascribing functions to them. The process may be less important than many scientists now assert, adds quantitative cell biologist Amy Gladfelter of the University of North Carolina, Chapel Hill. Some researchers, she says, have tried to make it “the answer to everything.” PHASE SEPARATION COULD ANSWER a fundamental question that has nagged biologists for more than 100 years: How do cells arrange their contents so that the molecules necessary to carry out a particular job are in the right place at the right time? One obvious way is with internal membranes, such as those fencing off the Golgi bodies and mitochondria. Yet many other well-known cellular structures, including the nucleolus—an organelle within the nucleus—and the RNA-processing Cajal bodies, lack membranes. Phase separation is an appealing answer. Many proteins sport sticky patches that attract other proteins of the same or a different type. Test tube studies have shown that under certain conditions, such as when protein concentration climbs above a certain level, the molecules may begin to huddle, forming dropletlike condensates. Researchers understand the mechanics best for proteins, but nucleic acids such as RNA could also aggregate with proteins. If the process happens in the cell, it could generate and maintain organelles and permit unique functions. “It's a principle that could explain how many things in the cell and nucleus are organized,” says biophysicist Mustafa Mir of the University of Pennsylvania, who as a postdoc once worked with Tjian. Although biologists mooted a role for intracellular droplets as far back as the 1890s, evidence that they are vital began to coalesce a little over 10 years ago. Brangwynne, then a postdoc at the Max Planck Institute of Molecular Cell Biology and Genetics, was tracing P granules, flecks of protein and RNA that, in nematode embryos, mark the cells that go on to produce sperm and eggs. To observe the granules' movements, Brangwynne squeezed worm gonads that harbor the structures between two microscope cover slips. Under pressure, P granules responded not like solids but like liquids, flowing along the surface of the nucleus and dripping off, he and colleagues reported in Science in 2009. The granules' watery behavior “was mind-blowing. It was so different than anything in cells,” says Weber, a former postdoc of Brangwynne's. In 2012, Brangwynne and colleagues saw similar fluid features in the nucleolus, a dense mix of proteins, RNA, and DNA that manufactures ribosomes, the cell's protein factories. The same year, biophysicist Michael Rosen of the University of Texas Southwestern Medical Center and colleagues showed that three proteins that collaborate to organize part of the cytoskeleton form liquid droplets in a test tube solution. They found that the process speeds the assembly of one type of skeletal fiber in vitro—and might do the same in the cell. Scientists have since reported dozens of examples of cellular structures that are round, prone to fuse, and tend to bead on or flow across surfaces—hallmarks of droplets formed by phase separation (see graphic, p. 338). To confirm that a molecular gathering in a cell is a liquid and not something more solid, scientists often deploy a technique called fluorescence recovery after photobleaching (FRAP). Using a cell that contains fluorescent proteins, researchers zap the region in question with a laser to darken the molecules and then trace how long the fluorescence takes to diffuse back in from other parts of the cell. A liquid, which the fluorescent proteins easily penetrate, should light up more quickly than a solid. Another test involves applying 1,6-hexanediol, a compound that fractures some of the molecular interactions that hold droplets together, to determine whether the structure dissolves. Rosen notes that three papers published last year in Cell offer some of the strongest evidence for phase separation in cells. One, from Brangwynne's lab, showed a particular protein had to reach a threshold concentration in cells to allow formation of stress granules—organelles that pop up during hard times and have been attributed to phase separation. The other two studies also identified threshold conditions for phase separation. Because a threshold is an attribute of the process, the studies provide “good but not perfect data that these structures are going through phase separation,” Rosen says. Many researchers are now convinced that phase separation explains many aspects of cell organization and function. Several research groups have reported that the mechanism helps convene the hundreds of proteins that carry out transcription, the process of reading DNA to produce the RNA instructions for making proteins. Similar molecular corralling may underlie functions including memory in fruit flies, immune cells' responses to pathogens, DNA silencing, transmission of nerve impulses across synapses, and reproduction of SARS-CoV-2, the pandemic coronavirus. Conversely, phase separation may cause disease when it goes awry. In 2018, for example, biophysicist Tanja Mittag of St. Jude Children's Research Hospital and colleagues revealed that mutations that promote several kinds of tumors disrupt the ability of the protein SPOP, which helps eliminate proteins that spur growth of cancer cells, to form droplets in test tube solutions. The researchers proposed that phase separation is key to SPOP's cleanup function in cells, and thwarting it allows cancer-promoting proteins to accumulate. Faulty phase separation could also spur damage by aiding the formation of the toxic intracellular inclusions, or protein globs, that amass in neurodegenerative illnesses such as ALS, Alzheimer's disease, and Parkinson's disease. For example, in some ALS patients the protein FUS is mutated and forms inclusions in their neurons. In the test tube, the mutated protein condenses into droplets that then morph into furry knots of fibers resembling the inclusions. In 2018, biochemist Dorothee Dormann of the Ludwig Maximilian University of Munich and colleagues discovered a possible reason: The mutated version of FUS shrugs off a protein bodyguard that prevents the normal variety from undergoing phase separation and clumping in the test tube. YET THAT SATISFYING PICTURE may be growing murky as more researchers have raised doubts about phase separation. In 2019, for instance, scientists organized a debate at Wiston House, a posh 16th century manor south of London, in part to mull whether the process helped control gene activity. About 30 participants hashed over the evidence that the process occurs in cells with the help of “free-flowing champagne,” recalls Mir, one of the presenters. The group's conclusion, he says, was that the support for many putative cases of phase separation in cells is shaky. Tjian, who was not at the meeting, came around to a similar conclusion because of new data from McSwiggen. McSwiggen's early evidence showed that in herpesvirus-infected cells, the replication compartments—clusters of protein and DNA that help produce new copies of the pathogen—are round and merge with each other, suggesting they result from phase separation. After tracking individual proteins within cells, though, McSwiggen and colleagues determined the molecules diffuse just as fast through the compartments as through the rest of the nucleus. In a true condensate, molecular crowding should have hindered diffusion. Other researchers found the negative evidence compelling when it was published later in 2019, soon after the Wiston House debate. The study is “a really important cautionary tale,” Weber says. The results spurred Tjian, McSwiggen, Mir, and Xavier Darzacq, a cell biologist who co-directs the UC Berkeley lab with Tjian, to scrutinize the phase separation literature. Later that year, in a December 2019 issue of Genes and Development , they published a scathing review of 33 studies that claimed to detect the process in cells. Tjian says he was “really disappointed by the quality of the papers.” The evidence, he and his co-authors wrote, was “often phenomenological and inadequate to discriminate between phase separation and other possible mechanisms.” Too often, he and the other review authors asserted, researchers looking for phase separation rely on qualitative indicators—shape, for example—rather than quantitative data. Moreover, because many intracellular structures possibly formed by phase separation are so small, they are near what's known as the diffraction limit of traditional light microscopes. As a result, the structures may look like fuzzy orbs, but their real shape isn't discernible. Tjian and colleagues also chastised researchers for often assuming the protein concentration in a cell is high enough to trigger phase separation, instead of actually measuring it. Overinterpretation “is rampant” in this type of research, Tjian says. The scientists questioned the FRAP measurements that underpin many claims of phase separation. In the hands of different scientists, the group noted, FRAP recovery rates for the same molecule can range from less than 1 second to several minutes, indicating the technique is too variable to confirm phase separation. Darzacq adds that FRAP “only shows you have a liquid. You have liquid everywhere in the cell.” Many of the congregations that researchers have identified with FRAP or other techniques are probably transient collections of molecules that only last a few seconds, Darzacq and Tjian say. ![Figure][1] Dropping inCREDITS: (GRAPHIC) V. ALTOUNIAN/ SCIENCE ; (IMAGE) C. BRANGWYNNE ET AL., SCIENCE , 324, 5935, 1729 (2020) The review was “an invitation for all of us to proceed with a more careful and thoughtful in-depth analysis of cellular condensates,” says molecular biophysicist Sua Myong of Johns Hopkins University. Although some scientists have been meticulous, “it has not been true of the field,” Rosen adds. Brangwynne says he, too, sees value in the critique. “I agree that we need quantitative approaches.” For example, he concurs that researchers need to be more rigorous when interpreting imaging results so that “every diffraction-limited blob” isn't declared an example of phase separation. Other recent papers have also raised doubts about cases of phase separation. In 2019 in Non-Coding RNA , Weber and a co-author weighed the support for phase separation in the cell nucleus and concluded that solid data back its role in forming three structures, including the nucleolus, but not two other structures commonly attributed to the process. And in April 2020 in Molecular Cell , biophysicist Fabian Erdel of the Center for Integrative Biology in Toulouse, France, and colleagues published a new investigation of heterochromatin—silenced regions of the genome in which DNA coils tightly with various proteins. Previous work suggested phase separation of the intracellular protein HP1 helped stretches of heterochromatin bunch up. But Erdel's team discovered that HP1 didn't form stable liquid droplets in mouse cells and that the size of the densely packed DNA regions didn't depend on the amount of the protein. Brangwynne and other researchers argue that even if some individual findings cited by Tjian and colleagues remain in dispute, the field is making progress toward more solid results. To provide some of the rigor of test tube studies, he and his team have developed a technique for seeding cells with what they call corelets, combinations of molecular fragments that cluster when exposed to light. The corelets trigger droplet formation in cells, allowing the researchers to more precisely probe what protein concentrations are necessary for phase separation and which parts of the molecule are required for the behavior. Even Tjian and colleagues give the approach high marks. Mir, who has been skeptical of much of the evidence for phase separation, agrees that the field seems to be moving away from the “everything is phase separation” stage to a more nuanced discussion of the formation and functions of condensates. “It's like any supertrendy thing in science. The noise subsides, and you are left with the truth.” To get to that truth, however, researchers “desperately need” new tools and a better understanding of the basic rules for how condensates form in cells, Gladfelter says. Scientists also need patience, she says, noting the field “tried to grow up and answer everything really fast.” But she's confident researchers will eventually sort out the real importance of phase separation in cells. “Give us time. We'll get there.” [1]: pending:yes

One Hundred Year Study on Artificial Intelligence (AI100) – a panel discussion at #IJCAI-PRICAI 2020


The mission of AI100 is to launch a study every five years, over the course of a century, to better track and anticipate how artificial intelligence propagates through society, and how it shapes different aspects of our lives. This IJCAI session brought together some of the people involved in the AI100 initiative to discuss their efforts and the direction of the project. The goals of the AI100 are "to support a longitudinal study of AI advances on people and society, centering on periodic studies of developments, trends, futures, and potential disruptions associated with the developments in machine intelligence, and formulating assessments, recommendations and guidance on proactive efforts". Working on the AI100 project are a standing committee and a study panel. The first study panel report, released in 2016, can be read in full here.

New study finds tech elites view the world with more meritocracy


A new study has revealed that while the top 100 richest people in tech share similar views to other wealthy people, they are also more focused on meritocracy. The research, published in PLOS One, used data sets based on tweets by these individuals who were named by Forbes as the top 100 richest people in the tech world, plus their statements on websites about their philanthropic endeavours. As part of the study, the researchers analysed 49,790 tweets from 30 verified Twitter account holders within the tech elite subject group and 60 mission statements from tech elite-run philanthropic websites, plus 17 statements from tech elites and other wealthy individuals not associated with the tech world for comparison purposes. The Twitter text analyses, according to the research, revealed tech elites used Twitter to tweet about subjects that placed emphasis on disruption, positivity, and temporality compared with the average user. Their most frequently used words were'new' and'great', and referred mostly to their peers and other tech firms. At the same time, the authors found that while tweets showed the tech elites did not see a significant difference between power and money or power and democracy, they did note the tech elites denied a connection between democracy and money, a view that was not shared by ordinary Twitter users.