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    A submerged Inca offering hints at Lake Titicaca’s sacred role

    A stone box fished out of Lake Titicaca contains tiny items that add an intriguing twist to what’s known about the Inca empire’s religious practices and supernatural beliefs about the massive lake.

    Divers exploring an underwater portion of the lake’s K’akaya reef found a ritual offering deposited by the Inca, say archaeologists Christophe Delaere of the University of Oxford and José Capriles of Penn State. The carved stone container holds a miniature llama or alpaca carved from a spiny oyster shell and a gold sheet rolled into a cylinder about the length of a paperclip, the scientists report in the August Antiquity. The meaning of these objects to the Inca are unclear.

    Inca offering boxResearchers suspect the Inca placed these two items in this stone box and then used ropes to lower it into the water during a religious ceremony of some kind.T. Seguin/Univ. libre de Bruxelles

    The location of the K’akaya offering indicates that Inca people regarded all of Lake Titicaca, which straddles the border between Bolivia and Peru, as sacred, not just its fabled Island of the Sun, the researchers say.

    Spanish documents described the Inca, who had no writing system (SN: 6/11/19), as believing that their ancestors had originated on the Island of the Sun, about 30 kilometers south of K’akaya Island. Inca rulers, whose empire lasted from 1400 to 1532, built a ceremonial center there. And until now, it’s the only place on Lake Titicaca where similar submerged stone boxes bearing figurines and gold sheets have been found. Of at least 28 stone boxes found there since 1977, many had been looted; only four had partially preserved or intact contents.

    Stone boxes containing figurines and gold items have also been uncovered at sites of Inca child sacrifices in the Andes. A connection may have existed between human sacrificial ceremonies that were intended to appease Inca deities and events held at Lake Titicaca, including the submerging of ritual offerings, the researchers suggest.

    in Science News on August 03, 2020 11:01 PM.

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    Water beetles can live on after being eaten and excreted by a frog

    For most insects, the sticky, slingshot ride straight into a frog’s mouth spells the end. But not for one stubborn water beetle.

    Instead of succumbing to the frog’s digestive juices, an eaten Regimbartia attenuata traverses the amphibian’s throat, swims through the stomach, slides along the intestines and climbs out the frog’s butt, alive and well.

    “This is legitimately the first article in a while that made me say, ‘Huh! How weird!’” says Crystal Maier, an entomologist at Harvard University’s Museum of Comparative Zoology. “There are still a lot of truly bizarre habits of insects that still wait to be discovered,” she says.

    Surviving digestion-by-predator is rare, but not unheard of in the animal kingdom. Some snails survive the trip through fish and birds by sealing their shells and waiting it out. But research published August 3 in Current Biology is the first to document prey actively escaping through the backside of a predator.

    Feeding beetles to predators to see what happens is a regular activity for Shinji Sugiura, an ecologist at Kobe University in Japan. In 2018, he discovered that bombardier beetles can force toads to vomit the insects back up by releasing a mix of hot, noxious chemicals from their rear ends (SN: 2/6/18). 

    On a hunch that R. attenuata might have evolved its own interesting evasive behaviors, Sugiura paired a beetle with a frog that the insect often encounters while swimming through Japanese rice paddies. In his laboratory, he watched.

    The frog made easy prey of the unsuspecting beetle. While the amphibians lack teeth that could kill prey with a crunch, a trip through the acidic, oxygen-poor digestive system should be sufficient to neutralize the insect. But as Sugiura monitored the frog, he saw the shiny black beetle slip out from the frog’s behind and scurry away, seemingly unharmed.

    About two hours before this video begins, this pond frog (Pelophylax nigromaculatus) ate a water beetle (Regimbartia attenuata). After traversing the digestive tract, the beetle emerges from the back end of the amphibian, alive. It’s the first documented example of prey actively escaping a predator through the digestive system.

    “I was very surprised,” he says. “I was expecting that the frogs might just spit out the beetles or something.”

    After more than 30 additional beetle-frog pairings, Sugiura found that over 90 percent of beetles survived being eaten, greatly outshining other animals known to survive digestion-by-predator. Those creatures typically survive less than 20 percent of the time. On average, it took six hours for the beetles to escape, though one intrepid individual completed the journey in just six minutes. 

    Sugiura confirmed that the beetles were actively escaping from the frog’s digestive tract by using sticky wax to fix some beetles’ legs together. None of these immobilized beetles survived, and their carcasses took a day or longer to pass through the frogs.

    R. attenuata’s aquatic lifestyle likely prepared the beetle to survive digestion, Sugiura says. Its streamlined, but sturdy, exoskeleton may shield the insect from digestive juices. And its ability to breath underwater via air pockets tucked under its hardened wings likely prevents suffocation.

    Sugiura plans to test the limits of R. attenuata’s abilities by pairing the insect with larger frogs, toads and even fish. “I’m looking forward to finding unimaginable types of antipredator defense,” he says.

    in Science News on August 03, 2020 03:00 PM.

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    Overconfidence Can Be Transmitted From Person To Person

    By Emma Young

    There will always be some people within a group who are more confident than others. But some groups as a whole tend towards modesty — as with the !Kung hunters of the Kalahari Desert, for example, who deliberately downplay their own achievements and efforts. However, the opposite can also occur — and widespread overconfidence can of course become a problem, as with the US energy company Enron, whose “culture of arrogance” ultimately led to its downfall.

    These two examples are highlighted in a new paper published in the Journal of Experimental Psychology, which reveals a route by which a bias towards overconfidence can develop. In their paper, Joey T Cheng at York University and colleagues first propose and then provide evidence for the idea that if we’re exposed to people who are overconfident, this rubs off on us. In other words, we calibrate our self-assessments based on the confidence level of those around us. Overconfidence can, then, be transmitted socially — and this could help to explain how groups, teams and organisations form their own, sometimes drastically different, confidence norms.

    The team ran a series of six studies to explore all this. In the first study, involving 104 participants, pairs of previously unacquainted students were put to work, first individually and then together, on a lab task. The task involved guessing the personality traits of 10 people from photographs. After completing the task both times, each participant ranked themselves according to how well they’d thought they’d done, relative to everyone else in the group. The team found that working with someone who’d over-ranked their own performance rubbed off on the other member of the pair — after the joint task, they became more confident in their own ability. (This happened though neither member knew what the other’s self-ranking had been.)

    As the researchers write, “after working together, initially non-similar strangers became more similar to each other in terms of over-placement, suggesting the convergence of over-confidence.”

    The subsequent five studies explored this effect further experimentally. A study that involved asking participants to guess the weights of people from photographs revealed that overconfidence (or in this study, at least, reduced under-confidence) can be transmitted indirectly, from person to person to person, “highlighting the extensive reach of confident peers”. (In this study, participants were indirectly influenced by a fictitious former partner of their own partner in the weight-guessing task.)

    Further work revealed that these confidence effects can persist, still being evident several days later. Importantly, two of the studies produced evidence that the influence of overconfident peers on a participant’s own self-estimations happened largely outside their conscious awareness. As the team writes, if you’re unaware of such a “stealthy” transmission of bias, this could make it harder to resist.

    The work also reveals one important qualifier to all these effects: overconfidence transmission occurs only within in-groups. In this case, student participants were influenced by the responses of “partners” who were identified as attending the same university, but not by responses from people identified as coming from a rival university sports team, for example. “That is, individuals do not copy indiscriminately”, the team writes. “Instead they are sensitive to whose mental representations are on display and selectively acquire the over-placement of in-group but not out-group members.” This is consistent with theories about cultural learning.

    However, as the researchers themselves point out, these studies focused on over-placement as one form of overconfidence. More work will be needed to investigate whether this kind of social transmission occurs for other forms, such as over-estimation, which relates strictly to your stand-alone performance — the belief that you did better than you actually did in a test, for example. Similarly, it’s not yet clear whether it applies to over-precision (being convinced that you scored at least 80 per cent, for example, when you didn’t.)

    Still, the work does contribute to our understanding of how an atmosphere of overconfidence (in the form of over-placement, at least) develops.

    The theory doesn’t negate the possibility that there are also cultural effects relevant to overestimation. For example, the researchers write, in the US, the most individualistic society in the world, unusually high levels of overconfidence might be triggered by cultural cues that emphasise success and self-sufficiency — and as those cultural values spread between people, so too can over-confidence.

    However, the work still suggests that overconfident beliefs among a few may lead to a cascade-like spread of biased beliefs through a social group, team, or society. A recognition that this happens, will surely be important for all kinds of organisations.

    The social transmission of overconfidence.

    Emma Young (@EmmaELYoung) is a staff writer at BPS Research Digest

    in The British Psychological Society - Research Digest on August 03, 2020 12:54 PM.

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    Some spiders may spin poisonous webs laced with neurotoxins

    Orb weaver spiders are known for their big, beautiful webs. Now, researchers suggest that these webs do more than just glue a spider’s meal in place — they may also swiftly paralyze their catch.

    Biochemical ecologist Mario Palma has long suspected that the webs of orb weavers — common garden spiders that build wheel-shaped webs — contain neurotoxins. “My colleagues told me, ‘You are nuts,’” says Palma, of São Paulo State University’s Institute of Biosciences in Rio Claro, Brazil. No one had found such toxins, and webs’ stickiness seemed more than sufficient for the purpose of ensnaring prey.

    The idea first came to him about 25 years ago, when Palma lived near a rice plantation where orb weavers were common. He says he often saw fresh prey, like bees or flies, in the spiders’ webs, and over time, noticed the hapless animals weren’t just glued — they convulsed and stuck out their tongues, as if they’d been poisoned. If he pulled the insects free, they struggled to walk or hold up their bodies, even if the web’s owner hadn’t injected venom.

    Palma had worked with neurotoxins for many years, and these odd behaviors immediately struck him as the effects of such toxins.

    Now, thanks in large part to the work of his Ph.D. student Franciele Esteves, Palma thinks he has found those prey-paralyzing toxins. The pair and their colleagues analyzed the active genes and proteins in the silk glands of banana spiders (Trichonephila clavipes) — a kind of orb weaver — and found proteins resembling known neurotoxins. The neurotoxins may make the webs paralytic traps, the team reports online June 15 in the Journal of Proteome Research. The prey-catching webs of other species probably have similar neurotoxins, Palma says.

    These neurotoxin proteins also showed up on the silk of webs collected in Rio Claro, packed into fatty bubbles in microscopic droplets on the strands. And when the researchers rinsed substances from webs and injected them into bees, the animals became paralyzed in less than a minute.

    The researchers also confirmed, as Palma’s lab had reported in 2006, that fatty acids are present in the droplets. These acids, Palma thinks, are the toxins’ way into prey. The molecules may dissolve the insect’s waxy outer cuticle, the chief barrier to topical toxins.

    “Toxic webs would certainly make sense,” says David Wilson, a venom researcher at James Cook University in Cairns, Australia, but he’d like to see evidence that the web toxins work quickly on contact. Alternatively, they might act as antimicrobials (SN: 10/30/19) or help deter ants and other animals that steal from webs or eat the spiders.

    Jolanta Beinaroviča, a synthetic spider silk designer at the University of Nottingham in England, says, “This paper was like a breath of fresh air.” She thinks many researchers have long oversimplified spider web silks, though she, too, would like to see further demonstration of the toxins’ topical action.

    Paralytic toxins may be just part of the underappreciated complexity of web design. Palma plans to have his students dive deeper into smaller, as of yet unidentified proteins his team found. He thinks they may help keep the prey alive until the spider’s ready for a fresh meal.

    in Science News on August 03, 2020 12:00 PM.

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    Antibiotic prescribing in England, and how this relates to the local area

    Promoting the appropriate use of antibiotics

    Since the discovery of penicillin by Alexander Fleming in the 1920s, there have been over 150 antibacterial drugs developed and marketed for human or veterinary use. The effect these drugs have had on infectious diseases and population health is remarkable. A once considered serious bacterial infection can now be successfully managed using antibiotics prescribed from the doctor. This was not always the case, as our grandparents may testify: bacterial infections were often fatal and the choices available to manage such infections were limited.

    Doctors have been urged to reduce the amount of antibiotics they prescribe when it is safe and appropriate to do so.

    This “golden age” of discovery may, however, soon come to an end, as more and more bacteria are becoming resistant to the antibiotics available to us. It is for this reason that healthcare organizations across the world have been focusing on developing stewardship policies to promote the appropriate use of antibiotics. In England, the situation is no different, and the Department of Health and Social Care have developed an antimicrobial resistance strategy. As part of the plan, doctors have been urged to reduce the amount of antibiotics they prescribe when it is safe and appropriate to do so. As the majority of antibiotic prescribing occurs in primary care, healthcare providers working in this setting are set specific prescribing targets.

    It is important to establish if the polices are working from an antibiotic stewardship perspective, but also that these polices are fair, and do not penalize communities in the most need of care. Our work aimed to address these questions. To do this, we used antibiotic prescribing data from the NHS, as well as working out the characteristics of the local areas in England using nationally available data sources.

    Our study

    In England, the plan to reduce antibiotic prescribing appears to be working

    Overall, we found that, in England, the plan to reduce antibiotic prescribing appears to be working: since 2014, antibiotic prescribing has reduced by around 14 per cent.  We also found that prescribing of certain classes of antibiotics, namely those considered broad spectrum, have also reduced.

    When we considered local factors in our analysis, we showed that the most deprived areas of England had the highest levels of antibiotic prescribing.  When we adjusted for two long-term conditions – diabetes and Chronic Obstructive Pulmonary Disease – both of which are associated with increased antibiotic use, we still found higher levels of antibiotic prescribing in the most deprived areas of England.  We also showed that geography was an important factor too: compared to London, all other areas of England had higher levels of antibiotic prescribing – with the East of England, and the North East of England having the highest levels.

    Considering local needs

    You might ask why this is important? Well, that’s a good question.  Our work shows that in addition to a national strategy to reduce antibiotic prescribing, it is important to consider local needs too. People living in more deprived areas might, for example, might have greater health need for antibiotics compared to people living in more affluent areas.  National one-sized-fits all targets might not necessarily account for this. If there is greater antibiotic need in deprived areas, doctors working in these areas might be unfairly penalized for prescribing them.  This is not fair on the doctors working in primary care, but may also impact on patients too.

    The antibiotic stewardship polices appear to be reducing overall antibiotic prescribing, which is a positive thing, although there is still significant variation in prescribing across England.  It would be appropriate for future prescribing targets to account for local factors to ensure the most deprived communities are not inappropriately penalized.

    The bottom line is if someone is in medical need of an antibiotic, they should be prescribed it, regardless of the characteristics of their local area or where they live.

    The post Antibiotic prescribing in England, and how this relates to the local area appeared first on BMC Series blog.

    in BMC Series blog on August 03, 2020 10:51 AM.

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    Ten takeaways from ten years at Retraction Watch

    As we celebrate our tenth birthday and look forward to our second decade, we thought it would be a good time to take stock and reflect on some lessons we — and others — have learned. Retractions are more common than we — or anyone else — thought they were. Two decades ago, journals were … Continue reading Ten takeaways from ten years at Retraction Watch

    in Retraction watch on August 03, 2020 10:00 AM.

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    Heavy drinking drove hundreds of thousands of Americans to early graves

    Heavy drinking is robbing Americans of decades of life.

    From 2011 to 2015, an average of 93,296 deaths annually could be tied to excessive alcohol use, or 255 deaths per day. Excessive drinking brought death early, typically 29 years sooner than would have been expected.

    All told, the United States saw 2.7 million years of potential life lost each year, researchers report in the July 31 Mortality and Morbidity Weekly Report.

    The researchers used a program developed by the U.S. Centers for Disease Control and Prevention that estimates annual deaths and years of potential life lost due to an individual’s own or another’s excessive drinking. The tool takes into account whether the cause of death is fully attributable to alcohol, such as alcoholic liver cirrhosis, or whether excessive drinking can partially contribute to a condition, such as breast cancer.

    Annually, about 51,000 of the deaths were from chronic conditions. The rest were sudden demises such as poisonings that involved another substance along with alcohol or alcohol-related car crashes.

    The CDC defines excessive alcohol use as binging — drinking five or more drinks at a time for men, four or more for women — or drinking heavily over the course of the week. Men qualify at 15 or more drinks per week; for women, it’s eight or more.

    The numbers of deaths and years of life extinguished due to excessive drinking have gone up since the last report. That assessment covered 2006 to 2010 and reported close to 88,000 deaths and 2.5 million lost years annually. Recommendations from the Community Preventive Services Task Force, made up of public health and prevention experts, to stem excessive drinking include raising taxes on alcohol and regulating the number of places that sell alcoholic beverages (SN: 8/9/17).

    in Science News on August 03, 2020 10:00 AM.

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    Retraction Watch turns 10: A look back, and a look forward

    Ten years. On Aug. 3, 2010, we published our first post on Retraction Watch. Titled, “Why write a blog about retractions?”, the welcome letter to readers outlined our hopes for the new blog. Retractions, we felt then, offered “a window into the scientific process,” as well as a source of good stories for journalists. In … Continue reading Retraction Watch turns 10: A look back, and a look forward

    in Retraction watch on August 03, 2020 10:00 AM.

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    Niyaz Ahmad’s technician did it

    "it makes more sense when you have consumed twice the recommended dose of San Pedro cactus and spent four hours staring at paisley wallpaper, or so I hear from a friend." - Smut Clyde.

    in For Better Science on August 03, 2020 06:00 AM.

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    Hydroxychloroquine can’t stop COVID-19. It’s time to move on, scientists say

    As a frontline doctor working with COVID-19 patients at Columbia University Medical Center in New York City, Neil Schluger had horrific days.

    “I would come into the ward in the morning to make rounds and say to the intern, ‘How did we do last night?’ And the intern said, ‘Well, I had 10 COVID admissions, and three of them have already died.’ It was like nothing I’ve experienced in 35 years of being a physician,” Schluger says.

    When he first heard about hydroxychloroquine, he hoped it would work for his patients. He and colleagues prescribed the antimalarial drug for 811 of the 1,446 patients hospitalized at the medical center from March 7 to April 8. But the drug didn’t seem to help, Schluger and colleagues reported May 17 in the New England Journal of Medicine.

    As a result, “we stopped giving hydroxychloroquine sometime in April,” he says.

    And yet the numbers of cases and deaths from COVID-19 in New York City have continued to fall. “If we’d taken away a lifesaving drug, you wouldn’t expect that to happen,” he says. Instead, Schluger, now a pulmonary critical care doctor and clinical epidemiologist at New York Medical College and Westchester Medical Center in Valhalla, credits old-fashioned public health measures — mask-wearing, staying home, and social distancing — for New York’s success against the virus.

    Hydroxychloroquine has been tested more than any other potential COVID-19 drug but has repeatedly fallen short of expectations. Although study after study has demonstrated no benefit of hydroxychloroquine for treating people with serious coronavirus infections, some people, including President Donald Trump, still insist the drug has merit. A viral video released July 27 that made the misleading assertion that hydroxychloroquine is an effective treatment for COVID-19 spread like wildfire online.

    But the overwhelming majority of scientific evidence doesn’t support that claim. It’s time to move on from hydroxychloroquine to test other drugs that may have more promise against COVID-19, Schluger and other experts say.

    Wrong cells

    Initial hope that hydroxychloroquine was useful in fighting the coronavirus stemmed from lab tests showing that the drug inhibits the virus’s growth in kidney cells from monkeys by blocking its entry. But it turns out that the virus doesn’t enter human lung cells in the same way.

    In those initial experiments, researchers tested the drug using African green monkeys’ kidney cells, known as Vero cells. Those cells are useful for virologists because they allow growth of a wide variety of viruses, says Stefan Pöhlmann, a virologist at the German Primate Center in Göttingen. But the way SARS-CoV-2, the coronavirus that causes COVID-19, infects monkey kidney cells is different from the way it infects human lung cells, Pöhlmann and colleagues report July 22 in Nature.

    To infect different types of cells, the coronavirus has at least two major possible routes of entry. In one, the virus’s spike protein (the knobby structures on its surface) attaches to ACE2 protein on the cell membrane, and then an enzyme called TMPRSS2 cuts the spike protein. That process allows the virus to inject its genetic material into the cell, where more copies of the virus are produced.

    The second way the virus gets inside cells is via a detour through special cellular compartments called endosomes. After attaching to ACE2, the virus is engulfed by an endosome, but the pathogen needs to get its genetic material out of the compartment and into the main part of the cell. So the spike protein needs to be cleaved by an enzyme to allow the viral and cellular membranes to fuse, releasing the virus’s genetic material, says Markus Hoffmann, a virologist also at the German Primate Center.

    In Vero cells from monkeys, that enzyme — called cysteine protease cathepsin L, or CatL — performs the fusion-promoting slice. But the enzyme needs a certain level of acidity to make the cut. Hydroxychloroquine and chloroquine increase the pH too much for CatL to snip the spike protein, thereby inhibiting infection.

    But when Hoffman, Pöhlmann and colleagues tested the drugs in human lung cells grown in lab dishes, the virus easily slipped into the cells. That’s because in lung cells, SARS-CoV-2 takes the more direct route using TMPRSS2, which isn’t found in the monkey cells and which chloroquine and hydroxychloroquine don’t inhibit, says Michael Farzan, a virologist and immunologist at Scripps Research Institute in Jupiter, Fla.

    He and colleagues posted a preprint to bioRxiv.org on July 22 also showing that hydroxychloroquine doesn’t block how SARS-CoV-2 enters human cells. That data has not yet been reviewed by other scientists for publication in a scientific journal.

    Very little, if any, CatL is made in human lung cells, Pöhlmann says. That leaves the virus with mainly the TMPRSS2 route of entry, which is impervious to hydroxychloroquine.

    Many other viruses, including the original SARS and MERS coronaviruses, use TMPRSS2 to activate their spike protein. But the TMPRSS2 entryway is much more important for SARS-CoV-2’s entry to human lung cells than it was for the original SARS virus, Farzan’s study demonstrates. That’s because SARS-CoV-2 also uses another enzyme called furin to snip the spike protein (SN: 3/26/20).

    That furin cleavage spot was not present in the original SARS virus, and may make it easier for SARS-CoV-2 to break into cells. Such furin cleavage sites often help make influenza and other viruses more infectious. In Farzan’s study, the furin cuts make the novel coronavirus more dependent on TMPRSS2 for entry, relegating the CatL pathway to a distant plan B.

    A compound called camostat mesylate effectively inhibits SARS-CoV-2 entry in cells that make TMPRSS2, both studies found. That drug is being tested against the virus in some clinical trials.

    Another study from researchers in France also found that hydroxychloroquine inhibits SARS-CoV-2 infection of Vero cells, but not human lung cells. In addition, the drug did not protect another kind of monkey, cynomolgus macaques, from coronavirus infection, the researchers reported July 22 in Nature.

    These results indicate the importance of using human lung cells to study the virus, the researchers say. “A lot of these [favorable hydroxychloroquine] studies that came out are sort of meaningless because they were done in the wrong cell [types],” says Katherine Seley-Radtke, a medicinal chemist at the University of Maryland Baltimore County.

    Farzan says he doesn’t blame anyone for trying hydroxychloroquine first. “We were grasping at straws” at the beginning of the coronavirus outbreak, he says. “There was a good deal of just trying things on people initially … that just ended up being essentially useless.”   

    The new studies’ implications are clear, says Seley-Radtke, who was not involved in any of the new studies. “We now have a lot more information about hydroxychloroquine, and it doesn’t work. It’s not a direct-acting antiviral.”

    That means chloroquine and hydroxychloroquine are also unlikely to prevent infection with the virus or protect people from developing serious illnesses, as some researchers had proposed. Some studies are still testing the drugs to determine whether they can prevent infection or lessen the risk of developing serious illness, although results of one such study conducted at the University of Minnesota were not encouraging (SN: 6/4/20). That study showed that hydroxychloroquine did not prevent coronavirus infections after exposure to the virus.

    No help for the hospitalized

    Antiviral activity aside, researchers had hoped hydroxychloroquine could calm the overactive immune system response, called a “cytokine storm,” that leads to tissue damage and even death in some COVID-19 patients. The reason for that hope is that hydroxychloroquine is also used to treat rheumatoid arthritis and lupus, and can help regulate the immune system in those patients (SN: 5/22/20).  

    But hydroxychloroquine and chloroquine have not panned out as effective COVID-19 therapies, Shmuel Shoham, an infectious-disease specialist at Johns Hopkins School of Medicine, said June 26 during a news conference sponsored by the Infectious Diseases Society of America announcing revised treatment guidelines. The evidence that “has come through is not encouraging that that’s going to be a great option,” he said. The U.S. Food and Drug Administration has withdrawn its emergency use authorization for hydroxychloroquine (SN: 6/15/20), and several large studies have stopped testing the drug for people who are hospitalized with COVID-19.

    Compared with a placebo, hydroxychloroquine did not relieve COVID-19 symptoms or prevent people from progressing to severe illness to a statistically meaningful degree, researchers reported July 16 in the Annals of Internal Medicine. Similarly, a randomized trial in Brazil of more than 600 COVID-19 patients with mild to moderate symptoms found no statistically meaningful benefit over a placebo of either hydroxychloroquine alone or in combination with another drug called azithromycin, researchers reported July 23 in the New England Journal of Medicine.

    Some studies, published after the FDA’s withdrawal, have found what appears to be a benefit of taking the drug. At Henry Ford Hospital in Detroit, researchers wanted to know how well the hospital was doing with treating COVID-19 patients. So infectious disease epidemiologist Samia Arshad and colleagues looked back at patient records from March 10 to May 2. Patients with moderate to severe disease were given hydroxychloroquine, and, if a bacterial infection was suspected, also got the antibiotic azithromycin. Overall, about 18 percent of COVID-19 patients died. That percentage was lower in the hydroxychloroquine group, with 13.5 percent dying, Arshad and colleagues reported July 1 in the International Journal of Infectious Diseases. But about 20 percent of those who got hydroxychloroquine and azithromycin died.

    Arshad says their results may differ from those of studies that didn’t show a benefit because the Henry Ford patients got treatment earlier (91 percent got the drug within 48 hours of being admitted to the hospital) and because a treatment algorithm the doctors used didn’t allow anyone with cardiac risk factors to take the drug. Anyone who did get the drug was closely monitored. The hospital stopped using the drug after the FDA withdrew emergency use authorization.

    Another retrospective study of almost 6,500 COVID-19 patients in New York City from March 13 to April 17 also found a reduced risk of death among people taking hydroxychloroquine, researchers reported June 30 in the Journal of General Internal Medicine.

    That’s not enough to recommend hydroxychloroquine for use against the coronavirus, says David Hsieh, an oncologist at the University of Texas Southwestern Medical Center in Dallas, who has been examining clinical trials of COVID-19 around the world.

    He and his brother Antony Hsieh of the Perelman School of Medicine at the University of Pennsylvania, and UT Southwestern colleague Magdalena Espinoza found that hydroxychloroquine has had more coronavirus clinical trials devoted to it and is mentioned in more publications than any other drug or therapy directed at COVID-19, the researchers reported July 4 in Med.  

    Studies that look back at outcomes, such as retrospective studies and meta-analyses (studies that combine data from multiple studies) are great for generating hypotheses, Hsieh says. “But we’re in real danger if we start using [them] to change our practice.”

    That’s because in retrospective or observational studies, there is no guarantee that patients who got the drug and those that didn’t are the same. In the Henry Ford trial, patients that got hydroxychloroquine were about five years younger, on average, than those who didn’t, Schluger says. “We know that age is the single strongest predictor of mortality from this illness.”

    And the patients who got hydroxychloroquine were also more likely than those not on the antimalarial drug to have also gotten steroids, which other studies have demonstrated can be lifesaving (SN: 7/22/20). So the patients who got the drug were different from those who didn’t in important ways.

    Researchers “who have looked at the data carefully consider the hydroxychloroquine story to be pretty much over,” Schluger says. “It would be a shame if we weren’t trying other potentially promising things because we were hung up chasing down something for which there’s a lot of evidence now that it doesn’t really do much.”

    in Science News on August 02, 2020 10:00 AM.

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    Weekend reads: ‘Self-promotion journals;’ co-authorship for money, flattening the COVID-19 publication curve

    Before we present this week’s Weekend Reads, a question: Do you enjoy our weekly roundup? If so, we could really use your help. Would you consider a tax-deductible donation to support Weekend Reads, and our daily work? Thanks in advance. We turn 10 years old on Monday. Can you help us celebrate? The week at Retraction … Continue reading Weekend reads: ‘Self-promotion journals;’ co-authorship for money, flattening the COVID-19 publication curve

    in Retraction watch on August 01, 2020 02:03 PM.

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    Coronavirus outbreak at a Georgia overnight camp infected over 200 kids and staff

    A coronavirus outbreak at an overnight summer camp in Georgia suggests that children of any age are susceptible to the virus and might have a key role in spreading it.

    At least 260 out of 597 attendees and staff members tested positive for the coronavirus, including campers younger than 10, researchers report in the July 31 Morbidity and Mortality Weekly Report. Younger children had the highest attack rates, or the total number of new cases per a specific group. Just over half of kids ages 6 to 10 tested positive.

    “This investigation adds to the body of evidence demonstrating that children of all ages are susceptible to [coronavirus] infection and, contrary to early reports, might play an important role in transmission,” the researchers write. Most infected people didn’t have symptoms, which may have helped the virus spread undetected.

    At the camp, a teenage staff member developed symptoms on June 22 — a day after campers arrived — and left the next day. On June 24, that teen’s coronavirus test result came back positive, and officials began sending attendees home. The camp was officially closed on June 27.

    Overall, 44 percent of people at the camp were infected with the virus, most of whom were campers. Kids’ ages ranged from 6 to 19 years old.

    Not everyone at the camp had test results available for analysis. Since some people were not tested or their test results were not reported, the number of people infected might have been underestimated, the researchers write.

    Camp officials had required anyone at the camp to provide proof of a negative coronavirus test conducted within 12 days of arriving. Campers also participated in activities like singing in clusters — made up of kids staying in the same cabin. Although all trainees and staff were required to wear cloth masks, campers were not. Staff also did not keep windows and doors open to ensure buildings were well-ventilated.

    It is still unclear how much of a role that children play in coronavirus transmission. Some contact tracing studies have suggested that kids younger than 10 are less likely than people in any other age group to transmit the virus to others. But younger people are more likely to have milder symptoms, and many cases in kids might go undetected (SN: 6/3/20).

    in Science News on July 31, 2020 09:55 PM.

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    The Correlation-Causation Taboo

    Should psychologists be more comfortable discussing causality?

    in Discovery magazine - Neuroskeptic on July 31, 2020 08:40 PM.

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    Human sperm don’t swim the way that anyone had thought

    Sperm have long fooled scientists. Instead of swimming straight by twirling their tails like propellers, human sperm flick their tails lopsidedly and roll to balance out the off-center strokes.

    Over 300 years ago, microscopy pioneer Antonie van Leeuwenhoek described sperm tails swaying in a symmetric pattern, like “that of a snake or an eel.” The prevailing view that sperm tails move in a balanced way, however, doesn’t capture what actually happens in three dimensions, researchers report July 31 in Science Advances.

    High-speed 3-D microscopy of human sperm swimming freely in the lab revealed that the cells corkscrew as they move, consistent with previous studies. The sperm almost seemed to be drilling into the surrounding fluid, says Hermes Gadêlha, a mathematician at the University of Bristol in England.

    Contrary to what people have thought, sperm tails don’t beat symmetrically. High-speed 3-D microscopy and mathematical analyses reveal that the tails wiggle to only one side as the cells roll. The combination of movements keeps sperm swimming straight ahead.

    Using automated tracking of swimming sperm and mathematical analyses of position data, Gadêlha and colleagues broke sperm tail movement down into two components. Surprisingly, one was a wiggle to only one side of the cell. It’s like someone swimming using just one side of the body, Gadêlha says. By itself, such a lopsided stroke would lead to swimming in circles.

    But a second component of tail movement causes the sperm to rotate, balancing out the lopsided strokes. From above, the sperm tail looks like it is beating symmetrically, as has been described historically. But a more complex, 3-D movement keeps the sperm swimming straight ahead.

    The new 3-D measurements are a big step forward in understanding sperm movement, says Allan Pacey, a male fertility specialist at the University of Sheffield in England. Additional investigation is needed, though, to know if sperm move the same way in the female reproductive tract, where they must contend with fluid movement and narrow passages to reach the egg (SN: 2/13/19). Such research may inform diagnosis and treatment of human infertility, Pacey says.

    in Science News on July 31, 2020 06:00 PM.

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    Springer Nature retracts paper that hundreds called “overtly racist”

    Less than two weeks after publication, an essay on poverty and race which critics decried as “unscholarly” and “overtly racist” has been retracted. The essay, by Lawrence Mead, of New York University, appeared in the journal Society on July 21. It immediately drew the ire of hundreds of academics and advocates who, in a pair … Continue reading Springer Nature retracts paper that hundreds called “overtly racist”

    in Retraction watch on July 31, 2020 04:49 PM.

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    To save Appalachia’s endangered mussels, scientists hatched a bold plan

    The emergency surgery took place in the back of a modified pickup truck in a McDonald’s parking lot in Pikeville, Ky. This scrappy plan to rescue a species of mussel on the edge of extinction made perfect sense: Meet somewhere between Indian Creek in Virginia, where the last known wild golden riffleshells lived, and Kentucky’s Center for Mollusk Conservation in Frankfort, where they would be saved.

    The strategy was a malacologist’s version of a Hail Mary pass. One scientist would gingerly pry open three golden riffleshells and remove their larvae to be nurtured in his lab. The other would return the three mussels to Indian Creek, and wait for the day he could introduce their grown offspring to the same habitat. If the plan didn’t produce enough offspring to sustain a new population, the mussels would probably vanish.

    Five years ago, Indian Creek was the only known remaining habitat for the golden riffleshell (Epioblasma florentina aureola). And like many other mussels, this bivalve’s future looked bleak. Biologists estimated that only about 100 remained in the wild. “They were the next species on the list for disappearing from the face of the Earth,” says biologist Tim Lane, who leads mussel recovery efforts at the Virginia Department of Wildlife Resources’ Aquatic Wildlife Conservation Center, near Marion. “We were literally watching the last of them.”

    Seeing a species vanish in real time is difficult, he says, and is in some ways worsened by the mussels’ near-invisibility beneath the surface. “They’re not charismatic like, say, the northern white rhino,” he says. When mussels go extinct, almost no one knows — or mourns them.

    Tim Lane holding a musselThe survival of mussel 6420 and thousands of its siblings started with an interstate rescue plan hatched by biologist Tim Lane.Gary Peeples/USFWS

    An avid amateur photographer who takes pictures of mollusks, snails, fish and various other small critters in the wild, Lane spends much of his time floating facedown in Appalachian waterways, suspended over rocky riverbeds like a float in the Macy’s Thanksgiving Day Parade. He came up with the plan and carried out phase one: delicately prying the bivalves from the Indian Creek river-bed and laying them in a cooler filled with pebbles, dirt and river water for the 90-minute trip to Kentucky.

    A full-grown golden riffleshell is about the size of a small biscuit, with a yellowy, fan-shaped case. Like other mussels, it anchors itself in gravel with a fleshy foot and rarely moves more than a few meters during its lifetime, which could last 15 years or more. The sedentary creatures have been listed as a federally endangered species since 1977.

    Malacologists, like Lane and others who study mollusks, are accustomed to championing underdogs. More than two-thirds of all identified North American freshwater mussel species are extinct or endangered. North America has the greatest diversity of freshwater mussels — with a heavy concentration in the Southeast. Tennessee’s Clinch River hosts about twice as many species as all of Europe.

    In every locale, the mussels’ problems arise from a mix of factors. Until about a century ago, enormous mussel populations thrived in the Midwest and Southeast, and mussels were often harvested to make shell buttons. But the construction of dams in major rivers divided these populations and separated the creatures from the fish that carry their larvae. “The dams suffocated the huge mussel beds in the most productive habitats,” says Paul Johnson, who runs Alabama’s Aquatic Biodiversity Center, in Perry County.

    Adding insult to injury, rampant pollution from industrial dumping and chemical spills led to massive die-offs before the 1972 Clean Water Act led to cleaner waterways. The animals have faced other threats, too, including microbial pathogens and predators.

    Just last December, more than 150 kilometers downstream of the confluence of Indian Creek and the Clinch, biologists with the U.S. Fish and Wildlife Service reported a massive die-off of pheasantshells (Actinonaias pectorosa) where the river passes through the town of Kyles Ford, Tenn. The researchers suspect some pathogenic fungi, bacteria or parasites are to blame. Myriad species in Europe and the Pacific Northwest, including the freshwater pearl mussel (Margaritifera margaritifera) and the depressed river mussel (Pseudanodonta complanata), have experienced similar die-offs.

    Against that backdrop of known and unknown hazards, researchers around the world are combining in vitro propagation, months of tedious observation and exhaustive laboratory trial and error to save these animals. But none of these evolving methods offer a quick fix.

    “It took us 100 years to get into this mess,” Johnson says. “It’s not going to take 10 to get out of it.”

    freshwater musselsA small group of biologists is getting creative to save freshwater mussels, animals that do a yeoman’s job of cleaning rivers.Gary Peeples/USFWS

    River cleaners

    Those who study and try to save mussels feel an irresistible calling, says Jessi DeMartini, a biologist in Illinois who works on mussel conservation in the Forest Preserve District of DuPage County. “It’s an addiction … that becomes a passion.” They see mollusks as the uncelebrated heroes of the world’s rivers.

    Mollusk shells stabilize riverbeds and create habitats for other creatures. The bivalves provide food to raccoons, muskrats and other critters. Most importantly, mollusks are nature’s water filters, able to clean up big messes.

    A single mussel can filter more than 50 liters of water per day, removing algae and pollution, including toxic substances dumped into rivers as industrial waste. Some researchers suspect that the ability to sop up toxic metals is contributing to the animals’ decline. Like canaries in coal mines, if a mussel population suddenly plummets, it’s a sign that something’s gone foul in the water. (Malacologists describe the smell of a living mussel as rich and sweet, like the river it comes from. But find a dead mussel and the stench is so bad you’d wish you had been born without a sense of smell.)

    By observing the health of juvenile mussels and analyzing tissue samples, researchers can effectively monitor water quality and acute die-offs, Monte McGregor, director of Kentucky’s Center for Mollusk Conservation, and others reported in December 2019 in Freshwater Science.

    The effort to save mussels has implications far beyond the rural and rugged riverways of Appalachia. More than two-thirds of U.S. homes get their drinking water from rivers, Johnson notes. Mussels provide an inexpensive way to safeguard that resource and do some of the work of water treatment plants. “Mussels allow us to provide cleaner water on a less per-cost basis,” he says.

    For all these reasons, conservation biologists keep returning to the rivers and take hope where they can find it. The golden riffleshell has been particularly vexing. To even begin the process of mussel propagation, which has a high rate of failure, biologists typically need to start with larvae, also known as glochidia. The golden riffleshell’s dwindling numbers mean that finding a gravid female — one filled with glochidia — is a rare occasion. But on an April morning in 2016, hope came with a find by Sarah Colletti, a mussel-loving biologist also at Virginia’s Aquatic Wildlife Conservation Center. Colletti had joined a small squad of biologists who donned tall rubber waders and spent hours hunched over viewscopes, which look like toy telescopes, pointed down into water to make it easy to tell rocks from mussels. Colletti was scanning the bottom of Indian Creek as part of what’s become an annual ritual, the search for the last remaining golden riffleshells.

    Sarah Colletti in Indian CreekBiologist Sarah Colletti found three gravid golden riffleshell females in Virginia’s Indian Creek in 2016, setting off a chain of events that might give the endangered species a chance at survival.G. Peeples/USFWS

    It’s a monotonous pursuit, she says, and “you’re second-guessing every rock.” When a mussel comes into view, “it’s kind of shocking.”

    Through her viewscope, Colletti spotted three golden riffleshells nestled among the rocks and silt. All were females displaying their lure, a section of tissue that resembles a tasty meal. Those exposed lures meant the mussels were gravid, ready to release millions of glochidia. Finding three gravid females was unusual. The biologists saw an opportunity — maybe one of the last — to help.

    Alluring display

    Just getting to the larval stage is an accomplishment for these bivalves. Eggs become fertilized only when females filter sperm released into the water by upstream males.

    Glochidia, each the size of a grain of salt, can’t survive on their own. They have to clamp onto the gills of a host fish and become parasitic passengers, embedding themselves in the gill tissue and thriving on a mix of nutrients in the water and in fish blood until undergoing a kind of metamorphosis.

    As mussels grow their first shells and become juveniles, they swell to the size of a well-fed deer tick, then drop from the fish. For each species of mussel, there’s often only one — or at most, a few — species of fish that can ferry larvae to the next stage of life.

    Mussels have evolved a staggering array of methods for infesting fish; almost all involve deception. Some mussels disguise their glochidia in alluring packages that look like minnows; others unspool wormlike appendages tipped with packets holding millions of larvae. The rainbow mussel (Villosa iris) has a lure that looks like a crawfish skittering along the river floor. When a fish tries to eat the minnow or worm or crawfish, the fish gets a mouthful of glochidia, released like dandelion seeds. With the fish’s next gulp of water, the glochidia wash over the gills and stick.

    Lampsilis mussel fish lureWhat looks like a tasty, spotted minnow is actually part of a Lampsilis mussel. When a fish goes in for a bite of this lure, it inhales a mouthful of mussel larvae that attach to the fish’s gills and grow into juveniles.M. Christopher Barnhart

    Members of the genus Epioblasma, including the golden riffleshell, have perfected a tactic that earned them the nickname “fish snapper.” The ritual begins when a mother mussel sends out a short thread, the end of which looks like a bug. When a hungry fish swims in for a bite, the shell snaps shut around the fish’s head and holds tight with short, sharp teeth just inside the shell’s rim. As the fish chokes, it inhales the glochidia, which install themselves in the gills. After a few minutes, the mussel relaxes and releases its captive. The fish that survive are stunned; smaller fish (which aren’t good hosts anyway) may die, their heads crushed by the mollusk’s snap.

    The handoff

    All the pieces of this choreographed sequence — fertilization to glochidia formation to infestation of a host — have to happen in just the right way, says McGregor, who with fellow Kentucky biologist Leroy Koch was waiting at the McDonald’s for Lane to arrive. “There are lots of strikes against these mussels,” he says. “The glochidia have to hit the right fish at the right time.”

    Ideally, mussels would reproduce on their own and people wouldn’t have to intervene. Malacologists step in when a species looks like it’s on the brink of extinction.

    Snuffbox mussel catching a fishA snuffbox mussel snaps shut on the head of a rainbow darter, giving the snuffbox larvae, or glochidia, enough time to attach to the fish’s gills.M. Christopher Barnhart
    logperch fish gillsA closeup photo shows nearly clear glochidia of an oyster mussel attached to the pink gills of a logperch.M. Christopher Barnhart

    That morning in April, Colletti marked the location of the mussels in the stream with three large stones and a bright orange flag. She phoned Lane, who had spent much of graduate school studying the diversity of life in Appalachian rivers. The golden riffleshell always seemed to be foundering. In previous years, when they found gravid females in Indian Creek, Lane and colleagues had attempted streamside infestations: catching host fish and manually transferring glochidia from the mussel into the fish gills. But the approach didn’t work.

    Lane called McGregor, who was well-known in the close-knit malacology community for having pioneered in vitro approaches to bring bivalves back. Biologists have sent him glochidia in test tubes via UPS and FedEx; he’s also been known to drive for hours to secure the larvae. At Kentucky’s Center for Mollusk Conservation, he closely monitors the temperature and quality of the water that flows through the lab, and he makes his own food for the mussels — often customizing a recipe to fit the needs of a species. After Lane called and proposed the plan, McGregor agreed to meet in Pikeville and carry out the glochidia-removing procedure in what he calls his “mobile lab” (the topped bed of his Ford F-250 super duty crew cab).

    Surgery took no more than 30 minutes per mussel. McGregor pried open the shell about five millimeters with his fingers, and used a silicone wedge to keep it open. Then, he filled a syringe with sterile water and flushed out the glochidia from the mussels into a lab dish. All the while, he had to pay attention to the patient and keep it cool.

     “You have to handle the mussel properly,” McGregor says. If the animal gets too warm, that could imperil both the larvae and the mother.

    Once the procedure was over, Lane replaced the mussels in the cooler and drove east to return them to Indian Creek. McGregor drove west, escorting thousands of golden rifflleshell larvae over 260 kilometers of twisting mountain roads, to the mussel recovery operation with the longest track record for propagating mussels in the lab without host fish. This would be the golden riffleshell’s best chance at survival.

    Take me to the river

    For nearly 20 years, researchers at the Kentucky facility have worked on bringing mussels back from the brink of extinction. The small collection of buildings sits near Elkhorn Creek, but McGregor says the water is often too polluted to use for the tanks that hold mussels during the most sensitive part of their development. The pollutants include raw sewage. “We can’t grow mussels in raw sewage,” he says.

    If such a thing as “artisanal algae” exists, it’s surely the stuff grown in this lab. Researchers grow algal cultures in giant incubators. McGregor has grown many algal varieties and has spent years matching the right algal slime to the right mussel.

    scientists prying open mussel shellBiologists have developed methods of propagating endangered mussel species in the lab, even without the host fish. To remove glochidia, scientists first pry open the shell.T. Lane
    Propagation processThen a scientist holds open the mussel shell with a silicone wedge to flush out the larvae with sterile water.T. Lane

    McGregor learned the basics of in vitro propagation in 2004 from Robert Hudson, a malacologist at Presbyterian College in Clinton, S.C. By 2016, McGregor had spent more than a decade improving his recipe, finding the right mix of algae, nutrients and rabbit serum to feed glochidia. Although he prefers to use host fish to grow mussels — and the lab contains dozens of tanks that hold fish as hosts for some other species — scientists have so far been unable to identify the fish that can carry golden riffleshell larvae (which is why streamside infestation doesn’t work).

    So McGregor had to grow the larvae without a host. After 18 days in an incubator with McGregor’s custom-made mussel-growing cocktail, about 1,600 larvae survived to become juveniles. They were transferred to silt-lined raceways with cool flowing water to simulate a river. Within a few months, the glochidia had grown to the size of nickels — large enough to survive in the wild.

    McGregor divided the spoils. “It was too risky for me to keep them all,” he says. He sent groups of mussels back over the mountains to two facilities in Virginia. One is the Aquatic Wildlife Conservation Center, where Colletti and colleagues have been studying and cultivating the bivalves. In a typical year, researchers there release up to 10,000 lab-grown mussels into the wild, representing up to 10 species.

    Colletti says she sees signs of hope for the golden riffleshell. Today, the progeny of those three mussels she found in 2016 are producing their own glochidia in the lab. “They were able to become gravid in captivity,” she says. Lane recently sent photos of those larval grandchildren to McGregor. Colletti and Lane hope the young mussels released into the river will do as well.

    There are other, scattered success stories emerging from recent mussel projects. Johnson, in Alabama, has spent years studying the pale lilliput (Toxolasma cylindrellus).

    After more than two years of work, Johnson pegged the northern studfish (Fundulus catenatus), which looks like a larger, prettier version of a minnow, as the pale lilliput’s host. Once he made that connection, Johnson began to infest a host fish to cultivate new populations of the endangered species.

    There are also big risks. Last year, Johnson propagated about 5,000 juveniles of the rare Louisiana pearshell mussel (Margaritifera hembeli). But just before he was going to release juveniles into a Louisiana river, disaster struck. On an unusually hot spring morning, the temperature of the water streaming into his facility’s raceways soared, killing thousands of the mussels before a researcher could close the valve. “One bad day can literally wreck several years of work,” Johnson says.

    He was left with only about 100 animals to return to nature. But those animals have been thriving in the lab. Johnson has grown new batches and plans to restore them to their natural habitat next year. It’s too soon to declare victory, he says, but he’s hopeful.

    gravid golden riffleshell musselThis gravid golden riffleshell began as a larva in Indian Creek, grew up in a Kentucky lab and is now in a Virginia lab. Its parted shell reveals pouches containing tiny larvae ready to infest an unwitting host fish.T. Lane

    The ultimate goal in mussel conservation, Johnson says, is to propagate animals that can complete an entire life cycle. That means glochidia get to the host fish, survive the tumultuous juvenile years and mature enough to reproduce. In the wild, the whole process takes a few weeks to a few months. In the lab, the timescale is bigger. “It’s a decadeslong effort,” he says.

    Hundreds of the next generation of golden riffleshells are now back at home, with two populations in the Clinch River and one in Indian Creek since 2017. These mussels now measure about the size of a quarter, though some are bigger. Of the 700 that Lane, Colletti and others installed in the wild, many have died and some are unaccounted for, but the researchers estimate that about 300 are still alive.

    The scientists placed transponders on about 100 of the mussels, and every year Lane and Colletti return for a census, waving a device that looks like a metal detector over the water surface and waiting for the satisfying chirp that indicates a lab-grown riffleshell is found.

    For now, the rescue of the golden riffleshell remains a good news story, but Lane says malacologists have to remain vigilant. “This gives us some time, but it’s not like we can pat ourselves on the back and stop.” To ensure the survival of the species, biologists will need to continue harvesting glochidia, shepherding mussels to the juvenile stage and returning them to the wild, year after year. The ultimate goal is to build a population that can sustain itself and reproduce without human intervention, rabbit serum or emergency surgery outside a rural McDonald’s.

    in Science News on July 31, 2020 03:00 PM.

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    Sex Differences And Happy Relationships: The Week’s Best Psychology Links

    Keyboard for ideaOur weekly round-up of the best psychology coverage from elsewhere on the web

    Researchers have reported on the unusual case study of a man, known as RFS, who could read letters but not numbers. When RFS saw numbers, they appeared as a jumbled up mess, writes Sam Kean at Science. Yet he could see the shape of an “8” once it was turned on its side, suggesting that the problem wasn’t a visual deficit, but something specific to number processing.

    A study has found sex differences in the volume of grey matter in certain areas of the brain — differences which may be related to the expression of genes on sex chromosomes. But the work brings up age-old questions about sex difference research, explains Grace Huckins at Wired. Do these kinds of differences have any actual real-world consequences?  And how do you prevent results from being misinterpreted or used to justify sexism?

    A new theory suggests that we dream so that our visual cortex continues to receive input and doesn’t suffer from a lack of stimulation. However, Neuroskeptic isn’t convinced over at Discover Magazine.

    A massive study on more than 11,000 couples has found that the key to a happy relationship may be the characteristics of the relationship itself, rather than of each individual partner. “Relationship-based variables” — things like conflict, feelings of appreciation and sexual satisfaction — accounted for a larger chunk of participants’ relationship satisfaction than their own personalities or traits, writes Emma Betuel at Inverse.

    Communication strategies during the coronavirus crisis haven’t always considered people’s cognitive biases. There are lessons to be learned from these failures that could help to improve messaging on climate change, argue Geoff Beattie and Laura McGuire at The Conversation.

    The crisis has been hard for all of us, but health workers have been placed in a particularly stressful situation. And preliminary evidence suggests that these workers may be at risk of developing mental health problems like PTSD and anxiety, writes Sabrina Weiss at Wired.

    Could lockdown also produce a lasting change to our personalities? It’s not implausible, writes Christian Jarrett at BBC Future: we know that personality traits are not set in stone, but can change throughout our lives. However, it’s too early to say exactly how our personalities might have changed — and any effects will likely be different for everyone.

    Compiled by Matthew Warren (@MattbWarren), Editor of BPS Research Digest

    in The British Psychological Society - Research Digest on July 31, 2020 02:50 PM.

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    $ How to profit from COVID-19 testing $

    Rapid testing has been a powerful tool to control COVID-19 outbreaks around the world (see Iceland, Germany, …). While many countries support testing through government sponsored healthcare infrastructure, in the United States COVID-19 testing has largely been organized and provided by for-profit businesses. While financial incentives coupled with social commitment have motivated many scientists and engineers at companies and universities to work hard around the clock to facilitate testing, there are also many individuals who have succumbed to greed. Opportunism has bubbled to the surface and scams, swindles, rackets, misdirection and fraud abound. This is happening at a time when workplaces are in desperate need of testing, and demands for testing are likely to increase as schools, colleges and universities start opening up in the next month. Here are some examples of what is going on:

    • First and foremost there is your basic fraud. In July, a company called “Fillakit”, which had been awarded a $10.5 million federal contract to make COVID-19 test kits, was shipping unusable, contaminated, soda bottles. This “business”, started by some law and real estate guy called Paul Wexler, who has been repeatedly accused of fraud, went under two months after it launched amidst a slew of investigations and complaints from former workers. Oh, BTW, Michigan ordered 322,000 Fillakit tubes which went straight to the trash (as a result they could not do a week worth of tests).
    • Not all fraud is large scale. Some former VP at now defunct “Cure Cannabis Solutions” ordered 100 COVID-19 test kits that do who-knows-what at a price of 50c a kit. The Feds seized it. These kits, which were not FDA approved, were sourced from “Anhui DeepBlue Medical” in Hefei, China.
    • To be fair, the Cannabis guy was small fry. In Laredo Texas, some guy called Robert Castañeda received assistance from a congressman to purchase $500,000 of kits from the same place! Anhui DeepBlue Medical sent Castańeda 20,000 kits ($25 a test). Apparently the tests had 20% accuracy. To his credit, the Cannabis guy paid 1/50th the price for this junk.
    • Let’s not forget who is really raking in the bucks though. Quest Diagnostics and LabCorp are the primary testing outfits in the US right now; each is processing around 150,000 tests a day. These are for-profit companies and indeed they are making a profit. The economics is simple: insurance companies reimburse LabCorp and Quest Diagnostics for the tests. The rates are basically determined by the amount that Medicare will pay, i.e. the government price point. Intiially, the reimbursement was set at $51, and well… at that price LabCorp and Quest Diagnostics just weren’t that interested. I mean, people have to put food on the table, right? (Adam Schechter, CEO of LabCorp makes $4.9 million a year; Steve Rusckowski, CEO of Quest Diagnostics, makes $9.9 million a year). So the Medicare reimbursement rate was raised to $100. The thing is, LabCorp and Quest Diagnostics get paid regardless of how long it takes to return test results. Some people are currently waiting 15 days to get results (narrator: such tests results are useless).
    • Perhaps a silver lining lies in the stock price of these companies. The title of this post is “$ How to Profit From COVID-19 Testing $”. I guess being able to take a week or two to return a test result and still get paid $100 for something that cost $30 lifts the stock price… and you can profit!Screen Shot 2020-07-31 at 2.03.23 AM
    • Let’s not forget the tech bros! A bunch of dudes in Utah from companies like Nomi, Domo and Qualtrics signed a two-month contract with the state of Utah to provide 3,000 tests a day. One of the tech executives pushing the initiative, called TestUtah, was a 37-year old founder (of Nomi Health) by the name of Mark Newman. He admitted that “none of us knew anything about lab testing at the start of the effort”. Didn’t stop Newman et al. from signing more than $50 million in agreements with several states to provide testing. tl;dr: the tests had a poor limit of detection, samples were mishandled, throughput was much lower than promised etc. etc. and as a result they weren’t finding positive cases at rates similar to other testing facilities. The significance is summarized poignantly in a New Yorker piece about the debacle:

      “I might be sick, but I want to go see my grandma, who’s ninety-five. So I go to a TestUtah site, and I get tested. TestUtah tells me I’m negative. I go see grandma, and she gets sick from me because my result was wrong, because TestUtah ran an unvalidated test.”

      P.S. There has been a disturbing TestUtah hydroxycholorquine story going on behind the scenes. I include this fact because no post on fraud and COVID-19 would be complete without a mention of hydroxycholoroquine.

    • Maybe though, the tech bros will save the day. The recently launched $5 million COVID-19 X-prize is supposed to incentivize the development of “Frequent. Fast. Cheap. Easy.” COVID-19 testing. The goal is nothing less than to “radically change the world.” I’m hopeful, but I just hope they don’t cancel it like they did the genome prize. After all, their goal of “500 tests per week with 12 hour turnaround from sample to result” is likely to be outpaced by innovation just like what happened with genome sequencing. So in terms of making money from COVID-19 testing don’t hold your breath with this prize.
    • As is evident from the examples above, one of the obstacles to quick riches with COVID-19 testing in the USA is the FDA. The thing about COVID-19 testing is that lying to the FDA on applications, or providing unauthorized tests, can lead to unpleasantries, e.g. jail. So some play it straight and narrow. Consider, for example, SeqOnce, which has developed the Azureseq SARS-CoV-2 RT-qPCR kit. These guys have an “EUA-FDA validated test”: Screen Shot 2020-07-31 at 2.14.45 AM
      This is exactly what you want! You can click on “Order Now” and pay $3,000 for a kit that can be used to test several hundred samples (great price!) and the site has all the necessary information: IFUs (these are “instructions for use” that come with FDA authorized tests), validation results etc. If you look carefully you’ll see that administration of the test requires FDA approval. The company is upfront about this. Except the test is not FDA authorized; this is easy to confirm by examining the FDA Coronavirus EUA site. One can infer from a press release that they have submitted an EUA (Emergency Use Authorization) but while they claim it has been validated, nowhere does it say it has been authorized.Clever eh? Authorized, validated, authorized, validated, authorized, .. and here I was just about to spend $3,000 for a bunch of tests that cannot be currently legally administered. Whew!At least this is not fraud. Maybe it’s better called… I don’t know… a game? Other companies are playing similar games. Gingko Bioworks is advertising “testing at scale, supporting schools and businesses” with an “Easy to use FDA-authorized test” but again this seems to be a product that has “launched“, not one that, you know, actually exists; I could find no Gingko Bioworks test that works at scale that is authorized on the FDA Coronavirus EUA website, and it turns out that what they mean by FDA authorized is an RT-PCR test that they have outsourced to others.  Fingers crossed though- maybe the marketing helped CEO Jason Kelly raise the $70 million his company has received for the effort; I certainly hope it works (soon)!
    • By the way, I mentioned that the SeqOnce operation is a bunch of “guys”. I meant this literally; this is their “team”:
      Screen Shot 2020-07-31 at 2.18.45 AM
      Just one sec… what is up with biotech startups and 100% men leadership teams? See Epinomics, Insight Genetics, Ocean Genomics, Kailos Genetics, Circulogene, etc. etc.)… And what’s up with the black and white thing? Is that to try to hide that there are no people of color?
      I mention the 100% male team because if you look at all the people mentioned in this post, all of them are guys (except the person in the next sentence), and I didn’t plan that, it just how it worked out. Look, I’m not casting shade on the former CEO of Theranos. I’m just saying that there is a strong correlation here.

      Sorry, back to the regular programming…

    • Speaking of swindlers and scammers, this post would not be complete without a mention of the COVID-19 testing czar, Jared Kushner. His secret testing plan for the United States went “poof into thin air“! I felt that the 1 million contaminated and unusable Chinese test kits that he ordered for $52 million deserved the final mention in this post. Sadly, these failed kits appear to be the main thrust of the federal response to COVID-19 testing needs so far, and consistent with Trump’s recent call to, “slow the testing down” (he wasn’t kidding). Let’s see what turns up today at the hearings of the U.S. House Select Subcommittee on Coronavirus, whose agenda is “The Urgent Need for a National Plan to Contain the Coronavirus”.



    in Bits of DNA on July 31, 2020 10:09 AM.

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    Cite yourself excessively, apologize, then republish the papers with fewer self-citations. Journal says: Fine.

    A journal has allowed a geophysicist who cited his own work hundreds of times across 10 papers to retract the articles and republish them with a fraction of the self-citations. From 2017 to 2019, Yangkang Chen published some of the papers in Geophysical Journal International, an Oxford University Press title, while he was a postdoc … Continue reading Cite yourself excessively, apologize, then republish the papers with fewer self-citations. Journal says: Fine.

    in Retraction watch on July 31, 2020 10:00 AM.

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    This parasitic plant consists of just flashy flowers and creepy suckers

    Doorknobs in skirts. Microphones in tutus. There are lots of ways to describe Langsdorffia flowers, but parasitic-plant specialist Chris Thorogood says they “absolutely look to me like deep-sea creatures.”

    Whatever you compare them to, the flowers are intricate, screaming red showpieces. That’s the total opposite of the unshowy rest of the plant. It has no leaves, just grayish, ropelike tissue that probes through soil and ranks in looks somewhere between blah and dried-up dog droppings.

    The mix of flashy sexual parts and super-simplified other structures makes sense for the plant kingdom’s extreme parasites, including the four known Langsdorffia species. Why grow a lot of greenery to feed yourself when you can steal what you need (SN: 8/23/16)?

    “They’re vampire plants,” says Thorogood, at the University of Oxford Botanic Garden & Arboretum. Langsdorffia’s underground rope sucks all the nutrition it needs from the roots of other plants, such as figs and mimosas. The burrowing freeloaders “challenge our notion of what plants even do,” he says.

    Langsdorffia hypogea parasiteScraping soil away from a Langsdorffia hypogea reveals the plant’s scam: It’s just a bouquet of flowers growing from ropy vampiric tissue that sucks on other species’ roots.Jean Carlos Santos

    Spotting such marvels requires finding just the right wild spot. Neither Oxford nor any other botanic garden grows them, and Thorogood has never seen a live one, he lamented in a Langsdorffia profile in the May 2020 Plants People Planet. But his lucky coauthor, ecologist Jean Carlos Santos, has.

    The flowers of L. hypogea species pop out of the ground here and there in Central and South America, including Brazil’s savanna, the cerrado. “Imagine the visual impact,” says Santos, of Universidade Federal de Sergipe in São Cristóvão, Brazil. The flowers bloom during the dry season, erupting in loud reds from a thin carpet of other plants’ dead, brown leaves.

    Unlike many flowers from apples to zinnias that sport both male and female parts, an individual L. hypogea plant is either all male or all female. Each of its knobby blooms burst from the soil as skirted masses of tiny same-sex nubbins. To attract the vital go-between pollinators, males ooze nectar among the nubbins. Females release it from their skirt and in a sweet zone at the base of the main bouquet. It’s a banquet in a parched season. Ants, beetles, cockroaches and even birds such as white-naped jays gather to feast.

    Beetles probably do some actual pollination for the plant, says Santos, who studies insect-plant interactions. But ants and most of the other guests are probably just freeloaders themselves on this freeloading plant.

    Blooming is an extraordinary event, and shows that even for a thief stripped to essentials, elaborate floral sex is apparently still worth the effort. Though, some observers have suggested, it may happen only once in each Langsdorffia lifetime.

    in Science News on July 31, 2020 10:00 AM.

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    Unbundling the Big Deal: An interview with SUNY’s Shannon Pritting

    The Big Deal has been a topic of heated discussion among librarians for some twenty or more years now. When first introduced, the attraction of the Big Deal was immediately obvious, since it allows a library to buy its faculty access to most, if not all, of a publisher’s journals at a much lower “cost per article” (discounted) rate. From the start, however, there were doubters.

    Shannon Pritting

    In 2001, the Director of Libraries at the University of Wisconsin, Madison, Kenneth Frazier, warned the library community of the dangers of signing big deals, or any comprehensive licensing agreement, with commercial publishers.

    “The current generation of library directors is engaged in a dangerous ‘game’ in which short-term institutional benefits are achieved at the long-term expense of the academic community,” he warned, adding that big deals would weaken libraries’ ability to manage their journal collections, foist on them journals they “neither need nor want” and increase their dependence on publishers “who have already shown their determination to monopolize the information marketplace.”

    Nevertheless, many libraries did sign big deals. And many later regretted it, not least because, having done so, they felt they had no choice but to keep renewing the contract, even as the cost kept going up and devoured more and more of their budget. 

    Libraries felt trapped, conscious that if they did not renew they would have to go back to subscribing to individual journals at list price, which would mean being able to afford access to fewer journals, and fearful that when they discovered that journals they wanted were no longer available, faculty would revolt.

    Over time, however, a greater willingness to think the unthinkable emerged, and some libraries began to cancel their big deals. And when they did so the sky did not fall in – which allowed other libraries to take heart.

    The list maintained here suggests that libraries began cancelling their big deals as long ago as 2008, but the number doing so has been accelerating in the last few years. What has really focussed minds are the recent decisions by both the University of California and MIT to walk away from their negotiations with Elsevier rather than renew their big deals.

    But it is not necessary to walk away completely in the way UC and MIT have done. Instead, libraries can “unbundle” their Big Deal by replacing the large package of several thousand journals they are subscribed to with a small à la carte bundle of a few hundred journals, and in the process save themselves a great deal of money.

    What is helping libraries to make the decision to unbundle is the knowledge that more and more research is becoming available on an open access basis. In addition, new tools like Unsub are available to advise them on which journals they can cancel without too great an impact, and which journals are essential and so should be retained. 

    Given the big savings that can be realised, and the pressure library budgets are under, unbundling is expected to grow, particularly in light of the straitened circumstances that libraries will find themselves in after the pandemic.

    This year a number of US universities have unbundled in favour of smaller packages of journals, including UNC Chapel Hill, Iowa State University and the State University of New York (SUNY) -- a system of 64 institutions. Coming in the wake of UC’s decision to walk away from Elsevier these little deals have attracted a lot of attention. 

    In Europe, by contrast, there is a greater focus right no on signing transformative agreements. In addition to providing reading rights, these new-style big deals include prepaid publishing rights to allow faculty to publish their articles on an open access basis. Amongst other things, these deals help assuage concerns about double dipping (where a university may end up paying both article-processing charges and subscriptions for the same journals). 

    So how is a decision to unbundle made, and what are the issues and implications of making the decision? To get a clearer picture I spoke recently by email with Shannon Pritting, Shared Library Services Platform Project Director at SUNY. In April, SUNY replaced its Big Deal of 2,200 journals with Elsevier with a “little deal” of just 248 journals. By doing so, it says, it has saved about $7 million.

    Unbundling raises a lot of questions, and I suspect we may not have answers to all of the questions for some time.

    For instance, as more and more universities unbundle, how accurate will the calculations informing the decisions about which journals to give up and which to keep prove to be over time? This could have implications for, amongst other things, how much of the money that has been saved will need to be spent on obtaining paywalled articles through Interlibrary Loan (ILL) and document delivery services.

    Moreover, since unbundling appears currently to be mainly a US thing (with Europe favouring transformative agreements) might we see a geographical divide emerge? If we do, what might the implications of this be, especially for the open access movement?

    In addition, might unbundling encourage more researchers to use illegal services like Sci-Hub, and might unbundling see university libraries marginalised to some extent, especially if they do not play an active role in funding open access?

    Please read on for the interview. 


    The interview begins …

    RP: SUNY consists of 64 campuses I believe. Do they all publish research papers, or is it primarily the 4 main campuses?

    SP: SUNY consists of 60 campuses. The additional 4 are Cornell Statutory colleges, which don’t rely on SUNY for services such as library access. The majority of publishing comes from the 4 University Centers, but there are many other faculty who publish research.

    SUNY has doctoral granting colleges with scholars who produce research in specialized areas, and it has 13 University Colleges with graduate programs and faculty who have publishing and research expectations for promotion and tenure. 

    RP: How many papers a year in total does SUNY publish?

    SP: According to data gathered through Dimensions, over the past five years (2015-2019), SUNY faculty and staff have published on average 9,960 papers.

    Over this term, publishing is split virtually evenly between Open Access and Subscription Based publishing.

    RP: You referred to 4 University Centers. I am thinking that these are Albany, Binghamton, Buffalo, and Stony Brook. You also referred to 4 Cornell Statutory colleges and said they do not rely on SUNY for services like library access. So the number of published papers you cite does not include all of the campuses?

    SP: The 4 University Centers (Albany, Binghamton, Buffalo, and Stony Brook) are included in the numbers of papers affiliated with SUNY authors. These 4 university centers participate fully with SUNY.

    But, there are 4 Cornell Statutory colleges that rely on Cornell for library and other support. These are NYS College of Agriculture & Life Sciences at Cornell University, NYS College of Human Ecology at Cornell University, NYS School of Industrial and Labor Relations at Cornell University, and NYS College of Veterinary Medicine at Cornell University.

    These statutory colleges are not included in the number of papers published.

    RP: How many of the open access papers you refer to are published as gold OA and how many as hybrid OA? And how do you expect these figures to change in the next few years? Also, how much do SUNY libraries pay each year in gold OA fees?

    SP: For 2019, there were 1,035 SUNY papers published as gold OA, with 461 being published as hybrid. Over the five-year period from 2015-2019, SUNY authors published on average 1,361 gold open access articles and 565 hybrid open access articles per year.

    No SUNY libraries currently pay for OA fees. These costs are paid directly by the author or the department, and payment data is not centrally managed.

    We expect that OA fees paid by SUNY authors will remain relatively stable, as most agencies who provide grant funding have already implemented OA requirements.

    RP: SUNY does not therefore know how much is spent on APCs each year by SUNY faculty?

    SP: No, SUNY does not have a reliable estimate of how much is spent on APCs by SUNY faculty.

    RP: Is there a SUNY-wide OA policy, or does each campus have its own separate policy?

    SP: There is a system wide open access policy, approved by the SUNY Board of Trustees in March 2018. This policy requires that the Universities (but not community colleges) should develop and adopt open access policies for each institution.

    The community colleges are encouraged, but not required, to adopt open access policies. Of the 30 universities, 21 currently have open access policies, with all 30 expected to have policies by December 2020.

    Three community colleges have open access policies, with the expectation that only a few more will develop open access policies. We have collected institutional open access policies into a repository that you can view here.

    For the most part, SUNY institutional OA policies leave the decision of whether to publish open access or deposit works into repositories with the faculty.

    A major focus of SUNY in open access has been through Open Educational Resources (OER), which has led to major improvements in college affordability, and improvements in teaching and learning.

    The investment in OER came from NY State Government, with $12 million invested in OER over three years, that has resulted in nearly $50 million in savings, and improved teaching and learning outcomes.


    RP: SUNY recently unbundled its Big Deal with Elsevier, reducing the number of journals it subscribes to from 2,200 to 248. As I understand it from a recent Sciencearticle, SUNY used Unsub to help it decide which journals to give up, and this estimated that a modest number of subscriptions would be enough to supplement the large numbers of Elsevier papers already available outside of paywalls. Of the papers SUNY researchers can access under the new arrangement, the calculation was that 30% of the papers that faculty are likely to need access to are available open access and, thanks to a post-termination agreement (PTA) with Elsevier, 25% will remain freely available to faculty from Elsevier. This does not imply that 45% will need to be ordered via document delivery services right?

    SP: SUNY partnered with Unsub (at the time Unpaywall Journals) to model costs and access options if we decided to cancel or unbundle our Elsevier Big Deal. The percentage you mention of 45% of content not being immediately accessible isn’t something that the Unsub data generally provided as a data point. Although the Unsub data varied by journal, the percentage that wouldn’t be immediately accessible was typically below 20%.

    Although there was a lot of scepticism about the reliability of Unsub data and modelling in predicting costs post-cancellation, the tool and services helped us to think critically about all other data we were using to determine value. In the end, most SUNYs found that Unsub data was useful, and as reliable as other sources that we were using to determine the value of a big deal.

    Certainly, Post-Termination Access helps with providing immediate access. However, I don’t think that any campus expects that either 45% or 20% of the usage would translate into document delivery purchases. Everyone understands that journal usage data is inflated, flawed, and doesn’t reflect true usage and value. Yet, most forecasts of costs after cancellation or unbundling are based on vendor provided usage data.

    Once you provide any barrier such as requesting a purchase, ILL, or anything but directly downloading a PDF or HTML document, the percentage of users who will actually try to request is very small.

    So we expect minimal increase in document delivery costs as a result of changing the Big Deal to a smaller, focused package. And, if libraries find that users are requesting via ILL or document delivery a high amount of articles from any specific journal, they can always subscribe to a single journal if it’s cost effective.

    Overall, the strategy was that the big deal provides access to a lot of content, but our big deal wasn’t an effective use of our money; it was worth it to see what actually happens after we changed our subscription.

    And, I expect that we’ll see the same trends and results that other consortia and libraries have seen: a cancellation of a big deal doesn’t lead to resulting increased costs for article purchasing or ILL that is anywhere near what a subscription to that large set of journals costs. Most users will find alternative sources as the user usually doesn’t need a specific article, but just needs an article that is relevant to the topic.

    In the end, SUNY’s decision was based on the simple equation of whether 2,200 journals was worth the amount we were paying for the Big Deal, and not the fear of what the costs would be for guaranteeing the same type of access to the 2,200 journals as we had when we subscribed to the bundle.  Just as important as determining whether we could provide access to papers we would lose from the bundled titles was determining how many of these 2,200 journals we needed.

    This work took just as much time or more than cost modelling. It involved outreach by many librarians with faculty and administration across SUNY. SUNY also hosted several coordinated open forums with faculty about the Elsevier deal, and engaged with Faculty governance and administration at the system and campus levels. Certainly usage data informed the journals we targeted for the 248, but equally important was input from our user community that was led by librarians.

    We certainly had to walk through various data-driven scenarios of costs after cancellation, value of the package based on usage (and what journals were most important) to ensure we were gathering input and managing the change that comes from moving away from a Big Deal. But, the decision for SUNY was based on whether we valued the journals enough to pay the amount the vendor required us to pay to maintain that access.

    In the end, it wasn’t in the best interests of SUNY to continue with the Big Deal. 

    Individual title subscriptions

    RP: As you indicate, the Elsevier unbundled deal assumes that any campus or department that needs access to journals not in the smaller bundle can subscribe separately. Do you have any sense of how many such subscriptions might be taken out/have been taken out? Presumably, they would need to be funded with money outside the library budget.

    SP: The expectation is that campuses who want to subscribe to journals outside of the 248 titles that most of SUNY gets is that the library subscribes to the journal separately at list price. This funding would be coming from the individual library budget, and would be funded with savings from the difference between what the library would have contributed to the previous big deal and the smaller 248 title deal.

    There have been very few individual title subscriptions for Elsevier titles that were lost in the change to the smaller unbundled deal. The global pandemic began to impact the US just after the new unbundled deal was finalized, which resulted in libraries immediately beginning to limit spending, and then begin to cut budgets.

    The savings from the change from the Big Deal to an unbundled deal provided campuses with the ability to weather drastic cuts, and many used the savings to help meet the need to quickly cut spending and budgets.

    RP: Presumably the figure of 25% of articles that will be freely available as a result of the PTA with Elsevier will grow over time, in line with the number of new papers published in Elsevier journals that are not covered by the PTA?

    SP: There will be some growth in the percentage of content that our users may want, but don’t have immediate access to as our Post Termination access grows less current. However, the percent increase and the costs of access will not be enough of a percentage to come close to the difference in what our previous deal cost our institutions, and what our current subscription will cost.

    SUNY would prefer to look at the aggregate savings built by the years it will take for our PTA to age as a major advantage to unbundling. In essence, as the industry shifts and more consortia and large libraries break subscriptions, the market for journal access will only be more advantageous to the subscriber in the future.

    Thinking of growth over time in the amount of content that our users can’t access via PTA, or a subscription, assumes that the value of a subscription or journal package will only grow. It’s clear that the value of big deals is declining, so future deals should only be more advantageous.

    If SUNY does find it more cost effective to enter into another big deal or “re-bundle” what it recently unbundled, future deals should be better than the deal we had, which was based on historical metrics.

    RP: Of those papers that will be available open access how many do you estimate will be the Version of Record (VoR) and how many are likely to be self-archived versions – e.g. preprint, Authors Accepted Manuscript (AAM), or some other version that is not the VoR? Does the version matter?

    SP: This is a tough question to answer, but based on experience searching for content and assisting users, I’d say that about half of the access would be content that is other than the Version of Record. In most cases, the Version of Record is not needed. But, when it is needed, this is where document delivery purchasing would be used. 

    ILL and document delivery services

    RP: So, SUNY uses both ILL and document delivery services for obtaining articles in journals it does not subscribe to. Can you say which services are used and how many documents on average are ordered each year via a) ILL and b) document delivery services? How do you expect those figures to change going forward?

    SP:Our primary vendor for document delivery is Reprints Desk. A few institutions also use Copyright Clearance Center’s “Get it Now” service, but this is only for a small percentage of the document delivery volume. SUNY Libraries use the lowest cost vendor for document delivery, and for all but a few percent of articles, Reprints Desk is the lowest cost option.

    Based on 5 years of ILL data (2015-19) SUNY has 300,000 total ILL requests per year (both lending and borrowing) for books and articles. Considering that half of ILL requests are for articles, and half of the requests are lending, about 100,000 requests are for ILL articles per year.

    Over this five-year span, total ILL volume has decreased a few percent per year. I expect that the total volume of ILL will continue to decrease, especially for articles. Every consortium that has cancelled big deals has found that there has been little impact on overall ILL volume.

    Of the 100,000 articles requested in SUNY each year, about 25% are for content published within the last five years, which has the potential to incur costs for access. ILL departments are already doing a fine job providing access to current content as a supplement or alternative to subscriptions, and will be a reliable source to provide access for any content that is needed but not available via subscription.

    SUNY libraries have regularly found that providing access to journals via ILL and document delivery is more cost effective than subscribing to journals that have high subscription costs.

    SUNY doesn’t currently have data on how many document delivery purchases are made per year, but we are working with our primary document delivery provider to gather this data to use as another point of consideration when we consider access options.

    RP: Do you have any sense of how much SUNY libraries generally pay for document delivery and ILL services each year?

    SP: The amount that SUNY pays for document delivery and ILL services each year varies between institutions. Typically, smaller institutions don’t pay for document delivery, with our largest few institutions paying from $50,000 to $100,000. But we don’t currently have reliable detailed data on this document delivery spending in aggregate across our 60 institutions as each campus pays separately.

    Although our campuses will continue to decrease the amount of content such as journals that they license, we expect to see only a slight increase in document delivery costs. Users typically find alternative paths to journal articles if libraries don’t subscribe, whether it’s open access or alternative versions of a paper.

    Document delivery is used only in limited circumstances, and we expect the percentage of articles that are available without a subscription to continue to increase. Most of the SUNYs also have enabled Unpaywall integration in their link resolvers, so open access is provided as an option whenever possible.

    RP: I understand it costs between $35 and $40 per article to order via Reprints Desk. In addition, there will be costs for ILL. An article from 2015 estimates the cost of ILL at between $8-$10 per item. Does that sound about right?

    SP: We have reasonably reliable data about the number of transactions where campuses have paid copyright (which in this case includes purchasing the article from a document delivery provider) and the number is 16,250 per year. Your estimate of $35-$40 per article is fair, so our document delivery and copyright spending would be roughly $568,750 dollars per year. However, some of the heaviest requested publications such as Nature, and even Elsevier publications, cost less than $25 per article.

    We think that there is a fair amount of open access that gets purchased or requested via ILL, especially in hybrid journals. This is why we’re excited that Reprints Desk has an open access filter that some libraries are using. As you’re likely aware, finding open access in hybrid publications is often not easy.

    Using your estimate of $8-10 per article for ILL, which I find reasonable, you’re correct that the spending on ILL for articles ordered from other libraries via resource sharing would be around $670,000 per year.  SUNY continues to try to minimize this cost by assessing costs of resource sharing systems and networks to ensure that we’re getting our best value for the resource sharing we need to serve our users.

    When we were using the Unsub post-cancellation cost modelling tool, they defaulted to $17 per request based on older estimates from ILL literature. Even with this higher ILL estimate, the model still indicated that most of our campuses should subscribe to only a small group of journals.

    RP: Ok, so as a rough estimate we can say that SUNY Libraries are receiving about 100,000 article requests a year from faculty. Of these about 16,250 will be supplied via document delivery services (at a cost of around $568,750) and some 83,750 will be supplied via ILL (at a cost of about $670,000). So the total cost of fulfilling individual article requests will be around $1.238 million a year. Does SUNY operate a mediated document delivery service, or can faculty go online and order documents without the library needing to be involved?

    SP: Some SUNY institutions provide an unmediated document delivery service, typically facilitated through an ILL workflow. However, most document delivery purchasing comes as a supplement to Interlibrary Loan requests, where libraries are purchasing articles rather than pay copyright royalties, lending fees, or to prevent slow service.  About half of the SUNY institutions are using a locally developed software middleware system called Article Gateway to facilitate unmediated document delivery through ILL.

    Unmediated document delivery is always provided for a limited number of titles that are most cost effective to use via document delivery article access rather than subscriptions for the entire campus.

    Many of our campuses are small, but offer advanced degrees in specialized areas. As many STEM publishers use metrics that utilize types and level of programs for subscription rates, document delivery is an attractive option to provide access to resources as subscription costs are often beyond the ability of these small campuses to afford. 

    Illegal services and big deals

    RP: You say you expect minimal increase in document delivery costs as a result of changing from a big deal to a smaller deal because “Once you provide any barrier such as requesting a purchase, ILL, or anything but directly downloading a PDF or HTML document, the percentage of users who will actually try to request is very small.” Is there any concern that by unbundling the library could encourage users to access illegal services like Sci-Hub?

    SP: Certainly, SUNY values the work that publishers do, including Elsevier. SUNY wishes to continue its relationship with Elsevier moving forward, as we’ll continue for multiple years to have at least a group of 248 titles.

    However, I think what unbundling does is focus the review not purely on cost per use, which inflates the value of a subscription. This point has been on Instead, the focus becomes more on the value of the usage you’re getting for the amount you’re paying, not purely letting usage drive the value discussion.

    By looking at link resolver data you can find that users often land on records of articles to which they have access, load the pdf into a browser, but never engage with the article. So, with content they do not have access to they may come to a record but never take the next step of ordering the article via ILL.

    We realize that the best case scenario for everyone would be that bundles of the highest quality content were available at prices that were slowly decreasing to acknowledge that the cost of IT infrastructure is going down, so journal hosting prices should go down. But, that’s not the offers that are typically coming from publishers. Library budgets, at least in SUNY, are declining, so increasing costs lead us to make tough decisions about which of the subscriptions to cut.

    The proposition that unbundling will lead to more use of illegal access and that this is a problem that the library or libraries should solve isn’t one that is fair to libraries. It’s not that libraries are seeking to offer less content to their users; they just can’t afford increasing prices.

    We hope that, instead of illegal services becoming more common open access and open science becomes more prevalent and shifts the readership models to open access rather than Sci-Hub or models that aren’t connected to legitimate organizations. 

    RP: How many big deals does SUNY currently have and with whom?

    SP: SUNY is not a consortium that has historically collaborated on big deals for content. This is partially due to the diversity of types of institutions, and partially due to capacity at the central office. The Elsevier Big Deal was the only major full-text deal SUNY had.

    SUNY has historically had a large package of aggregator content labelled SUNYConnect that all campuses subscribe to. However, beyond the Elsevier deal and SUNYConnect, there is currently very little content that the 60 institutions or large groups within the system coordinate purchasing on.

    SUNY is working to do more coordinated collection activity, and will consider big deals if the offer is appropriate.

    However, with most big deals, there is such a wide variety of content that we don’t anticipate finding many deals that will benefit enough of SUNY to pursue. The overall management overhead for big deals is also something we thought about in depth as we moved from the Elsevier big deal to an unbundled group.

    With smaller unbundled coordinated collecting, the opportunity to change strategies or to cancel is less overwhelming, and outweighs the benefit of access to journals in bulk. 

    Transformative agreements

    RP: Has SUNY signed any transformative agreements? If so, with whom? If not does it plan to?

    SP: SUNY as a system, or as individual institutions, has not signed any transformative agreements. At this point, it seems unlikely that SUNY would enter into any large-scale transformative agreements in the near future.

    The culture and organizational structure of SUNY is such that individual authors have been paying open access fees. Although SUNY libraries are largely supportive of movements towards open such as open access and open educational resources, the financial implications of transformative agreements would be difficult for most SUNY libraries to justify.

    SUNY library budgets will continue to be negatively impacted, so the focus will likely be on getting the most relevant access over the next 3-5 years. However, SUNY will continue to ask for terms and discounts for publishing open access as much as possible.

    When a commitment to dedicate funds away from current access to supporting open access comes into play with negotiations, SUNY will likely continue to prioritize current access. An overlooked portion of the SUNY-Elsevier unbundled deal was a 10% discount on Elsevier APCs for SUNY Authors, which is typical of the approach we’ll likely be taking with other deals.

    If we can include terms that are advantageous to authors moving towards open access, we’ll do so, but won’t sacrifice access or incur more costs to move from a read to read and publish strategy.

    RP: You say that SUNY libraries are not responsible for paying any gold OA fees and that payment data is not centrally managed. Do you think there is a danger that by not being involved in the management of APCs, and by unbundling, SUNY libraries might be risking marginalising themselves to some extent? I note in this paper the authors say, “Studies have shown that interlibrary loan often does not increase following journal cancellations, but rather than being good news, this may represent a decrease in perceived library value by researchers. Open Access will also play a critical and increasing role in this environment, and understanding its relation to the content at hand will be important in building a robust and sustainable research support system.”

    The paper also suggests that unbundling could, over the longer term, have a negative impact on smaller institutions that rely on their larger peers to supply ILL requests. I wonder also if, as we see more institutions breaking their Big Deals, the ILL system could start to come under pressure.

    Do you have any thoughts on these matters?

    SP: As a direct response to the quote about ILL volume not increasing after big deal cancellations representing a decrease in “perceived library value,” this statement indicates something that I’ve never fully understood.

    Libraries see it as their responsibility to figure ways to keep providing the same content, even if the deals get worse and cripple the organization further. Why wouldn’t libraries see this not as a referendum on the value of the library, but as an indicator of how much the exact content they were subscribing to mattered. I realize things are always complex in these situations, but libraries shouldn’t tie up their value with keeping specific subscriptions. Libraries offer so much more than just access to articles.

    Regarding risking being marginalized if SUNY doesn’t focus on transformative agreements or continuing to find ways to subscribe to large journal packages: I agree that unbundling should signal a shift in how libraries focus on access. And, SUNY certainly isn’t against transformative agreements or subscribing to bundles of journals that make sense financially.

    However, focusing on licensing agreements with publishers as the main vehicle will likely lead to further issues in the future where libraries again cannot sustain the costs of the endeavours they’re focusing on.

    SUNY will be focusing on ways we can help our system’s faculty and staff participate more in open access publishing to make their intellectual property and research more accessible to all.  We can be sure that publishers and vendors will be partners with us as we begin to move more into open access strategies. But, APCs and transformative agreements should be analysed in our overall context regarding increasing access for SUNY faculty, staff, and students and making the output of SUNY faculty, staff, and students more accessible to the larger community.

    Certainly, ILL and availability of articles is something to be aware of, especially if more large subscription reductions and unbundling continue. ILL departments have seen staffing reductions, which has led to a focus on streamlining workflows, and has brought about a decade’s worth of focus in ILL (at least in the US) that has seen most of the innovation going towards automation.

    What ILL has lacked is a large-scale investment in focusing on the larger ecosystem, which includes better terms in licensing and the ability to offer new services rather than just offering the same services more efficiently. But, I think there’s going to be a real shift in libraries moving more towards collections services, which includes ILL.

    For example, Princeton has adopted this model, which focuses on both access and collections. There needs to be better structural support for ILL, so that consortial coordination of collection and access for things like journals can happen. SUNY discussed all of this when we were considering unbundling, and although we focused for the past six months on showing libraries how to arrange and configure alternative access, we’re at a point now where we can focus on more structural issues that use multiple data points when making collection decisions or setting strategic directions.

    This spirit has been strong in SUNY with coordinated collection development via resource sharing and demand driven acquisitions for books for some time, with many libraries seeking to diversify SUNY’s collection if a title isn’t available in SUNY.

    We’re hoping that we can coordinate journal access in a similar way, where we have programs where SUNYs cooperate on what journals they subscribe to in order to provide the best access to e-journals for all of SUNY.

    Additionally, vendors will likely be offering more in the way of access options that allows consortia to blend ILL-like access and subscriptions. The SILLVR project for streaming video at the Colorado Alliance of Research Libraries is one such pilot where the larger consortium is looking to secure both subscriptions and access in a single license.

    With ILL and collections access departments blending, libraries should be prepared to look at licensing and subscriptions differently, and find the best blend of subscriptions and bundled access that will get the best value for their institutions.

    RP: Thank you very much for taking the time to speak with me.








    in Open and Shut? on July 31, 2020 06:13 AM.

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    What Color is Your Mental Parachute?

    Aphantasia and Occupational Choice

    NOTE: This isn't a real test of visual imagery. Click HERE for the Simple Aphantasia Test, which assesses whether (and how well) you can imagine pictures in your mind's eye.

    Do you prefer to learn by studying material that is visual, auditory, verbal (reading/writing), or kinesthetic (“by doing”) in nature? A massive educational industry has promoted the idea of distinct “learning styles” based on preference for one of these four modalities (take the VARK!). This neuromyth has been thoroughly debunked (see this FAQ).

    But we humans clearly vary in our cognitive strengths, and this in turn influences our choice of career. This should come as no surprise.

    A recent study queried the occupational choices of self-selected populations of people at the extremes of visual imagery abilities: those with Aphantasia (n=993 male/981 female) or Hyperphantasia (n=65 male/132 female). This was assessed by their scores on the Vividness of Visual Imagery Questionnaire (VVIQ). There was also a control group with average scores on the VVIQ, but they were poorly matched on age and education.

    Fig. 4 (Zeman et al., 2020). Percentage of participants with aphantasia and hyperphantasia reporting their occupation as being:
    1 = Management, 2 = Business and financial; 3 = Computer and mathematical/Life, physical, social science; 4 = Education, training, and library; 5 = Arts, design, entertainment, sports and media; 6 = Healthcare, practitioners and technical.

    As expected, people with fantastic visual imagery were more likely to be in arts, design, entertainment, and media, as well as sports (an excellent ability to imagine a pole vault or swing a bat would be very helpful). People with poor to no visual imagery were more likely to choose a scientific or mathematical occupation. These categories are rather broad, however. For instance, “media” includes print media. And artists and photographers with Aphantasia certainly do exist.

    The study had a number of limitations, e.g. washing out individual differences and relying on introspection for rating visual imagery ability (as noted by the authors). There are more objective ways to test for imagery, but these involve in-person visits. Although the authors were circumspect in the Discussion, they were a bit splashy in the title of their paper (Phantasia–The Psychological Significance Of Lifelong Visual Imagery Vivdness Extremes). And the condition of “Aphantasia” existed long before it was named and popularized. But these researchers have caught the imagination of the general public, so to speak:
    The delineation of these forms of extreme imagery also clarifies a vital distinction between imagery and imagination: people with aphantasia–who include the geneticist Craig Venter, the neurologist Oliver Sacks and the creator of Firefox, Blake Ross–can be richly imaginative, as visualisation is only one element of this more complex capacity to represent, reshape and reconceive things in their absence.


    Zeman A, Milton F, Della Sala S, Dewar M, Frayling T, Gaddum J, Hattersley A, Heuerman-Williamson B, Jones K, MacKisack M, Winlove C. (2020). Phantasia–The Psychological Significance Of Lifelong Visual Imagery Vivdness Extremes. Cortex. 2020 May 4; S0010-9452(20)30140-4.

    in The Neurocritic on July 30, 2020 11:09 PM.

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    Hand surgeon in South Korea loses seven papers for “serious misconduct”

    A surgery journal has retracted seven papers by a group in South Korea after an institutional investigation found evidence of “intentional, repetitive, and serious misconduct” in the work.  The articles, by a team at Ewha Womans University and Seoul National University College of Medicine, appeared in the Journal of Hand Surgery (European Volume) between 2016 … Continue reading Hand surgeon in South Korea loses seven papers for “serious misconduct”

    in Retraction watch on July 30, 2020 11:00 PM.

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    The physics of solar flares could help scientists predict imminent outbursts

    Space weather forecasting is a guessing game. Predictions of outbursts from the sun are typically based on the amount of activity observed on the sun’s roiling surface, without accounting for the specific processes behind the blasts.

    But a new technique could help predict the violent eruptions of radiation known as solar flares based on the physics behind them, researchers report in the July 31 Science. When applied to old data, the method anticipated several powerful flares, although it missed some as well.

    Radiation released in solar flares and associated eruptions of charged particles, or plasma,can be harmful. This space weather can disrupt radio communications, throw off satellites, take down power grids and endanger astronauts (SN: 9/11/17). More accurate forecasts could allow operators to switch off sensitive systems or otherwise make preparations to mitigate negative effects.

    Current prediction methods rely on tracking flare-linked phenomena such as large, complex sunspots — dark regions on the sun’s surface with powerful magnetic fields. But that leads to some false alarms.

    In contrast, the new prediction method is rooted in the intricacies of how and when the sun’s tangled loops of magnetic fields rearrange themselves, in a process known as magnetic reconnection, releasing bursts of energy that mark solar flares.

    On the sun’s surface, magnetic fields can get gnarly. Magnetic field lines, imaginary contours that indicate the direction of the magnetic field at various locations, loop and cross over one another like well-mixed spaghetti. When those lines break and reconnect, a burst of energy is released, producing a flare. The details of how and under what conditions this happens have yet to be unraveled.

    In the new study, physicist Kanya Kusano from Nagoya University in Japan and colleagues propose that the largest flares result when two arcing magnetic field lines connect, forming an m-shaped loop, as a smaller loop forms close to the sun’s surface. This “double-arc instability” leads to more magnetic reconnection, and the m-shaped loop expands, unleashing energy.

    Using 11 years’ worth of data from NASA’s Solar Dynamics Observatory spacecraft, the researchers identified regions on the sun with high magnetic activity. For each region, the team determined whether conditions were ripe for a flare-inducing double-arc instability, and then aimed to predict the most powerful flares the sun produces, called X-class flares. The technique correctly predicted seven of nine flares that passed a threshold that the researchers chose, called X2, the second strength subdivision of the X-class.

    The successful predictions suggest that researchers may have identified the physical process that underlies some of the largest outbursts.

    “Prediction is a very good benchmark for how well we can understand nature,” Kusano says.

    The unsuccessful predictions are likewise illuminating: “Even if it fails, it tells us something,” says solar physicist Astrid Veronig of the University of Graz in Austria, who wrote a commentary on the result, also published in Science. The two flares that the technique missed had no associated ejection of plasma from the sun’s surface. “This kind of instability is maybe not a good way to explain these other flares,” Veronig says. They may instead have resulted from magnetic reconnection high above, instead of close to, the sun’s surface.

    The mechanism on which the researchers based their prediction “is really interesting and very insightful,” says solar physicist KD Leka of NorthWest Research Associates in Boulder, Colo. But, she notes, the method couldn’t predict how soon the flares will occur — whether the burst would come an hour or a day after the right conditions first occurred — and it didn’t identify slightly weaker X1 flares, or the next class down, known as M-class flares, which could still be damaging.

    “The mantra that I live by,” Leka says, “is any rule you think you’ve figured out about the sun, it’s going to figure out how to break it.”

    in Science News on July 30, 2020 06:16 PM.

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    An immune system quirk may help anglerfish fuse with mates during sex

    For deep-sea anglerfishes, sex resembles an organ transplant. It’s hard to find a partner in the dark depths, so a tiny male anglerfish fuses its tissues to a more massive female during mating, allowing the two to share not only sperm but even blood and skin (SN: 7/26/75). The creatures are the only animals known to mate in this parasitic way. 

    How males and females fuse and avoid being rejected by each other’s immune systems — like a mismatched organ transplant — has been a mystery. Now, a study finds that anglerfish might not have to evade the immune system in the first place. Some species lack key genes involved in the body’s immune response, which may make fusion without deadly consequences possible, researchers report online July 30 in Science.

    In vertebrates, immune protection typically involves a bodily response called adaptive immunity that identifies and eliminates foreign threats like viruses. Immune cells, such as T cells, recognize fragments of invaders and present those pieces to other cells that then mount an attack. In another line of defense, proteins called antibodies bind to trespassers to mark them for removal by the immune system. In organ transplants, such responses can cause the new organ to fail.

    The deep-sea anglerfishes’ missing genes are involved in making those systems work.

    “When you look at [these fish], you scratch your head and think, ‘How is that possible?’” says Thomas Boehm, an immunologist at the Max Planck Institute of Immunobiology and Epigenetics in Freiburg, Germany. In humans, it’s often difficult to find the right match for organ transplants because of the adaptive immune system, “but these creatures seem to be doing it without knowing what’s going on.” 

    Boehm and colleagues isolated DNA from 31 preserved anglerfish representing 10 deep-sea species. In four of the species, males attach to females only temporarily. In the other six, the fusion is permanent, with either one or multiple males attached to a single female. The researchers also scanned the genetic blueprints of three species that live in shallow waters and don’t attach during mating.

    Photocorynus spiniceps femaleTwo deep-sea anglerfish species, including Photocorynus spiniceps (a preserved female is shown with a tiny male attached on her back), don’t have genes involved in developing antibodies or immune cells that identify invaders and kill foreign or infected cells.Theodore W. Pietsch/Univ. of Washington

    Compared with anglerfishes that don’t fuse to their mates, species that fuse are missing genes that help produce new antibodies that get better at binding to perceived threats in future encounters. Not having those antibodies might be helpful for a female that is exposed to multiple males throughout life, Boehm says. Some anglerfishes that unite permanently also lack genes needed to make the parts of T cells that help identify foreign tissue and pathogens.

    Two of the species in which multiple males can attach to a single female — Photocorynus spiniceps and Haplophryne mollis — may not make antibodies at all. “If I had to diagnose [those two fish] … I would say, ‘OK, this is red alert, we really have to do something because this is severe combined immunodeficiency. Fatal prognosis,’” Boehm says. People with severe combined immunodeficiency — a condition in which genetic defects result in a weak immune system — often die within the first year of life.    

    The researchers didn’t do any laboratory experiments to confirm how the missing genes might affect the immune system’s behavior. Without such data, it’s hard to know what the lack of these genes means for things like fighting off pathogens. “How are they balancing … reproduction and response to infections?” asks Natalie Steinel, an immunologist at the University of Massachusetts Lowell. “It seems, at least genetically, that they’ve put all their chips on reproduction.”

    The researchers’ findings highlight the various forms creatures’ immune systems can take — not only within vertebrates at large, but also within a single group of fishes, Steinel says. “It’s really interesting to see the diversity of immune systems within these different species.”

    It’s possible, though not probable, that anglerfishes have an adaptive immune system that is completely different from that of other vertebrates. Or the creatures may have evolved a nonspecific immune response that protects them from infections but not parasitic sex.

    The fish “must have done something to compensate for adaptive immunity,” Boehm says. “We don’t know what that is, but that is for the future.”

    in Science News on July 30, 2020 06:00 PM.

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    Many U.S. neighborhoods with the worst air 40 years ago remain the most polluted

    Not all air is created equal. 

    While air quality has improved across the United States in recent decades, significant disparities persist in terms of who breathes the worst air. Communities exposed to the most air pollution in the 1980s — often poor and with high proportions of Black and Hispanic residents — are largely in the same position today, researchers report in the July 31 Science.

    Lots of different pollutants can clog the air, but scientists are especially interested in particulate matter less than 2.5 microns in diameter. Called PM2.5, the tiny particles are associated with myriad health problems, including cardiovascular disease, respiratory illness, diabetes and neurological problems (SN: 9/19/17). 

    Marginalized communities, often closer to factories or major roadways than whiter, wealthier communities, bear the brunt of PM2.5 pollution. That exposure contributes to stark racial health inequities in the United States. “There hasn’t been clear documentation of how these disparities have evolved over time,” says Jonathan Colmer, an economist at the University of Virginia in Charlottesville. The U.S. Environmental Protection Agency only began measuring PM2.5 in 1999. Addressing current inequities requires an understanding of the past, Colmer says.

    He and colleagues estimated annual average PM2.5 levels for each square kilometer in the country from 1981 to 2016 using published data derived from satellites and simulations of pollutant movement through space. The team then mapped those estimates onto about 65,000 census tracts to rank neighborhoods from most to least polluted annually, and noted how rankings changed over time.

    Whereas average PM2.5 concentrations decreased by 70 percent across the entire country, the relative ranking of neighborhoods hardly budged.

    On average, whiter, more affluent neighborhoods were less polluted throughout the 36-year time frame. Disadvantaged neighborhoods with more Black or Hispanic people remained more polluted, despite experiencing a larger absolute drop in PM2.5 levels.

    “It’s really good news that air pollution is dropping for everyone,” says Anjum Hajat, an epidemiologist at the University of Washington in Seattle who wasn’t involved in the research. But even relatively low levels of pollution pose significant health risks, and the reductions might not translate to improved health for the hardest-hit communities. “To me, the take-home message is that inequity is very stubborn.”

    The study wasn’t designed to address why these inequities persist, though a move away from manufacturing or coal production was associated with air quality improvements in certain neighborhoods. 

    More important, Hajat says, is power structure. “The communities that were the most marginalized and had the least political power in the 1980s are likely the same communities that continue to have the least power today.”

    White, wealthy communities have been able to prevent polluting facilities from being placed in their communities, she says, while marginalized communities often haven’t had this power. To see real change, “marginalized communities need to be included in discussions about their future,” she says, for instance through community members holding decision-making roles.

    in Science News on July 30, 2020 06:00 PM.

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    Whistleblowers bring receipts, journal retracts swiftly

    A group of researchers in China have lost a 2018 paper after whistleblowers informed the journal that the authors had misreported their data.  The paper, “Long‐term outcomes of 530 esophageal squamous cell carcinoma patients with minimally invasive Ivor Lewis esophagectomy,” appeared in the Journal of Surgical Oncology, a Wiley publication. It has been cited five … Continue reading Whistleblowers bring receipts, journal retracts swiftly

    in Retraction watch on July 30, 2020 02:50 PM.

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    How To Get The Most Out Of Virtual Learning

    By Emily Reynolds 

    When the coronavirus hit, many of us had to quickly adapt to remote working — and even post-pandemic, many of us are likely to continue at least some of these tasks online.

    Demands for more flexible working practices continue to grow, and for good reason — it can make life easier for employees with parenting or caring responsibilities, health problems or disabilities, and some argue it can also increase productivity. Online webinars and conferences also allow continued professional development without workers ever having to leave their home office.

    Things are no different in the world of education: many undergraduate courses now provide lecture recordings for students to watch in their own time, and online masters programmes are offered by some of the UK’s top universities. Freshers’ Week this year is also likely to be very different, with many students experiencing a wholly virtual first year of university.

    But learning online is not always easy. How do you concentrate when staring at a screen for hours at a time? How do you manage your workload? And what is the best strategy for note-taking? Here’s our digest of the findings that could help to make online learning stick.

    Learn how to make notes effectively

    Writing down what’s said during lectures may seem fairly straightforward. But there is evidence that some strategies are better than others — and knowing what those are could help you take notes more efficiently.

    In 2019, a team from Kent State University looked at how often students were following best practice on note-taking. Writing with pen and paper is encouraged, for example, because laptops can distract both the note-taker and those sitting near them, and notebook notes tend to be more varied, not simply copied from the lecturer verbatim. Both organising information and using it to test your knowledge, rather than just passively writing and rereading notes, is also likely to boost your memory.

    The researchers found that students weren’t always using these techniques — and when it came to those taking online courses, only half of participants were even taking notes. This is concerning, the team notes, because to really learn properly, you can’t just rewatch recordings. So brush up on the research if you want to avoid these students’ mistakes.

    Ask yourself a “prequestion”

    Working out what you want to get out of a lecture before it happens might help, as research from Journal of Applied Research in Memory and Cognition suggests. Students were shown an informational video before answering questions about what they’d seen. Those who had been given two “prequestions” related to the information before watching outperformed those who had not.

    Researchers believed that this technique was especially effective for learning from videos: it’s not easy to skip through video content to find answers to those prequestions, so viewers likely end up paying more attention.

    Thinking about what you want to get out of a video lecture or webinar before you watch it might therefore help you retain more information.

    Set your goals early

    Prequestions can work on a small scale — and asking yourself questions about wider goals can also help in the grander scheme of things.

    One piece of research suggested that students were generally unprepared for the levels of self-directed learning that online courses necessitate — there is far less direction and routine, after all, than in a traditional learning setting.

    The team suggests that students consider a number of factors before they start online courses. First, think about what your learning needs are and what resources are available to help you with them. Then, consider what specific strategies you think might be helpful for you personally.

    Finally, try to set yourself learning outcomes and evaluate how successfully you achieved them at the end of the course — this may help you hone your study technique for future classes, courses or modules.

    Work on your concentration

    Looking at a screen all day can be tiring — after several hours of Zoom, it can be hard to keep focused. So working out how best to boost your concentration might help you out, and there’s lots of different research that might inspire you. One study claimed that treadmill desks helped memory and concentration; another suggests that doodling can do the same.

    If you’re reaching for your fidget spinner, however, you might be disappointed: one 2019 study suggested that they can impede learning.

    Get socialising

    Unlike traditional methods, online learning can be solitary: you’re at home on your own, with minimal time to socialise with your coursemates. But as well as boosting your social life, encouraging discussions between peers can help learning stay on track too.

    One study suggested that discussing course material with other students in online forums may improve outcomes: the students who were most active in the learning forums were more likely to achieve a higher final grade. Some of this will obviously be to do with motivation and effort — students who put in a lot of effort studying and working on papers are also more likely to put effort into engaging with classmates. But active learning can’t hurt, either.

    Start later if you need to

    For the night owls out there, online learning is somewhat perfect: there’s no need to do much more than roll out of bed and switch on a computer to make that pesky 9am lecture, and if you miss it you can always watch later.

    And according to one 2017 study, later start times may benefit many undergraduates:  students who started and finished later, working between 11am and 9.30pm, had the best learning outcomes. The team suggested that asynchronous online classes might help provide for people with all kinds of sleep schedules — so whenever you get out of bed, online learning may work for you.

    Manage boundaries

    Smartphones have made work easier in lots of ways, but they can also come with an added helping of stress, pinging with notifications even outside of working hours. This is such a problem that the French government has taken action, giving workers the “right to disconnect” from out of hours correspondence from colleagues or bosses — and it can be even more difficult when your home is also where you work or learn.

    A study from the University of Illinois published this year also highlighted the stress of this always-on approach. Looking at a group of teachers, the team found that those with better boundary tactics — keeping work email alerts turned off on smartphones, for example — experienced less work intrusion. Setting such boundaries may help you concentrate when you’re online for work or university.

    Get enough sleep

    Getting enough sleep has many cognitive benefits. Periods of sleep between studying can help you learn faster and retain those memories for longer, for instance — so you might want to stock up on herbal teas before term starts.

    Even thinking you’ve got a good night’s sleep may act as an effective placebo, regardless of how much sleep you’ve actually had or how high quality it was. And if you can’t sleep? Don’t stress. Some research suggests insomnia doesn’t have to ruin your life, and how we think about sleep is nearly as important as how much we get.

    Find your own strategies

    Following advice is all well and good — but you might be better off finding your own strategies when it comes to productive work. A recent study published in Proceedings of the National Academy of Sciences looked at behavioural interventions in online learning, finding that general strategies were not that helpful for students.

    Instead, the team suggests, students and teachers alike should understand their specific needs and the context in which they’re working; if a student has ongoing issues with their internet connection, they’re not going to need advice about self-regulation, while those who find it hard to wake up in the morning might. Working on personalised strategies, therefore, might benefit you the most in the long run.

    Emily Reynolds is a staff writer at BPS Research Digest

    in The British Psychological Society - Research Digest on July 30, 2020 01:57 PM.

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    The Perseverance rover caps off a month of Mars launches

    NASA’s Perseverance rover took off at 7:50 a.m. EDT on July 30 from Cape Canaveral, Fla., and is now on its way to Mars with a suite of instruments designed to search for ancient life. The launch is the third this month of spacecraft en route to the Red Planet.

    This is the 22nd spacecraft NASA has aimed at Mars (16 of those missions were successful). But Perseverance will be the first mission to cache rock samples from the Red Planet for a future mission to bring back to Earth.

    It will also be the first NASA mission in more than 40 years to directly search for life on Mars. The rover will land in a region called Jezero crater (SN: 7/28/20). That crater was once an ancient lake bed, and scientists think its rocks and sediments could preserve signs of life, if life was ever there (SN: 7/29/20). The spacecraft will take video and audio recordings of its own landing as it touches down — another first for a NASA Mars mission.

    “This mission has more cameras on it than any we’ve ever sent before,” said Lori Glaze, director of NASA’s Planetary Science Division, on July 30 during a news conference. “It’s going to feel like we’re actually there, riding along with Perseverance on the way down.”

    Perseverance, shown here in an artist’s illustration, will seek signs that Mars once hosted alien life.JPL-Caltech/NASA

    Mars launches tend to come in clumps thanks to Mars’ and Earth’s orbits. The planets line up on the same side of the sun every two years, so scientists have narrow windows to launch for the most efficient trip. All three of this year’s missions will arrive in February 2021.

    The other missions launched in July represent firsts for their respective countries. The United Arab Emirates’ first interplanetary mission, which carries an orbiter called the Hope Probe, launched from Japan on July 19. Hope will measure Mars’ weather, from daily temperature changes to the significance of dust in the planet’s atmosphere (SN: 7/14/20).

    Next up was China’s first Mars mission, Tianwen-1, which means “questions to heaven” and launched on July 23. China has previously sent spacecraft to orbit and land on the moon (SN: 1/3/19). And it is the first nation to send an orbiter, lander and rover all at once on its first attempt to reach Mars. “No planetary missions have ever been implemented in this way,” mission scientists wrote July 13 in Nature Astronomy. “If successful, it would signify a major technical breakthrough.”

    Tianwen-1’s lander and rover will touch down in Utopia Planitia in April 2021. Instruments on the rover and lander will test Mars’ soil composition and magnetic and gravitational fields and will probe Mars’ interior.

    Utopia Planitia is the same region where the first long-lived Mars lander, NASA’s Viking 1, touched down in 1976 (SN: 7/20/16). Viking was the first spacecraft to search for life on Mars, but its results were inconclusive. Perhaps with the rush of spacecraft this year, and the plans to bring red rocks home, scientists will finally learn whether Mars ever did — or does — host alien life.

    in Science News on July 30, 2020 11:56 AM.

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    Journal retracted 46 articles in one fell swoop for faked peer review

    In Retraction Watch world, it’s like finding long-buried and forgotten treasure. A now-defunct journal retracted nearly four dozen papers in a single sweep, citing questions about the integrity of the peer review process for the articles.  The Open Automation and Control Systems Journal, formerly published by Bentham, released a list of 46 articles, which it … Continue reading Journal retracted 46 articles in one fell swoop for faked peer review

    in Retraction watch on July 30, 2020 10:28 AM.

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    Exploring hypothetical thinking

    What is hypothetical thinking? We do it continually. Consider making a decision, from choosing what to eat to choosing what to do about a dangerous disease. In deciding between options, you have to consider each of them, working out what’s likely to happen if  you take it, then compare the results. A natural human way to do that is by imagining taking the given option, and following through that scenario, still “offline” in imagination, but constrained by your background sense of reality. That sense includes innate or learned patterns of expectation about what will happen next, of how things and people in general tend to behave; it also includes your knowledge of your local environment and its particular inhabitants. It may be informed by modern science. Unfortunately, it may also be distorted by various sorts of prejudice and error. Still, we often have to rely on our ability to preview options hypothetically, because we cannot try them all before deciding. Choosing the right option first time can be a matter of life or death.

    Hypothetical thinking is used for theoretical purposes as well as practical ones. For example, when a mathematician wants to prove that every number with a property P also has a property Q, the most straightforward way to do it is by supposing that an unspecified number x has P, then proving from that hypothesis that x also has Q. For that shows that if x has P, then x has Q. Since x could be any number with P, the argument establishes that every number with P also has Q.

    We can get more precise about what such cases have in common. They all involve a procedure for assessing conditional statements of the form “If X, then Y.” For instance, “X” could be “It rains” and “Y” “The match will be cancelled”, or “X” could be “I try to swim across the river” and “Y” “I’ll reach the other side.” The procedure is this. First, suppose X. Then, on that hypothesis, assess Y, using whatever background information is appropriate. Finally, whatever attitude you take to Y on the hypothesis X, take the same attitude unconditionally to “If X, then Y.” Thus, if you accept the conclusion “I’ll reach the other side” on the hypothesis “I try to swim across the river” (the current is slow, you are a strong swimmer), you unconditionally accept the conditional statement “If I try to swim the river, I’ll reach the other side.” But if you reject the conclusion “I’ll reach the other side” on the hypothesis “I try to swim across the river” (the current is fast, you are a weak swimmer), you unconditionally reject the conditional statement. We may call that procedure the Suppositional Rule. Although its explicit articulation in words is quite abstract, we implicitly use it in practice all the time. It comes so naturally to us that it may seem almost trivial.

    What we fail to realize, in unreflectively applying the Suppositional Rule, is that it contains a hidden logical inconsistency. That can be proved in several different ways; Suppose and Tell has the details. Thus it cannot be 100% reliable. But that does not mean that it is completely useless. It works well enough for practical purposes in most ordinary applications. When restricted to acceptance on the basis of mathematical proof, it works perfectly. But the unrestricted rule, which we use in everyday life, subtly generates contradictions in some cases.

    The Suppositional Rule is what psychologists call a heuristic, a way of answering questions of some kind which is quick and easy to use, but only imperfectly reliable. For example, when we are asked which personal names in a list are the most common, with no access to statistics, we may use their psychological accessibility as a heuristic, a guide to their frequency. In vision, we may use discontinuities in colour as a guide to the edges of solid objects; camouflage exploits the limitations of that heuristic.

    The inconsistency of our heuristic for conditionals helps explain why logicians have had so much trouble understanding the meaning of conditional statements in natural languages. It was already a matter of controversy amongst the ancient Greeks, more than two thousand years ago. The poet Callimachus wrote: “Even the crows on the rooftops are cawing about the question ‘Which conditionals are true?’” It is just as hotly contested today amongst philosophers and linguists. The trouble was that we didn’t realize just what rule we were applying, so its inconsistency was unclear. This affected even the data on which discussion relied, which largely consisted of sample sentences classified as “correct” or “incorrect”—using the inconsistent heuristic!

    How can such a logically flawed heuristic serve us so well in practice? As with other paradoxes uncovered by philosophers, in practice we can get a long way by backing off whenever we bump into a paradox, without trying to understand what it is we have stumbled across.

    Featured Image Credit: by Thanos Pal via Unsplash

    The post Exploring hypothetical thinking appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on July 30, 2020 09:30 AM.

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    Paper called “unscholarly, overtly racist” earns an editor’s note

    The journal that recently ran a controversial essay on poverty and race has flagged it with an editor’s note letting readers know about an investigation into the work.  As we reported last week, Society, a Springer Nature title, published a paper by Lawrence Mead, of New York University, who argued that poor Blacks and Hispanics … Continue reading Paper called “unscholarly, overtly racist” earns an editor’s note

    in Retraction watch on July 29, 2020 03:09 PM.

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    An Antarctic ice dome may offer the world’s clearest views of the night sky

    An observatory in the heart of Antarctica could have the world’s clearest views of the night sky.

    If an optical telescope were built on a tower a few stories tall in the middle of the Antarctic Plateau, it could discern celestial features about half the size of those typically visible to other observatories, researchers report online July 29 in Nature. The observatory would achieve such sharp vision by peering above the atmosphere’s lowermost layer, known as the boundary layer, responsible for much of the undulating air that muddles telescope images (SN: 10/4/18).

    The thickness of Earth’s boundary layer varies across the globe. Near the equator, it can be hundreds of meters thick, limiting the vision of premier optical telescopes in places like the Canary Islands and Hawaii (SN: 10/14/19). Those telescopes usually cannot pick out celestial features smaller than 0.6 to 0.8 arc seconds — the apparent width of a human hair from about 20 meters away.

    “But in Antarctica, the boundary layer is really thin,” says Bin Ma, an astronomer at the Chinese Academy of Sciences in Beijing, “so it is possible to put a telescope above.”

    Ma and colleagues took the first-ever measurements of nighttime atmospheric blur from the highest point in East Antarctica, called Dome A. From April to August 2019, instruments on an 8-meter-tall tower at China’s Kunlun research station tracked how Earth’s atmospheric turbulence distorted incoming starlight. A nearby weather station also monitored atmospheric conditions, such as temperature and wind speed. Using these observations, researchers characterized the boundary layer at Dome A and its effect on telescope observations.

    Kunlun research stationFrom April to August 2019, instruments atop an 8-meter-tall tower at China’s Kunlun research station in East Antarctica observed how the local atmosphere distorted light from celestial objects.Zhaohui Shang

    The boundary layer was, on average, about 14 meters thick; as a result, the light sensors at the top of the 8-meter tower were completely free of boundary layer blur only about one-third of the time. But when these instruments were above the layer, atmospheric interference was so low that a telescope could pick out details on the sky 0.31 arc seconds across, on average. The best recorded atmospheric conditions would let a telescope see features as small as 0.13 arc seconds.

    “One-tenth of an arc second is extremely good,” says Marc Sarazin, an applied physicist at the European Southern Observatory in Munich who was not involved in the work. This is “really something you rarely achieve in Chile or on Mauna Kea” in Hawaii.

    Researchers have found similarly excellent visibility above the boundary layer at another spot on the Antarctic Plateau, known as Dome C. But the boundary layer there is around 30 meters thick — making it more difficult to build an observatory above it. An optical telescope planned for construction on a 15-meter tower at Kunlun could take advantage of Dome A’s stellar views above the boundary layer, Ma says. Such crisp telescope images could help astronomers study a range of celestial objects, from solar system bodies to distant galaxies.

    in Science News on July 29, 2020 03:00 PM.

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    Researchers Assume White Americans Are More Representative Of Humankind Than Other Groups, According To Analysis Of Psychology Paper Titles

    By Matthew Warren

    It’s well-known that psychology has a problem with generalisability. Studies overwhelmingly involve “WEIRD” participants: those who are western and educated, from industrialised, rich and democratic societies. And while there is increasing recognition that other populations need better representation in research, many psychologists still often draw sweeping conclusions about humanity based on results from a narrow portion of the world’s population.

    A new study published in Social Psychological and Personality Science suggests that this problem may have had another, more insidious effect. The authors argue that because of psychology’s traditionally narrow focus, we’ve ended up implicitly assuming that results of studies on WEIRD groups — particularly white Americans — are somehow more universally generalisable than those from other populations.

    The study, led by Bobby Cheon at Nanyang Technological University in Singapore, looked at the way in which participant samples were described in the titles of psychology papers. Their logic was simple: article titles are written to get across the most important bits of information about a study, which includes highlighting key features of the sample that might constrain how applicable the results are. For instance, if a study is conducted on children, this will probably be mentioned in the title, so that the reader immediately knows that the results may not apply to adults.

    Similarly, some study titles include information about participants’ ethnicity or country of origin. Again, the implication is that the results might not apply to people outside of that group. So if I’m a US-based researcher looking at how access to parks influences our mental health, I might call my study either “The role of green space in the mental wellbeing of adults”, or “The role of green space in the mental wellbeing of American adults”. The latter suggests that the results might not apply in, say, the United Kingdom or India.

    The team looked at the titles of 2,088 articles published in 49 prominent psychology journals between 2004 and 2017, all of which were picked out because the title specifically mentioned the ethnicity, nationality, culture or race of participants. Just 14.7% of these titles mentioned that participants were of American origin, and 34.8% mentioned a sample from a WEIRD region outside of the US (e.g. “Exercise improves healthy diet: Evidence from an Australian sample”). These figures were both significantly lower than the 50.5% that mentioned a sample from a non-WEIRD region (e.g. “Bidirectional engagement among Indian students and teachers”).

    The fact that research on non-WEIRD groups so often mentions participants’ origins in the title implies a belief that these studies might not generalise but rather only apply to that specific culture. By comparison, the fewer instances of titles mentioning participants’ origin for research conducted on WEIRD groups, and on Americans in particular, suggests these groups are considered more representative of humanity as a whole.

    It’s important to note that the vast majority of psychology research is conducted on WEIRD participants and North American samples in particular; according to some analyses, participants from Asia, Africa and Latin America are included in just a small percentage of papers in leading psychology journals. So it’s not the case that the small number of titles specifying American samples is due to there being fewer papers on Americans in general.

    Of course, there may often be the best of intentions behind calling out under-represented groups in the title of papers, particularly when we are used to psychologists studying white, Western participants by default. But as the authors point out, “the bias in the tendency to qualify sample characteristics in titles may reflect and/or reinforce a subtle form of infrahumanization … in which the nature, experiences, and behaviors of some populations are assumed to be a better reflection of humanity than others.” And, unfortunately, the team found that this bias has actually got worse in recent years.

    In a second analysis, the researchers looked at the titles of a further 945 articles from around the world which specified that the research had been conducted on a minority group from that country. The vast majority of these (85.4%) were from the United States (e.g. “Developmental trajectories of African American youths”). In contrast, the team only found 32 titles which specified that a sample consisted of white Americans. This suggests that within the United States, results from white Americans are considered more generalisable than those from minority groups.

    So what’s the solution? The researchers say there should be standardised practices for reporting the population being studied. Editors also have a responsibility, they add:  journals should avoid framing research conducted outside of the United States as “cultural”.

    I’d add that outlets reporting on psychology research — including Research Digest! — also need to be more aware of the way they frame research.  It’s important to acknowledge the limitations of research, and that often involves explaining who the participants in a study were. But it becomes a problem if you consistently highlight the limitations of generalising from studies on participants from China or Brazil, for instance, while describing American or UK-based research in generic terms.

    How USA-Centric Is Psychology? An Archival Study of Implicit Assumptions of Generalizability of Findings to Human Nature Based on Origins of Study Samples

    Matthew Warren (@MattBWarren) is Editor of BPS Research Digest

    in The British Psychological Society - Research Digest on July 29, 2020 02:20 PM.

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    A South American mouse is the world’s highest-dwelling mammal

    A yellow-rumped leaf-eared mouse has shattered the world record as the highest-dwelling mammal yet documented.

    The mouse (Phyllotis xanthopygus rupestris) was found 6,739 meters, or 22,110 feet, above sea level on the summit of Volcán Llullaillaco, a dormant volcano on the border of Chile and Argentina. For comparison, Mount Everest is 8,848 meters high (29,029 feet).

    The record was previously held by the large-eared pika (Ochotona macrotis), reported at an altitude of 6,130 meters during a 1921 Mount Everest expedition. Birds have been found at even higher altitudes (SN: 2/13/14).

    That mammals can live at these heights is astonishing, considering there’s only about 44 percent of the oxygen available at sea level. “It’s very difficult to sustain any kind of physical activity, or mental activity for that matter,” says Jay Storz, an evolutionary biologist at the University of Nebraska–Lincoln. The temperature is also rarely above freezing and can drop as low as –60° Celsius.

    Storz and colleagues captured several yellow-rumped leaf-eared mice, including the summit-topping one, plus mice from three other species from a range of high altitudes, the team reports July 16 in Proceedings of the National Academy of Sciences. Next, the team plans to look for genetic changes that might have equipped these animals to survive at high elevations. Surprisingly, another yellow-rumped leaf-eared mouse was found at sea level, indicating that this species has the broadest altitude distribution of any mammal, in addition to the altitude record.

    Researchers captured a yellow-rumped leaf-eared mouse (Phyllotis xanthopygus rupestris) at a record altitude of 6,739 meters, or 22,100 feet, above sea level. Jay Storz, an evolutionary biologist at the University of Nebraska–Lincoln, and mountaineer Mario Pérez Mamani discovered the animal at the summit of Volcán Llullaillaco, a dormant volcano on the border of Chile and Argentina.

    “It’s so amazing that they’re up there,” says Graham Scott, a physiologist at McMaster University in Hamilton, Canada who was not involved in the study. Understanding how these and other animals survive under low-oxygen conditions could provide insight into how humans could overcome diseases that cause reduced oxygen levels, he says.

    in Science News on July 29, 2020 12:00 PM.

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    USC-Children’s Hospital Los Angeles researcher out following misconduct probe

    An infectious diseases researcher found by a federal U.S. watchdog to have “recklessly” faked data in grants worth millions left his job as the investigation was coming to a close, Retraction Watch has learned. As we reported last week, Prasadarao Nemani, of Children’s Hospital Los Angeles (CHLA) and the University of Southern California (USC), “engaged … Continue reading USC-Children’s Hospital Los Angeles researcher out following misconduct probe

    in Retraction watch on July 29, 2020 10:00 AM.

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    To rehearse Perseverance’s mission, scientists pretended to be a Mars rover

    Megan Barrington watched the sun rise over the rocky outcrop. When light struck at exactly the right angle, she mounted a gizmo that looked like eye exam equipment on a tripod and aimed it at the spot. The goal: gather evidence that this windswept wilderness once teemed with life, and then beam the information to her colleagues back home.

    Soon, a version of that setup (minus Barrington) will be deployed on Mars. The state-of-the-art, zoomable, multispectral camera is part of the toolkit on NASA’s Perseverance rover (SN: 7/28/20). “That instrument is going to allow me to look at the mineralogy of Mars at Jezero crater,” the rover’s landing spot, says Barrington, a planetary scientist at Cornell University.

    The rover is scheduled to launch to Mars on July 30. A February role-playing exercise in the Nevada desert by Barrington and six colleagues was a kind of dress rehearsal for the rover’s various instruments. Another 150 team members around the world played the “Earth” team during those two weeks, sending commands from remote mission control and receiving data as it would appear coming from the real rover.

    “We’re not just simulating a Mars mission,” says engineer Raymond Francis of NASA’s Jet Propulsion Laboratory in Pasadena, Calif., who organized and led the trip. “We’re simulating a specific Mars mission by presenting data … to the people who designed the instrument that will take that data. So the standard is high not to look like clowns.”

    Perseverance has the most demanding and ambitious to-do list of any rover yet: seek signs of past Martian life, prepare the way for future human missions and collect at least 20 samples of Martian rock for eventual return to Earth. And that’s just in its first two years. For contrast, Curiosity rover has drilled a few dozen holes over eight years on Mars, and didn’t store any of those samples for later (SN: 7/7/18, p. 8).

    The dress rehearsal in the desert will help ensure that when Perseverance lands on the Red Planet in February 2021, its handlers on Earth can get straight to the science.

    “We don’t want to get there and learn how to explore Mars while on Mars,” Francis says. “We want [team members] to be ready when the rover hits the ground.”

    Water marks the spot

    The first order of business was to find the right spot for the dry run. “We had to pick a site that kind of looked like Mars,” Francis says. “The parking lot would not do.” The team wanted the site to look as Mars-like as possible, no factories, footprints or foliage to break the illusion.

    An ideal site would have geology that echoed Jezero crater, which is thought to be the remnants of an ancient lakebed and river delta (SN: 11/19/18). It also had to be within a few hours’ drive of JPL, and not totally off the grid — the rover team slept in hotels, ate dinner in restaurants and had reliable Wi-Fi to send data to the Earth team every night.

    The final requirement was that it be someplace the Earth team hadn’t seen before. If mission control members recognized the site, they could bias their findings with what they already knew.

    Raymond FrancisEngineer and team leader Raymond Francis gets up close with the rocks to make a measurement.JPL-Caltech/NASA

    “Most of the popular Mars analogs are already well known to the Mars community,” Francis says. “So we had to be a little sneaky.”

    Previous exercises, in November 2017 and February 2019, were run in the Mojave Desert in California. For 2020, the rover team headed to Walker Lake in western Nevada. The lake’s water has been receding for a thousand years, so there are spots near the ancient shoreline where the present-day lake is invisible.

    Walker Lake’s rocks preserved a cornucopia of biological signals for the ground team to discover: fossilized fish bones and shells of tiny shrimplike crustaceans called ostracods, which are not expected on Mars; and microbial fossils called stromatolites, which could plausibly be found in Jezero crater (SN: 10/17/18).


    Francis and his team brought handheld versions of almost all the rover’s instruments to gather whatever data the Earth team requested. They had a drill, handheld spectrometers, lasers, a ground-penetrating radar that they transported in a jogging stroller, plus several elaborate camera setups to represent the rover’s navigation, hazard avoidance and zoomable 3-D science cameras.

    Perhaps the most important piece of equipment was the broom used for sweeping away footprints. It became a running joke, Francis says: “We’ve got all this equipment, a multibillion-dollar mission, and it’s all hinging on this 99-cent broom.”

    Almost everything went smoothly. But a few days into the mission, Barrington’s zoomable camera had “a major malfunction,” she says. She framed her shot, and…. nothing happened. The camera wasn’t getting any power, she realized. “I took it apart and rewired many pieces, to no avail,” she says.

    She and her teammates finally realized one of the power adapters had completely blown. She had to drive two hours to the nearest city to get a new one.

    Of course, driving into town to get a new part won’t be an option on Mars. The real camera, called Mastcam-Z, has been through weeks of rigorous testing and calibration, and is probably up to the task. But “we all go into missions knowing that sometimes irreversible mistakes occur,” Barrington admits. “All we can do at that point is use the instruments to the fullest capacity of which they are capable of operating.”

    Megan BarringtonPlanetary scientist Megan Barrington adjusts her instrument, a multispectral, zoomable camera standing in for Perseverance’s Mastcam-Z.JPL-Caltech/NASA

    Signs of life, big and small

    There was one major giveaway that the team was actually on Earth. “This is very much middle-of-nowhere desert, which is good,” Francis says. But the rover site was mere steps from a U.S. Department of Defense munitions facility, one of the largest in the world.

    “It was really something to behold,” Barrington says. “They had hundreds of bunkers lined up in rows as far as you could see…. All of that was one very crooked metal fence away from us.”

    More than once, military police showed up to check the team’s credentials. “I had to approach them and say, hello, people with the guns, I need you to stop walking now,” Francis says. “We’re running a Mars rover simulation and we don’t want you to put your footprints in this sand.”

    Despite Francis and colleagues’ best efforts, the bunkers showed up in a few photos. The ground team gamely ignored them, apart from a few jokes about SpaceX founder Elon Musk building a Martian city.

    By the end of the two-week exercise, the remote science team reviewing the data had noticed the ostracods and fishbones, and started exploring the stromatolites. “They were doing a good job of finding the biomarkers,” Francis says, who now has hope that “if Mars is hiding stromatolites, maybe we’ll see them.”

    Coming home to quarantine

    The field trip ended on February 27, just as awareness of the novel coronavirus SARS-CoV-2 was rising in the United States. By March 15, JPL told employees to work from home. “We only had a few days together before we were all on remote work,” Francis says.

    The pandemic has already contributed to the delay of the launch of the European and Russian ExoMars rover, which was also supposed to launch in July (SN: 3/12/20).  If Perseverance misses the late July to early August launch window, the rover can’t head to Mars until 2022.

    If the pandemic is still an issue by the time the rover lands in February, Francis doesn’t know what the team will do. “But,” he says, “the good news is the mission is designed for remote operations.”

    in Science News on July 29, 2020 10:00 AM.

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    Close relatives of the coronavirus may have been in bats for decades

    Viruses from the coronavirus lineage responsible for COVID-19 have been circulating in bats for decades, long before the virus started infecting people last year, a new study suggests.

    How exactly the virus jumped to humans is still a mystery. But the study suggests the coronavirus most likely evolved in bats — such as intermediate horseshoe bats (Rhinolophus affinis), the source of the coronavirus that caused the 2003–2004 SARS outbreak — not snakes or pangolins as some researchers have suggested (SN: 1/24/20). Pangolins or another animal might still have been an intermediate host before the virus made it to humans.

    Maciej Boni, an epidemiologist at Penn State, and his colleagues examined the genetic blueprints of the new coronavirus, or SARS-CoV-2, and 67 related viruses. The analysis aimed to uncover the evolutionary history of SARS-CoV-2 and see if the virus had exchanged bits of genetic material with other coronaviruses, a process called recombination, to become the formidable pathogen it is now.

    SARS-CoV-2 is not the result of genetic shuffling among known coronaviruses, the researchers report July 28 in Nature Microbiology. Previous studies had suggested that recombination with coronaviruses from pangolins may have contributed a portion of the virus’ spike protein, which is used to break into human cells (SN: 3/26/20). But the spike’s ability to attach to a protein on host cells called ACE2, which allows the virus to gain entry, appears to be an ancestral trait, rather than one gained from recombination.

    Based on the evolutionary relationship among the 68 coronaviruses, the researchers estimate that the branch of the virus family tree that leads to SARS-CoV-2 diverged from related viruses between 1948 and 1982. Those dates suggest that the coronavirus lineage that gave rise to the virus behind the pandemic has been present in bats for decades.

    That long period hints that more bat viruses with the potential to infect humans are circulating in horseshoe bats. Searching for such bat viruses can help identify potential threats before the pathogens make the jump, the team writes.   

    in Science News on July 28, 2020 09:21 PM.

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    These ancient seafloor microbes woke up after over 100 million years

    Even after 100 million years buried in the seafloor, some microbes can wake up. And they’re hungry.

    An analysis of seafloor sediments dating from 13 million to nearly 102 million years ago found that nearly all of the microbes in the sediments were only dormant, not dead. When given food, even the most ancient microbes revived themselves and multiplied, researchers report July 28 in Nature Communications.

    Scientists have pondered how long energy-starved microbes might survive within the seafloor. That such ancient microbes can still be metabolically active, the researchers say, just goes to show that scientists are still fathoming the most extreme limits to life on Earth.

    The microbes’ patch of seafloor lies beneath a kind of ocean desert, part of a vast abyssal plain about 3,700 to 5,700 meters below sea level. Researchers, led by microbiologist Yuki Morono of the Japan Agency for Marine-Earth Science and Technology in Kochi, examined sediments collected in 2010 from part of the abyssal plain beneath the South Pacific Gyre. That region of the Pacific Ocean contains few nutrients that might fuel phytoplankton blooms and thereby support a cascade of ocean life. As a result, very little organic matter makes its way down through the water to settle on the seafloor.

    The extremely slow accumulation of organic material and other sediments in this region does allow oxygen in the water to seep deep into the sediments. So Morono and colleagues wondered whether any aerobic, or oxygen-liking, microbes found there might be revivable. After “feeding” microbes from the collected sediments with nutrients including carbon and nitrogen, the team tracked the organisms’ activity based on what was consumed.

    The aerobic microbes in the sediments turned out to be a highly diverse group, consisting mostly of different types of bacteria belonging to large groups such as Alphaproteobacteria and Gammaproteobacteria (SN: 9/14/17). Nearly all the microbes responded quickly to the food. By 68 days after the experiment’s start, the total number of microbial cells had increased by four orders of magnitude, from as little as about 100 cells per cubic centimeter to 1 million cells per cubic centimeter.

    Those increases weren’t just among the youngest microbes. Even in the sediment sample containing the most elderly — about 101.5 million years old — up to 99.1 percent of the microbes were revived.

    in Science News on July 28, 2020 03:00 PM.

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    Having Realistic Expectations Could Make You Happier Than Being Over-Optimistic

    By Emily Reynolds

    There are fairly good arguments for optimism and pessimism both. Optimists, who see the best in everything, are likely to have a sunnier disposition; pessimists, on the other hand, would argue that their negative expectations never leave them disappointed when the worst actually happens.

    But in the end, it might be realists who win out. According to a study published in Personality and Social Psychology Bulletin, being realistic about your life outcomes is likely to make you happier than overestimating them.

    David de Meza from the London School of Economics and Chris Dawson from the University of Bath examined data from 1,601 individuals who took part in the British Household Panel Survey between 1991 and 2009. This longitudinal survey covers a range of topics including health, finances, household composition and more.

    The team looked first at unrealistic optimism. Unlike optimism, this isn’t simply a belief that something good might happen, but an “excessive belief in the probability of good realisations” that is so strong you are likely to make mistakes in your predictions. To measure levels of unrealistic optimism, two questions were pulled out of the survey: “how do you think you will be financially a year from now?” and “would you say that you are better off, worse off or the same financially than you were a year ago?”. Comparing these expectations year on year with participants’ actual financial situation was the basis for measuring optimism.

    The researchers looked at how this unrealistic optimism was related to participants’  psychological wellbeing and life satisfaction. (They also took into account demographic information which has been linked to wellbeing, including marital status, children, monthly income, education attainment, location and consumption of tobacco.)

    As expected, those with realistic beliefs had higher psychological wellbeing than those with both low and high expectations. The most pessimistic participants had a 37.2% higher level of psychological distress than realists, with optimists not faring much better: they had an 11.8% higher level of distress. Life satisfaction also suffered for both parties: for those holding the most pessimistic expectations there was a 21.8% reduction and for the most optimistic a 13.5% reduction in general wellbeing compared to realists.

    Why this was the case, however, is unclear. It could be that optimists end up perpetually disappointed as their expectations fail to materialise, and although pessimists may avoid that disappointment, they may be more likely to experience dread or anxiety before anything even happens. The team also points out that any plan made based on an inaccurate belief is likely to deliver a worse outcome than one based on rationality. Both over- and under-estimating financial outcomes, for example, is unlikely to yield good results: optimists may fail to adequately save, whilst pessimists could avoid profitable opportunities.

    Whether unrealistic optimism would also have the same effect in a non-financial domain is yet to be seen. Finances are particularly susceptible to unrealistic optimism, which research has shown tends to be greatest in areas perceived to be under an individual’s control. It would be interesting to know whether similar results are found for an outcome that is completely out of someone’s control — their genetic susceptibility to a particular medical condition, for example.

    None of this is to say that optimism in general is a bad thing, and some research has suggested it has benefits of its own. But being overly or unrealistically optimistic may not provide those same effects.

    For those who consider themselves more realistic than optimistic, however, the study’s results could come as a relief. Culturally, positive thinking is fairly influential, with self-help gurus and wellness influencers often promoting it as a way to achieve life goals; it’s also been the basis of many bestselling books. But, as this study shows, rejecting positive thinking doesn’t have to make you miserable.

    Neither an Optimist Nor a Pessimist Be: Mistaken Expectations Lower Well-Being

    Emily Reynolds is a staff writer at BPS Research Digest

    in The British Psychological Society - Research Digest on July 28, 2020 01:26 PM.

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    NASA’s Perseverance rover will seek signs of past life on Mars

    NASA’s next rover is a connoisseur of Martian rocks. The main job of the Perseverance rover, set to launch between July 20 and August 11, is to pick out rocks that might preserve signs of past life and store the samples for a future mission back to Earth.

    “We’re giving a gift to the future,” says planetary scientist Adrian Brown, who works at NASA Headquarters in Washington, D.C.

    Most of the rover’s seven sets of scientific instruments work in service of that goal, including zoomable cameras to pick out the best rocks from afar and lasers and spectrometers to identify a rock’s makeup. After the rover lands in February 2021, it’s capable of collecting and storing 20 samples within the first Martian year (about two Earth years). The NASA team plans to collect at least 30 samples over the whole mission, says planetary scientist Katie Stack Morgan of NASA’s Jet Propulsion Laboratory in Pasadena, Calif.

    Fortunately, Perseverance is headed to a spot that should be full of collection-worthy rocks. The landing site in Jezero crater, just north of the Martian equator, contains an ancient river delta that looks like it once carried water and silt into a long-lived lake.

    “We can already predict which parts of that delta might give us the highest return for possible biosignatures,” Stack Morgan says. The crater has a “bathtub ring” of carbonates, minerals that settle in shallow, warm waters that are especially good at preserving signs of life. “That makes Jezero special,” she says.

    But Perseverance is more than a rock collector. The rover will probe the ground beneath its wheels, fly a helicopter, track the weather and test tech for turning Martian air into rocket fuel. Every part of the rover has a job to do.

    icon of Perseverance rover with dot on Rimfax location


    RIMFAX, or Radar Imager for Mars’ Subsurface Experiment, will use radio waves to probe the ground under the rover’s wheels. The instrument will take a measurement every 10 centimeters along the rover’s track and should be able to sense 10 meters deep, depending on what’s down there. The InSight lander, currently on Mars, has a seismometer that listens for Marsquakes, but a ground-penetrating radar to understand the Martian interior is a first.

    icon of Perseverance rover with dot on MOXIE location


    Human explorers will need oxygen on Mars, but not just for breathing, says former astronaut Jeffrey Hoffman. “It’s for the rocket,” says Hoffman, now an engineer at MIT. To take off from the Martian surface and return home, astronauts will need liquid oxygen rocket fuel. Bringing all that fuel from Earth is not an option.

    To demonstrate how to make fuel from scratch, MOXIE, or Mars Oxygen In-Situ Resource Utilization Experiment, will pull carbon dioxide out of the Martian atmosphere and convert it to oxygen. MOXIE will produce about 10 grams of oxygen per hour, which is only about 0.5 percent of what’s needed to make enough fuel for a human mission over the 26 months between launch windows. But the effort will teach engineers on Earth how to scale up the technology.

    icon of Perseverance rover with dot on Mastcam-Z location


    Set atop Perseverance’s neck, Mastcam-Z, the rover’s main set of eyes, can swivel 360 degrees laterally and 180 degrees up and down to view the surrounding landscape. Like its predecessor on the Curiosity rover, the camera will take color, 3-D and panoramic images to help scientists understand the terrain and the mineralogy of the surrounding rocks. Mastcam-Z can also zoom in on distant features — a first for a Mars rover.

    icon of Perseverance rover with dot on SuperCam location


    How can Perseverance look for signs of ancient microbes in rocks too far away to touch? Enter SuperCam, a laser spectrometer mounted on the rover’s head. SuperCam will shoot rocks with a laser from more than seven meters away, vaporizing a tiny bit of the minerals. Researchers will then analyze the vapor to help figure out what the rocks are made of, without having to drive the rover down steep slopes or up rugged crags. The laser will also measure properties of the Martian atmosphere and dust to refine weather models.

    icon of Perseverance rover with dot on MEDA location


    MEDA, or Mars Environmental Dynamics Analyzer, is the rover’s weather station. Six instruments distributed across the neck, body and interior will measure air temperature, air pressure, humidity, radiation and wind speed and direction. The tools will also analyze the physical characteristics of the all-important Mars dust. Scientists hope to use the information from these sensors to better predict Mars weather.

    icon of Perseverance rover with dot on instrument location


    Geologists never go into the field without a hand lens. Likewise, Perseverance will be prepared with three arm-mounted magnifying instruments. PIXL, the Planetary Instrument for X-ray Lithochemistry, will have a camera that can resolve grains of Martian rock and dirt to scales smaller than a millimeter. It will also detect the chemical makeup of those rocks by zapping them with X-rays and measuring the wavelength of light the rocks emit in response. SHERLOC, or Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals, will take similar measurements using an ultraviolet laser. WATSON, the Wide Angle Topographic Sensor for Operations and Engineering, will take pictures with a resolution of 30 micro­meters to put the chemistry in context. The instruments will seek signs of ancient microbes preserved in Martian rocks and soil, and help scientists decide which rocks to store for a future mission to return to Earth.


    This helicopter will be a test case for future reconnaissance missions to help the rover see further on Mars.JPL-Caltech/NASA

    Perseverance will also carry a stowaway folded up origami-style in a protective shield the size of a pizza box: a helicopter called Ingenuity. At a smooth, flat spot, Ingenuity will drop to the ground and unfold, then take about five flights in 30 Martian days. These flights are mainly to show that the copter can get enough lift in the thin Martian atmosphere. If Ingenuity is successful, future helicopters might help run reconnaissance for rovers. “There’s always a question with the rover, what’s over that cliff? What’s over that rise?” says planetary scientist Briony Horgan of Purdue University in West Lafayette, Ind. “If you have a helicopter, you can see those things ahead of time.”

    in Science News on July 28, 2020 10:00 AM.

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    A black hole circling a wormhole would emit weird gravitational waves

    Gravitational wave detectors have already spotted mysterious black holes. But something even stranger might be next: wormholes.

    A black hole spiraling into a wormhole would create an odd pattern of ripples in spacetime that the LIGO and Virgo gravitational wave observatories might be able to pick up, physicists report July 17 at arXiv.org. The waves would blink off and on as the black hole passed through the wormhole and then came back.

    Wormholes are hypothetical objects in which spacetime is curved into a tunnel that connects distant cosmic locales or potentially different universes (SN: 8/5/13). From the outside, wormholes can appear similar to black holes. But while an object that falls into a black hole is trapped there, something that falls into a wormhole could traverse through it to the other side.

    No evidence has been found that wormholes exist. “These are speculative for sure, with a capital S,” says physicist William Gabella of Vanderbilt University in Nashville. But if they do exist, researchers have a chance of detecting the wormholes via gravitational waves.

    Gabella and colleagues considered a black hole with a mass five times the sun’s, orbiting a wormhole about 1.6 billion light-years from Earth. As the black hole swings around the wormhole, the researchers calculated, it would begin by spiraling inward as if it were orbiting another black hole. At first, the resulting gravitational waves would look like a standard signature for two black holes, a pattern of waves that increase in frequency over time called a chirp.

    But when it reaches the wormhole’s center, called the “throat,” the black hole would pass through. The researchers considered what would happen if the black hole emerged in a distant realm, such as another universe. In that case, the gravitational waves in the first universe would abruptly die off. In the second universe, the black hole would shoot outward before spiraling back in. Then, it would pass back through the wormhole to the first universe.

    As the black hole returns, it would initially spiral outward from the wormhole, perhaps producing an “anti-chirp,” a pattern of gravitational waves opposite to a chirp’s, before plunging back in with a chirp. The black hole would continue bouncing between the two universes, causing repeated bursts of gravitational waves punctuated by silence. Once the black hole lost enough energy to gravitational waves, its journey would end as it settled down in the wormhole’s throat.

    “You can’t reproduce that with two black holes, so it’s a clear-cut signal of a wormhole,” says physicist Dejan Stojkovic of the University at Buffalo in New York, who was not involved with the research. The waves “should be sticking [out] like a sore thumb,” he says.

    According to the general theory of relativity, which describes gravity as the result of the curvature of spacetime, wormholes are possible. But actually detecting one would imply that there exists a strange type of matter that physicists don’t understand. That’s because a substance with negative mass would be necessary to prop open a wormhole’s throat to prevent it from collapsing, and no known type of material fits the bill.

    The United States–based Advanced LIGO, or Laser Interferometer Gravitational-Wave Observatory, and Advanced Virgo in Italy detect ripples from black holes or dense stellar corpses called neutron stars. Those massive objects orbit around one another before they merge.

    Scientists are now skilled at spotting such mergers, having confirmed more than a dozen since 2015, with more awaiting confirmation. But at some point, physicists will need to start focusing on more unusual possibilities, says physicist Vítor Cardoso of Instituto Superior Técnico in Lisbon, Portugal. “We need to look for strange but exciting signals.”

    in Science News on July 27, 2020 04:00 PM.

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    Vets Show “Weight Bias” Against Obese Dogs And Their Owners

    By guest blogger Ananya Ak

    The concept of weight bias or “fatphobia”, the social stigma around obesity, has been around for quite a while. Studies have shown that such stigma is present even among medical professionals, which negatively impacts quality of care for patients with obesity. Over the years, there have been several instances of doctors attributing medical symptoms to obesity when the symptoms were actually caused by something more serious, like a tumour.

    But what about social stigma towards obese pets? Over 50% of cats and dogs in the USA are obese and, like humans, pets with obesity have a higher risk of metabolic, respiratory and other diseases. A new paper in the International Journal of Obesity examines whether the same weight bias that affects the delivery of healthcare in humans is prevalent among pet doctors as well.

    The investigation, conducted by a team led by Rebecca Pearl at the University of Pennsylvania, involved two online studies exploring the attitudes of the participants towards obese and lean dogs, and the treatment recommendations they gave the dogs for hypothetical symptoms. One of the studies was conducted on 205 veterinarians and the other on 103 veterinary students, with the methodology remaining identical for both the studies.

    The studies were done in two parts. In the first part, the participants were each randomly shown one of four images featuring either a lean dog and lean owners, an obese dog and lean owners, a lean dog and obese owners, or an obese dog and obese owners. The dogs and owners in each of the vignettes were identical except for their weight status. The participants were then asked questions to determine their emotional response towards the dogs and owners, and perceived causes of the dogs’ weight (e.g. biology/genetics, environmental factors, the owners’ feelings of responsibility, and their behaviours). They were also asked whether they had ever recommended weight loss treatment to the overweight owners.

    In both the studies, the participants reported stronger feelings of blame, contempt, disgust and frustration towards the overweight dogs and their owners (irrespective of the owners’ weight) compared to the lean dogs and their owners. They also felt that the owners of the obese dogs were less likely to comply with weight-related treatment recommendations.

    Moreover, the participants also seemed biased against the heavier owners. They saw the obese owners as more responsible for their dog’s weight if it was obese than if it was lean. Similarly, the lean owners got the “credit” if their dog was lean, but weren’t seen as so responsible if their dog was obese. So, the veterinarians appeared to make the stereotypical assumption that the overweight owners had poorer health behaviours than the lean owners and were transferring their own bad behaviours to their dogs, making them obese as well. Across both studies, 7-10% of participants also reported that they had previously recommended that pet owners seek weight loss treatment. This might seem like a small number, but, as the authors say, “It is surprising that any participants reported counseling owners about weight, considering that veterinarians are not trained to give health advice to humans.”

    In the second part of the study, the participants were told that the dog they had seen was presenting at their clinic with respiratory problems. They were first asked to recommend diagnostic procedures. Then, after being told that the dog was diagnosed with a collapsed trachea, they were asked how they would treat it. The participants gave similar diagnostic recommendations for the dogs irrespective of their weight. But when asked for treatment recommendations, the participants were more likely to recommend weight treatment for the obese dog than the lean dog. This is an acceptable treatment, of course, since weight is one of the causes of poor respiratory health. But focusing on weight may lead veterinarians to miss other potential causes of illness.

    This investigation had its limitations, including that all participants were either students or alumni of the same veterinary school. The sample size was thus quite limited. The focus was also solely on dogs vs. other pets like cats. A larger study with a wider selection of participants and more variety in pets is required to be able to truly generalise the results.

    But even with the limitations, this study provides empirical evidence of weight bias among veterinarians. This is significant considering that unlike humans, pets cannot voice their concerns and a wrong diagnosis or treatment recommendation could prove dangerous to our beloved animal friends. Thus, just as interventions are put in place to reduce bias among doctors, steps may need to be taken to ensure that veterinarians remain mindful of their biases while diagnosing and treating pets.

    Who’s a good boy? Effects of dog and owner body weight on veterinarian perceptions and treatment recommendations

    Post written for BPS Research Digest by Ananya Ak. Ananya is a long-time reader of the Research Digest, studying to be a clinical psychologist. As a freelance copywriter, she’s also interested in the psychology of bias, persuasion and communication. You can find her on LinkedIn and read about her personal life and the books she reads on her blog.

    At Research Digest we’re proud to showcase the expertise and writing talent of our community. Click here for more about our guest posts.

    in The British Psychological Society - Research Digest on July 27, 2020 10:58 AM.

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    A New Theory of Dreaming

    Do dreams exist to protect the brain's visual cortex?

    in Discovery magazine - Neuroskeptic on July 26, 2020 01:44 PM.

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    Pensioner Jan van Deursen and postdoc engage Hoecker Lawyers against me

    Jan van Deursen, together with his postdoc Bennett Childs, engaged a notorious German law firm against me. The former Mayo Clinic professor denies accusations of bullying and discrimination and obviously seeks to prevent his lab members from talking to the press. Hoecker Lawyers claim van Deursen resigned as pensioner on 24 July 2020, voluntarily.

    in For Better Science on July 26, 2020 06:35 AM.

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    Magic Tricks And Brain Art: The Week’s Best Psychology Links

    Keyboard for ideaOur weekly round-up of the best psychology coverage from elsewhere on the web

    Recent work has cast doubt on many previously reported priming effects — but the kind of priming used by magicians may in fact work, writes Jennifer Ouellette at Ars Technica. Researchers used the gestures and verbal cues employed by illusionist Derren Brown to try and encourage participants to think of a 3 of diamonds when given the choice of any card from a deck. And it worked: participants picked that card 18% of the time, much higher than would be expected by chance.

    Psychologist Stuart Ritchie has a new book out, Science Fictions, which explores the flaws, biases and outright fraud that undermines psychology and science more generally. He talks about the book with Shamini Bundell for this week’s Nature podcast.

    The Netherlands Institute for Neuroscience has announced the winners of their “Art of Neuroscience” competition. The images are pretty cool, ranging from straightforward microscopy photos to the rather more abstract. Check them out at Scientific American.

    Yet another study has concluded that playing violent video games doesn’t lead to aggression, reports Alex Hern at The Guardian. Researchers conducted a meta-analysis of longitudinal studies investigating the link between playing violent games and later aggression or violence. Although the team found an overall significant effect, this effect was so small to be meaningless from a practical perspective

    It’s a common idea that pregnant women are biologically and evolutionarily hardwired to “nest” — tidy, decorate and so on — in the weeks and months before their child is born. But there’s no scientific evidence that that’s the case, writes Arianne Shahvisi at Psyche.  In fact, to claim that it has a biological basis obscures the much more likely explanation that “nesting” is the result of cultural stereotypes about the role of women in the home.

    Having a “strategic mindset” could help you to achieve your goals, reports David Robson at BBC Worklife.  Researchers found that the kind of people who adapt and refine their approach when faced with obstacles are ultimately more likely to reach a goal, such as learning a new language or losing weight.

    Most of us have been on the receiving end of a rude email from a co-worker — and can relate to the way it really gets under your skin. Impolite emails can lead workers to experience more negative emotions and even experience more stress when back at home. And now a study has shown that even “passive” rudeness — ignoring a co-worker’s request, for instance — can create stress. We should all think about improving our “netiquette”, write the researchers, Zhenyu Yuan and YoungAh Park, at Scientific American.

    Compiled by Matthew Warren (@MattbWarren), Editor of BPS Research Digest

    in The British Psychological Society - Research Digest on July 24, 2020 02:12 PM.

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    The Ethics of Dangerous Code

    Who should get to decide which software is safe to share?

    in Discovery magazine - Neuroskeptic on July 23, 2020 06:00 PM.

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    Receiving Money-Saving Gifts Can Make People Feel Ashamed And Embarrassed

    By Emily Reynolds

    Looking for the perfect gift can be a pleasure and a curse: the joy of picking exactly the right thing vs. the anxiety that you’ve completely missed the mark. Whether to get somebody something luxurious but impractical or something with utility is another common dilemma.

    It’s also one that may have unintended consequences: while some practical gifts — those that save someone time, for example — can be appealing and well-received, others may fall short. If you were thinking of getting that special someone a gift with the intention of saving them money, for example, think again — you might end up making them feel ashamed, according to research recently published in the Journal of the Association for Consumer Research.

    If someone is short on money, it’s possible that a gift designed to help them save more could be well received. But, Alice Lee-Yoon from UCLA and colleagues hypothesise, the opposite is actually more likely to happen: people are likely to feel ashamed of such a gift and see it as an indication of either a lower status overall or a greater differential in status between themselves and the gift-giver.

    In the first study, 405 participants were asked to write about a gift they had recently been given: either a gift that they felt was intended to save them time, or one intended to save them money. They then rated how much the gift made them feel guilty, embarrassed, ashamed, proud, brave and good, and ranked their status in society and where they felt the gift-giver would rank their own status.

    As expected, recipients experienced greater feelings of shame, embarrassment and other negative emotions when they felt a gift had been given to save them money — gift cards, coupons or memberships, for example — and also believed that the gift-giver saw themselves as higher in status compared to the participant.

    A second study looked at real-life gift-giving. Two hundred students were given a $5 Starbucks gift card and instructed to give it to another person within the week. Half of the cards displayed a message indicating the gift was designed to save the recipient time, while the other messages explained the card was designed to save money.

    The card included a survey similar to that in the first study for the recipient to fill in. And again, those receiving a gift intending to save money experienced more negative emotions, and believed that the gift-giver saw a greater status differential between the giver and receiver, than those receiving a gift to save time. However, three months later, cards with time saving messages were equally likely to have been redeemed as those with money saving messages.

    In a third study participants were asked to imagine coming home after a long day to a friend bringing them dinner from Chipotle, either to save them time or money. They then answered the same questions about negative emotions from the previous study, as well as indicating their experience of resource scarcity — how often had they been short of time or money? Not only did participants again feel more negative emotions when a gift was given to save them money, these were intensified when they had more experience of being short of money. Gifts intended to save the recipient time, however, were not particularly influenced by experience of time scarcity.

    A final study looked at whether the intended purpose of a gift could influence decisions about what to buy. The team asked 303 participants to imagine a friend had given them a gift card, this time $30 to spend on Amazon. In the control condition, participants were told their friend was giving them the card with no explanation; in the money stress condition their friend said “I know you’ve been stressed for money”; and in the inadequate money condition said “I know you’ve felt you have had an inadequate amount of money lately”. Participants were also asked how they would use the card — either on a Boston University hoodie or a Harvard University hoodie.

    Status, again, seemed to play a large part. Those in the control condition were less likely to buy the Harvard sweater (which was perceived to be higher status) than those in the money stress or inadequate money conditions, and there was a higher power differential in the latter conditions too. How choosing hoodies in the lab would translate to real world decisions, however, is unclear.

    Why do gifts fall flat when picked out to save the recipient money? The team suggests that gift-givers may be focusing too heavily on their own perspective, failing to predict the emotional responses that a recipient low on money might experience. This may be particularly true if the giver has never experienced money scarcity themselves.

    The team also notes that the effect seen in this study might change over time: someone who felt ashamed in the moment might later appreciate having received a money-saving gift from a friend, particularly if their financial situation changes in some way. But for the time being, you’re probably best off avoiding any mention of money when you next hand over that carefully-selected gift.

    Overcoming Resource Scarcity: Consumers’ Response to Gifts Intending to Save Time and Money

    Emily Reynolds is a staff writer at BPS Research Digest

    in The British Psychological Society - Research Digest on July 23, 2020 02:58 PM.

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    Working toward racial and social equality: research and commentary

    Free access to curated research related to systemic racism, healthcare bias, racial violence, law enforcement reform and social justice movements

    in Elsevier Connect on July 23, 2020 01:22 PM.

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    CRL and East View Release Third Open Access Collection | CRL

    "CRL and East View Information Services have released the Independent and Revolutionary Mexican Newspapers (link is external), the third Open Access collection of titles digitized under the Global Press Archive (GPA) CRL Charter Alliance. This collection adds to the growing collection of Open Access material(link is external) available through East View's Global Press Archive program. The Independent and Revolutionary Mexican Newspapers collection, with a preliminary release of 135,000 pages from 477 titles, will ultimately include approximately 1,000 titles from Mexico’s pre-independence, independence and revolutionary periods (1807-1929). The collection traces the evolution of Mexico during this pivotal period and provides rare documentation of the dramatic events of this era, including coverage of Mexican partisan politics, yellow press, political and social satire, as well as local, regional, national and international news...."

    in Open Access Tracking Project: news on July 23, 2020 12:11 PM.

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    Plant “Cognition” Deserves Greater Attention In Comparative Psychology, Paper Argues

    By Emma Young

    Comparative psychology is the study of animal behaviour, and its psychological underpinnings. But the term wasn’t always this restrictive. Until about 1935, plant behaviour also featured in texts in the field. Now Umberto Castiello at the University of Padua argues that it’s high time that plants regained their rightful place in the study of the psychology of non-human organisms.

    In a paper published in the Journal of Comparative Psychology, Castiello gathers together a selection of recent evidence that plants can communicate, remember, recognise kin, decide and even count — “all abilities that one would normally call cognitive if they were observed in animals”. Far from being hard-wired, inflexible respondents to a changing world, they can adapt to change, benefit from classical conditioning, and even come to make predictions about the future.

    There’s more than an improved understanding of plants at stake, writes Castiello: “As plants should be considered cognitive agents, as such, they offer us a unique opportunity for a comparative approach, which can potentially lead us to the ‘roots’ of cognition.”

    Plants are clearly capable of all kinds of sensing — they can detect everything from changing levels of daylight to levels of the vital nutrient phosphorus in the soil, to signals from each other.

    And when it comes to communication, plants have various methods at their disposal. Their sophisticated use of a suite of volatile organic chemicals (VOCs) could be considered a language, as varying groups of VOCs can be used flexibly in new interactions and new contexts, Castiello argues. A combination of different VOCs allows the plant to transmit information about attack by a herbivore, or a more general wound, for example. There’s even evidence for dialects among different species, and that plants that are more closely related understand each other better. This could mean that predator-attack signals would work to protect relatives more than unrelated plants.

    Evidence for plant learning is also growing. For example, after being repeatedly dropped on the floor, Mimosa pudica (often known as “sensitive plant” or “touch-me-not”) stops responding with its normal leaf-folding response to a shock — it comes to “realise” that being dropped on the floor is “normal” — but remains sensitive to other types of assault. Even more remarkably, a lab study found that garden pea seedlings can learn that a sudden increase in airflow, caused by a fan, is followed by the occurrence of (desirable) blue light, and will then grow towards the fan, even in the absence of light. This work demonstrates training by classical conditioning.

    In other research, pea plants have been found to make “decisions” that resemble those that a human would make. In this study, each plant’s roots were split between two different pots, one of which received a constant level of nutrients, the other a variable level. The overall level of nutrients in these pairs of pots was also varied, so that some pairs had high levels, and some low.

    In overall low-nutrient situations, the plants went for the safe option of the pot with the stable (if unsatisfying) level of nutrients, focusing root growth in this pot. But in higher nutrient conditions, they took a punt on the variable-level pot. As Castiello writes: “The experiment showed that plants are able to respond to risk and to switch to risk-prone or risk-averse behaviour depending on resource availability.”

    Castiello also outlines evidence that though plants will compete for resources, they can also support each other, exchanging nutrients via the mycorrhizal network of funghi, which connects tree root systems. As he reports, one study even found that Paper birch and Douglas fir trees growing together in a forest in British Columbia were aware when one was in need of help to dispose of excess carbon, and readily gave it. This kind of reciprocal generosity, based on need, to benefit all, looks very like the need-based giving observed in human societies.

    In his paper, Castiello also considers research demonstrating that plants can learn the shape of a structure on which they’re growing and adapt to match, choose where to live (by directing their growth), cooperate with ants, and so much more.

    “The question should no longer be if plants are cognitive organisms but how plants make use of their cognitive capacities,” Castiello writes. And as the work suggests that a complex, centralised brain  is not necessary for cognitive behaviour, it has implications for how we understand cognition.

    Over the past century or so, research on plants has focused on their physiology. Castiello, for one, would like that to change. As he says, psychologists have a suite of tools and techniques available to study plant behaviour — and they are also in an ideal position to theorise about the mechanisms that underlie them.

    (Re)claiming Plants in Comparative Psychology

    Emma Young (@EmmaELYoung) is a staff writer at BPS Research Digest

    in The British Psychological Society - Research Digest on July 22, 2020 02:00 PM.

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    What robots can teach about inclusive education

    A technology course for underserved youth in Amsterdam shows them they can achieve what they set their minds to

    in Elsevier Connect on July 22, 2020 08:56 AM.

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    Religious People In The US — But Not Elsewhere In The World — Have More Negative Attitudes Towards Science

    By Matthew Warren

    It’s a common view among the public — and certain intellectuals — that science and religion are in fundamental opposition to each other, despite claims to the contrary. As Richard Dawkins put it in his essay The Great Convergence, “To an honest judge, the alleged convergence between religion and science is a shallow, empty, hollow, spin-doctored sham.”

    Part of this conviction that science and religion cannot be reconciled comes down to a belief that the two doctrines are psychologically incompatible. How can someone put their faith in a divine being while also trying to make sense of the world through careful observation and hypothesis testing?

    But a new study in Social Psychological and Personality Science casts doubt on the idea that religious people tend to be less scientifically-minded. Jonathon McPhetres from Massachusetts Institute of Technology and colleagues find that while the link between religiosity and negative attitudes towards science is pretty robust in the United States, in other countries that relationship is very different.

    The team first explored Americans’ religiosity and attitudes towards science across a series of nine studies comprising more than 2,300 participants. Each study used the same measure of religiosity: participants rated themselves on six statements like “I believe in God” or “I consider myself religious”. But the studies varied in their approach to measuring participants’ stance on science. For instance, in some studies participants rated their own interest in scientific topics (e.g. robotics) vs neutral topics (e.g. music), while in others they responded to statements about their attitudes towards science (e.g. “The world is better because of science”).

    In pretty much all of the studies, scores on the religiosity scale were negatively associated with scores on the science scales. That is, people who were more religious tended to have less interest in science, or more negative attitudes towards it.

    (Interestingly, these studies also included an experimental manipulation: some participants were first “primed” to think of religion, by listing reasons that religion is good, for instance, or by copying a snippet of text about religion. But this had no impact on the results, adding to other recent findings which have cast doubt on many priming effects).

    So far, so unsurprising. But would the same relationship hold up outside of the United States? To test this, the team conducted a couple of further studies. Firstly, they looked at data that had already been collected from a large, global survey. As part of that assessment, participants had rated their agreement with three items concerning science (e.g. “Science and technology are making our lives healthier, easier, and more comfortable”), and had answered three questions about religiosity (e.g. “How important is religion in your life?”).

    The team looked at data from more than 66,000 participants across 60 countries. And, overall, they found a small negative correlation between religiosity and science attitudes. But this was far from consistent between the different countries: some nations showed positive correlations, while others showed no relationship between the two at all.

    To delve further into differences between countries, the team asked people from Brazil, the Czech Republic, the Philippines, South Africa, and Sweden to complete the same measures of interest in science and attitudes towards science as in the first set of studies.  This time — and in stark contrast to the American results — there were small positive correlations in each country: those who were more religious tended to be a little more interested in science and had more positive attitudes.

    Overall, the results suggest that, for much of the world, rejection of science is not necessarily a feature of religion. Instead, the authors write, “apparent conflicts may be the product of other sociocultural and historical features of specific countries.” For instance, American Christianity has certain aspects of religious fundamentalism, such as a literal interpretation of the bible, and many political conservatives in the US have strong ties to the Christian right. These sorts of factors may help to explain why the country seems to have developed a unique conflict between science and religion.

    There are other interpretations, of course: perhaps scientifically-minded Americans tend to reject religion, rather than the other way around. I also expect that some people would label the simultaneous holding of both scientific and religious views as “irrational”, and argue that the research says little about reconciling the two ideologies.

    Fine — those kinds of philosophical arguments are unlikely to end any time soon. More interestingly to me, the study neatly illustrates the problem of relying solely on data from American participants (or participants from other Western, industrialised societies) in psychological research. Whatever your take on the results, it’s clear that making sweeping generalisations based on such a narrow group can lead to stories about how we think and behave that are just not true for vast swathes of humanity.

    Religious Americans Have Less Positive Attitudes Toward Science, but This Does Not Extend to Other Cultures

    Matthew Warren (@MattBWarren) is Editor of BPS Research Digest

    in The British Psychological Society - Research Digest on July 21, 2020 01:51 PM.

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    Teeth Marks from Anna Dumitriu on Vimeo.“Teeth...

    Teeth Marks from Anna Dumitriu on Vimeo.

    “Teeth Marks” is a body of work and exhibition by artist Anna Dumitriu explores the strange histories and emerging futures of dentistry from teeth worms, false teeth and the development of anaesthetics to 3D printing and the DNA of dental microbes. It looks at the societal and psychological impacts of this defining field of medicine through a deep investigation of the Birmingham Dental Hospital Historic Collection and collaboration with present day researchers who work at the cutting edge of medical science. annadumitriu.co.uk/portfolio/teeth-marks/

    in Anna Dumitriu: Bioart and Bacteria on July 21, 2020 01:46 PM.

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    Our commitment to diversity, equity and inclusion

    The Black Lives Matter movement in the US and elsewhere has rightly brought about a much-needed reexamination of deeply rooted issues around diversity and equity for minorities and marginalized populations. Structural racism and other inequities, for example around gender or status, continue to affect academia world-wide. At PLOS we recognize that we can do better — our journals can and must play a role in addressing concerns around diversity, equity and inclusion. 

    These are not new concerns, and we have been working to make our journals a home for diverse voices. However, we recognize that we need to step up our efforts in a number of areas and commit to doing so. For our journals, this means:

    • We will assess and survey the diversity of our contributors, from the thousands of Academic Editors handling submissions at our journals to our authors and reviewers. This will establish a baseline and allow us to hold ourselves accountable for making measurable positive changes. 
    • We need to improve the diversity of our journals and their leadership. This includes our internal staff but also our Academic Editors appointed to senior roles. We need to ensure that our journals are representative of broader society as well as the academic community, and that the voices of different communities or groups of researchers are heard and play an integral role in our journals. We commit to proactively seeking out underrepresented communities to redress the balance.
    • We will continue our efforts to ensure that all manuscript handling processes are set up to recognize and minimize bias. We are reflecting internally on how we can improve our understanding of these issues and minimise any of our own biases, and will work with our Academic Editors and peer reviewers to address any form of bias against authors or their origin in the handling of submitted manuscripts. 
    • Within the scope of each of our journals we aim to be a publishing platform for research that studies inequalities, racism, and inequities facing minority and/or marginalized populations. In doing so, we need to ensure that the study of these populations recognizes the problem of racism and inequalities, and that the topic is covered appropriately in published papers. We need to be mindful of inappropriate discussions of race in relationship with genetics traits for example. Inequalities and racism do affect the well-being of minority populations, and this needs to be considered in public health research settings as well.
    • We have the obligation to continue to uphold the highest standards of ethics. Research about minorities or other affected populations needs to be conducted to the highest editorial standards and ethics guidelines, and should award credit to contributors from these communities as appropriate.  We will not publish research intended to directly support oppression or persecution. 

    Some of these commitments are items that we will be able to address swiftly, whereas others will take more time to achieve. This topic will therefore be a regular feature on PLOS Blogs, so watch this space. We are committed to pursue these activities in the short as well as long term, and to facilitate change not just at PLOS’ journals, but also in the broader academic community where possible. We count on your support in this endeavor and will appreciate any feedback, help or suggestions for specific actions to take. Thank you!

    The post Our commitment to diversity, equity and inclusion appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on July 20, 2020 02:39 PM.

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    Early Sharing: Should You Take the Plunge?

    What does early sharing accomplish?

    Scientific discovery is a process of continuous vetting and refinement. While immediate access to the latest findings allows for accelerated discoveries, sharing early and transparently also results in more checkpoints throughout the research process for communities to provide feedback. The need for effective and time-sensitive global collaboration has been further emphasized by the COVID-19 pandemic. Adopting early sharing practices helps ensure your research is available as soon as it’s needed, regardless of your field. 

    Early sharing allows for the latest research to be connected without waiting for the final publication. Whether it’s through a preprint, open data set, or accessible protocol, researchers are empowered to cite the latest discoveries in their current research. Learning how and when researchers have adopted early sharing is the first step to contributing to this global movement. 

    Sharing Before the Study Takes Place

    The research question being pursued and the resulting study design create the foundation of a research project. These core elements are often internally reviewed to ensure the resulting study is as sound and focused as possible, but the greater research community typically doesn’t see the methodology of a study until the results and conclusions are published. By preregistering your study protocol early, you enable broader research assessment to begin at the foundation of a study. The study design itself goes through peer review so that potential improvements or flaws are detected before the study actually takes place. When the final research article is ready to be assessed, editors can consider the study’s rigor and adherence to the study design.   

    To help ensure a study follows the highest standards and has long-term reproducibility, PLOS ONE and PLOS Biology both offer preregistration options. Preregistration can help reduce confirmation bias of editors and reviewers by confirming the underlying validity of your research. Additionally, having your protocol published allows others to pursue your study, or to tweak your design to fit their available resources. 

    Sharing Initial Findings

    Earlier this year, PLOS Biology announced two new linked articles types: Discovery Reports and Update Articles. To alleviate the pressure of having to wait for a fully formed story to develop, Discovery Articles give researchers the flexibility to publish novel initial findings and as a first step. Once the Discovery Report is published, both the original authors and other research groups can augment the initial report by submitting Update Articles for review. 

    As multiple Update Articles can be linked to a single Discovery Report, your initial finding can spring into a series of interconnected advancements. 

    Sharing Before Publication

    Preprints provide a platform for open, public review that is independent from a journal and doesn’t depend on an invitation from the editor. While the original preprint can be viewed and cited prior to publication, the preprint can be updated as the manuscript is revised to ensure the most recent version of your paper is always available. 

    PLOS makes the interaction between preprint servers and our journals as simple as possible. You can directly submit your preprint to our journals from medRxiv and bioRxiv, or you can include the DOI of your preprint on the submission form if you used a different server. For those in other subjects, there is an ever-growing collection of active preprint servers. Alternatively, authors of life science articles can opt-in to have the paper uploaded to bioRxiv during submission, without any additional work. Our editors are encouraged to consider comments left on a preprint, allowing for the open review platform that preprints provide to potentially accelerate and deepen the review process. 

    That said, open and accessible data sets are another opportunity to collaborate among far-spanning researchers. Recent research has shown that publications that link to data in a repository are cited more frequently on average. As many researchers around the world don’t have access to the infrastructure required to generate their own data sets, making your data available without restrictions is an easy way to ensure your research is maximizing its contribution and usefulness. 

    Early sharing opens up opportunities throughout the research process to share study designs, initial findings, and data at a global scale. Involve your communities with early sharing practices so that vetting happens throughout the research process, ultimately improving the credibility of your final research output.

    The post Early Sharing: Should You Take the Plunge? appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on July 20, 2020 02:19 PM.

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    COVID-19: The Health Inequity Magnifier

    The COVID-19 pandemic and efforts to mitigate its spread have affected people across the entire world—but not equally. Many of the same groups of individuals known to suffer a disproportionate burden of poor health outcomes are faring especially poorly during this pandemic. In many ways, the disparate outcomes being documented in COVID-19 are simply offering a magnified view of longstanding health inequities.

    The Robert Wood Johnson Foundation stated that “Health equity means that everyone has a fair and just opportunity to be healthy“. To achieve health equity, obstacles to health must be removed. Socially disadvantaged people, who have been historically marginalized and/or disfavored by social and political institutions, have faced significant obstacles to health equity in the midst of COVID-19.

    To achieve health equity, obstacles to health must be removed.

    Social distancing, a key recommendation for preventing the spread of COVID-19, has proven to be very difficult for socially disadvantaged persons. Housing insecurity and homelessness are established risk factors for chronic health conditions, including kidney disease. In the setting of COVID-19, these challenges have meant that many individuals cannot feasibly maintain the recommended physical distance from others. Further, for people in service professions that require they interact daily with the public, their ability to socially distance has also been quite challenged. Racial and ethnic minorities and low income persons are overrepresented in such professions, which has increased their risk of COVID-19 exposure.

    For people who have sought testing for COVID-19, inequities in health care access and services have been on full display. One report noted that African Americans patients with potential symptoms of COVID-19 (e.g. cough and fever) were less likely to be given a COVID-19 test than were white persons with the same symptoms. This type of biased delivery of health services can lead to socially disadvantaged individuals presenting later (e.g. for hospitalization) with severe symptoms or even death.  As vaccines and treatments for COVID-19 are developed and disseminated, individuals who have directly, or vicariously, experienced bias in the health care setting may be reticent to seek these options, out of fear of inequitable treatment.

    COVID-19 mitigation efforts have led to shortages of food in many communities due to store closures as well as bulk purchases by individuals who can afford to do so. Low-income communities have been particularly affected. A consequence of structural inequities including residential segregation, food access is known to vary by community demographics. In this pandemic, diet-sensitive health conditions such as diabetes, hypertension and kidney disease, may be exacerbated, particularly for persons facing food insecurity.

    Solutions for addressing the inequities magnified by COVID-19 have been offered and include expanding access to testing and health care, and providing social services to keep vulnerable groups safe. People with kidney diseases are particularly vulnerable to COVID-19 infection, hospitalization and death. Because many are also socially disadvantaged, it will be important to evaluate and expand the services they are provided, including those addressing social needs.

    The post COVID-19: The Health Inequity Magnifier appeared first on BMC Series blog.

    in BMC Series blog on July 20, 2020 01:53 PM.

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    BMC Series highlights: June 2020

    Colorectal cysts: A simple model system for testing the efficacy of CAR-T cells against malignancies

    Optimal CAR T therapy validation requires a 3-D cellular system that mimics the complex tumour cellular architecture. In a study published in BMC Biotechnology Dillard et al. report the development of colorectal cysts from a single colorectal cell line Caco-2 as simple and reliable tools to validate CAR T-mediated therapy.

    Method principle, taken from the original publication.

    CAR T cells are T lymphocytes, genetically engineered to express a Chimeric Antigen Receptor (CAR) on their surface that recognizes CD19 marker on the surface of B lymphocytes and also promotes signalling events that control the activation of lysis. This results in the destruction of the B lymphocyte. Since CD19 is a widespread marker in cancerous B cells, CAR-T cells are being used as an allogenic treatment of B-cell malignancies.  The CAR T-mediated immunotherapy for cancer has revolutionized the treatment of ‘liquid tumors’, i.e, haematological, however, it hasn’t been so effective in the treatment of solid tumors, as CAR-T cells are unable to survive in the complex tumour microenvironment and target successfully all the tumor-generating cells.

    For this reason, using a two-dimensional (2-D) cellular system, in which CAR-T cells are added in a monolayer of cultured target cancer cells, to validate CAR-T cell functionality and specificity, is inadequate, as the 2-D system does not mimic the challenging 3-D morphology and organization of solid tumors. Moreover, it has been demonstrated that cancer cells acquire a different gene expression profile when cultured in 3-D spheroids compared to 2-D, which may affect their recognition by CAR-T cells.

    In order to create a simple 3-D cellular system that could be used for the validation of CAR-T cells, the authors took advantage of a colorectal cancer cell line, Caco-2, that has been shown to form 3-D cyst-like structures by self-organisation, with the apical surface of the epithelial cells facing a central lumen. First, they transduced Caco-2 cells with the CD19 gene, in a way that ensured cell-surface expression of the CD19 antigen on their surface (CD19Caco-2 cells). Next, they showed that CD19CAR-T cells were able to kill CD19Caco-2 cells, as effectively as in a 2-D culture, while Caco-2 cells remained intact. Finally, they demonstrated that the system was compatible with super-resolution microscopy, high-throughput live imaging and bioluminescence assays; hence the ability of the CAR-T cells to kill the cancer cells and destroy the cyst can be monitored with both qualitative and quantitative methods.

    This is a simple and versatile method that can be adapted to the use of a variety of cancer lines that have been shown to form similar simple 3-D structures. It could therefore, constitute a powerful tool for the therapeutic validation of CAR-T cells in different contexts.



    Bipolar disease is prevalent in homeless people

    Numerous studies have shown that bipolar disease (BD) is a common disorder among homeless people. In a study published in BMC Public Health Ayano et al. performed a systematic review and meta-analysis by pulling existing data from the literature, which confirmed and estimated more accurately the high pooled prevalence of BD among homeless people.

    Bipolar disorder (BP) is a mental health condition characterized by lengthy periods of extreme mood swings. BP has a prevalence of about 1-2.4 % in the general population, but has been shown to affect 2.41 to 42.42% of homeless people, depending on the study. BD has a severe negative effect in homeless people and is associated with an increased risk of disability, substance/drug abuse. In order to provide recommendations for future research and clinical practice, the authors performed a systematic review and meta-analysis using the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines. From a total of 3236 articles identifies, only 10 articles met the inclusion criteria for the final systematic review and meta-analysis that was conducted. The studies were performed in five countries/continents (Canada, USA, Brazil, Germany, Ireland and France) and were published between 2001 and 2017.

    Based on the random-effects model to account for existing heterogeneity the pooled BD prevalence among homeless people was estimated at 11.4%. Subgroup analysis by country/continent showed the prevalence of BD to be 10% in Europe and 13.2 %  in other countries, while subgroup analysis by the quality of the studies showed a pooled BD prevalence of 9.9% for high-quality studies and 11.8% for both low and moderate-quality studies. These numbers are significantly higher than the ones reported for the general population.

    Likely reasons for this increased between BD and homelessness is the co-occurrence of other medical conditions, such as tuberculosis, HIV/AIDS, which have been associated with an increased risk of bipolar and other mental illnesses. Also, the possible exposure of homeless people to physical and sexual trauma, which is associated with the onset of manic episodes and bipolar disease in risky groups, may also be a factor. Moreover, the higher co-existence of depression, anxiety, psychosis and alcohol-related disorders in homeless people may also constitute a possible reason for the higher prevalence of BD.

    This study demonstrates the importance of further high-quality studies to determine the etiologies of the high prevalence of BD observed in homeless people and of targeted interventions to prevent and diagnose BD in these individuals. The authors recommend the strengthening of the mental health services for homeless people.



    Calculating committed CO2 emissions of the shipping industry

    The shipping industry has one of the highest carbon dioxide (CO2) emissions and needs to take action to reduce such emissions as soon as possible. In a study published in BMC Energy Bullock et al. analyses for the first time the committed emissions of the shipping sector taking into consideration individual ship type data from existing and new ships and assesses which measures should be taken to reduce baseline committed emissions to meet the Paris agreement goals for action on climate change.

    The United Nations Framework Convention on Climate Change (UNFCCC) Paris agreement goal is to keep the increase of global temperature below 2oC above pre-industrial levels and to pursue efforts to keep the temperature rise below 1.5 oC. For this to be achieved global CO2 emissions need to be reduced as soon as possible.

    The shipping sector is the main contributor of CO2 emissions, estimated at around 800 MtCO2 per year, hence it has set a target of at least 50% reduction in CO2 emissions by 2050 compared to 2008.  However, until now the committed emissions of shipping, i.e., the CO2 emissions expected based on existing energy infrastructure, are based on assumptions of ship lifetimes extrapolated from other transport systems. The average scrappage age of ships is 28 years, which is much higher than road transport vehicles, therefore, this practice underestimates committed emissions in shipping. As a result, the ‘carbon budget’, which is the amount of CO2 that can be emitted over time while limiting global warming to the accepted levels of the Paris agreement for shipping industry is estimated to be higher for the shipping industry, than it really should.

    In this study the authors analysed committed emissions in 11,000 existing and new ships in the European Union’s new emissions monitoring scheme (EU MRV), taking into account the wide range of ship types, as well as their different sizes and scrappage age, using datasets published for the first time in 2019. It was found that five ship types: container, bulk carriers, ro pax, oil tankers and passenger ships are responsible for 71% of committed emissions, with the highest baseline committed emissions estimated for container ships. In particular, the new containers account for the highest committed emissions, as although they are more efficient, they are much larger than older containers and this has a greater impact. Moreover, passenger ships were found to have disproportionately high emissions, despite their small numbers, due to their long life time. Overall the baseline committed emissions from all existing ships in the EU MRV fleet was found to be 2260 MtCO2, much larger than estimated in previous studies. This is equivalent to 85-212% of the carbon budget to achieve the 1.5 oC target that is available for the EU MRV fleet, therefore, significant mitigation measures are required to reduce these figures.

    Committed emissions for existing ships, from the 10 largest ship types through time, taken from the original article.

    The authors found that the combination of four measures: slow speed, technical and operational improvements, fuel blending and the use of zero-carbon fuel, if implemented between 2020s-2030s has the potential to reduce the baseline committed emissions by 65% to 793 MtCO2 and achieve the target of keeping within the Paris agreement carbon budgets, without the need for premature scrappage. However, any delay in appropriate implementation would result in a reduction of only 13% of committed emissions.

    This study demonstrates that we cannot rely on measures to improve the efficiency of new ships in order to deliver what is decided in the Paris agreement and highlights the need to implement measures on existing ships, as soon as possible.



    Pilot study finds: Modified short-term fasting reduces chemotherapy toxicity in gynaecological cancer patients

    Chemotherapy-induced toxicity results in patients postponing chemotherapy or in the reduction of the drugs dose used, thus compromising therapy. There’s a lot of evidence to suggest that short-term fasting prior to the onset of chemotherapy has beneficial effects in tolerating chemotherapy. In study published in BMC Cancer Zorn at al. report a significant reduction of toxicity-related symptoms in patients with gynecological cancer, achieved in a controlled cross-over pilot study that used a modified short-term fasting (mSTF) protocol.

    Toxicity is a common side effect of chemotherapy, a consequence of healthy cells being destroyed together with the cancer cells by the drug cocktail. Fasting is believed to protect normal cells from the detrimental effects of chemotherapy, as they enter a state of reduced cell division and stress resistance, upregulation of DNA repair and induced autophagy. In tumor cells on the other hand, growth pathways remain activated, which renders them more sensitive to chemotherapy.

    In a case series study human patients under various fasting regimens were reported to show significantly fewer toxicity-induced symptoms, such as fatigue, vomiting and diarrhea, while a randomized control trial showed that a 48-h fasting reduced bone marrow toxicity and DNA damage in peripheral blood mononuclear cells. Moreover, a dose-escalation fasting study demonstrated that 72h fasting during chemotherapy was safe and tolerated by the patients, while it resulted in reduced chemotherapy-related toxicity and low-grade fasting-related toxicity.

    In this pilot study the authors evaluated the effect of a 96-h fasting on the chemotherapy-induced toxicity in women with gynecological cancer. For the first time the effect of a 6-day intervention of Ketone diet (KD) prior to mSTF on ameliorating the negative effects of fasting was also assessed. The mSTF itself had a ketogenic composition (75% fat, 15% protein and 10% carbohydrate), as it has been shown that fasting achieves best results in a state of ketosis (elevated levels of ketone bodies in the blood). The patients, who underwent a calorie restriction to 25% of their daily requirement, as a result of mSTF tolerated the fasting well and experienced much less severe symptoms of chemotherapy-induced toxicity: significantly fewer patients suffered from stomatitis, headaches and weakness and patients also showed significantly less haematological parameters of toxicity during mSTF cycles. Although previous studies had reported reduced cases of nausea, vomiting and diarrhea after STF, in this particular study, this was not observed, possibly because the patients had already overcome these conditions due to preventive medication. Importantly, the patients on mSTM postponed much fewer chemotherapy appointments than the ones on normal diet, which reflects their better tolerance of their treatment and physical condition in general. It was also found that the KD neither reduced fasting-related discomfort nor improved compliance of the fasting regimen.

    These results clearly show the potential of mSTF in counteracting chemotherapy-related toxicity and enhancing tolerance of treatment. Further larger randomized controlled trials are needed to confirm the efficacy of mSTF as a supportive approach to chemotherapy, before recommending this treatment to cancer patients.




    The post BMC Series highlights: June 2020 appeared first on BMC Series blog.

    in BMC Series blog on July 20, 2020 01:39 PM.

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    Jan van Deursen’s bullying: lab members speak out

    "There is a clear difference between being a taskmaster and a bully. There just is. Jan was definitely both." - Robin Ricke, former postdoc in van Deursen's Mayo Clinic lab

    in For Better Science on July 17, 2020 02:01 PM.

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    The evolving world of article and journal metrics – what you need to know

    To attract the best authors to your journal or find the best journal for your research, it’s essential to understand the role of metrics and the options available

    in Elsevier Connect on July 17, 2020 08:40 AM.

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    Why do so many women find it challenging to stay in postpartum HIV care?

    Despite availability of free HIV care in many low- and middle-income countries, fewer women living with HIV (WLHIV) remain in care in the first year after childbirth than during pregnancy. WLHIV who do not stay in care do not receive antiretroviral therapy and are at increased risk of passing HIV to their child or partner and may also experience worse HIV-related health outcomes. UNAIDS estimate that about 1 in 5 HIV-exposed children in Ghana become infected with HIV by the time of cessation of breastfeeding. This rate of mother-to-child transmission (MTCT) is the second-highest in West Africa and the fourth-highest among the 21 focus countries UNAIDS tracks.

    The reasons why the drop-out rates of HIV care are higher in the postpartum year than during pregnancy are not well understood. Researchers have offered several theories:  women may fall out of care due to fewer scheduled encounters with the healthcare system, due to a decline in perceived susceptibility of MTCT after childbirth, due to prioritization of their child’s health over their own, or due to challenges with childcare — but there is little evidence to support any one of these theories over the others.

    To contribute toward a better understanding of this issue, we conducted qualitative interviews with thirty postpartum WLHIV in Ghana, recruited in 2016 from two tertiary hospitals in the urban city of Accra. Our new paper in BMC Pregnancy and Childbirth presents the barriers women themselves described.

    Multiple barriers

    Women’s accounts suggest that social, economic, and physical health factors, more than a change in individual motivation, may explain why fewer women remain in HIV care in the postpartum year than during pregnancy. Broadly, we found that the social and economic costs of staying in HIV care became higher in the postpartum year and many who dropped out experienced multiple barriers.

    Ghana has the potential to eliminate MTCT of HIV; doing so will require a concerted and deliberate effort to support postpartum WLHIV to stay in HIV care.

    ART-related side-effects and HIV denial were the strongest barriers during pregnancy and the fear of re-experiencing the ART-side effects continued to keep mothers away from HIV care even after childbirth. One participant shared her story:

    During pregnancy, I suffered when I took the drugs due to the side-effects. Thus, anytime I thought of going back for the drugs [after the birth], the thoughts of the side effects came to my mind and troubled me. I became afraid. 

    The challenge of travel and transport

    One unique barrier in the early postpartum months was difficulty traveling to HIV care due to complications from childbirth or prolonged recovery from a cesarean section. For example, one mother remarked:

    Most mothers will tell you that the first six months are very tough. Many women take the time to work on themselves since some undergo an operation [i.e., C-section]. Others, too, had a vaginal tear, so they may need some time to take care of themselves. It takes six months or more for a mother to return to a normal life after childbirth [i.e., to be healthy and to visit the HIV treatment centers for care]. Some, too, are single mothers who have no support at home.

    Relatedly, for a few of the women who had dropped out of care, childbirth was associated with debt, unemployment, or underemployment. This led to a new reliance on others, such as a partner or relative, to give them money before they could make their HIV care visits, even when their motivation to stay in HIV care was high.

    Mode of transportation was the most significant barrier, with increasing costs to mothers facing new sociocultural pressures unique to the postpartum year. Postpartum mothers were motivated to protect their children’s health, and often felt obligated to take a taxi to their clinical appointments instead of the cheaper local bus, called trotro, which they typically took during pregnancy. Taxis could protect their children from the risk of illness and excessive heat common to the hot and crowded trotros, but they were more expensive, costing one participant 70% of her monthly salary.

    HIV stigma also contributed to high transportation costs, as some mothers established their HIV care far from their home to avoid being recognized. Further, those who now needed to rely on financial or childcare support to make it to appointments in their postpartum year would find it difficult to do so without disclosing their HIV status.

    Priority of pediatric care

    As a result of these economic and social challenges, one would expect that mothers who had discontinued from HIV care would also be unable to adhere to their pediatric HIV testing or child well-baby visit schedules. However, we found that all the mothers who had dropped out of HIV care, except one, were engaged with the healthcare system for their child’s health. This behavior suggests that in the context of limited resources, mothers prioritized their children’s health over their own.


    To close the pregnancy-postpartum HIV-care retention gap, our results call for a package of interventions that minimize the economic burden of accessing HIV care, diminish stigma, and enhance the management of ART-related side effects. The women in our study recommended that HIV-care providers in Ghana consider extending their medication refills from three to six months. This option will not only reduce transportation costs, but it will also allow mothers to recover physically from childbirth. Ghana has the potential to eliminate MTCT of HIV; doing so will require a concerted and deliberate effort to support postpartum WLHIV to stay in HIV care.

    The post Why do so many women find it challenging to stay in postpartum HIV care? appeared first on BMC Series blog.

    in BMC Series blog on July 17, 2020 08:00 AM.

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    Six books to help us understand eating disorders

    Some 70 million people worldwide have an eating disorder and, with the prevalence of disordered eating on the rise,  it’s clear that this presents a significant public health issue. Despite this, many myths and misconceptions abound that are significant barriers to both treatment and public understanding of eating disorders. Anyone can develop an eating disorder, regardless of age, gender, or cultural background.

    We’ve put together a list of books that provide practical information to dispel misconceptions, as well as guidance for people affected by eating disorders and their loved ones.

    1. If Your Adolescent Has An Eating Disorder: An Essential Guide for Parents by B. Timothy Walsh and Deborah R. Glasofer
    This is an authoritative guide to understanding and helping a teenager with an eating disorder. It is designed for parents of teens who have recently been diagnosed with an eating disorder, or who are at risk of developing one, and for other adults, such as teachers and guidance counselors, who are regularly in contact with at-risk adolescents. The book combines the latest science–including the newest treatments and most up-to-date research findings on eating disorders–with the practical wisdom of parents who have been raising teens with eating disorders.

    2. Eating Disorders: What Everyone Needs to Know by B. Timothy Walsh, Evelyn Attia, and Deborah R. Glasofer
    Practical yet authoritative, this book defines eating disorders, explains what we know about them based on the latest science, and describes how treatment works. The book dispels common myths about eating disorders, such as the notion that they occur only amongst the affluent, that they affect only girls and women, or that they simply result from environmental factors such as the fashion industry and society’s obsession with thinness. This book is essential reading for those seeking authoritative and current information about these often-misunderstood illnesses.

    3. The Void Inside: Bringing Purging Disorder to Light by Pamela K. Keel
    This book chronicles the growing recognition of purging disorder at the turn of the millennium, reviews what science has taught us about the illness, and explains the medical complications that purging may bring. The author, known for her work identifying and naming purging disorder, presents irrefutable evidence that it can no longer be considered a subset of better-known eating disorders. Keel illuminates how the illness impacts the lives of real people to underscore the severity of this hidden eating disorder and the need for greater awareness.

    4. Exposure Therapy for Eating Disorders  by Carolyn Black Becker, Nicholas R. Farrell, and Glenn Waller
    This book is designed to augment existing eating disorder treatment manuals by providing clinicians with practical advice for maximizing the effectiveness of exposure, regardless of clinical background or evidence-based treatment used. Suitable for use with a range of diagnoses, this easy-to-use guide describes the most up to date empirical research on exposure for eating disorders. The book also provides strategies for overcoming obstacles, including institutional resistance to implementation of exposure therapy.

    5. Handbook of Positive Body Image and Embodiment  by Tracy L. Tylka and Niva Piran
    This book is the first comprehensive, research-based resource to address the breadth of innovative theoretical concepts and related practices concerning positive ways of living in the body. Presenting chapters by world-renowned experts in body image and eating behaviors, the handbook explores how therapeutic interventions and public health and policy initiatives can inform scholarly, clinical, and prevention-based work in the field of eating disorders.

    6. Eating Disorders: The Facts by Suzanne Abraham
    Sympathetically and clearly written, this guide considers why eating disorders occur, and then looks at each in turn, describing the eating behaviours, diagnosis, and treatments available. Case histories and patient perspectives provide insights into the mind of the eating disorder sufferer, making it easier for patients and their families to relate to the topics discussed. The book provides an authoritative resource on eating disorders that will prove valuable for sufferers and their families.

    These titles highlight some of the most pressing issues in the field of eating disorder research. Greater awareness among stakeholders – including healthcare workers, researchers, policymakers, and the general public – can address ongoing challenges and inform future directions.

    Featured Image Credit: Image by jannoon028 via Freepik

    The post Six books to help us understand eating disorders appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on July 16, 2020 12:30 PM.

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    A balancing act: gender and welfare regimes in the association between work-life conflict and poor health

    Many of us find it increasingly difficult to separate our work from our personal lives. Modern technologies exacerbate the problem, with our inability to ‘switch off’ and tendency to take calls and check emails outside of working hours. What’s more, the COVID-19 pandemic has created a new challenge for those of us working from home, where the line between our jobs and family lives has become even more blurred, and for those working longer shifts in hospitals, supermarkets or elsewhere.

    It is already known that work-life imbalances can negatively affect both our physical and mental health. However, we know little about the factors that strengthen or weaken this association. New research published in BMC Public Health looks at the influence of gender and level of welfare provision by the state on the link between work-life balance and health.

    In their study, Mensah and Adjei analyze data from over 32,000 workers, aged 16 to 64, from 30 European countries. This data was collected as part of the 6th European Working Conditions Survey, carried out in 2015 by the European Foundation for the Improvement of Living and Working Conditions (Eurofound).

    The authors perform statistical analysis on the association between work-life balance and self-reported health, which previous studies have found to be a reliable proxy of overall health, and factor in other variables such as gender and welfare regime. Validating earlier studies, the results show that there is a significant association between work-life balance and health.

    Gender differences in the association between work-life conflict and health

    Traditional gender roles permeate our everyday levels such that, in many cultures, women more often take on a caring role within the family unit and men are seen as the so-called ‘breadwinner’. This is changing, with the last 40 years seeing increased participation of women in the labor market and a rise in the number of dual-earning families.

    There is generally a stronger association between poor work-life balance and poor health among women.

    How, then, does gender affect the association between work-life conflict and self-reported health? Mensah and Adjei find that while men more often report a poor work-life balance across different European countries, there is generally a stronger association between poor work-life balance and poor health among women.

    There may be a number of reasons for this. Women still bear the greater burden of childcare responsibilities, for example, creating additional pressures at home as well as in the workplace. Women also face increased discrimination at work and lower rates of pay, both of which may contribute to the impact of work-life conflict on health.

    The role of the welfare state

    The strength of this study’s large cross-European sample is that it enables comparison between groups of countries with different welfare regimes, with countries classified as Nordic (Sweden, Denmark, Finland and Norway), Conservative (such as Germany and Switzerland), Liberal (UK and Ireland), Southern Europe (such as Greece, Spain and Italy) and Central and Eastern Europe (including Estonia, Latvia, Poland, Croatia and others).

    Mensah and Adjei report that work-life balance is best for both working men and women in the Nordic countries. There is also a weaker association between poor work-life balance and poor self-reported health in these countries, which the authors attribute to their substantial welfare provision including availability of childcare, universal healthcare and long parental leave.

    The association between work-life conflict and poor health is strongest in countries with Liberal and Conservative welfare regimes, with Conservative states also being the only ones where the association is stronger in men than in women.

    Multiple factors may be at play here, including increased emphasis on the male breadwinner role, weaker employment regulation and unions, and more stringent social welfare than the Nordic states. However, it remains to be established why Southern European states, with the least generous welfare policies, fared better. Further work is also needed to determine the specific contribution of individual policies on work-life conflict and health.

    Striking a healthy balance in future

    On a personal level, the findings of this study may help us to reflect on how often we allow commitments at work encroach on our personal lives and negatively impact our health. So how might we guard against the stresses and strains of work-life conflict in future?

    The Mental Health Foundation, a UK charity, recommends a number of measures including better prioritization of tasks at work, taking proper breaks in the working day, dedicating time for exercise or hobbies, and keeping a record of time spent working or thinking about work.

    The differential impact of working practices, employment law and welfare policies on women and men’s health must be considered.

    The study also points to systemic differences to be addressed by governments and policymakers. As we strive towards equality, the differential impact of working practices, employment law and welfare policies on women and men’s health must be considered.

    Of course, countries vary widely in political and economic landscape and so too does the level of social and financial intervention by the state, but strategies to help minimize work-life conflict would surely pay dividends in fostering a healthier population and workforce.

    The post A balancing act: gender and welfare regimes in the association between work-life conflict and poor health appeared first on BMC Series blog.

    in BMC Series blog on July 16, 2020 07:59 AM.

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    Mr ACE2 Josef Penninger, Greatest Scientist of Our Time

    As a young Wunderkind, Josef Penninger discovered the ACE2 receptor. Now he invented the cure for the coronavirus which will work in his hands where Big Pharma failed. He was never found guilty of research misconduct and never retracted a paper. Dr Penninger is a Genius making a COVID-19 vaccine.

    in For Better Science on July 16, 2020 06:00 AM.

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    Towards a new approach to reveal dynamical organization of the brain using topological data analysis

    This week on Journal Club session Emil Dmitruk will talk about the paper "Towards a new approach to reveal dynamical organization of the brain using topological data analysis".

    Little is known about how our brains dynamically adapt for efficient functioning. Most previous work has focused on analyzing changes in co-fluctuations between a set of brain regions over several temporal segments of the data. We argue that by collapsing data in space or time, we stand to lose useful information about the brain’s dynamical organization. Here we use Topological Data Analysis to reveal the overall organization of whole-brain activity maps at a single-participant level—as an interactive representation—without arbitrarily collapsing data in space or time. Using existing multitask fMRI datasets, with the known ground truth about the timing of transitions from one task-block to next, our approach tracks both within- and between-task transitions at a much faster time scale (~4–9 s) than before. The individual differences in the revealed dynamical organization predict task performance. In summary, our approach distills complex brain dynamics into interactive and behaviorally relevant representations.


    Date: 17/07/2020
    Time: 16:00
    Location: online

    in UH Biocomputation group on July 15, 2020 05:35 PM.

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    Spiking Neural Networks Evolved to Perform Multiplicative Operations

    This week on Journal Club session Amir Khan will talk about the paper "Spiking Neural Networks Evolved to Perform Multiplicative Operations".

    Multiplicative or divisive changes in tuning curves of individual neurons to one stimulus ("input") as another stimulus ("modulation") is applied, called gain modulation, play an important role in perception and decision making. Since the presence of modulatory synaptic stimulation results in a multiplicative operation by proportionally changing the neuronal input-output relationship, such a change affects the sensitivity of the neuron but not its selectivity. Multiplicative gain modulation has commonly been studied at the level of single neurons. Much less is known about arithmetic operations at the network level. In this work we have evolved small networks of spiking neurons in which the output neurons respond to input with non-linear tuning curves that exhibit gain modulation—the best network showed an over 3-fold multiplicative response to modulation. Interestingly, we have also obtained a network with only 2 interneurons showing an over 2-fold response.


    Date: 17/07/2020
    Time: 16:00
    Location: online

    in UH Biocomputation group on July 15, 2020 05:35 PM.

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    The new ARRIVE 2.0 guidelines are here

    For BMC Series journals, it is important that the research we consider and publish can be utilised and is trusted.  We have a responsibility to ensure that the welfare of animals has been considered and that the harm involved is justified by the expected benefit of the research. To support us, we utilise tools such as the Animal research: reporting In Vivo Experiments (ARRIVE) guidelines to evaluate the integrity and soundness of submissions that report on animal experiments.

    In 2010, the NC3Rs developed the ARRIVE guidelines; a 20 point checklist covering measures associated with bias (randomization, blinding, sample size calculation, data handling) with the aim to improving the quality of both scientific research design and reporting of animal studies. The guidelines prompt authors to provide sufficient detail in their research paper that would allow the reader to assess the methodological rigour of the experiment, determine the reliability of the findings, and to reproduce and build upon the work. Unfortunately, the argument for the success of ARRIVE has been varied since its launch, and despite being widely endorsed by journals, funding bodies and research institutions, the quality of reporting in animal research publications is still far from roubust.

    Problems encountered using the ARRIVE 2010 guidelines

    As an Editor, I have noticed that authors use the ARRIVE checklist in different ways. Given the inconsistent adoption of ARRIVE by journals, many authors, and editors, are still not aware of these guidelines, or see them as an unnecessary box ticking exercise. This lack of awareness can also affect how authors plan their research where issues related to bias may not have been appropriately considered, and this has a knock-on-effect at the manuscript writing stage. At BMC Veterinary Research, we often receive ARRIVE checklists that are incomplete or don’t correspond to what is reported in the paper. These issues could be related to language barriers or differences in research culture where authors are still not fully aware of the consequences of incomplete reporting. Alternatively, it may be related to the misconception that admitting to non-compliance of an ARRIVE item will disqualify a manuscript from being published. Overall, comparing an ARRIVE 2010 checklist against a manuscript can be an onerous task for editors and reviewers when evaluating the robustness of the methods and results.

    comparing an ARRIVE 2010 checklist against a manuscript can be an onerous task

    Therefore, in an attempt to improve uptake, an international working group was formed to review the original ARRIVE 2010 guidelines and develop a strategy that would make ARRIVE easier for researchers, editors and reviewers to use. We are pleased to announce that the new ARRIVE 2.0 guidelines have been published today in PLOS Biology and re-published by BMC Veterinary Research.

    ARRIVE 2.0 – what has changed? 

    The overall guidelines have been simplified. Items from the original checklist have been updated and reorganised and are now presented in two categories: the ‘ARRIVE Essential 10’ and ‘Recommended Set’.

    The ‘ARRIVE Essential 10’ is a list of key items that authors should address in their manuscript text as a minimum standard and represents best practice. If adhered to, reporting of these items should have the biggest impact on improving the quality and reliability of animal research studies.

    The second list of recommendations is designed to provide greater context and background to the study. This includes items such as conflicts of interest, protocol registration, and animal housing and welfare aspects. While not strictly essential, these points will add value to the review process, enhancing the transparency of the study design and reporting.

    A useful Explanation and Elaboration (E&E) document has also be made available. This helps to describe each of the ARRIVE 2.0 items in greater context and detail, and includes best practice examples from the published literature.

    The ARRIVE 2.0 update joins a host of other ongoing initiatives in an attempt to address factors contributing to poor reproducibility.  There is still much work to be done to engage key stakeholders to create a process whereby these standards can be consistently implemented and enforced at the research planning stage, and then hopefully mandated by all journals.

    Support provided at BMC Veterinary Research

    At BMC Veterinary Research, we encourage all authors to adhere to ARRIVE 2.0 and offer the following services and resources to our authors and readers.

    Plan your research
    The sooner you adhere to ARRIVE standards the better.  We encourage authors to publish their study protocol with us, which is a great opportunity to ensure that your planned study follows ARRIVE 2.0 standards and 3Rs principles. Publishing study protocols help to improve the transparency and reproducibility of animal and veterinary research, in addition to reducing publication bias and post hoc revisions of the study’s objectives and methodologies.

    Make writing easier
    A copy of the BMC Veterinary Research manuscript template is available for authors to download, which follows our formatting guidelines and includes requests relating to Landis criteria and ARRIVE 2.0 items making it easier for authors to ensure that their reporting is complete.

    Available resources
    Further information and resources about standards of reporting can be found via the BMC Veterinary Research Instructions for Authors page and in the BMC editorial policies.

    Our commitment to reproducible science
    We have also recently launched a new section in the journal dedicated to animal ethics, policy and research integrity practices in animal and veterinary science and will publish research and opinion articles on this important topic.

    Author support
    We have a dedicated editorial board that are happy to support our authors with any queries they may have regarding adherence to ARRIVE 2.0 and reproducible research practice. If you would like further information, please contact me at hayley.henderson@biomedcentral.com

    The post The new ARRIVE 2.0 guidelines are here appeared first on BMC Series blog.

    in BMC Series blog on July 15, 2020 03:32 PM.

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    MOOCs help researchers and librarians in developing countries access the latest scientific information

    In new online courses, Research4Life users are finding the information they need to improve life in low-income countries

    in Elsevier Connect on July 15, 2020 12:18 PM.

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    ‘The new system’: How will healthcare organizations navigate COVID-19 and beyond?

    With our healthcare system under pressure, Elsevier’s Patient Safety and Innovation Manager writes about ways to ensure high quality care and safety

    in Elsevier Connect on July 15, 2020 11:37 AM.

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    Let’s Take a Look at Your Kidneys

    The number one cause of chronic kidney disease and end-stage kidney disease is diabetes, and the gold standard for diagnosing any kidney disease is through biopsy. Unfortunately, kidney biopsies are not without risks, and although minimal, there is a risk of bleeding and damaging the kidney further by performing this invasive procedure. In addition, some patients cannot have a kidney biopsy when they truly need one because of other comorbidities, anti-coagulant medications, and other factors that make them high risk for complications. Usually for patients with diabetes that present no other concerning findings, the nephrologist might assume its diabetic nephropathy, a complication of diabetes, without performing a kidney biopsy.  Could they be making a mistake?  It might be something else that is treatable.  Is there another test we could do?  What if there was an alternative for diagnosing diabetic nephropathy that is noninvasive and low risk?

    Is there another test we could do?  What if there was an alternative for diagnosing diabetic nephropathy that is noninvasive and low risk?

    In a BMC Neprhology publication, Li et al., examine the potential use of specialized ultrasound – three-dimensional ultrasound and contrast-enhanced ultrasound – to diagnose diabetic nephropathy.  This technology takes a large series of 2-D ultrasound images in rapid succession which are then assembled by a computer to create a 3-dimensional image. For pregnant women, a 3-D ultrasound may have been offered to you to look at your growing baby.  Contrast enhanced ultrasound uses intravenous contrast agents consisting of microbubbles/nanobubbles of gas, which oscillate creating an “echo” when exposed to ultrasound waves. This is a better alternative when a patient cannot get contrast agents for a CT or MRI.

    Li and colleagues used these two technologies to examine 115 patients with diabetes and kidney disease that underwent kidney biopsy to see if they could differentiate between diabetic nephropathy from non-diabetic renal disease (i.e., IgA nephropathy, membranous nephropathy).  Sixty-four had diabetic nephropathy and 51 had non-diabetic renal disease. We know that diabetic nephropathy is more likely with longer history of diabetes and with other microvascular complications (like retinopathy).  Li et al.’s data was consistent with these previous studies. They didn’t find any differences with contrast-enhanced ultrasound.  However, they did find that using a logistic regression model for BMI and right kidney volume was statistically significant.  They concluded that 3-D ultrasound has the potential to be an option in our arsenal for diagnosing diabetic nephropathy.

    Li et al. is one of a many researchers looking at utilizing 3-D ultrasound for diagnosing and managing kidney pathology.  Not surprisingly it’s been looked at for determining kidney volume in autosomal dominant polycystic kidney disease.  And Calio et al. examined 3-D contrast-enhanced ultrasound use in surveillance for renal cell carcinoma recurrence after ablation.

    In my clinical practice, I’m not running out to get a 3-D ultrasounds just yet, but I’m keeping it in mind for the future. After further studies, I might be ordering it for that diabetic patient with chronic kidney disease to make sure I’m not missing something.

    The post Let’s Take a Look at Your Kidneys appeared first on BMC Series blog.

    in BMC Series blog on July 14, 2020 03:02 PM.

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    Improving Research Assessment in the Triage Phase of Review

    Authors: Helen Sitar is the community coordinator for DORA and a Science Policy Programme Officer at EMBO and Anna Hatch is DORA’s program director. DORA receives financial support from PLOS via organizational membership, and PLOS is represented on the steering committee of DORA.

    When seeking to fill an open faculty position, it’s common for universities to receive hundreds of applications for a single job. Unsurprisingly, such a high level of competition creates a bottleneck early in the hiring process. The ‘triage’ phase of review therefore becomes a critical point, as it determines which applicants receive further consideration.

    The ability to efficiently yet effectively triage applications has been a long-standing challenge for the academic community. Time constraints make triage prone to the influence of unintended biases and proxy measures of success, such as the journals where the candidate has published or their institutional affiliations.

    Meanwhile, consistency between reviewers presents another challenge.  Even when selecting for the same purpose, processes and standards can vary greatly between individual reviewers or committees, due to differing assumptions about the process or the criteria for making judgments. Reviewers may prefer certain institutions, labs, or journals, or attach different values to funding track records. If reviewers are unaware of their own biases for certain community affiliations, these can influence decision-making. Ultimately, biased hiring processes impede underrepresented and minoritized scholars from making progress in their academic careers, resulting in inequalities in academic leadership and more. Without any intervention, one current model of postdoc to faculty transitions suggests that faculty diversity will not increase significantly until 2080.

    Testing three approaches to triage

    To stimulate discussion of the challenges associated with the triage process, and to identify possible solutions, DORA organized an interactive session for the 2019 ASCB | EMBO Meeting. Through a mock-review exercise, participants worked in small groups to test different approaches to the triage process. The seventeen participantsーrepresenting different groups and career stages, including postdocs, faculty members, administrators, publishers, and staff from other non-profit initiativesーwere given the description of a faculty position to ‘hire,’ general instructions on how to conduct the triage, and a set of anonymized application materials (CVs and cover letters). Because the session was limited to 75 minutes, other application materials, including letters of reference, teaching statements, and diversity statements, were not included in our informal exercise.

    The application materials were anonymized, and the author names from the references listed in the bibliographies were also removed. A note under each reference, however, indicated the applicant’s position in the author list (e.g. “2nd author, 8 authors total”). The CVs and cover letters provided to two of the participant groups were further altered, by removing institutional names and journal titles when they were presented. One of these groups was provided with an assessment matrix to guide the evaluation of different competency areas: research, teaching and mentorship, equity and inclusion, and service to scientific or academic communities.

    By informally experimenting with these triage approaches, our goal was to understand what information people use to make judgments during the triage phase. We were also keen to surface ideas about improving the triage process. Below we summarize the discussion and insights that emerged from our exercise.

    What’s in a name?

    CVs are littered with names, including those of applicants’ advisors, collaborators, coauthors, and references, which may yield strong associations for reviewers. These names can divert the reviewer’s focus from the work presented and onto the context and community in which it has been conducted. One way that names have the potential to mislead reviewers is through ingroup favoritism, wherein reviewers may gravitate towards the individuals that present affiliations most like themselves.

    Surprisingly, some individuals did not notice that names had been omitted from the application materials in our exercise. And others reported that it did not negatively impede the review process. Without names, participants found they became more attentive to the remaining details. For example, one group reported paying greater attention to the institutions where candidates received their training.  But relying on the names of institutions is also problematic, because they do not speak directly to the accomplishments or contributions of an individual, which should be the focus when hiring.

    Institution and journal prestige

    Interestingly, the lack of institutional and journal names in materials did not detract from the participants’ ability to understand an applicant’s profile, as long as sufficient detail on their academic record had been included. Specifically, participants were interested in knowing how an applicant had contributed to the community at large, or to their department or research group, as this is a better indicator of their skills than their institutional affiliation.

    Journal names were deemed generally unnecessary as well, especially when an applicant had provided a brief 2-4 sentence explanation summarizing what an article achieved and their specific contribution. This is not the first time DORA has received this feedback; it was suggested at a previous conference session in 2018.

    The participants who saw journal names in the application materials reported that they realized they were using them as a way of evaluation; these participants proposed that their assessments might have been fairer had the journal titles been removed. However, participants still wanted access to the articles’ DOIs to make papers easier to find, read, and evaluate.

    One group reported that in the absence of journal names, they paid more attention to the author order and used this to determine the importance of the applicants’ contributions to each work. But others argued that knowing the authorship order for a publication did little to indicate an applicant’s role in contributing to a paper or project, and therefore was not particularly useful information. Tools like the Contributor Roles Taxonomy (CRediT) can help parse apart how an individual contributed to an article or project.

    Details instead of names

    The problem with preferring candidates with well-known labs, institutions or awards named on their CVs is that by valuing reputation, departments narrow their search for talent to within known spheres. In doing so, they will miss out on hiring great researchers who have yet to be recognized by a prestigious award or hired into a well-known lab. When personal, institution, and journal names were removed at the same time in our exercise, some participants noticed that many CVs lacked details necessary to understand applicants’ skill areas. Some such details may have been in materials, such as teaching statements or reference letters, not available for the exercise. The reaction of participants to omission of these details from applicants’ CVs and cover letters underscores the importance of communicating one’s own research interests, approach to science, unique skills, and teaching and mentoring abilities. Only with this information can reviewers accurately evaluate candidates and suitability to a particular faculty role.

    There was some disagreement regarding the necessity of including several details common to applicant CVs, including assessing candidates based on their receipt of awards or grants. Some participants paid close attention to mentions of grants, and attributed great value to the fact that an applicant had received an independent grant. Others debated the level of confidence one should have in a person’s abilities based on their receipt of grants, as this can contribute to the “Mathew effect” of people already recognized receiving further recognition because of previous awards.

    Consistency is key

    In the triage process, it is clearly important for reviewers to be able to quickly find relevant information. The necessity of this was a major topic of discussion in our session, particularly when it came to the question of being able to compare candidates with ease. The lack of consistent organization of CVs made it complicated for participants to find the relevant information needed to make judgments of applicant’s strengths in various areas (e.g. research, teaching, leadership, inclusivity, service). Moreover, some applicants’ CVs were much longer than others, which reviewers found cumbersome as the length made finding specific pieces of information even more challenging.

    To address the need for organized CVs, the concept of a structured narrative format was mentioned in our discussions as an option to build consistency into the triage process. The Royal Society in the United Kingdom, the Dutch Research Council, and the Swiss National Science Foundation are each experimenting with standard structured narrative CV formats. So far, the Dutch Research Council has received mostly positive feedback on its new narrative. Reviewers report appreciating the added context the narrative format provides, and the Council has found that it leads to a more diverse selection of researchers. Some participants in our session, however, were skeptical of enforcing a standard template CV, noting that it could restrict creativity and limit applicants in describing work which may not fit neatly into any of the preconceived categories.

    Standardizing judgments

    Every reviewer has their own ‘way’ of sorting through applications, and specific criteria that they look for when deciding who to ‘keep’ or ‘eliminate’ in a triage round of review. In our session, participants using an assessment matrix advocated for a short discussion between reviewers to find a common set of standards before embarking on the triage process, as a way to increase consistent decision making and help minimize the effects of implicit bias. The Germans call this process towards reaching a collective agreement—‘abstimmen’. Directly translated it means “off-voting,” or voting before one begins something. Asking reviewers to calibrate how they interpret the categories in the rubric would ideally result in more consistent assessment of all individuals.

    The overarching framing for the discussion was the tension between the need for efficient, accurate assessment versus the burden of devoting attention to details in every application. While some participants stated firmly that the use of rubrics may slow down the triage process, the group generally agreed that rubrics allow for uniform standards to be applied and that consistency should be valued. Still, a few others were resistant, stating that it was not desirable to ‘over-engineer’ the process.

    Looking ahead

    Universities and research funders are increasingly reconsidering the relevance and importance of researchers’ contributions when assessing them for hiring, promotion or funding. Across the DORA and wider research communities, there are numerous discussions on how to demonstrate the value of different contributions, whether it be via descriptive narratives, article-level metrics, teaching evaluations, or other means. The triage process is the front line to further review and consideration—and is therefore both important and influential in determining the makeup of the research community and its leadership.

    The scholarly community has not yet reached a consensus regarding which methods for evaluation are best suited to different purposes or situations, and many believe that there will never be a ‘one-size-fits-all’ solution to research evaluation. Yet demands for employment and funding continue to grow, resulting in more challenges for applicants and review committees in every selection process. And as the number of PhD graduates continues to exceed the number of available positions in academia, academics can expect the triage process for applications to become ever more challenging.

    Instilling standards and structure into research assessment processes, especially during the triage phase of review for faculty searches, appears to be a particularly robust option for reducing bias. To achieve this, universities can ask applicants to use a structured narrative CV template. Institutions can also develop evaluation assessment matrices and have conversations amongst reviewers to set standards and identify desirable applicant qualities and characteristics. By removing journal titles and replacing them with 2-4 sentence article summaries that articulate key findings and specify the researcher’s contributions, reviewers would be provided with information better suited to judging researchers’ contributions at the triage stage. When researchers and institutions reflect on and carefully choose what types of information are used to judge scholarly contributions, evaluation processes can be brought into alignment with community values.


    We thank the participants at our career enhancement programming session at the 2019 ASCB|EMBO Meeting for a robust and thoughtful discussion about research assessment. Thanks to Stephen Curry, Chris Pickett, and Gary Ward for very helpful comments.

    The post Improving Research Assessment in the Triage Phase of Review appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on July 14, 2020 02:37 PM.

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    Dr. Ignarro has suffered stigma, and was denied at least two interviews on television

    "The presence of such articles online have severely affected Dr. Louis J. Ignarro’s public reputation, and his personal life. Dr. Ignarro disputes any accusations of wrongdoing. There was no fabrication of data, although there was a mistaken duplication of data which occurred due to error. None of the data was false." -J.L. Perez, Esq.

    in For Better Science on July 14, 2020 08:06 AM.

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    6 things to consider when transitioning from academia to industry

    Thinking about switching from academia to industry? These skills and mindsets will help you make the most of your new career

    in Elsevier Connect on July 13, 2020 10:32 AM.

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    Extraordinary results of the Olomouc Nano-con

    This is a guest post by two whistleblowers from the Palacky University in Olomouc. In the centre of the growing research misconduct and retaliation scandal: the nanotechnology professor Radek Zboril

    in For Better Science on July 13, 2020 06:00 AM.

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    Going beyond what we know – how we can break down barriers between disciplines

    As a research leader in chemical engineering, Prof. Jarka Glassey talks about venturing beyond traditional educational siloes to address global issues

    in Elsevier Connect on July 10, 2020 09:54 AM.

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    Now Hiring: arXiv Senior Software Architect

    Thanks to generous funding from the Allen Institute for Artificial Intelligence, arXiv will hire an experienced software engineer to serve as the senior software architect for supporting the technological innovation of arXiv.org, the premier open access platform serving scientists in STEM. As a member of the arXiv team, the senior software architect will extend and implement a highly modular, micro-service based architecture that will give arXiv a strong foundation for the future. For nearly 30 years, arXiv has enabled scientists to share research within scientific communities and to publish pre-prints, which are scientific papers shared prior to publication in journals. Around the world, arXiv is recognized as an essential resource for the scientists that it serves.  The new arXiv senior software architect will play a key role building out the next generation system to continue this legacy.

    The arXiv organization is led by the Executive Director based at Cornell Tech, and is composed by staff working from Cornell University in Ithaca and remotely across the country. Cornell Tech serves as the steward organization for arXiv, ensuring that arXiv has reliable technical infrastructure and providing new opportunities for innovative software development. arXiv relies on the advice and collaboration from a Scientific Advisory Board, a Member Advisory Board, and an international community of scientific subject area moderators.  Since arXiv’s inception in August 1991, more than 1.7 million scientific papers have been uploaded and shared. arXiv receives direct support for innovating is services from, among others, the Sloan Foundation and the Allen Institute for Artificial Intelligence with ongoing arXiv support from Cornell Tech, the Simons Foundation, and a global collective of 200 institutional members.

    This is a one year position with the potential for renewal, located at either of the Cornell University campuses in Ithaca, NY or New York, NY. Remote work is also a possibility. Click here for the full job description and application.

    in arXiv.org blog on July 09, 2020 02:00 PM.

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    Update: Submission Agreement and Instructions

    arXiv has updated its submittal agreement terms and conditions and instructions for submissions. These changes will go into effect this week.

    Among other updates, these agreements clarify the submitter’s representations and warranties, the license granted to arXiv, the waiver of rights and indemnification, and management of copyright. Authors who submit their work to arXiv will now be presented with the new agreements during the submission process. Authors who have currently have submissions in progress will be prompted to view and accept the new agreements before finalizing their submissions.

    arXiv encourages authors to review the agreements thoroughly before submitting their work. The full text of the updated agreements can be found here: submittal agreement and instructions for submissions.


    in arXiv.org blog on July 08, 2020 02:00 PM.

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    Il Piccolo Mulino Verduci Frodatore

    "I choose to think of the paper-mills as something like a mediaeval monastic scriptorium, with one table of tonsured monks working on the text, while the limners at another table illuminate the Figures." - Smut Clyde

    in For Better Science on July 08, 2020 07:56 AM.

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    “The amount of data you get to apply to a real-world problem is huge”

    Using machine learning, an NLP Specialist at Elsevier helps institutions see the impact of their research and where to direct their funding

    in Elsevier Connect on July 07, 2020 09:31 AM.

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    “Want a Drink? Go on, you know you want to.” – Peer pressure to drink alcohol among UK adults

    You have probably been in situations where someone offers you an alcoholic drink and you feel like you have to drink it. Or perhaps you offer people a drink and make sure that they join in the fun. Peer pressure to drink alcohol is common in our everyday lives; from parties, your local pub, to nowadays COVID-19 pandemic friendly social distancing beers on Zoom with your mates.

    Based on our systematic review of 13 qualitative research studies here are five key lessons:

    1. Peer pressure is not just experienced by adolescents and young people:

    A common perception is that peer pressure exists mainly in young people. However, peer pressure can affect people of all ages. The review found the adults often saw themselves as ‘older and wiser’ compared to when they were young. But many still experienced pressures to drink and continue drinking. Who hasn’t had the offer of ‘one for the road’?

    2. People can feel threatened by peer pressure:

    Peer pressure experiences varied from friendly banter to aggressive forms of pressure where people felt alcohol was ‘forced on you’. Being encouraged to ‘keep up’ with others’ drinking was a common reason for drinking too much.

    3. Peer pressure can have a negative impact:

    Ironically, to get rid of peer pressure many people gave in and drank more alcohol. They either had a drink when they didn’t want to drink, or drank more than they had intended. Drinking alcohol in response to peer pressure was seen as ‘caving in’. Most people who drank as a result of peer pressure regretted this decision later.

    4. Our wider social context matters to build and keep up peer pressure:

    Drinking provided connections to other people, and those who didn’t drink were often seen as boring or outsiders.

    The social surroundings often influenced peer pressure to drink. Drinking was seen as ‘a sociable thing’ – as normal and helping you to fit in. For men, drinking could also be seen as a way to show their masculinity, which included ‘drinking like a man’ and choosing manly drinks.  Drinking provided connections to other people, and those who didn’t drink were often seen as boring or outsiders.

    5. People develop strategies to deal with peer pressure.

    Many reported using strategies to avoid pressure. Strategies included ‘nursing your drink’, drinking alcohol-free options which mimic alcoholic in flavor and appearance, or driving their car to provide an excuse for not drinking which would usually be accepted. Some people who did not drink much alcohol ‘came out’ out about their drinking preference, but this seemed to be rare. Others selected their group of friends to make sure it included non-drinkers or those who only drank moderate amounts.

    The next time that you’re at a party, in the pub or having social distancing beers on Zoom, will you recognize when you are pressured to drink? Will you cave into the peer pressure, or have a strategy to deal with it? And what can you do to make sure that people don’t feel like they have to drink alcohol if they don’t want to?

    The post “Want a Drink? Go on, you know you want to.” – Peer pressure to drink alcohol among UK adults appeared first on BMC Series blog.

    in BMC Series blog on July 07, 2020 06:35 AM.

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    Science misconduct

    Scholarly publishing is broken, and no repair is possible. At least let's point fingers at the elites and laugh. Can science trust Science?

    in For Better Science on July 07, 2020 06:01 AM.

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    Call for Papers! BMC Oral Health Collection: Something in the Water – Fluoridation and Caries

    Water fluoridation is a measure to prevent caries, a disease of significant public health importance. Caries, when not managed, result in pain and discomfort for individuals and have further implications for the health and well-being of the affected individual, such as retarded growth and development of pre-school children. The huge cost of managing caries has significant impact on the allocation of public health funding.

    Different management strategies have been employed to prevent caries. Behaviour based interventions to reduce individual’s exposure to caries’ risk factors such as a reduction in sugar consumption, have limited success. Public water fluoridation is a cost-effective approach to facilitate access of populations to systematic fluoride and, in turn, reduce caries.

    © samopauser / stock.adobe.com

    The effectiveness of water fluoridation is still being extensively debated globally.  First, there is contradictory evidence on its effectiveness in preventing caries and there are reported risks of adverse effects such as dental and skeletal fluorosis. There are also debates weighing up the potential health benefits in the context of ethical principles and personal liberties.  Fluoridation reduces the risk of ill health in a manner which protects the vulnerable and reduces health outcome inequality between the different socioeconomic groups. Those who oppose fluoridation do so on the grounds that it is unethical to coerce individuals to live healthy lives, and emphasises the importance of consent before any health intervention.

    Given the level of interest in public water fluoridation, the range and complexity of the public debate, and its implication for policy making, this Collection aims to bring together empirical research papers, and theoretical and conceptual analyses about water fluoridation and caries. The Collection will consider manuscripts on the following three themes:

    • Population level impact of the introduction or the cessation of water fluoridation on health
    • Barriers to the implementation of fluoridation and reasons for its cessation, including the assessment and evaluation of the attitudes and knowledge of members of the public, dental professionals and policy makers on water fluoridation
    • Ethical arguments for and against water fluoridation

    If you have any research you would like us to consider, please submit directly to BMC Oral Health stating in your cover letter that you wish to be considered for the Collection “Something in the Water”

    To view the articles already published in this Collection, please visit our website: https://www.biomedcentral.com/collections/Fluoride

    Alternatively you can email your pre-submission queries to Anne Menard (anne.menard@biomedcentral.com).

    The post Call for Papers! BMC Oral Health Collection: Something in the Water – Fluoridation and Caries appeared first on BMC Series blog.

    in BMC Series blog on July 02, 2020 01:45 PM.

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    Research 2030 podcast: Looking beyond lockdown — PhD student Comzit Opachaloemphan

    An international PhD student shares how he has adjusted to life under lockdown, from the essential work of caring for ants to continued learning in a paused world

    in Elsevier Connect on July 02, 2020 09:39 AM.

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    Buy Professor Seeberger’s Artemi-Tea to survive COVID-19!

    Science communication by press release. No paper is published, no data available, but a Max Planck Institute director is eager to announce a possible cure for COVID-19: artemisia extracts, by his own company.

    in For Better Science on July 02, 2020 06:43 AM.

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    Seventy Teams of Scientists Analysed the Same Brain Data, and It Went Badly

    What the latest fMRI “crisis” means for the rest of science

    in The Spike on July 01, 2020 02:27 PM.

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    NWO announces implementation guidelines for Plan S

    Plan S – an initiative of European research funders to accelerate the transition to open access – will apply to all new NWO [Dutch Research Council] calls published as of 1 January 2021. To give researchers sufficient time to prepare, NWO is already announcing how it will implement the guidelines for Plan S in its grant rules.

    in Open Access Tracking Project: news on July 01, 2020 08:19 AM.

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    Traces of Fear in Aphantasia

    When reading a vivid story that describes a shark attack, do you imagine yourself in the ocean, seeing the dorsal fin approach you?
    “...sun glints off the waves / suddenly a dark flash / in the distant waves / maybe it was a shadow / you turn to the beach / more people are pointing / they look anxious / looking back out to sea / a large fin / slices the surface / moving closer...”

    Or is your “mind's eye” — your visual mental imagery of the evocative scene ⁠— essentially a blank?

    early warning: picture of snake below

    One's subjective internal life of thinking, perceiving, imagining, and remembering belongs to oneself and nobody else. [Brain scanning is still not a mind reader.] An increasing number of media reports (and scientific studies) have shined a light on this fact: the mental life of one person differs from that of another, sometimes in startling ways. It's always been that way, but now it's out in the open.

    The cat is out of the bag.

    When reading that sentence, did you have a fleeting mental picture in your mind's eye? Maybe it was clear, maybe it was hazy. Or maybe you saw no visual image at all... if that was the case, you might have a condition known as Aphantasia, the inability to voluntarily generate mental imagery. This is a normal variant of human experience, albeit an uncommon one.

    What are the “consequences” of having Aphantasia? You may be more likely to choose a scientific or mathematical occupation, although artists and photographers with Aphantasia certainly exist. Aphantasia is often associated with poor autobiographical memory (diminished ability to recall the past episodes of your life).

    Does Aphantasia affect your emotional reactions to ordinary experiences like looking at pictures or reading a story? If visual imagery is important for having an affective response to the shark story, would people with Aphantasia show physiological (bodily) signs of emotion while reading? Wicken and colleagues (2019) asked this question by comparing the skin conductance response (sweaty palms) evoked by reading vs. looking at pictures. This was a pilot study reported in a preprint (not yet peer reviewed).

    If visual imagery is necessary for an affective response to evocative stories, then A-Phantasics should have diminished (or absent) skin conductance responses (SCRs) compared to Typical-Phantasics. In contrast, SCRs to unpleasant pictures should not differ between the two groups, because the picture-viewing experience doesn't require imagery. However, it's still possible that imagery-based elaboration (or verbal elaboration, for that matter) could amplify the SCR, especially since each picture was presented for 5 seconds.

    For the reading condition, stories were presented as sequential short phrases (to match reading speed across subjects). The control conditions weren't well-matched, unfortunately. This was especially true for Stories, where reading the task instructions served as the neutral comparison condition (instead of reading a neutral story).


    The participants were 24 individuals with intact imagery (based on the Vividness of Visual Imagery Questionnaire and binocular rivalry priming1 scores within the typical range) and 22 self-identified Aphantasics (who were older, on average, than the control participants).2 For the Aphantasia group, seven (out of the original 29) were excluded because their VVIQ or priming scores exceeded the cut-off.


    For the Pictures (Perception) condition, the physiological response to Unpleasant vs. Neutral stimuli was not significantly different for the two groups. Incidentally speaking, the skin conductance level (SCL = SCR) was quite variable, as shown in the shaded portion of the graph below.

    Adapted from Fig. 1D (Wicken et al., 2019).  Left: Aggregated progressions of baseline-corrected SCL across the duration of the frightening photos sequence (sampled as average across 5 sec time bins). Right: Mean and standard error across time bins.

    The Stories were another story... For the Stories (Imagery) condition, the Aphantasic group did not show an elevated SCL for the scary stories, unlike the controls.

    Adapted from Fig. 1B (Wicken et al., 2019).

    Or as the authors suggested, “[Aphantasia] is associated with a flat-line physiological response to frightening written, but not perceptual scenarios, supporting imagery’s critical role in emotion.”

    I'd say “flat-line” is a little judgy, with the semantic implication that the Aphantasics were dead or something.

    I'd like to see subjective ratings of emotion (affect and arousal) for the Pictures and Stories, especially since the primary means of identifying people with Aphantasia is based on subjective report. Nonetheless, this is an intriguing finding, with additional evidence forthcoming (or so I imagine)...


    1 See: Is there an objective test for Aphantasia? Binocular rivalry priming can be a useful “objective” measure of aphantasia (Keogh & Pearson, 2018), but it's not necessarily diagnostic at an individual level.

    2 Mean age = 33.7 yrs for Aphantasia, mean = 23.0 for controls. I don't know why they didn't recruit age-matched controls from the community, other than the convenience of recruiting university students.


    Wicken M, Keogh R, Pearson J. (2019). The critical role of mental imagery in human emotion: insights from Aphantasia. bioRxiv. 2019 Jan 1:726844.

    in The Neurocritic on July 01, 2020 05:19 AM.

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    The Strange Case of the Homeopathic Sex Enhancer

    A retracted paper points to a strange story of homeopathy rebranded.

    in Discovery magazine - Neuroskeptic on June 30, 2020 08:00 PM.

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    Five questions about PTSD

    Post-traumatic stress disorder is an often discussed, and often misunderstood, mental health condition, that affects up to 7% of adults during their lifetimeHere we answer five questions related to misconceptions that often prevent people from seeking care. 

    1. Is PTSD a veteran disease? 

    While a significant minority of veterans suffer from PTSD, this disorder can impact anyone who has experienced life-threatening trauma. Approximately 70% of people will experience a potentially traumatic event. Sexual assault, natural disasters, serious and traumatic illness, physical attack, etc. are all experiences that can become the stuck memories of PTSD. Trauma survivors with PTSD are haunted by these experiences, impacting everything from sleep to relationships.  

    2. Are people with PTSD violent? 

    Traumatic experiences sometimes include exposure to physical violence and many trauma survivors have histories that include violence even if their target trauma does not. Sadly, violence is much too common.  Most people with PTSD are not violent. Most people with PTSD do not have problems with aggression or violence. When PTSD happens with alcohol or substance misuse, the risk for violence increases.

    3. Can PTSD only be managed but not really treated?

    Effective treatments for PTSD exist and include psychotherapy as well as medication. While these options do not work for all people suffering with PTSD, most people will see reduction in symptoms, and many will even see remission of PTSD over time. 

    4.  If someone has mental health problems after a trauma, is it always PTSD? 

    PTSD is just one possible mental health problem that can occur following trauma. Since PTSD involves being haunted by a trauma memory, it is easily connected to a traumatic event. However, studies following people after exposure to trauma show that for some people trauma may result in other issues, such as depression, panic disorder, substance abuse, or even obsessive-compulsive disorder. Good assessment beyond just trauma exposure is necessary to provide the best insight into diagnosis and treatment of trauma survivors.

    5. Is it all in your head?

    PTSD can feel like it is all in your head with the intrusive memories, feeling that you cannot connect to others, and sense of feeling out of control. The impact of PTSD goes beyond just your brain and includes changes in how your body reacts to stress and other normal processes. These changes can even result in weight gain and cardiovascular problems

    Misunderstanding PTSD and its causes contributes to many people never seeking care or dropping out of care before they have had a chance to experience the benefits. In getting the word out about PTSD and the good news that there are effective treatment options, we hope that more people will seek care and experience taking their lives back from PTSD.

    Feature image: Silhouette by Isai Ramos via Unsplash.

    The post Five questions about PTSD appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on June 30, 2020 12:30 PM.

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    What does the pandemic mean for research in biodiversity conservation?

    As with many areas of research, conservation has been hit by COVID-19 restrictions – but it also offers unique opportunities

    in Elsevier Connect on June 30, 2020 12:08 PM.

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    LGBTQ2S+ People as a Disadvantaged Group in Healthcare

    Pride parade

    Pride Month is celebrated around the world in June to commemorate the 1969 Stonewall Uprising. Pride is both a celebration and a protest and encourages acceptance, solidarity, and visibility of LGBTQ2S+ people and their rights, including their right to healthcare.

    Compared to the general population, it is well documented internationally that LGBTQ2S+ people experience poorer health outcomes, both psychologically and physically. These poorer health outcomes are a consequence of healthcare disparities. That is, LGBTQ2S+ individuals face unequal burdens in healthcare which increases the incidence, or prevalence, of poorer health outcomes.

    This is a vicious circle that continues due to the lack of attention on the poorer health outcomes and underserved healthcare needs that LGBTQ2S+ people experience.

    In healthcare settings, LGBTQ2S+ people are more likely to not receive appropriate healthcare and experience discrimination and harassment. Barriers to accessing healthcare bring harmful experiences for LGBTQ2S+ people. These experiences can have detrimental effects, including decreasing the likelihood of seeking healthcare in the future, consequently leading to poorer health outcomes. This is a vicious circle that continues due to the lack of attention on the poorer health outcomes and underserved healthcare needs that LGBTQ2S+ people experience.

    What are some of the common barriers in LGBTQ2S+ healthcare?


    There are multiple unsolved barriers for LGBTQ2S+ people to access healthcare and here we touch on some examples. It is especially important to acknowledge that these barriers can be further exacerbated by a number of factors, including the current COVID-19 pandemic, where, as an example, transgender people have been found to face unprecedented and enlarged healthcare disparities.

    Firstly, there are limited numbers of healthcare staff trained to deliver healthcare that recognizes the needs of the LGBTQ2S+ people. Considering the risks of facing discrimination, LGBTQ2S+ people could hesitate to disclose information such as sexual orientation and how they identity to healthcare staff. This makes it difficult for healthcare personnel to appreciate the specific needs of the patient and to provide the most appropriate and holistic care.

    Secondly, The LGBTQ2S+ community continues to face severe inequalities in their access and provision of care, which is closely linked to governmental policy. Most recently, the revised US Affordable Care Act has narrowed the definition of sex discrimination to the extent that it omits protections for transgender people in the US.

    Thirdly, LGBTQ2S+ people can also experience discrimination and harassment in the workplace. LGBTQ2S+ people are more likely to have a lower income, which can be a financial pressure and barrier to LGBTQ2S+ people accessing and using health services.

    How can we remove the barriers in the future?

    Removing Barriers

    Researchers have previously presented an LGBTQ2S+ Health Equity Promotion Model, guiding LGBTQ2S+ people to consider both positive and negative health-related circumstances to reach full psychological and physical health potentials. But more research and work is needed to involve LGBTQ2S+ people in guiding the research agenda to promote the recognition of specific healthcare needs, whilst respecting the differences amongst the community.

    Significant efforts need to be made to reduce health disparities and remove barriers to healthcare. Society should work together to promote healthcare equity, address and prevent LGBTQ2S+ poorer health outcomes, support LGBTQ2S+ people to access safe and inclusive healthcare, and work to eliminate healthcare disparities. It is essential to translate negative research findings in this context into reformative and progressive practices.

    The post LGBTQ2S+ People as a Disadvantaged Group in Healthcare appeared first on BMC Series blog.

    in BMC Series blog on June 30, 2020 11:30 AM.

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    Motherisk crook Gideon Koren now at Ariel University

    The Israeli Ariel University recruited a doctor from hell to their newly established medical school: Gideon Koren, infamous for Motherisk and deferiprone scandals.

    in For Better Science on June 29, 2020 10:10 AM.

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    Are There Purposeless Behaviors?

    Are habits goal-free behaviors, or does every habit actually serve a purpose?

    in Discovery magazine - Neuroskeptic on June 27, 2020 11:00 PM.

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    Academic precarity and the single PI lab model

    Brilliant young scientists are struggling to obtain a stable faculty position, all over the world. It seems that “publish or perish” was actually quite hopeful. Now clearly, at least in biology, it is more like “publish in Science, Nature or Cell every other year or perish”. Only a small proportion of PhD holders manage to obtain a stable academic position, and only at an advanced age after multiple postdocs. Of course, this competition for publishing in certain venues also has a great impact on science; encouraging dishonesty and discouraging both long-term creative work and solid incremental science. Everyone complains about the situation.

    What should we do about it? What I hear most frequently is that governments should increase the budget and create more faculty positions. That is certainly necessary but I think it is a reductionist view that largely misses the point. Of course, at the time when you start hiring more faculty, the proportion of young scientists who get a faculty position increases. However, if each of them then opens their lab and hire dozens of postdocs, then this proportion quickly reverts to what it was before.

    What is at stakes is the general organization of research, in particular the “X lab” model (e.g. the Brette lab), with one group leader (the “PI”) surrounded by a number of graduate students and postdocs (I will discuss only the research staff here), with a complete turnover every few years. It seems that in many countries, to get a faculty position means to start their “own” lab. This is not the case yet in France, but this lab model is spreading very, very fast. With the new law on research currently in discussion (“discussion” might not be the appropriate word, though), it is planned that about 25% of all new recruitments will follow this model (a tenure-track system).

    The math is easy. In a stable world, each faculty member will train on average one student to become a faculty member. For example, if a typical lab consists of 1 PI with 3 graduate students, rotating every 4 years, then over 40 years the PI will have trained 30 students, one of which would become a PI. The “success rate” would therefore be 1/30. Even with just one student at any given time, the chance for a student to end up getting a faculty position is 1/10.

    Of course, one does not necessarily pursue a PhD with the goal of obtaining a faculty position. It is completely respectable to do a PhD then go to the industry. In many countries, holding a PhD is an asset. It is generally not the case in France, though. One may also want to do a PhD not for career, but because it is interesting in itself. This seems perfectly valid. Note that in that case, implementing a subtask of the PI’s project and doing all the tedious bench work might not be ideal. In any case, it must be emphasized that in this lab model, training students for research is only a marginal aim of a PhD.

    How about postdocs? A postdoc is not a diploma. It typically doesn’t improve employability much. Of course, it could be done just for its own interest. But the experience I hear is mostly that of a highly stressful situation, because many if not most postdocs are hoping to secure a stable faculty position. Let us do the math again, with a simplified example. Suppose each lab has just 1 postdoc, rotating every 4 years. Compared to the above situation, it means that 1 out of 3 graduate students go on to do a postdoc. Then each of these postdocs has a 10% chance of getting a faculty position.

    Let us have a look at funding questions now. What seems very appreciated is that when you start a lab, you get a “start-up package”. There is a blog post on Naturejobs entitled “The faculty series: Top 10 tips on negotiating start-up packages” that describes it. We can read for example: “There’s no point having equipment if you don’t have any hands to use it. One of the largest costs you can expect to come out of your start-up fund are the salaries of PhD students and postdocs. They’re the most crucial components of the lab for almost all researchers.”. It is very nice to provide the PI with these “components of the lab”, but as argued above, a direct consequence is to organize academic precarity on a massive scale. This remains true even if the entire budget of the State is allocated to research.

    The same goes for the rest of the funding system. Project-based funding is conceived so that you hire people to implement your project, which you supervise. Part of these people are students and postdocs. For example, an ERC Starting Grant is 1.5 million euros for 5 years, or 300 k€ per year. In France, a PhD student costs about 30 k€ / year and a postdoc about the double. Of course, to that must be added the indirect costs (25%) and the grant also covers equipment and your own salary. But this is generally sufficient to hire a few students and postdocs, especially as in many countries graduate students are funded by other sources. Then the budget goes up to 2 million € for the consolidator grant and 2.5 million € for the advanced grant. The ERC has become a sort of model for good funding schemes in Europe, because it is so generous. But is it? Certainly it is for the PI who receives the grant, but a world where this mode of funding is generalized is a world where research is done by a vanishingly small proportion of permanent researchers. It is a world that is extremely cruel to young scientists, and with a very worrying demographic structure, most of the work being done by an army of young people with high turnover. You might increase the ERC budget several fold because it is such a great scheme, it will not improve this situation, at all.

    Ending academic precarity is a noble cause, but one has to realize that it is inconsistent with the one PI - one lab model, as well as with project-based funding. I want to add a couple of remarks. Precarity is obviously bad for the people who experience it, but it is also bad more generally for the academic system. The excessive competition it generates encourages bad practices, and discourages long-term creative work and solid incremental science. We must also look beyond research per se. The role of academia in society is not just to produce new science. It is also to teach and to provide public expertise. We need to have some people with a deep understanding of epidemiology that we can turn to for advice when necessary. You would not just hire a bunch of graduate students after a competitive call for projects to do this advising job when a new virus emerges. But with a pyramidal organization, a comparatively low proportion of the budget is spent on sustaining the most experienced persons, so for the same budget, you would have much lower expertise than in an organization with more normal demographics. This is incredibly wasteful.

    What is the alternative? Well, first of all, research has not always been organized in this way, with one PI surrounded by an army of students and postdocs. The landmark series of 4 papers by Hodgkin and Huxley in 1952 on the ionic basis of neural excitability did not come out of the "Hodgkin lab"; they came out from “the Physiological Laboratory, University of Cambridge”. The Hubel and Wiesel papers on the visual cortex were not done by graduate student Hubel under the supervision of professor Wiesel. Two scientists of the same generation decided to collaborate together, and as far as I know none of their landmark papers from the 1960s involved any student or postdoc. What strikes me is that these two experienced scientists apparently had the time to do the experiments themselves (all the experiments), well after they got a stable faculty position (in 1959). How many PIs can actually do that today, instead of supervising, hiring, writing grants and filling reports? It is quite revealing to read again the recent blog post cited above: “There’s no point having equipment if you don’t have any hands to use it.” - as if using it yourself was not even conceivable.

    In France, the 1 PI - 1 lab kind of organization has been taking on gradually over the last 20 years, with a decisive step presumably coming this year with the introduction of a large proportion of tenure tracks with “start-up packages”. This move has been accompanied by a progressive shift from base funding to project-based funding, and a steady increase in the age of faculty recruitment. This is not to say that the situation was great 20 years ago, but it is clearly worsening.

    A sustainable, non-pyramidal model is one in which a researcher would typically train no more than a few students over her entire career. It means that research work is done by collaboration between peers, rather than by hiring (and training) less experienced people to do the work. It means that research is not generically funded on projects led by a single individual acting as a manager. In fact, a model where most of the working force is already employed should have much less use of “projects”. A few people can just decide to join forces and work together, just as Hubel and Wiesel did. Of course, some research ideas might need expenses beyond the usual (e.g. equipment), and so there is a case for project-based funding schemes to cover for these expenses. But it is not the generic case.

    One of the fantasies of competitive project-based funding is that it would supposedly increase research quality by selecting the best projects. But how does it work? Basically, peers read the project and decide whether they think it is good. Free association is exactly that, except the peers in question 1) are real experts, 2) commit to actually do some work on the project and possibly to bring some of their own resources. Without the bureaucracy. Peer reviewing of projects is an unnecessary and poor substitute for what goes on in free collaboration - do I think this idea is exciting enough to devote some of my own time (and possibly budget) on it?

    In conclusion, the problem of academic precarity, of the unhealthy pressure put on postdocs in modern academia, is not primarily a budget problem. At least it is not just that. It is a direct consequence of an insane organization of research, based on general managerial principles that are totally orthogonal to what research is about (and beyond: teaching, public expertise). This is what needs to be challenged.

    in Romain Brette on June 20, 2020 11:27 AM.

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    Probabilistic Optimization Algorithms for Real-Coded Problems And Its Application in Latin Hypercube Problem

    This week on Journal Club session Mohammad Tayarani-Najaran will talk about paper "Probabilistic Optimization Algorithms for Real-Coded Problems And Its Application in Latin Hypercube Problem".

    This paper proposes a novel optimization algorithm for read-coded problems called the Probabilistic Optimization Algorithm (POA). In the proposed algorithm, rather than a binary or integer, a probabilistic representation is used for the individuals. Each individual in the proposed algorithm is a probability density function and is capable of representing the entire search space simultaneously. In the search process, each solution performs as a local search and climbs the local optima, and at the same time, the interaction among the probabilistic individuals in the population offers a global search. The parameters of the proposed algorithm are studied in this paper and their effect on the search process is presented. A structured population is proposed for the algorithm and the effect of different structures is analyzed. The algorithm is used to solve Latin Hyper-cube problem and experimental studies suggest promising results. Different benchmark functions are also used to test the algorithm and results are presented. The analyses suggest that the improvement is more significant for large scale problems.


    Date: 19/06/2020
    Time: 16:00
    Location: online

    in UH Biocomputation group on June 17, 2020 12:30 PM.

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    Nerd Food: Notes on Computational Finance, Part I: Introduction

    Nerd Food: Computational Finance, Part I: Introduction

    Welcome to the first part of what we hope will be a long series of articles exploring QuantLib, Open Source Risk Engine (ORE), libbitcoinand other interesting finance-related FOSS (Free and Open Source) projects. However, I'm afraid this will be a bit of a dull first post, as we need to clarify our objectives before we can jump into the fray.


    Even though I've been a software engineer in the financial sector for over fifteen years, I've always felt I lacked a deep understandingof the foundational concepts that make up the domain. As a self-confessed reductionist, I find this state of affairs extremely uncomfortable, akin to hearing a continuous loop of David Hilbert's words: wir müssen wissen, wir werden wissen1. The situation had to be remedied, somehow, and the material you are now reading is the proposed fix for my ailments. As to the methodology: given I've had some success in applying the Feynman Technique2 to other complex domains, it seemed only natural to try to use it for this endeavour as well. Past experience also demonstrated writing is an adequate replacement for in vivocommunication, which is just as well in this brave new world of social distancing.

    So that's that for the why and the how. But, just what exactly are we researching?


    These posts shall largely amble where our fancy takes us, within the porous boundaries of finance. Alas, we can hardly keep calling our target domain "trading, accounting, crypto and a bit of quantitative finance, when viewed through the lens of FOSS" - descriptive though that might sound. We are Software Engineers after all, and if there is one thing we do is to name things, especially when we lack competence to do so3. In this vein, I decided to call this motley domain of ours "Computational Finance". Should the name have merit, I'm afraid I have little claim to it, as it was shamelessly stolen from this passage in Wolfram's writings:

    Doctors, lawyers, teachers, farmers, whatever. The future of all these professions will be full of computational thinking. Whether it’s sensor-based medicine, computational contracts, education analytics or computational agriculture - success is going to rely on being able to do computational thinking well.

    I’ve noticed an interesting trend. Pick any field X, from archeology to zoology. There either is now a “computational X” or there soon will be. And it’s widely viewed as the future of the field.

    These seemed like inspiring words for anyone embarking on a long and uncertain journey, so we made them our own and, in turn, it gave us a name to rally around. But what of its boundaries? One of the biggest challenges facing the reductionist is that, in the limit, everything is interconnected with everything else, for there is no natural halting function. Thus, if you are not careful, all paths will eventually lead you into the realm of quarks and particle physics, regardless of your starting point. Now, that would not be an entirely useful outcome. I have never found a completely satisfactory answer to this question in any on my previous meanderings, but in general I tend to follow an empiric approach and let taste be my guide4. Granted, its probably not the scientific solution you were expecting, but it seems that there are "intuitive" boundaries in subjects, and when we hit one of those we shall stop5. As an example, for our purposes we need not look in detail at legal frameworks when trying to understand financial concepts, though the two disciplines are deeply intertwined.


    An issue which is closely interrelated with the previous one is on how to strike a balance between computational exploration versus domain definitions. Too much exploration and you proceed full steam ahead without knowing the meaning of things; too many boring definitions and they become just words without bringing any light to the subject under scrutiny. The sweet spot lies somewhere in the middle.

    Our approach can be described as follows. We shall try to progress very slowly and methodically through the concepts in the domain, building them up as we climb the abstraction ladder but without making them too dense and technical. We'll make extensive use of Wikipedia definitions, where possible, but keeping these focused only on the point at hand rather than exploring the myriad of possibilities around a theme.

    Finally, we shall try to marry domain concepts with our chosen implementations - the computational experiments part - in order to illustrate their purpose and get a better understanding at what it is that they are trying to do. So, each post will be focused on one fairly narrow subject area, start with a bunch of definitions which are hopefully self-explanatory and then proceed to explore the available implementations on that topic, or code that we write ourselves.


    The target audience for this material is the fabled homo developus, that non-existent "standard developer" - in this particular case, one moderately competent on C++ but unfamiliar with computational finance. On the "finance" part, if you are already familiar with the domain, you will no doubt find the content very slow going. I'm afraid this is by design: the objective is to try to build the concepts on a solid foundation for those not in the know, so slowness is unavoidable6.

    With regards to the computational part: the astute reader will likely point out that there are a great deal of tutorials on QuantLib, ORE and many other libraries of a similar ilk, and many books have been written on quantitative finance. One could be forgiven for wondering if there is a need to pile on more literature onto a seemingly already crowded subject.

    In our defence, we are yet to find work that directly targets "plain" software developers and provides them with a sufficiently broad view of the domain. In addition, most of the existing material is aimed at either those with strong mathematical abilities but no domain knowledge, or its converse, leaving many gaps in the understanding. What we are instead aiming for is to target those with strong programming abilities but no particular knowledge of either computational finance or mathematics. And this leads us nicely to our next topic.


    Our assumption is that you, dear reader, are not able to attain deep levels of understanding by staring at page after page of complex mathematical formulae. I, for one, certainly cannot. Unfortunately, non-trivial mathematics is difficult to avoid when covering a subject matter of this nature so, as a counterweight, we shall strive to use it sparingly and only from a software engineering applicationperspective. Note that this approach is clearly not suitable for the mathematically savvy amongst us, as they will find it unnecessarily laboured; then again, our focus lies elsewhere.

    Our core belief is that an average reader (like me) should be able to attain a software engineer's intuition of how things work just by fooling around with software models of formulae. The reason why I am very confident on this regard is because that's how developers learn: by coding and seeing what happens. In fact, it is this very tight feedback loop between having an idea and experimenting with it that got many of us hooked into programming in the first place, so its a very powerful tool in the motivational arsenal. And, as it turns out, these ideas are related to Wolfram's concept of Experimental Mathematics. Ultimately, our aspiration is to copy the approach taken by Klein in Coding the Matrix, though perhaps that sets the bar a tad too high. Well, at least you get the spirit of the approach.


    Another rather peculiar idea we pursued is the use of cryptocurrencies throughout, to the exclusion of everything else. Whilst very popular in the media, where they are known as cryptos, in truth cryptocurrencies still have a limited presence in the "real" world of finance, and nowhere more so than in derivatives - i.e., the bulk of our analysis. So at first blush, this is a most puzzling choice. We have decided to do so for three reasons.

    Firstly, just because I wanted to learn more about cryptos. Secondly, because there is a need to bridge the knowledge gap between these two distinct worlds of finance; to blend the old with the new if you will. Personally, I think it will be interesting to see what the proliferation of derivatives will do to cryptos - but for that we need to disseminate financial knowledge. Finally, and most important of all, because in order to properly illustrate all of the concepts we shall cover, and to drive the open source libraries to their potential, one needs vast amounts of data of the right kind. Lets elaborate further on this point.

    One of the biggest problems with any material in quantitative finance is in obtaining data sets which are sufficiently rich to cover all of the concepts being explained. This, in my opinion, is one of the key shortcomings with most tutorials: they either assume users can source the data themselves, or provide a small data set to prove a very specific point but which is insufficient for wider exploration7. This document takes a slightly different approach. We will base ourselves on a simulated world - a parallel reality if you'd like, thinly anchored to our reality by freely available data taken from the crypto markets. We shall then generate all of the remaining data, to the level of precision, richness and consistency required both to drive the code samples, but also to allow for "immersive" exploration. In fact, the very processes for data generation will be used as a pathway for domain exploration.

    Of course, generated data is not perfect - i.e., realistic it is not, by definition - but our point is to understand the concepts, not to create new quant models that trade in the real world, so it is adequate for our needs. In addition, the data sets and code samples, as well as the means used to derive them shall be part of a git repository under an open source licence, so they can be extended and improved over time.

    If you are not familiar with cryptos, don't worry. For starters, we can assume the intricate mechanistic details to a large extent - the blockchain and so forth - and introduce key concepts as required. We need not concern ourselves with this because there is plenty of freely available material covering it in excruciating detail, and designed specifically for software engineers. Instead, we shall treat cryptos as if they were regular currencies, except where they are just too different - in which case we'll point out the differences. Its a bit of a strange approach, but hopefully it will produce the desired results.

    Non Goals

    If you are trying to learn techniques on how to trade, this is not the material for you. Even when we discuss trading strategies and other similar topics, our focus is always on trying to understand how the machinery works rather than on how to make money with it. Similarly, if you are a quant or are trying to become one, you are probably better off reading the traditional books such as Hull or Wilmott rather than these posts, as our treatment of mathematics will be far too basic for your requirements. However, if you are an expert in this subject area, or if you find any mistakes please do point them out.


    As with anything to do with finance, we need to set out the standard disclaimers. To make sure these are seen, we shall add them to each post.

    Legal Disclaimer

    All of the content, including source code, is either written by the author of the posts, or obtained from freely available sites in the internet, with suitable software licences. All content sources shall be clearly identified at the point of use. No proprietary information of any kind - including, but not limited to, source code, text, market data or mathematical models - shall be used within this material.

    All of the views expressed here represent exclusively myself and are not those of any corporation I may be engaged in commercial activities with.

    The information available in these blog posts is for your general information and use and is not intended to address your particular requirements. In particular, the information does not constitute any form of financial advice or recommendation and is not intended to be relied upon by users in making (or refraining from making) any investment decisions.8

    All software written by the author for these posts is licensed under the Gnu GPL v3. As per the licence, it is "distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details."


    With all of the preliminaries out of the way, we can move on to the meat of the subject. On Part II we shall discuss our first real topic, and it could not be much more fundamental: Money.



    "We must know, we will know". As per Wikipedia:

    The epitaph on his tombstone in Göttingen consists of the famous lines he spoke at the conclusion of his retirement address to the Society of German Scientists and Physicians on 8 September 1930. The words were given in response to the Latin maxim: "Ignoramus et ignorabimus" or "We do not know, we shall not know".


    The Feynman Technique is a well-established learning methodology. For more details, see Richard Feynman: The Difference Between Knowing the Name of Something and Knowing Something.


    There are no circumstances under which I have seen software developers lacking confidence. I feel that the motto of our profession should be the Latin translation of Make up with confidence that which you lack for in competence.


    An idea that was most likely inspired by Linus' views on good taste. For details see Applying the Linus Torvalds “Good Taste” Coding Requirement.


    Of course, your intuition is not my intuition. I'm afraid you will have to take my taste as a given, even where you disagree. Feel free to make your views heard though.


    As they say in my home country of Angola, malembe malembe. The expression can be loosely translated to English as "slowly but surely", or "slowly does it".


    As an example, the latter approach is taken by a library I respect very much, the Open Source Risk Engine (ORE).


    This paragraph was obtained from the Truly Independent Ltd and modified to suit our needs.

    in Marco Craveiro on June 16, 2020 09:29 PM.

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    The emotional toll of the COVID-19 pandemic on teenagers

    A growing body of evidence supports my clinical experience that younger people, high schoolers especially, are having more psychological problems during the pandemic than adults. There are many reasons for this. Adolescents are in the developmental stage of forming a new social world away from their parents. Social needs tend to dominate their lives and yet currently this growth has come to a bit of a standstill. In addition, teenagers are not fully cognitively developed; their moods still dominate compared to the planning and attention that are controlled by the prefrontal cortex, which doesn’t fully develop until about age 25. We all need to create a new and different worldview, but adults have more history and neurological development to take the long view.

    We can help support our teens in many ways. Here are some recommendations for how to communicate and foster mental health during this difficult time; many of them will benefit the entire family.

    Listen.  Remember that no matter how much teens might protest, they are still dependent on their parents; the family is still the go-to support system. We need to show our teens that they can still count on us; that are we are emotionally there for them. I don’t mean a rose-colored glasses approach, but a realistic and strong view. Listen rather than trying to solve problems and try to check in often. It may be painful to hear teens’ worries because in the current situation, we are all struggling with a variety of anxieties. Communicate that although this is an extremely challenging situation, we can get through it together.

    Communicate what you know as well as uncertainty. We’re are all under enormous stress. Our children can see it in us. Rather than try to avoid the sadness, it is better to communicate what you can. For example, if you know that if you get sick a relative or family friend is ready to step in, that will reassure your teens. On the other hand, if your teen wants to know when they will be able to go out in groups, you can reply that you don’t know but are monitoring the guidelines. Clarify that all this hardship is about keeping us as safe as possible.

    Remember coping skills and resilience. Although teens are still developing psychologically, they may be aware of their strengths and weaknesses. Under this enormous stress, however, they may overlook how they have coped during hard times in the past. You can remind them how, for example, when there was illness in the family, they read certain types of books, baked, or wrote in a journal. Many of us, in the hopes of protecting our children from pain, do not help them learn distress tolerance. Even though we are in the midst of a worldwide trauma, building on a teen’s existing strengths can help increase distress tolerance.

    Pay attention.  Most of us are struggling with some level of anxiety or sadness. This is a natural response to a surreal situation. Clinical anxiety or depression is something different. If you observe panic attacks, extreme worry, or avoidance, those are some symptoms of an anxiety disorder.  Similarly, some symptoms of a major depressive episode include feeling sad or empty, feeling hopeless, experiencing changes in appetite or sleep, expressing guilt, and having suicidal thoughts. Remember, too, that in adolescents, irritability may be a more prominent symptom than sadness. Even now, you can contact your pediatrician for a referral to a mental health professional. Getting in touch with a previous psychotherapist or psychiatrist can be in enormously helpful, even if just for a “check in.” Most psychotherapists are now comfortable using teleconferencing or telephone sessions.

    Don’t forget to take care of yourself. It is an axiom in mental health that if a parent is feeling psychologically healthy, so will a child.  This is an upsetting time and parenting is one of life’s most challenging (also rewarding) experiences. Try to include some time for yourself for restoration, fun or a conversation with a close friend. Reach out to family, friends, or close co-workers for specific assistance. Some of the tips suggested may not be easy or even possible for you given your economic or social situation. You may be a single parent. You may be a member of a minority group or frontline healthcare professional. If so family, religious groups, neighborhood networks, or community agencies can also provide the support that you need. Please don’t hesitate to get help; we can get through this if we all work together.

    Featured Image Credit: Image by rawpixel.com via Freepik

    The post The emotional toll of the COVID-19 pandemic on teenagers appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on June 14, 2020 09:30 AM.

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    Mental Disorder in a Healthy Brain: The Goose, the Fox and Addiction

    Can there be mental disorder without brain disease?

    in Discovery magazine - Neuroskeptic on June 12, 2020 11:00 PM.

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    5 Lessons I Learned From My Neuroscience Degree

    A call to celebrate with reflection in the absence of convocation.

    in The Spike on June 11, 2020 11:27 AM.

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    Black lives matter

    Today, June 10th 2020, black academic scientists are holding a strike in solidarity with Black Lives Matter protests. I strike with them and for them. This is why:

    I began to understand the enormity of racism against blacks thirty five years ago when I was 12 years old. A single event, in which I witnessed a black man pleading for his life, opened my eyes. I don’t remember his face but I do remember looking at his dilapidated brown pants and noticing his hands shaking around the outside of his pockets while he plead for mercy:

    “Please baas, please baas, … ”

    The year was 1985, and I was visiting my friend Tamir Orbach at his house in Pretoria Tshwane, South Africa, located in Muckleneuk hill. We were playing in the courtyard next to Tamir’s garage, which was adjacent to a retaining wall and a wide gate. Google Satellite now enables virtual visits to anywhere in the world, and it took me seconds to find the house. The courtyard and retaining wall look the same. The gate we were playing in front of has changed color from white to black:

    Screen Shot 2020-06-09 at 1.36.08 AM

    The house was located at the bottom of a short cul de sac on the slope of a hill. It’s difficult to see from the aerial photo, but in the street view, looking down, the steep driveway is visible. The driveway stones are the same as they were the last time I was at the house in the 1980s:

    Screen Shot 2020-06-09 at 1.08.38 AM

    We heard some commotion at the top of the driveway. I don’t remember what we were doing at that moment, but I do remember seeing a man sprinting down the hill towards us. I remember being afraid of him. I was afraid of black men. A police officer was chasing him, gun in hand, shouting at the top of his lungs. The man ran into the neighboring property, scaled a wall to leap onto a roof, only to realize he may be trapped. He jumped back onto the driveway, dodged the cop, and and ran back up the hill. I remember thinking that I had never seen a man run so fast. The policeman, by now out of breath but still behind the man, chased close behind with his gun swinging around wildly.

    There was a second police officer, who was now visible standing at the top of the driveway, feet apart, and pointing a gun down at the man. We were in the line of fire, albeit quite far away behind the gate. The sprint ended abruptly when the man realized he had, in fact, been trapped. Tamir and I had been standing, frozen in place, watching the events unfold in front of us. Meanwhile the screaming had drawn one of our parents out of the house, concerned about the commotion and asking us what was going on. We walked, together, up the driveway to the street.

    The man was being arrested next to a yellow police pickup truck, a staple of South African police at the time and an emblem of police brutality. The police pickup trucks had what was essentially a small jail cell mounted on the flat bed, and they were literal pick up trucks; their purpose was to pick up blacks off the streets.


    Dogs were barking loudly in the back of the pickup truck and the man was sobbing.

    “Please baas, not the dogs. Not the dogs. Please baas. Please baas…”

    The police were yelling at the man.

    “Your passbook no good!! No pass!! Your passbook!! You’re going in with the dogs and coming with us!”

    “Please… please… ” the man begged. I remember him crying. He was terrified of the dogs. They had started barking so loudly and aggressively that the vehicle was shaking. The man kept repeating “Please… not with the dogs… please… they will kill me. Please… help me. Please… the dogs will kill me.”

    He was pleading for his life.


    The passbook the police were yelling about was a sort of domestic or internal passport all black people over the age of 16 were required to carry at all times in white areas. South Africa, in 1985, was a country that was racially divided. Some cities were for whites only. Some only for blacks. “Coloureds”, who were defined as individuals of mixed ancestry, were restricted to cities of their own. In his book “Born a Crime“, Trevor Noah describes how these anti-miscegenation laws resulted in it being impossible for him to legally live with his mother when he was a child. Note that Mississippi removed anti-miscegenation laws from its state constitution only in 1987 and Alabama in 2000.

    The South African passbook requirement stemmed from a law passed in 1952, with origins dating back to British policies from the 18th century. The law had the following stipulation:

    No black person could stay in a white urban area for more than 72 hours unless explicit permission was granted by an employer (required to be white).

    The passbook contained behavioral evaluations from employers. Permission to enter an area could be revoked by any government employee for any reason.

    All the live-in maids (as they were called) in Pretoria had passbooks permitting them to live (usually in an outhouse) on the property of their “employer”. I put “employer” in quotes because at best they would earn $250 a month (in todays $ adjusted for inflation) would sleep in a small shack outside of a large home, and receive a small budget for food which would barely cover millie pap. In many cases they lived in outhouses without running water, were abused, beaten and raped. Live-in-maids spent months at a time apart from their children and families- they couldn’t leave their jobs for fear of being fired and/or losing their pass permission. Their families couldn’t visit them as they did not have permission, by pass laws, to enter the white areas in which the live-in-maids worked.

    Most males had passbooks allowing them only day trips into the city from the black townships in which they lived. Many lived in Mamelodi, a township 15 miles east of Tswhane, and would travel hours to and from work because they were not allowed on white public transport. I lived in Pretoria for 13 years and I never saw Mamelodi.

    I may have heard about passbooks before the incident at Tamir’s house, but I didn’t know what they were or how they worked. Learning about pass laws was not part of our social studies or history curriculum. At my high school, Pretoria Boys High School, a Milner school which counts among its alumni individuals such as dilettante Elon Musk and murderer Oscar Pistorius, we learned about the history of South Africa’s white architects, people like Cecil Rhodes (may his name and his memory be erased). There was one black boy in the school when I was there (out of about 1,200 students). He was allowed to attend because he was the son of an ambassador, as if somehow that mitigated his blackness.

    South Africa started abandoning its pass laws in 1986, just a few months after the incident I described above. Helen Suzman described it at the time as possibly one of the most eminent government reforms ever enacted. Still, although this was a small step towards dismantling apartheid, Nelson Mandela was still in jail, in Pollsmoor Prison at that time, and he remained imprisoned for 3 more years until he was released from captivity after 27 years in 1990.



    We did not stand by idly while the man was being arrested. We asked the police to let him go, or at least to not throw him in with the dogs, but the cops ignored us and dragged the man towards the back of the van. The phrase “kicking and screaming” is bantered about a lot; there is even a sports comedy with that title. That day I saw a man literally kicking and screaming for his life. The back doors of the van were opened and the dogs, tugging against their leash, appeared to be ready to devour him whole. He was tossed inside like a piece of meat.

    The ferocity of the police dogs I saw that day was not a coincidence or accident, it was by design. South Africa, at one time, developed a breeding program at Roodeplaat Breeding Enterprises led by German geneticist Peter Geertshen to create a wolf-dog hybrid. Dogs were bred for their aggression and strength. The South African Boerboel is today one of the most powerful dog breeds in the world, and regularly kills in the United States, where it is imported from South Africa.


    After encounters with numerous Boerboels, Dobermans, Rottweilers and Pitbull dogs as a child in South Africa I am scared of dogs to this day. I know it’s not rational, and some of my best friends and family have dogs that I adore and love, but the fear lingers. Sometimes I come across a K-9 unit and the terror surfaces. Police dogs are potent police weapons here, today, just as they were in South Africa in the 1980s. There is a long history of this here. Dogs were used to terrorize blacks in the Civil Rights era, and the recent invocation of “vicious dogs” by the president of the United States conjures up centuries of racial terror:

    I learned at age 12 that LAW & ORDER isn’t all it’s hyped up to be.


    I immigrated to America in August 1988, and imagined that here I would find a land free of the suffocating racism of South Africa. In my South African high school racism was open, accepted and embraced. Nigg*r balls were sold in the campus cafeteria (black licorice balls), and students would tell idiotic “jokes”  in which dead blacks were frequently the punchline. Some of the teachers were radically racist. My German teacher, Frau Webber, once told me and Tamir that she would swallow her pride and agree to teach us despite the fact that we were Jews. But much more pernicious was the systemic, underlying, racism. When I grew up the idea that someday I would go to university and study alongside a black person just seemed preposterous. My friends and I would talk about girls. The idea that any of us would ever date, let alone marry an African girl, was just completely and totally out of the realm of possibility. While my school, teachers and friends were what one would consider “liberal” in South Africa, e.g. many supported the ANC, their support of blacks was largely restricted to the right to vote.

    Sadly, America was not the utopia I imagined. In 1989, a year after I immigrated here, Yusef Hawkins was murdered in a hate crime by white youths who thought he was dating a white woman. That was also the year of the “Central Park Five“, in which Trump played a central, disgraceful and racist role. I finished high school in Palo Alto, across a highway from East Palo Alto, and the difference between the cities seemed almost as stark as between the white and black neighborhoods in South Africa. I learned later that this was the result of redlining. My classmates and teachers in Palo Alto were obsessed, in 1989, with the injustices in South Africa. but never once discussed East Palo Alto with me or with each other. I was practicing for the SAT exams at the time and remember thinking Palo Alto : East Palo Alto = Pretoria : Mamelodi.

    Three years after that, when I was an undergraduate student studying at Caltech in Los Angeles, the Rodney King beating happened. I saw a black man severely beaten on television in what looked like a clip borrowed from South Africa. My classmates at the time thought it would be exciting to drive to South Central Los Angeles to see the “rioters” up close. They had never visited those areas before,  nor did they return afterwards. I was reminded at the time of the poverty tourism my friends in South Africa would partake in: a tour to Soweto accompanied by guides with guns to see for oneself how blacks lived. Then right back home for a braai (BBQ). My classmates came back from their Rodney King tour excitedly telling stories of violence and dystopia. Then they partied into the night.

    I thought about my only classmate, one out of 200, who was actually from South Los Angeles and about the dissonance that was his life and my classmates’ partying.

    Now I am a professor, and I am frequently present in discussions on issues such as undergraduate and graduate admissions, and hiring. Faculty talk a lot, sometimes seemingly endlessly, about diversity, representation, gender balance, and so forth and so on. But I’ve been in academia for 20+ years and it was only three years ago, after moving to Caltech, that I attended a faculty meeting with a black person for the first time. Sometimes I look around during faculty meetings and wonder if I am in America or South Africa? How can I tell?


    Today is an opportunity for academics to reflect on the murder of George Floyd, and to ask difficult questions of themselves. It’s not for me to say what all the questions are or ought to be. I will say this: at a time when everything is unprecedented (Trump’s tweets, the climate, the stock market, the pandemic, etc. etc.) the murder of George Floyd was completely precedented. His words. The mode of murder. The aftermath. It has happened many times before, including recently. And so it is in academia. The fundamental racism, the idea that black students, staff, and faculty, are not truly as capable as whites, it’s simply a day-to-day reality in academia, despite all the talk and rhetoric to the contrary. Did any academics, upon hearing of the murder of George Floyd, worry immediately that it was one of their colleagues, George Floyd, Ph.D., working at the University of Minnesota who was killed?

    I will take the time today to read. I will pick up Long Walk to Freedom, and I will also read #BlackintheIvory. I may read some Alan Paton. I will pause to think about how my university can work to improve the recruitment, mentoring, and experience of black students, staff and faculty. Just some ideas.

    All these years since leaving South Africa I’ve had a recurring dream. I fly around Pretoria. The sun has just set and the Union Buildings are lit up, glowing a beautiful orange in the distance. The city is empty. My friends are not there. The man I saw pleading for his life in 1985 is gone. I wonder what the police did to him when he arrived at the police station. I wonder whether he died there, like many blacks at the time did. I fly nervously, trying to remember whether I have my passbook on me. I remember I’m classified white and I don’t need a passbook. I hear dogs barking and wonder where they are, because the city is empty. I wonder what it will feel like when they eat me, and then I remember I’m white and I’m not their target. I hope that I don’t encounter them anyway, and I realize what a privilege it is to be able to fly where they can’t reach me. Then I notice that I’m slowly falling, and barely clearing the slopes of Muckleneuk hill. I realize I will land and am happy about that. I slowly halt my run as my feet gently touch the ground.




    in Bits of DNA on June 10, 2020 12:30 PM.

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    Extraordinary performance of semiconducting metal oxide gas sensors using dielectric excitation

    This week on Journal Club session Ritesh Kumar will talk about impedance spectroscopy and its use in the design of electronic tongue and nose systems. Specifically, he will refer to the paper by Radislav A. Potyrailo et al. along with some of his previous works.

    Impedance spectroscopy is a powerful technique which has been applied to the design of instruments for characterising liquids and solids. The ‘impedance fingerprints’ obtained at various frequencies can be used to classify, define sensitivity, selectivity, linearity of systems. It uses a sweep of sinusoidal frequencies as perturbation signal at low voltage so as to remain in the linear and causal domain. In this talk, I will be presenting about impedance spectroscopy and its use in the design of electronic tongue and nose systems in general and specifically the paper by Radislav A. Potyrailo et al. along with some of our previous works in the design of Electronic Tongue systems. The paper by Radislav A. Potyrailo et al. shows that the run-of-the mill metal oxide gas sensors can act as high performance sensors using the impedance measurements. They show exemplary performance in terms of linearity, limit of detection, cross-sensitivity etc. This can pave way for the design of low cost and efficient electronic nose systems.


    Date: 12/06/2020
    Time: 16:00
    Location: online

    in UH Biocomputation group on June 10, 2020 12:00 PM.

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    Published Peer Review: 1 Year Across PLOS

    Last May, PLOS announced a new option for authors to publish their peer review history, and the support from our communities has been loud and clear. Since our update 6 months ago, we’ve jumped from 800 to over 3,500 articles with published peer review history!

    Why Publish Peer Review

    Opening access to the reviewer comments benefits readers who wish to dive deeper into a specific study. Comments from experts who reviewed the article that would traditionally remain unseen helps contextualize the research. Upcoming researchers can get a glimpse behind the curtains and see what sort of requests authors in their field were asked to address during revisions. If an author chooses to publish both a preprint and their peer review history, the process from first draft to final article can be learned from. 

    Those involved in the peer review process also benefit, as the potential for reviews to be made public further fosters an environment where authors, editors, and reviewers respectfully collaborate to deliver the best possible manuscript for their community.

    Our First Year Publishing Peer Review

    By leaving the decision to opt-in for published peer review history with authors, we’ve seen a steady 39% opt-in rate among eligible manuscripts across all of PLOS. Of those 3,500 publications that agreed to participate in the last year, 60% have at least one signed review! 

    With this increased number of publications with peer review history under our belt, we’ve continued to see the highest opt-in rates in our journals publishing work in health or life-sciences. 

    Within PLOS ONE, Oral Health (57%), Clinical Trials (51%), and Women’s Health (51% and 67 opt-ins) lead the pack in terms of opt-in percentage for subjects with over 20 opt-ins. We’re ecstatic to see so many articles dealing with public health providing access to expert reviewer opinions to further validate the studies.

    Choosing to Collaborate

    We believe authors and reviewers should be in control of how their work is portrayed. Reviewers are given the choice to sign their comments, and authors choose to opt-in when they’ve received and had an opportunity to respond to all reviewer feedback, and their paper has been accepted. 

    Through this system, both roles work in tandem to drive a transition to more diverse, transparent peer review options. A reviewer who signs their name and provides substantial comments backed by evidence may entice an author to opt-in and have the reviewer’s comments published. 

    Alternatively, an author may entice a reviewer to sign their name if their paper is already participating in other aspects of open science, such as publishing a preprint or sharing data and code in a repository. Regardless of your role on a specific paper, you have the choice with PLOS to enact transparency in peer review.

    The Transforming Landscape of Open Review

    Different forms of Open Review are taking hold and changing the evaluation process. Preprint commenting and other opportunities are being realized due to the shift in research attitudes. The greater research community is more accepting than ever to Open Review concepts such as portable peer review (reviews that can be transferred across journals) or Review Commons, a platform providing independent peer review prior to journal submission. 

    Recognizing the essential role of peer review, reviewers have more opportunities to claim credit for their difficult and constructive work. These changes are all opportunities for researchers to cultivate transparency in peer review and, across all sectors of science, improve context and trust.

    The post Published Peer Review: 1 Year Across PLOS appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on June 08, 2020 05:32 PM.

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    arXiv staff to participate in the #strike4blacklives

    The arXiv staff is deeply saddened and angered by the recent killings of George Floyd, Regis Korchinski-Paquet, Tony McDade, Breonna Taylor, Ahmaud Arbery, and so many others. We recognize that Black people live with the injustices of systemic racism every day — and have for centuries — in North America and around the world.

    We acknowledge that in research, as in life, people often perpetuate bias and systemic racism, both consciously and unconsciously. Members of arXiv’s own physics community asked us to pause business-as-usual this week and join scientists participating in the #strike4blacklives. Our US-based staff agreed.

    arXiv is an essential, daily tool for most physicists, and Black physicists are faced with the simultaneous tasks of writing and reading papers, while also fighting for their rights.

    “The strike is an idea that grew out of discussions among Black physicists and astronomers, and importantly one thing that it offers us is a day of rest,” says Dr. Chanda Prescod-Weinstein, professor of physics at the University of New Hampshire and co-organizer of the #strike4blacklives. “I want a day where I don’t have to worry that I’ve missed an important paper on the arXiv because I am stressed out while my non-Black colleagues happily keep going. The strike is not just about gathering people together to begin to take action, but it is also about a day of rest for the people most affected by this heated moment.”

    arXiv will not mail a daily announcement on the evening of Tuesday, June 9, 2020. Submissions received at or after 14:00 ET Monday, June 8 and before 14:00 ET Wednesday, June, 10 will be announced at 20:00 ET Wednesday, June 10.
 We also encourage authors to pause their submissions on Wednesday, June 10 to participate in the #strike4blacklives.

    We encourage arXiv readers to use the time they would normally spend reading the daily announcement or submitting an article to instead read about and discuss racism and how they will work in their own local and professional communities to address it. If you choose to participate, please consider tagging @arXiv on Twitter to let us know what you are doing.

    arXiv was founded as an open and freely available service to disseminate scientific research, and, as such, is an equalizer and democratizer. The arXiv staff is proud of this heritage and at the same time we recognize there is still much work to be done. The staff is participating in the #strike4blacklives and #shutdownSTEM at the request of our community, and we encourage members of minority groups around the world who are underrepresented in science to reach out to arXiv to help us understand how to serve you better.

    in arXiv.org blog on June 08, 2020 03:31 PM.

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    PLOS and Carnegie Mellon University announce APC-free open access publishing agreement

    The following joint press release was issued on June 8, 2020.

    SAN FRANCISCO — Carnegie Mellon University (CMU) and the Public Library of Science (PLOS) today announced a two-year open access agreement that allows researchers to publish in PLOS’ suite of journals without incurring article processing charges (APC). This partnership brings together two organizations that believe researchers should be able to access content freely and make their work available publicly, regardless of their access to funds.

    “The evidence is undeniable — open access research enables the convergence of disciplines that drives scientific innovations,” said Keith Webster, dean of Libraries and director of Emerging and Integrative Media Initiatives for Carnegie Mellon University. “This agreement with PLOS gives our researchers more avenues to provide their work to the public, and, in doing so, increases readership and opportunities for societal impact.”

    Under the agreement, which will be implemented in July, Carnegie Mellon will be charged an annual fixed flat rate over the two-year term, which will be based on prior years’ publication levels. CMU researchers will have unlimited opportunity to publish in PLOS journals over these two years and will not be charged any APC. This pilot will further PLOS’ mission of making open access publishing available to all while ensuring that its journals include research from authors representing a diverse array of disciplines, career stages and geographies.  

    “The agreement with Carnegie Mellon University is yet another step in our goal of empowering authors who want to participate in open access publishing, and it continues the momentum following our recent agreements with the University of California and Iowa State University,” said Sara Rouhi, director of Strategic Partnerships for PLOS. “Both agreements demonstrate our effort to build a truly ‘open to read, open to publish’ environment for authors as well as our commitment to experimentation with our library partners.”

    The post PLOS and Carnegie Mellon University announce APC-free open access publishing agreement appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on June 08, 2020 07:01 AM.

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    arXiv at the American Astronomical Society


    On June 2, 2020, arXiv’s executive director, Dr. Eleonora Presani, presented at the American Astronomical Society’s 236th meeting, held virtually. Below is a summary, first published on AAS Nova and Astrobites, of her talk.


    AAS Publishing Exclusive: A Discussion with the arXiv Executive Director

    by Alex Pizzuto

    Day 2 of the meeting started strong, featuring a discussion with arXiv Executive Director Eleonora Presani, who detailed the current status and future outlook of the open access archive service many of us know and love. Not only is Presani new to the role of executive director, but the role itself is only two months old, marking a step towards engaging with the scientific community more efficiently and productively. As someone equipped with both a PhD in astroparticle physics and more than 6 years of experience from a career in scientific publishing, Presani is extremely qualified to help execute the vision of arXiv.

    Presani began her presentation with her own mantra on the dissemination of scientific research: “knowledge only exists if it is accessible.” As an organization, Presani believes that arXiv functions as the “enablers” for the sharing of this knowledge, and seeks to make accessible environments like arXiv; those which are for researchers, by researchers. To get a sense of the sheer volume of knowledge that passes through the arXiv servers, Presani quizzed her audience, revealing some dumbfounding statistics about the quantity of preprints that have been submitted:

    Tweets from Astrobites

    The fact that about half of the funding for arXiv is from the community is a testament to the fact that arXiv exists to serve the community.

    Although many organizations have been slowed to a halt by the tragic global pandemic, Presani assures us that arXiv is still working hard. Over the last few months, arXiv has rolled out user-driven classification, which alerts authors when they assign their papers to a category that disagrees with arXiv’s classification algorithm. They have also been executing operational stability drills and developing a COVID-19 moderation plan, to make sure that no matter what is going on in the world, scientists can stay connected through their research.

    Looking more to the future, we were then told about arXiv’s 3-year strategic plan (picture below). This plan is broken down into three distinct user categories (readers, authors, moderators) and discusses how each of these users can benefit in three different areas (control, impact, and collaboration). In order to successfully execute this plan, however, arXiv requires our help and wants to hear from scientific communities like the AAS, in order to learn what researchers believe are the highest impact deliverables.

    There are also some specific tasks that the arXiv team is focusing on over the next 18 months. These include distributing some of their classification data to Kaggle, allowing users to contribute to classification algorithms. Additionally, arXiv will be rolling out an update to TeXLive2020 and is actively working on improving their user disambiguation techniques.

    Focusing arXiv’s resources to decide which of these goals is completed first is no simple task. Presani highlighted how challenging it is to balance all of the lofty goals of arXiv with their limited resources and discussed how no changes should be rolled out until they are up to arXiv’s high standards, noting that “arXiv was launched in 1991, and when it launched, it was an extremely cutting-edge product and it stayed the same for 30 years. It’s important to find the right balance between being quick and keeping the high quality of the work.”

    Tweet from Astrobites

    Interested in helping arXiv execute their vision? There are a variety of ways to contribute. Start by joining arXiv’s user testing or read their blog and news/announcements. They are also looking for volunteers to help with developing a better moderator workflow, and they are soliciting applications for volunteers (if interested, you can send your CV and a motivation letter to moderation@arxiv.org). Best of all, continue to use the arXiv and engage in discussion with the administrators about what your perfect arXiv would look like in the future.


    This article first appeared on AAS Nova and Astrobites. It is reposted here with permission from AAS.


    in arXiv.org blog on June 03, 2020 07:31 PM.

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    A Kirchhoff-Nernst-Planck framework for modeling large scale extracellular electrodiffusion surrounding morphologically detailed neurons

    This week on Journal Club session Reinoud Maex will talk about the paper "A Kirchhoff-Nernst-Planck framework for modeling large scale extracellular electrodiffusion surrounding morphologically detailed neurons".

    Many pathological conditions, such as seizures, stroke, and spreading depression, are associated with substantial changes in ion concentrations in the extracellular space (ECS) of the brain. An understanding of the mechanisms that govern ECS concentration dynamics may be a prerequisite for understanding such pathologies. To estimate the transport of ions due to electrodiffusive effects, one must keep track of both the ion concentrations and the electric potential simultaneously in the relevant regions of the brain. Although this is cur- rently unfeasible experimentally, it is in principle achievable with computational models based on biophysical principles and constraints. Previous computational models of extracel- lular ion-concentration dynamics have required extensive computing power, and therefore have been limited to either phenomena on very small spatiotemporal scales (micrometers and milliseconds), or simplified and idealized 1-dimensional (1-D) transport processes on a larger scale. Here, we present the 3-D Kirchhoff-Nernst-Planck (KNP) framework, tailored to explore electrodiffusive effects on large spatiotemporal scales. By assuming electroneu- trality, the KNP-framework circumvents charge-relaxation processes on the spatiotemporal scales of nanometers and nanoseconds, and makes it feasible to run simulations on the spatiotemporal scales of millimeters and seconds on a standard desktop computer. In the present work, we use the 3-D KNP framework to simulate the dynamics of ion concentra- tions and the electrical potential surrounding a morphologically detailed pyramidal cell. In addition to elucidating the single neuron contribution to electrodiffusive effects in the ECS, the simulation demonstrates the efficiency of the 3-D KNP framework. We envision that future applications of the framework to more complex and biologically realistic systems will be useful in exploring pathological conditions associated with large concentration variations in the ECS.


    Date: 05/06/2020
    Time: 16:00
    Location: online

    in UH Biocomputation group on June 02, 2020 09:09 AM.

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    The COVID Stress Scales

    Danger. Deprivation. Xenophobia. Contamination. These are some of the fears related to COVID-19. Scores of COVID questionnaires have popped up recently to assess fear, anxiety, stress, and depression related to the novel coronavirus and its massive disruption to daily life. Most are freely available for use as research tools, but few have been validated and peer reviewed.

    The COVID Stress Scales (CSS) developed by Taylor and colleagues (2020) were recently published in the Journal of Anxiety Disorders. The authors propose a new COVID Stress Syndrome, and present evidence that the CSS subscales are intercorrelated (which is suggestive of a “coherent” condition).

    To develop the CSS, representative samples of people in Canada (n=3,479) and the US (n=3,375) completed a 58-item survey on Qualtrics. Factor analysis identified five subscales...
    1. COVID danger and contamination fears
    2. COVID fears about economic consequences
    3. COVID xenophobia
    4. COVID compulsive checking and reassurance seeking
    5. COVID traumatic stress symptoms

    ...and limited the questionnaire to 36 items. I'll note that “fears about economic consequences” were restricted to a lack of supplies at grocery stores and pharmacies, rather than fears of crushing debt, eviction, hunger, and homelessness because of unemployment.

    One can view this new syndrome as a context-related extension of OCD contamination fears, compulsive checking, and health anxiety (preoccupation with the possibility of serious illness). Indeed, convergent validity was confirmed by showing correlations with established measures of those conditions. Unique aspects of COVID Stress Syndrome not seen in other diagnoses include fears that grocery stores would run out of toilet paper,1 and especially a fear of foreigners (xenophobia). Xenophobia is promulgated by politicians and amplified by bad actors on social media and IRL. I don't think xenophobia (specifically, anti-Asian sentiment) is on the list of symptoms for any DSM diagnosis.

    Basically, it seems that a coherent condition called COVID Stress Syndrome would require racist beliefs and a fear of people who are Chinese, Chinese-American, or Chinese-Canadian.2 The prevalence of COVID Stress Syndrome in their Canadian and American samples was not specified, nor was the cut-off point for such a diagnosis. Plenty of Americans are xenophobic, but they don't have bad dreams about coronavirus.

    In an editorial, Taylor and Asmundson (2020) said:
    It appears that people who develop COVID Stress Syndrome have pre-existing psychopathology, particularly pre-existing high levels of health anxiety and obsessive-compulsive checking and contamination symptoms. It remains to be seen whether the COVID Stress Syndrome is simply an adjustment disorder, abating once the pandemic is over, or whether it will become chronic for some individuals.

    So much about COVID-19 “remains to be seen”, and this level of uncertainly is a major source of anxiety on its own.


    1 The toilet paper question just missed the cut...included were worries about water, cleaning supplies, medications, etc. The original version also included “worry about looting & rioting.”

    2 One could really say East Asian people more broadly. Or actually, anyone considered “Other”.


    Taylor S, Asmundson GJG. (2020). Life in a post-pandemic world: What to expect of anxiety-related conditions and their treatment. J Anxiety Disord. 2020; 72:102231.

    Taylor S, Landry CA, Paluszek MM, Fergus TA, McKay D, Asmundson GJG. Development and initial validation of the COVID Stress Scales. J Anxiety Disord. 2020; 72:102232.

    Additional Scales (from a compendium of COVID questionnaires on Google docs)

    Epidemic-Pandemic Impacts Inventory Racial/Ethic Discrimination Addendum (15 items).

    COVID-19 Stressful events (13 items)

    COVID-19 Concerns (9 items)

    Coronavirus Stressor Survey (9 items)

    CRISIS (The CoRonavIruS Health Impact Survey V0.3) - more here

    Covid-19 Staff Needs and Concerns Survey (18 items)

    COVID-19 Family Stress Screener (10 items)

    ADDENDUM (June 1, 2020): MORE!

    UCLA Brief COVID-19 Screen for Child/Adolescent PTSD

    Fear of COVID-19 Scale (10 items)
    Ahorsu DK, Lin CY, Imani V, Saffari M, Griffiths MD, Pakpour AH. The Fear of COVID-19 Scale: Development and Initial Validation. International Journal of Mental Health and Addiction. 2020 Mar 27:1-9.
    Coronavirus Anxiety Scale (5 items)
    Lee SA. Coronavirus Anxiety Scale: A brief mental health screener for COVID-19 related anxiety. Death Studies. 2020 Apr 16:1-9.

    in The Neurocritic on June 01, 2020 06:46 PM.

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    The PLOS Blogs Network: Fascinating Perspectives from Independent Writers and Staff Contributors

    You may have noticed our PLOS Blogs Network has a fresh new look.  What’s changed? A cleaner design, better user experience and enhanced search. What hasn’t? The same great content from our independent bloggers and staff contributors.  Here’s a brief overview of what you’ll find on the ‘new and improved’ Network.

    Independent Blogs

    Absolutely Maybe: Meta-scientist Hilda Bastian writes about evidence and bias in medicine, and the culture of science. The blog is illustrated with her own cartoons.

    DNA Science: Geneticist Ricki Lewis blogs from the cutting edge of genomics, including genetic testing, stem cells, gene therapy and more

    All Models are Wrong: Dr. Tamsin Edwards tackles climate science in her blog, while at work at King’s College London and advising policymakers.

    SciComm: PLOS SciComm helps scientists, physicians, and journalists become better communicators with the general public and policy makers. Krista Hoffmann-Longtin, Jason Organ, and Bill Sullivan of the Indiana University School of Medicine are the writers and editors at PLOS SciComm. If you would like to contribute to PLOS SciComm, please email them at scicommplos@gmail.com. Follow them on Twitter @SciCommPLOS. 

    The ECR Community: Andreas Vilhelmsson, a public health researcher at Lund University, Sweden, oversees this blog, which attracts the next generation of scientists and science writers who are currently at the undergrad, graduate or post-doctoral levels (up to 5 yrs post PhD). Posts provide unique insights into the current state of science education, research developments in individual disciplines, science communication and Open Access issues with special attention paid to education and career choices facing early career scientists at these critical stages of their work lives. 

    Your Say: is the site on PLOS BLOGS Network for guest posts from scientists and science writers who wish to express individual points of view on issues in science, medicine and scholarly publishing.  We encourage voices and perspectives from any scientific discipline. If you would like to contribute to Your Say, please email your submission to us at:community@plos.org.

    Staff Blogs:

    The Official PLOS Blog: Announcements, perspectives, and policy updates from PLOS Staff. This is your go-to source to learn more about our collective mission and the ways in which we’re experimenting to help researchers transform scholarly communication and open science.

    Speaking of Medicine: This blog encourages researchers and health policy experts to share their experiences from the field, views on critical health issues, hopes for the future of medicine, opinions on the medical education system, as well as any other thoughts about topics relevant to global health issues.

    PLOS Biologue: This blog helps the community stay abreast of groundbreaking biological research and discussions in the field, on topics ranging from Open Access publishing developments and science policy, to science outreach and education, and the implications of new discoveries in biological research.

    EveryONE: This blog covers a range of topics, from staff perspectives on publishing and Open Access developments to posts highlighting the breadth and variety of scientific research published in PLOS ONE.

    PLOS Collections: Aggregates and curates related content from PLOS journals and the PLOS Blogs Network to provide structured access to papers of interest in the PLOS corpus and demonstrate innovative approaches to the assessment, organization and reuse of research, data and commentary.

    The post The PLOS Blogs Network: Fascinating Perspectives from Independent Writers and Staff Contributors appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on June 01, 2020 04:59 PM.

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    How Much Color Do We Really See?

    Most people don’t notice massive color distortion in their peripheral vision.

    in Discovery magazine - Neuroskeptic on May 30, 2020 11:00 PM.

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    Moving beyond toxic masculinity: a Q&A with Ronald Levant

    In 2018, the American Psychological Association released its first ever Guidelines for Psychological Practice with Boys and Men. At the time of the release, these guidelines were met with criticism by some who viewed them as pathologizing masculinity, but since the guidelines were released the discussion of “toxic masculinity” has spread to all areas of our society and culture. Ronald F. Levant has served as president of American Psychological Association as well as president of the association’s Society for the Psychological Study of Men and Masculinities. Levant has been a leader in the research on the psychology of men. We spoke with him about how traditional masculinity ideology is conceptualized by psychologists, how it plays out in our society, and why it’s important from a psychological standpoint to move beyond the concept of toxic masculinity.

    Sarah Butcher: You observe that the feminist movement opened up more options for girls and women to express their identity but that there was no corresponding movement for men. Why do you think that is?

    Ronald Levant: In the 1960’s amid the civil rights and LGBTQ movements, women decided once again (think of the suffrage movement) to address their oppression.  The result is what is called second wave feminism. Over the 70s to the 90s many men felt defensive in the face of women’s newfound assertiveness, resulting in what was then called a masculinity crisis (think Bridges over Madison County). This led to several different types of movements. One that gained prominence was the mythopoetic movement (remember Robert Bly and Iron John?), which did help some men become more comfortable with their emotions but was also was suffused with misogyny. Others like the Promise Keepers and the Men’s Rights Organization were even more blatantly misogynistic. What we advocate is a movement that is inspired by the ideals of gender equality, one that would help men ditch the burdens of dominance, and teach men that they can be men without the trappings of masculinity.

    SB: You coined the term Traditional Masculinity Ideology—how do you define it, and how do you see it playing out in the lives of men?

    RL: The most current definition is the holistic set of beliefs about how boys and men should, and should not, think, feel and behave. As far as current research is concerned, we’re typically looking at seven sets of prescriptive and proscriptive norms–avoidance of femininity; negativity toward sexual minorities; self-reliance through mechanical skills, toughness, dominance, importance of sex, and restrictive emotionality.

    SB: Do you see any biological component to masculinity, or is it entirely socially constructed?

    RL: There may be a biological basis to masculinity, but I am not aware of any solid support for this proposition. More importantly, we are psychologists not biologists, and we study masculinity as a social and psychological phenomenon.

    SB: In recent decades, men have begun shouldering more of the burden of domestic labor and childrearing (although far from an equal share). Why does that pose a challenge to traditional masculinity ideology?

    RL: Good questions. It poses a challenge to traditional masculinity ideology because it violates the avoid all things feminine norm, because childcare (and nurturance in general) is considered feminine.

    SB: Research has shown that men have a harder time expressing (and even naming) their emotions. Why is that and what are the consequences for themselves and others?

    RL: Decades ago, I noticed this in my work in the Boston University Fatherhood Project, and curiosity drove me to study the emotion socialization research literature in developmental psychology. Boys start out life more emotionally expressive than girls as neonates and retain this advantage over the first year of life, but from ages two to six—due to the childhood socialization of emotions, in which boys are made to feel ashamed of themselves for expressing vulnerable and caring emotions—many lose this expressive ability. This study formed the base for my normative male alexithymia hypothesis. “Alexithymia” means no words for emotions. My hypothesis is that socialization guided by traditional masculinity ideology, and in particular the norm of restrictive emotionality, produces a mild form of alexithymia in men, who cannot give a good account of their inner lives. This has enormous implications for relationships, stress management, and mental health. I later developed a treatment for such men called Alexithymia Reduction Treatment.

    SB: As you argue, most violence is committed by men, yet most men aren’t violent. What is it that leads a minority of men to engage in violent behavior, and what role does traditional masculinity ideology play?

    RL: This is a good question. The short answer is that we don’t know why some men are violent and others are not. Various theories have been proposed, with social-situational factors having more weight than personality factors. What we do know is:

    • The vast majority of boys and men are not violent.
    • The vast majority of adult men do not endorse traditional masculinity ideology.
    • There are literally 40 + years of research showing correlations between all of the masculinity scales and harmful outcomes, and many of these are related to violence.
    • We think that the correlation is due to the boys and men who score at the very high end of these scales. Thus, high endorsement of or conformity to the norms of traditional masculinity is associated with rape myth acceptance, disdain for racial and sexual minorities, or aggression, for example.

    SB: What role does traditional masculinity ideology play in sexual violence, ranging from sexual harassment to rape?

    RL: Based on the avoid femininity norm, boys prefer playing with other boys rather than girls, and thus rarely get to know girls as persons. In puberty boys become very interested in girls, but as sex objects. Objectifying women is at the very foundation of sexual violence.

    SB: You also examine different versions of masculinity ideology such as African American masculinity and Latinx masculinity. How can the theory of intersectionality help us understand these different masculinities?

    RL: The theory of intersectionality says that our overall identity and sense of self is a composite of a number of specific identities that may relate to our race/ethnicity, gender identity, sexual orientation, age cohort, etc. So, for example, African American men have to fulfil the requirements of the male role (e.g., providing for one’s family) impeded by racism, which has reduced educational and employment opportunities for black men.

    SB: What is the role of traditional masculinity in mental and physical health?

    RL: Traditional masculinity ideology emphasizes toughness, self-reliance and never revealing vulnerability. In the areas of physical and mental health this translates into taking health risks, not seeking professional help when needed, and relying on alcohol for stress reduction.

    SB: Based on your clinical experience, what are some of the most effective techniques for men who want to escape the prison of traditional masculinity ideology?

    RL: The most effective techniques I have found is helping men who are unable to verbalize their emotions to learn how to do that, to open up their hearts to their families. This often involves first dealing with their fears that this will somehow emasculate them, strip them of their ‘man card,’ and along the way dealing with their sense of shame resulting from violating the male code.

    SB: What role do fathers play in the propagation of traditional masculinity ideology, and what are some tips for fathers wishing to model a more gender-neutral approach?

    RL: The “essential father hypothesis” posits that the father’s essential role is to model masculinity and heterosexuality for his sons. Although this idea has been largely discredited in academia it is still very prominent among the public. A better alternative is the involved father role, in which dads share parenting duties equally with their female partners.

    Featured image by Aarón Blanco Tejedor on Unsplash.

    The post Moving beyond toxic masculinity: a Q&A with Ronald Levant appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on May 30, 2020 09:30 AM.

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    Did Freud ‘Borrow’ His Ideas on Sexuality?

    Freud’s ideas were not the unprecedented breakthrough he claimed.

    in Discovery magazine - Neuroskeptic on May 29, 2020 11:00 PM.

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    On Robot Compliance: A Cerebellar Control Approach

    This week on Journal Club session Volker Steuber will talk about the paper "On Robot Compliance: A Cerebellar Control Approach".

    The work presented here is a novel biological approach for the compliant control of a robotic arm in real time (RT). We integrate a spiking cerebellar network at the core of a feedback control loop performing torque-driven control. The spiking cerebellar controller provides torque commands allowing for accurate and coordinated arm movements. To compute these output motor commands, the spiking cerebellar controller receives the robot's sensorial signals, the robot's goal behavior, and an instructive signal. These input signals are translated into a set of evolving spiking patterns representing univocally a specific system state at every point of time. Spike-timing-dependent plasticity (STDP) is then supported, allowing for building adaptive control. The spiking cerebellar controller continuously adapts the torque commands provided to the robot from experience as STDP is deployed. Adaptive torque commands, in turn, help the spiking cerebellar controller to cope with built-in elastic elements within the robot's actuators mimicking human muscles (inherently elastic). We propose a natural integration of a bioinspired control scheme, based on the cerebellum, with a compliant robot. We prove that our compliant approach outperforms the accuracy of the default factory-installed position control in a set of tasks used for addressing cerebellar motor behavior: controlling six degrees of freedom (DoF) in smooth movements, fast ballistic movements, and unstructured scenario compliant movements.


    Date: 29/05/2020
    Time: 16:00
    Location: online

    in UH Biocomputation group on May 27, 2020 12:44 PM.

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    Be a TA at Neuromatch Academy

    Neuromatch Academy is an online summer school in computational neuroscience at scale, and we need TAs like you! Here’s what we’re planning:

    • 1500 students spread over 50+ countries
    • 9 timezones
    • 15 days
    • 45 hours of content (sample day)
    • 60 colab tutorials (sample day)
    • Teaching by 200 TAs (one of which could be you!)

    It’s an experiment in democratizing computational neuroscience education, and we can’t do it without TAs. As a TA, you’ll teach a small group of people (aiming for 6:1 student:TA ratio) who are slightly earlier in their careers (typically early masters and early PhD students in neuroscience). You’ll:

    • help students from diverse background get quality education
    • learn more about computational neuroscience – there’s no better way to master a subject than to teach it
    • get access to NMA’s network of mentors
    • receive teacher training by seasoned educators specialized in project-based learning
    • see and help this huge project being built in realtime (like Asaph says in his vid, it really feels like an adventure). If you wanna learn about project management, education, building tech at scale, etc. this is the place.
    • (bonus) have something great to talk about in your teaching statement
    It really feels like an adventure

    You’ll get compensated for your time (1500$ for three weeks). Round 2 applications for Teaching Assistants are due Monday May 25th. If you’re interested in being a TA and haven’t received a Round 2 application or did not apply to Round 1, you can still apply.

    Fill out an application now.

    in xcorr.net on May 23, 2020 06:17 PM.

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    Why anti-vaxxers are rising again

    In the midst of a health crisis when our only hope is a new vaccine, many have begun to wonder how those with anti-vaccination sentiments might respond to the current COVID-19 crisis. Many have guessed that the only natural, rational response would be for anti-vaxxers to change their minds and wholeheartedly embrace the prospect of a new vaccine. After all, there is a prevailing theory that anti-vaccine sentiment arises at least in part from a collective amnesia about the true scourge of vaccine-preventable diseases. Vaccines, so the argument goes, are a victim of their own success, resulting in a situation in which people do not remember why they are getting vaccinated because the diseases that the vaccines prevent against have been absent for so long. If this theory is true, then in a situation in which we are face-to-face with the ill effects of an infectious pathogen, we should all readily embrace a new vaccine.

    It turns out that the anti-vaxxer response to COVID-19 and the prospect of a new vaccine, much like science denialism more generally, is much more complex than that. The response also seems to suggest that the idea that amnesia about diseases that have been largely conquered by vaccines is probably not the primary reason for anti-vaccine sentiments. So how have people with anti-vaccine tendencies responded to COVID-19? While it’s still too soon to have a complete picture of this, especially since no new vaccine has been rolled out yet, several interesting patterns have emerged.

    Staunch anti-vaxxers still oppose vaccines, including potential new coronavirus vaccines, and are active at spreading misinformation. Those who have not made up their minds about whether vaccines are safe are now wavering more than they were previously. Whereas before they may have been slightly more inclined in the anti-vaccine direction, now they are questioning those viewpoints more. They do seem to remain amenable to being persuaded.

    Public figures, such as politicians and musicians, who are staunch anti-vaxxers are facing more opposition now. Crisis situations have the tendency to bring certain background issues into high relief. People who may have found anti-vaxxers to be somewhat irritating but not a direct threat are now viewing them differently and thus more social pressure is being placed on anti-vaxxers to abandon their views and change their behaviors.

    Still, anti-vaxxers are very active and very vocal, both about potentially refusing a new vaccine for coronavirus but also increasingly voicing conspiracy theories about coronavirus itself. These conspiracy theory claims run the gamut, from claiming the virus is not as bad as public officials note to warning people that public officials and government bodies like the CDC are not to be trusted.

    Another very disturbing development is the migration of objections to a putative coronavirus vaccine away from a scientific and health basis and toward a more general political basis. Anti-vaxxers are now linking stay-at-home orders and the hoped-for vaccines as assaults on liberty and freedom. Although anti-vaxxers have always made personal liberty a part of their message, by incorporating objections to a coronavirus vaccine into the broader context of freedom, they have taken this link to an extreme.

    Heidi Munoz Gelisner, a leader in anti-vaccine and anti-lockdown protests, told a reporter at the New York Times, “we have always been about freedom.” This adds a new dimension to our efforts to ensure that there is swift uptake of a coronavirus vaccine as soon as it becomes available. Targeting the pro-vaccine message on issues of vaccine safety and efficacy may not address this broader issue. Of course, the notion that vaccines involve a personal liberty aspect is faulty: it is long recognized that no one has the right to jeopardize the health of others, especially children, and therefore that democracies can legitimately enforce vaccine requirements. Nevertheless, Americans are perhaps more insistent about a broad range of personal liberties than citizens of any other country and therefore we will have to consider ways to address this aspect of anti-vaccination sentiment as well.

    More than 90 vaccines against the virus that causes COVID-19 are now in various stages of development and the most optimistic predictions would give us a viable one in a year to 18 months. Research by Kathleen Hall Jamieson, director of the Annenberg Public Policy Center at the University of Pennsylvania, indicates that we can no longer rely on debunking myths about vaccines after they have been promulgated throughout the media. Rather, her work calls for “proactive messaging,” in which groups of experts begin to thwart anti-vaccination messages before a crisis promoted by misinformation begins. Thus, we need to start immediately to use evidence-based communication methods to preempt the different varieties of misinformation about a vaccine for COVID-19. There is no time to waste.

    Featured Image Credit: Photo by pressphoto via Freepik

    The post Why anti-vaxxers are rising again appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on May 23, 2020 09:30 AM.

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    The Dream of ‘Disconnected Psychology’

    Does psychology need researchers who ‘don’t follow the discipline’s norms and conventions’?

    in Discovery magazine - Neuroskeptic on May 22, 2020 11:00 PM.

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    We Don’t Know How You Make a Decision

    A new study shows we cannot tell how you’re using the evidence before you

    in The Spike on May 21, 2020 02:46 PM.

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    arXiv.org Moderator for Rapid Screening of COVID-19 Research

    Update May 26, 2020: Thanks for your interest. We’re pleased to report that this position has been filled.

    Make an impact on COVID-19 research as a Google-sponsored moderator for arXiv.org. This is a temporary contract position with flexibility, up to 12 hours per week, for up to six months.

    arXiv is currently receiving a flood of papers related to COVID-19 and is engaging additional paid support to help ensure quality and accuracy of this important work.

    The selected candidate will work with a globally distributed team of volunteers and staff performing quality control checks on article submissions. Moderators work independently following arXiv’s moderation standards.


    The successful candidate must be familiar with standards for research on human subjects, patient data, and clinical trials. This could be related fields of medicine, biology, biological modeling and may extend to statistics, computer, or information science.

    This is an ideal position for PhD or MD graduates, Post Docs, or early career researchers who want to support and learn about open access information sharing.

    More information on arXiv’s moderation standards can be found here: https://arxiv.org/help/moderation. Accepted papers can be found here: https://arxiv.org/covid19search

    arXiv is the world’s premiere open access platform for dissemination of scientific works, for researchers by researchers. It is a community-centered, non-commercial and impartial archive, and its cutting edge platform enables fast distribution and discovery of recent results, facilitating downstream innovation in scholarly communication. arXiv aims to empower its community to share and advance research together.

    Interested candidates, please send your resume or CV to moderatorsearch@arxiv.org.

    in arXiv.org blog on May 20, 2020 04:03 PM.

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    New User-Driven Classification Tool Released

    The correct categorization of scholarly works is vitally important. It helps readers find the information they seek — and assures authors that their research will be found by the right audience. Recently, arXiv released a new user-driven classification tool to help authors choose the correct category for their papers during the submission process.

    “I think this is a great addition, and I am already seeing positive effects,” said Frank Simon, Max-Planck-Institute for Physics, Munich, Germany and arXiv moderator. “Since the feature has been in operation, submitters tend to classify things for my category (physics.ins-det) correctly more often.”

    When submitting to arXiv, authors select a category for their paper, such as computational geometry or quantum physics. Now, in real time, the automated classifier double checks that selection by comparing the paper to those already hosted on arXiv.org. If the author’s selection doesn’t match the classifier’s recommendation, an alternate category is proposed. The author can review the suggestion, accept or decline it, and continue the submission process, as shown below.

    This is a screen shot of arXiv's classifier recommendation tool.

    In the past, only moderators had access to the automated classifier recommendations, after submission. Moderators reviewed the recommendations, and, if necessary, reclassified papers. This added time to the process and often led to delays.

    Integrating the classifier recommendations into the submission process empowers authors and increases transparency when reclassification is necessary. Additionally, this feature is expected to reduce the workload for moderators and lower the number of papers put on hold due to misclassification. Improved category selection during the submission process will provide more accurate classification at the outset and therefore reduce delays in announcing papers.

    “In my category, the most common issue is the case where instrumentation papers that should have physics.ins-det as primary category are instead submitted to hep-ex, nucl-ex, physics.optics or the like, and subsequently need to be reclassified,” Simon said. “Alerting the submitters that their instrumentation paper should be submitted to the instrumentation category rather than one of the others will reduce moderation workload and speed up the release of the articles, so it is a win-win situation for both submitters and moderators.”

    Other moderators have also expressed enthusiasm about the new feature, calling it important, worthwhile, a fantastic idea, and a big step forward, “even if there will be hiccups” in the beginning. In the first four days after release, 17.4% papers received category recommendations and 67.5% of authors accepted the suggested category.

    arXiv continues to welcome feedback on this feature, which was first tested by volunteer moderators. Authors who receive a category recommendation will have the opportunity to complete a survey about their experience. Moderators are sharing their observations and experiences with arXiv staff, and staff members are monitoring server log statistics.

    Moving forward, arXiv is developing a new version of this machine learning classifier tool that will be trained by feedback from users and moderators in order to provide better category recommendations in the future.

    We encourage the arXiv community to participate. Join the user testing group here and share your experiences on Twitter with the hashtag #arXivexperience.

    in arXiv.org blog on May 20, 2020 01:50 PM.

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    Preprints and the Media: A change to how PLOS handles press for papers previously posted as preprints

    This post was written by Beth Baker, PLOS’ Senior Media Relations Manager.


    PLOS actively encourages the posting of preprints – please see https://plos.org/open-science/preprints/ for all the ways authors can engage. Posting of preprints and discussion of preprints will never affect editorial decisions to publish work in a PLOS journal.

    From today, articles accepted at PLOS journals that were previously posted as a preprint will be under a press embargo which lifts upon publication. This alters our prior practice of not applying an embargo to articles that were previously posted as a preprint and means that we will be applying a consistent press embargo to all articles published at PLOS. We have made this decision after conducting research revealing the positive impact of press embargoes for PLOS papers. The change will optimize authors’ opportunities to disseminate their work to the public via the press and will ensure that authors who have posted preprints are not disadvantaged by this choice, nor are authors disincentivized to post preprints.

    Open communication of research, and the value of embargoes

    PLOS’ press embargo policy is designed to positively impact researchers and to aid the communication of their work. We work to facilitate open communication of research wherever possible. PLOS encourages the discussion of research between scientists at all stages in the publication process. Researchers are free to present and discuss their work for scientific purposes prior to publication. This includes talking about research at conferences and on preprint servers.

    While we know that preprints play a crucial role in the efficiency of scientific communication, establishing priority sooner, increasing attention, and opening up the review process to all, we also believe that public attention at scale via the media should focus on the most reliable science: published, peer-reviewed research. Press embargoes continue to be the best tool to facilitate that. 

    Embargoes enable authors to achieve accurate, high-quality media coverage which disseminates their peer-reviewed research to non-expert readers. Since our articles are accessible to everyone, everywhere upon publication, our embargoes also ensure that peer-reviewed published articles are accessible to the public when first reported in the media.

    Embargoes provide fair and equal access for journalists to allow them time to research their stories and to speak with experts. They give press officers adequate time to coordinate coverage with scientists at their institutions, and give researchers the opportunity to provide comments.

    Discussion of research prior to publication, whether in the scientific community or in the media, will never affect editorial decisions to publish work in a PLOS journal. Prior coverage in the media may simply affect if and how PLOS promotes that research at the time of publication.

    Background to our research

    PLOS partnered with preprint server bioRxiv in May 2018 to help authors opt in to preprints. Soon after, we decided not to embargo for media purposes any published papers which had previously been posted as preprints, believing that embargoes might not be meaningful, necessary, or practical for these papers. Instead, we distributed press releases for such research without embargo at the time of publication, and encouraged institutions to do likewise.

    Following implementation of this embargo exception for preprinted papers, we heard concerns from journalists, press officers and the UK Science Media Centre about this policy. Some parties felt that releasing preprinted research without embargo could result in less media coverage, or in lower quality, less accurate coverage, as journalists would race to report on research immediately or decide not to cover it at all. Concerns were also raised that not embargoing preprinted research meant forfeiting a valuable tool to help journalists focus on covering peer-reviewed published research rather than non-peer-reviewed preprints.

    PLOS’ media team therefore investigated the claim that non-embargoed preprinted papers received less media coverage.

    What we researched and what we found

    We took all the preprinted papers we’d press released without embargo between October 1, 2018 (when we introduced the policy) and September 11, 2019 and paired each with a paper we’d press released under embargo that published at around the same time. Each paired paper was from the same journal as the preprinted paper, and for our multidisciplinary journal PLOS ONE, we also ensured the paired paper was in the same broad scientific area.

    We examined the amount of media coverage each paper had received by measuring the number of mentions of the paper in the media, using media intelligence software Meltwater. We used paired t tests to assess if differences found were statistically significant. 

    We found that the preprinted papers press released without embargo received significantly less media coverage than the paired papers press released under embargo. This was true both in terms of total media mentions (74.60 more media mentions (19.27 vs 93.87); 95% CI: 14.07 – 135.13) and in terms of media mentions in the highest profile outlets (1.47 fewer high profile mentions (0.07 vs 1.53); 95% CI: 0.55 – 2.39). We note that our sample size was small, comprising 30 preprinted papers press released without embargo and 30 paired papers, and we only examined two broad measures of media attention. However, these results support the anecdotes we had previously heard.

    How we are reacting

    Our research indicates that embargoed papers receive more media coverage, including in the most high-profile news outlets, than papers which are not embargoed. A practice of not embargoing papers previously posted as preprints therefore risked disadvantaging authors who posted preprints, and/or disincentivizing the posting of preprints, which PLOS actively encourages. We have decided to change our practice to treat all our authors equally, and to maximize authors’ opportunities to work with the press to disseminate their work to the public.

    From today, all PLOS publications promoted to the press will be embargoed until the time of publication. We believe that this change will enable all our authors to reap the benefits of the embargo system – whether or not they have previously posted preprints – and will facilitate continued high-quality science communication to the public.

    The post Preprints and the Media: A change to how PLOS handles press for papers previously posted as preprints appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on May 19, 2020 05:05 PM.

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    Pandemic practicalities and how to help teenagers manage time at home

    It’s May and many of us have fond memories of springtime when we were in high school. There was some stress from exams and final papers to be sure, but also more outdoor activities, sports, banquets or awards assemblies, proms, and most of all, looking forward to the summer. High school students today, however, have lost all of that. Seemingly in an instant, they are confined at home, with little access to friends, no organized sports, arts, music, journalism, or other activities. Education via teleconferencing is of variable quality and is no substitute for the interactive learning with other students and a skilled educator. Most of all, our students face an uncertain future. It is especially difficult for teens to foresee or plan for a future with the current disruption. Adolescents may well not be able to deal with these multiple concerns, so it’s predictable and understandable that many high school students are struggling with anxiety and depressed mood. Even before the pandemic adolescents had high rates of clinical anxiety and depression. We are facing an enormous mental health crisis.

    As parents there’s a lot we can do to help support our teens. Here are some practical tips to alleviate anxiety and promote stability during this uncertain time.

    Create a schedule. Maintaining a regular schedule can provide a sense of stability for the whole family. Teens still have school; many parents are working and those form the basic skeleton of the day. Online learning can be draining so I suggest periodic breaks, at least 15 minutes of stretching, running in place, or going outside (if possible) every two hours or so. Teens with attentional issue may need more frequent breaks.  Add structured time for meditation, pleasant events, and physical activity. Many schools, online programs, and apps can support a meditation practice.  At the minimum we can teach our children to take just a few minutes to breathe deeply as a break from the stresses of the day. I am partial to Dr. Andrew Weil’s simple 4-7-8 approach, breathing in for four seconds, holding the breath for seven seconds, and then exhaling very slowly for eight seconds.  I can feel a sense of relaxation at about number five during the exhale. This small exercise is helpful to everyone and can quell anxiety. Evenings might be a time to reclaim long-forgotten family activities from when the teens were younger: baking, doing puzzles, working on family history projects, or even watching television together can foster connection and emphasize the family as foundational.

    Limit access to the news. Normally I think that high schoolers learn about government and global issues and develop a critical eye from reading or watching the news. Right now, however, it can be overwhelming to see the stories, not only of death and pain but also unemployment and the plight of our most vulnerable citizens. You can share with your teen why watching too much coronavirus or political news can be demoralizing. Everyone is different, but 30 minutes is plenty of time to catch up on the news and you can add some time for discussion. You can also help yourself and your teen by being a good role model of having boundaries about watching the news.

    Help them stay connected. Teens can continue to find ways to relate to their friends even during this time of social distancing and sheltering in place. In the past I viewed too much time on social media as destructive, especially to young women. However, in the current situation, social media can, if used responsibly, provide a sense of connection, shared goals, and distraction. I recommend being more flexible about screen time.  Email, texts, and even writing letters will help (and older relatives will appreciate the letters). In addition to connections to their friends, we can encourage teens to form connections to the larger community. We’ve seen that teens can be creative and generous by volunteering, whether making masks, raising money for charity online or contributing art work.

    Foster self-efficacy. In isolation, it is can be difficult for teenagers to feel any sense of competence other than academics. Teens with learning differences may be having an especially difficult time adjusting to virtual learning. Assign tasks at home, including daily chores and longer-term ones like organizing family photos, building a table, creating new menus, and so on.  Older teens can help their siblings or cousins with schoolwork. Ask your high schoolers how they think they can help out; their creativity may surprise you. All these activities help the family and teens still appreciate your acknowledgment of a job well done. Learning a new skill or completing a project also elicits the “I’ve got this” feeling, that leads to improved mood and can foster independence.

    Featured Image Credit: by Anastasia Gepp via Pixabay

    The post Pandemic practicalities and how to help teenagers manage time at home appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on May 19, 2020 09:30 AM.

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    Open positions: NeuroFedora is looking to take on trainees

    Teamwork by Perry Grone on Unsplash

    Photo by Perry Grone on Unsplash.

    After the recent release of the Computational Neuroscience installable OS image, the NeuroFedora team is looking to work on to the next set of deliverables. For this, we need to expand the team.

    I want to note that we are not only looking for people that may already have the necessary skills. We are looking for anyone interested in working in these areas that would perhaps like to acquire the required skills. We will teach the skills that we can, and where we cannot, we will involve experienced members of the Free/Open Source software community to help us. All one really needs is a few hours a week of free time.

    We are looking for people interested in:

    • Scientific communication, marketing, outreach, and community engagement:
      • To spread information on the staggering amount of Free/Open Source Software that is available for Neuroscience to researchers and the community in general,
      • To disseminate the progress that the NeuroFedora team makes regularly to the community.
      • To just generally monitor our various communication channels to answer queries and participate in discussions with the team and users.
    • Software development:
      • There are still about 200 tools to include in NeuroFedora, so still lots of work to do here. Some tools related to computational neuroscience remain, so we are working on those. However, we want to start making some headway on the next deliverable that will be focussed on neuroimaging and data analysis. Not only do we need to build these tools from source, we also need to test them regularly, and push new versions to our users when developers make new releases.
      • We also want to provide easy to use containers for all the tools that we are including in NeuroFedora.
    • Neuro-imaging and data analysis in Neuroscience:
      • A lot of tools on our list are related to Neuro-imaging and data analysis. To effectively integrate these with the rest of NeuroFedora, we need more people with domain knowledge. If you work these areas or want to work in them and would like to learn more about these tools, NeuroFedora is a great informal environment to start in.

    It is common knowledge that joining Free/Open source communities is an excellent way to pick up skills and experience. So, I especially encourage students to join one, even if it is not NeuroFedora.

    I also have first hand experience of how busy a PhD candidate can get, but in my experience I also found it possible to free up a few hours a week to work on developing general skills that one may not necessarily be able to learn from daily research work. So, I also strongly encourage undergraduate/postgraduate research students and Ph.D. candidates to do the same.

    Get in touch with us today!

    in NeuroFedora blog on May 17, 2020 10:38 PM.

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    TeX Live 2020 Update Planned

    This summer, the arXiv development team will begin work on the next major release of the arXiv TeX compilation system, which will be based on the official TeX Live 2020 update. TeX is an open source markup language that allows precision formatting of various aspects of academic writing, including mathematical formulas and bibliographies.

    This year’s update will provide enhanced local add-ons and support for newer font sets. The development team will also use this opportunity to address outstanding bugs and feature requests and further modernize how the compilation system is packaged and run. arXiv’s previous major release was based on TeX Live 2016.

    arXiv accepts more than ten thousand articles every month, and continues to provide access to all arXiv papers since the service was founded in 1991. A stable TeX compilation system is critical to reprocess articles from TeX sources from any point in time. arXiv maintains all past TeX trees so that existing papers are processed using the TeX tree that was in place when the article was originally submitted. This preserves the original presentation of the article.

    arXiv’s new TeX Live release is expected to become available Fall 2020.

    in arXiv.org blog on May 12, 2020 05:41 PM.

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    Understanding guilt in mother-child relationships

    “You never write…you never call….” The guilt-tripping mother is common stereotype in movies and TV. But how many adult children harbor feelings of guilt toward their aging parents? Who experiences this guilt, and why?

    About one in five adult children experience feelings of guilt toward their ageing mothers, based on data from a nationally representative survey of 2,450 Dutch adults in 2015 who have a mother aged 55 or older. Feelings of guilt in the family have rarely been measured in a systematic fashion but researchers have long argued that guilt is not only something moral, but also a fundamental social emotion. Guilt refers to negative feelings that arise from having done something that is – or is perceived to be – wrong. Guilt is not the same as shame; guilt is the awareness that one has done something wrong, shame is the translation of that feeling to one’s self-image: the feeling of not being a good person. Guilt and shame are emotions that have been linked to depression and low self-esteem.

    People who have negative feelings about their relationships with their mothers more often report feelings of guilt. Surprisingly, people who have both negative and positive feelings about their mothers have more guilt. This may be because children who have negative feelings about their mothers are afraid that this will hurt their mothers’ feelings. This fear of hurting a person is more difficult if one also cares about that other person. Most people have positive feelings about their mothers. However, cultural expectations about positive and warm relationships with mothers leave little room for irritation, anger, and embarrassment, and it is exactly when such feelings arise in a warm relationship that people may feel guilty.

    Adult children are an important source of support for their ageing parents. However, even at older ages, parents continue to support their adult children. The flow of support does not necessarily shift from downward (from parents to children) to upward (from children to parents) with age and for that reason, some children with older parents may feel that they are not doing enough to help. Feelings of guilt are associated with a lack of reciprocity in the support relationship. The less support people give to their mother, in comparison to how much support they receive, the stronger the feelings of guilt. With an increasing number of ageing parents in most high-income societies, demand for social and practical support from children increases and this may create more occasion for guilt to develop. It also seems that children who have strong norms about what people should do for their parents feel guilty more often. People set high standards for themselves, which in turn may lead to a feeling of not having done enough.

    It was expected that infrequent contact would be associated with guilt but while people who had only monthly contact with their mothers feel guiltier, people with less than monthly contact did not report significantly more guilt than those with weekly contact. That primarily the monthly-contact group feels more guilt fits with a pattern of a good relationship that carries a cultural expectation of more frequent contact than can be achieved.

    In psychological theory, guilt is often seen as a negative emotion that motivates positive behavioral change. This theory can also be applied to the mother-child bond. For example, guilt that arises from not visiting enough may motivate children to visit more, hence, reducing guilt. But guilt may also be reduced when parents exercise moderation in their downward support, letting the stream of support turn more quickly in the expected upward direction, from children to parents. Guilt is not always productive. When guilt arises from negative emotions such as anger and irritation, both of which are measured in this study, it is less clear which productive changes a person could make. Guilt that stems from ambivalence may therefore be perceived as more awkward. Adult children may visit their parents more often or offer more support when they feel guilty, but changing the way they feel about their parents is a different matter. This would require a change of expectations and a change in norms. Such mental and cultural changes are more difficult to achieve.

    Featured image by congerdesign via Pixabay.

    The post Understanding guilt in mother-child relationships appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on May 09, 2020 12:30 PM.

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    What are your priorities for data sharing?

    This blog was written by Iain Hrynaszkiewicz, Publisher, Open Research, PLOS.

    We’ve been working to identify important problems faced by researchers in the practice of open research. And, to deepen understanding of researchers’ priorities with regards to sharing research data, we’ve launched a new study. If you are a researcher residing in the US or Europe who has shared or reused research data please take a few minutes to take part in the survey.

    The results of the survey will also help determine if and how well researchers’ needs are met by existing tools and services for sharing research data, and inform future PLOS initiatives and partnerships – beyond the publication of open access journals.

    Researchers’ experiences and attitudes about sharing research data are arguably already well studied. The annual State of Open Data reports from Digital Science, and Carol Tenopir’s research are valuable, recurring examples. And a bibliography of studies we’ve read, or re-read, recently is included below [1–24].

    So, why do we need another survey?

    Considering the results of numerous studies, researchers’ concerns about misuse and scooping are amongst the most common concerns about, or barriers to, data sharing. These concerns are followed, in their frequency, by the more practical concerns about copyright and licensing (ownership) and the time and effort required to make research (data) openly available.

    In principle there are numerous solutions available for some of the problems, barriers and concerns represented by these findings – from repositories, institutional research support, training programmes, to journal policies and procedures. Yet in practice — to give one example of assumed good practice in open research — today only about a fifth of researchers use repositories to share data supporting published papers.

    Having reviewed this prior research and having spoken with different groups of researchers ourselves in the last few months, we’ve concluded:

    • There is considerable evidence for various cultural and practical concerns with sharing of research data, and growing evidence of how sharing and reusing data can benefit research, the economy and researchers’ careers. But, 
    • we are less certain about how important each of these problems are, and if and how well existing tools, products, and services help solve these problems.

    Data sharing, research data, and open data are very important at PLOS — reflected in our long-standing policies on data sharing. But there is more that we can do to enable research data sharing and reuse, which may help realise more of its benefits. We expect that this study will help identify researchers’ priorities, which in turn will guide our priorities for new initiatives.

    We’re very grateful for any time researchers can lend to completing the survey and, naturally, we plan to share data from the survey publicly in the future.


    1. Eynden VVD, Knight G, Vlad A, Radler B, Tenopir C, Leon D, et al. Survey of Wellcome researchers and their attitudes to open research. Figshare. 2016; doi:10.6084/m9.figshare.4055448.v1
    2. Tenopir C, Christian L, Allard S, Borycz J. Research data sharing: practices and attitudes of geophysicists. Earth and Space Science. 2018;5: 891–902. doi:10.1029/2018EA000461
    3. Tenopir C, Allard S, Douglass K, Aydinoglu AU, Wu L, Read E, et al. Data sharing by scientists: practices and perceptions. PLoS ONE. 2011;6: e21101. doi:10.1371/journal.pone.0021101
    4. Tenopir C, Rice NM, Allard S, Baird L, Borycz J, Christian L, et al. Data sharing, management, use, and reuse: Practices and perceptions of scientists worldwide. PLoS ONE. 2020;15: e0229003. doi:10.1371/journal.pone.0229003
    5. Tenopir C, Dalton ED, Allard S, Frame M, Pjesivac I, Birch B, et al. Changes in Data Sharing and Data Reuse Practices and Perceptions among Scientists Worldwide. PLoS ONE. 2015;10: e0134826. doi:10.1371/journal.pone.0134826
    6. Borghi JA, Van Gulick AE. Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers. PLoS ONE. 2018;13: e0200562. doi:10.1371/journal.pone.0200562
    7. Houtkoop BL, Chambers C, Macleod M, Bishop DVM, Nichols TE, Wagenmakers E-J. Data sharing in psychology: A survey on barriers and preconditions. Advances in Methods and Practices in Psychological Science. 2018;1: 251524591775188. doi:10.1177/2515245917751886
    8. Rathi VK, Strait KM, Gross CP, Hrynaszkiewicz I, Joffe S, Krumholz HM, et al. Predictors of clinical trial data sharing: exploratory analysis of a cross-sectional survey. Trials. 2014;15: 384. doi:10.1186/1745-6215-15-384
    9. Rathi V, Dzara K, Gross CP, Hrynaszkiewicz I, Joffe S, Krumholz HM, et al. Clinical trial data sharing among trialists: a cross-sectional survey. BMJ. 2012;345: e7570.
    10. Schmidt B, Gemeinholzer B, Treloar A. Open data in global environmental research: the belmont forum’s open data survey. PLoS ONE. 2016;11: e0146695. doi:10.1371/journal.pone.0146695
    11. Gregory K, Groth P, Scharnhorst A, Wyatt S. Lost or found? discovering data needed for research. Harvard Data Science Review. 2020; doi:10.1162/99608f92.e38165eb
    12. Faniel IM, Frank RD, Yakel E. Context from the data reuser’s point of view. Journal of Documentation. 2019;75: 1274–1297. doi:10.1108/JD-08-2018-0133
    13. Open Data: the researcher perspective – survey and case studies [Internet]. 4 Apr 2017 [cited 15 Nov 2018]. Available: https://data.mendeley.com/datasets/bwrnfb4bvh/1
    14. Allagnat L, Allin K, Baynes G, Hrynaszkiewicz I, Lucraft M. Challenges and Opportunities for Data Sharing in Japan. Figshare. 2019; doi:10.6084/m9.figshare.7999451.v1
    15. Lucraft M, Allin K, Baynes G, Sakellaropoulou R. Challenges and Opportunities for Data Sharing in China. Figshare. 2019; doi:10.6084/m9.figshare.7326605.v1
    16. Stuart D, Baynes G, Hrynaszkiewicz I, Allin K, Penny D, Lucraft M, et al. Whitepaper: Practical challenges for researchers in data sharing [Internet]. 2018. Available: https://figshare.com/articles/Whitepaper_Practical_challenges_for_researchers_in_data_sharing/5975011
    17. Science D, Fane B, Ayris P, Hahnel M, Hrynaszkiewicz I, Baynes G, et al. The State of Open Data Report 2019. Digital Science. 2019; doi:10.6084/m9.figshare.9980783.v1
    18. Science D, Hahnel M, Fane B, Treadway J, Baynes G, Wilkinson R, et al. The State of Open Data Report 2018. 2018;
    19. Science D, Hahnel M, Treadway J, Fane B, Kiley R, Peters D, et al. The State of Open Data Report 2017. 2017;
    20. Federer LM, Lu Y-L, Joubert DJ, Welsh J, Brandys B. Biomedical data sharing and reuse: attitudes and practices of clinical and scientific research staff. PLoS ONE. 2015;10: e0129506. doi:10.1371/journal.pone.0129506
    21. Perrier L, Blondal E, MacDonald H. The views, perspectives, and experiences of academic researchers with data sharing and reuse: A meta-synthesis. PLoS ONE. 2020;15: e0229182. doi:10.1371/journal.pone.0229182
    22. Linek SB, Fecher B, Friesike S, Hebing M. Data sharing as social dilemma: Influence of the researcher’s personality. PLoS ONE. 2017;12: e0183216. doi:10.1371/journal.pone.0183216
    23. Oushy MH, Palacios R, Holden AEC, Ramirez AG, Gallion KJ, O’Connell MA. To share or not to share? A survey of biomedical researchers in the U.S. southwest, an ethnically diverse region. PLoS ONE. 2015;10: e0138239. doi:10.1371/journal.pone.0138239
    24. Wallis JC, Rolando E, Borgman CL. If we share data, will anyone use them? Data sharing and reuse in the long tail of science and technology. PLoS ONE. 2013;8: e67332. doi:10.1371/journal.pone.0067332

    The post What are your priorities for data sharing? appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on May 06, 2020 12:00 AM.

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    PLOS Pathogens & PREreview Live COVID-19 Preprint Journal Club

    On Monday, May 11, 2020, at 9am PST / 12pm EST / 5pm BST / 6pm CEST, PLOS Pathogens is  teaming up with PREreview to bring together scientists from around the world to discuss and review a COVID-19-related preprint — live. #PLOSPREreviewLIVE

    The preprint under review is: Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus. (Full preprint citation at the end of this post).

    Please register here to participate in this important event. (Registration is required.) 

    Monday, May 11, 9am PST / 12pm EST / 5pm BST / 6pm CEST


    We will be using Zoom video conference software, which is free to download. Once registered you will receive the information on how to join the live journal club before the event. Therefore registration is required.

    You will spend one hour with your fellow scientists diving straight into the preprint and resurfacing with constructive feedback for the authors. This is a great opportunity to play a role in tackling the COVID-19 pandemic by sharing your expertise with your peers from all over the world. You will also learn about preprints (and reviewing them), build your network, and get credit for your feedback because reviews are citable as each is assigned a digital object identifier (DOI).

    PLOS is proud to collaborate with PREreview to shine a spotlight on our shared goals: to encourage more scientists to post feedback on preprints, which is never more important than during a time of crisis.

    Preprint citation in full:

    Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus

    Tieying Hou, Weiqi Zeng, Minling Yang, Wenjing Chen, Lili Ren, Jingwen Ai, Ji Wu, Yalong Liao, Xuejing Gou, Yongjun Li, Xiaorui Wang, Hang Su, Bing Gu, Jianwei Wang, Teng Xu

    medRxiv 2020.02.22.20025460; 

    doi: https://doi.org/10.1101/2020.02.22.20025460


    The post PLOS Pathogens & PREreview Live COVID-19 Preprint Journal Club appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on May 04, 2020 12:00 AM.

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    A Selfish Reason To Share Research Data

    This blog was written by Giovanni Colavizza, Isla Staden, Kirstie Whitaker and Barbara McGillivray of the Alan Turing Institute and Iain Hrynaszkiewicz, PLOS and first appeared on their website.

    As many of us adapt to the benefits of remaining connected with our peers and colleagues digitally, new evidence suggests that scholarly papers might get increased citations by staying digitally connected to the research data that support their results.

    To promote open, reproducible research, many journals have started to encourage or even mandate that researchers share their research data and provide statements about the availability of their data in their published papers. These Data Availability Statements (DAS’s) in published papers (see Table for examples) provide a way to study if and how researchers share their data, and if data sharing correlates with citations of research.

    Previous studies have explored researchers’ data-sharing practices and their associations with citation counts in specific journals, or in specific research disciplines only. We analysed more than half a million papers across multiple journals and research disciplines, to explore the following questions: 

    • Are authors taking up the challenge of data sharing? 
    • Is this beneficial for them as well as for the scientific community? 

    We analysed published articles from the PubMed Open Access collection to help answer these questions, and made all our code and data available for replication. 

    Using an automated approach designed for the study, we classified different kinds of data availability statements, according to their main categories (illustrated in Table 1). The outcome is important as statements that contain a link to research data available in a public repository (category 3) are considered to be preferable over all other types of statements. However, depositing data in a repository may be more time-consuming for researchers than other approaches.

    Key findings

    We found that data availability statements are now very common in published papers. We also found that journal mandates to include these statements are effective, with big increases in the number of statements in 2014 and 2015, when PLOS (Public Library of Science) and BMC (BioMed Central), respectively, mandated them. When journals only encourage that authors provide a statement, only a small percentage of papers include them. In 2018 93.7% of 21,793 PLOS articles and 88.2% of 31,956 BMC articles had data availability statements. Yet, data availability statements containing a link to data in a repository are just a fraction of the total. In 2017 and 2018, 20.8% of PLOS publications and 12.2% of BMC publications provided DAS containing a link to data in a repository. Figure 1 gives an overview of data availability trends over time in PLOS journals, while Figure 2 exemplifies distinct approaches to data sharing from two BMC journals.


    Figure 1: Data availability statements over time in PLOS. The histogram shows the number of publications from specific subsets of the dataset and DAS categories: No DAS (0), Category 1 (data available on request), Category 2 (data contained within the article and supplementary materials), and Category 3 (a link to archived data in a public repository). The vertical solid line shows the date when a mandated DAS policy was introduced.

    Figure 2: Data availability statements over time in articles from the BMC Genomics journal (left; selected to illustrate a journal that had high uptake of an encouraged policy) and from the Trials journal (right; published by BMC, selected to illustrate a journal that has a very high percentage of data that can only be made available by request to the authors). The vertical solid line shows the date when a mandated DAS policy was introduced. A dashed line indicates the date an encouraged policy was introduced.

    We also find that papers that link to data in a repository can have up to 25.36% (± 1.07%) higher citation impact on average, using a citation prediction model. While our results show that higher citations to a paper are correlated with linking to data in a repository, we cannot be certain this is the cause for the higher citations. However, this result may be encouraging for researchers, journals, publishers, funders and policymakers who are interested in data sharing and reproducible research. It suggests there might be a further incentive—beyond increasing transparency and reproducibility of resultsto authors to make their data available using a repository.

    There might be a variety of reasons for this effect. More efforts and resources are put into papers sharing data, thus this choice might be made for better quality articles. It is also possible that more successful or visible research groups have also more resources at their disposal for sharing data. Sharing data likely also gives more credibility to an article’s results, as it supports reproducibility. Finally, data sharing encourages re-use, which might further contribute to citation counts.


    Researchers are concerned that there are insufficient resources and incentives to share their research data, and that more effort is required to publish data when publishing papers. However, this extra effort is really an investment rather than a cost. It is an investment in more reliable and reusable research for the scientific community, and this new evidence suggests it could also be a reasonable, “selfish” investment in researchers’ own reputations. 

    Read the authors’ paper in PLOS ONE: The citation advantage of linking publications to research data

    Access the data in the following repository.

    The post A Selfish Reason To Share Research Data appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on May 04, 2020 12:00 AM.

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    A pandemic of boredom

    It was just the two of them: on a raft, lost, floating off the coast of Africa—the lone survivors of a shipwreck. Years before, struck with stupendous boredom, Hymie Basteshaw decided to become boredom’s master. He read what others wrote about boredom, studied its physiology, and discovered its secrets in the wavering folds of human cells. Mid-sea, he now shares with Augie March his first and “obvious” findings. Boredom is “the shriek of unused capacities, the doom of serving no great end or design, of contributing to no master force. The obedience that is not willingly given because nobody knows how to request it. The harmony that is not accomplished.” Basteshaw is but a minor character—a psycho-biologist, a carpenter, a genius, a “maniac”—in Saul Bellow’s long picaresque novel, The Adventures of Augie March. He offers not a minor or obvious feature of boredom, but a discerning appraisal of its intimate nature. Boredom, Basteshaw tells March, although not in these exact words, is hybrid, both personal and social.

    Our current situation is one of crisis, of resources, values, and priorities. It’s also a crisis for the study of boredom. It’s a call to understand boredom both as a psychological and social phenomenon. If our aim is to capture what it means to experience boredom right now—the boredom of social distancing, quarantine, and the pandemic—we can’t rely exclusively on lessons that we’ve drawn from willing participants in on-line or in-person studies. Yes, we are bored with more or less the same things that previously bored us. But we are bored because of our newfound and newly imposed social condition. In social distancing, we find ourselves in an unusual position. Both restrained and acutely aware of the meaninglessness of our everyday actions we are under the threat of a new boredom—a boredom that looks and feels just like our ordinary boredom, but which has grown out of a much different and more fertile ground.

    What is boredom most fundamentally? Boredom is an unpleasant state that signals to us the presence of an unsatisfactory situation and which, at the same time, contains a strong desire to do something else. During boredom, we feel both frustrated and listless. We’re disengaged from and dissatisfied with what we do. Our situation doesn’t hold our attention. It doesn’t interest us and doesn’t strike us as meaningful. In a state of boredom, we’re moved to think of alternative situations and goals, ones that are more interesting, engaging, and meaningful to us than our current ones. We itch to leave boredom behind and are propelled to try to do just that.

    Boredom is a problem—a disruption of agency, a deficit of meaning, or a block in our ability to engage cognitively and satisfactorily with our situation at hand. And yet, it’s also a solution. Or better, it’s the promise of a solution. The unpleasantness of boredom, along with its effects on our psychological processes and behavior, offers us a possible way out. Boredom is that disagreeable reminder that we should be doing something other than what we are currently doing. It’s also a repellent force, a drive that could, under the right conditions, allow us to overcome our discontent.

    What I have just described sounds a lot like a psychological state that exists in a social vacuum, but that isn’t so. Boredom can arise out of a perceived dissatisfaction with our situation, a mismatch between our wishes and reality, or even a lack of sufficient engagement with the task at hand. All of these prompts of boredom can be both personal and social. Any social condition that either begets or supports them would be one that promotes boredom.

    We are currently experiencing a change in social order. Compared to our recent past, the present of the pandemic is one characterized by excessive order. Out of necessity, caution, concern, or fear, we are constrained. There’re real and tangible limits to our opportunities and obstacles to free action. And so, out of this new social order, boredom grows. “Boredom arises when we must not do what we want to do, or must do what we do not want to do,” psychoanalyst Otto Fenichel once observed. In Melancholy and Society, German sociologist Wolf Lepenies warned us of how socially frustrated agency is a fertile ground for boredom. Experimental studies agree that conditions over which individuals have little control can give rise to boredom. And a recent study examining the attitudes of people living in quarantine in Italy appears to confirm it.

    There’s another element of our social condition that contributes to the rise of boredom. Boredom is related not just to the perceived control or autonomy that we have over a situation but also to how meaningful our situation strikes us. Studies report that perceived meaninglessness is both a component of and a likely antecedent to boredom. While social distancing, we often feel that our actions and activities are lacking in meaning. Why? In the face of the pandemic, our everyday activities seem insignificant. For those of us who are not nurses, doctors, first respondents, essential workers, or actively involved in helping others or fighting the spread of the virus, our actions seem to have little effect on the situation.

    When faced with the boredom of the pandemic it helps to bring to mind the function of boredom. It offers us a productive way to think about our boredom, for it underlines its existential import. We are fortunate not for this or that experience of boredom, but for the capacity to experience boredom. Boredom—in its non-chronic form—is a valuable tool and perhaps now, more than ever, a privilege. It’s both an affective reminder that we are stuck with ourselves and a call to become more than what we are right now.

    But boredom can only do so much. Once it has made itself known to us, we are on our own. We have to decide how to act and what to do. We can turn to diversions or reflection, act rashly or prudently, give up or stand up, help others or look after ourselves. The possible outcomes of boredom are many and varied.New habits, opportunities, and careers often start with the thought “I am bored.” But so can unhealthy eating habits, binge drinking, drug use, or even destruction.

    One hopes that in times like these boredom’s call can be put into productive and compassionate use. To borrow Voltaire’s words, one hopes that we can cultivate our garden: the ground out of which our personal and social existence can grow and flourish—not as an act of quietism but as a sign of resilience and as way to realize change.

    It’s worth a try, even if it is done out of boredom.

    Featured Image Credit: by Rhett Noonan on Unsplash 

    The post A pandemic of boredom appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on May 02, 2020 09:30 AM.

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    Do Peer Reviewers Prefer Significant Results?

    An experiment on peer reviewers at a psychology conference suggests a positive result premium, which could drive publication bias.

    in Discovery magazine - Neuroskeptic on April 30, 2020 10:27 PM.

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    PhD Studentship in Computational Neuroscience and Rehabilitation Robotics

    Biocomputation Research Group

    Centre for Computer Science and Informatics Research

    University of Hertfordshire, UK

    Application deadline 1 June 2020

    Bursary GBP 15,285 p.a.

    Applications are invited for PhD positions in the Biocomputation Research Group at the University of Hertfordshire. (http://biocomputation.herts.ac.uk/).

    Project description

    Stroke is a major cause of disability in adults. More than 15 million strokes occur every year in the world, and more than 100,000 of these affect patients in the UK. Stroke patients often have an impaired ability to control their upper limbs and need assistance with every-day tasks. Relearning motor skills after stroke is similar to learning new motor skills, for example learning to play tennis, but a problem for stroke survivors is that their impaired movements often restrict the ability to use sensory feedback for re-learning.

    Rehabilitation robotics has shown promise to augment the rehabilitation process and to offer feedback on performance. However, the personalisation of the therapy to individual needs remains a major challenge to date.

    The proposed project will use a computational model of the cerebellum that is being developed by the Biocomputation Research Group (biocomputation.herts.ac.uk) to optimise robotic rehabilitation for individual subjects. The cerebellum has been optimised throughout vertebrate evolution to become an adaptive controller of biological skeletomuscular structures that is unrivalled by any artificial adaptive motor control algorithm. This has led and is still leading to the development of a rapidly increasing number of computational models of cerebellar learning, and to the successful applications of these cerebellar models to controlling simulated and real robots. The PhD project will involve the development and application of personalised cerebellar models in order to optimise rehabilitation robots for individual subjects.

    Applicants should have excellent computational and numerical skills and a very good first degree in computer science, biology, maths, physics, neuroscience, or a related discipline. Successful candidates are eligible for a research studentship award from the University (GBP 15,285 per annum bursary plus payment of the student fees). Applicants from outside the UK or EU are eligible.

    Research in Computer Science at the University of Hertfordshire has been recognised as excellent in the latest Research Excellence Framework Assessment, with 50% of the research submitted rated as internationally excellent or world leading. The Centre for Computer Science and Informatics Research provides a very stimulating environment, offering a large number of specialised and interdisciplinary seminars as well as general training and researcher development opportunities. The University is situated in Hatfield, in the green belt just north of London.

    Please contact Dr Volker Steuber or Prof Farshid Amirabdollahian for informal enquiries. Application forms are available under https://www.herts.ac.uk/study/schools-of-study/engineering-and-computer-science/research-in-engineering-and-computer-science/the-phd-programme-in-computer-science and should be returned to doctoralcollegeadmissions AT herts DOT ac DOT uk.

    The short-listing process will begin on 1 June 2020.

    in UH Biocomputation group on April 30, 2020 03:40 PM.

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    How childhood trauma resurfaces during COVID-19

    Children who are victims of bullying often suffer a sense of helplessness. They don’t know what to do during bullying episodes and they don’t really believe anything will change or anyone can intervene effectively. Children subjected to bullying say it makes them feel sick, afraid, and helpless. It can also lead to feelings of anxiety, anger and depression. We know that as adults former victims can undergo similar feelings in the right circumstances.

    Due to my research in the area of childhood bullying, I am contacted by many people about their own bullying incidents as children. They describe how they coped at the time. Often, they comment on how they’ve managed their lives in the wake of bullying.   The great majority have survived and gone on to live productive lives. However, during this world-wide COVID-19 crisis, adults relate that their mental state is similar to how they felt as children. I have received messages describing the reactivation of childhood memories of being captive to someone while feeling powerless.  In the face of the uncertainty generated by the coronavirus, the same emotions are rekindled: fear, anxiety, anger, and a certain amount of depression. While most are doing what they can in terms of preparedness and health precautions, helplessness is once again a prevailing emotion. Substance abuse held at bay has reemerged as a problem.

    By this point, perhaps the majority of people are aware of a sense of helplessness while trying to outwait and outwit COVID-19 by using every best effort. It is a helpless feeling to see the numbers of deaths and to witness the struggles in the healthcare system. While everyone may feel some amount of anxiety related to the virus, survivors of bullying experience a heightened degree of fear, anxiety, and depression based on triggered childhood feelings. Helplessness is a familiar but unwelcome manifestation impacting their daily mood. Sheltering-in-place is difficult emotionally in general. But for victims of childhood bullying it is reminiscent of and activates the loneliness that was an everyday burden.

    Trauma is an aspect of this health crisis. The loss of family and friends, and the fear of their loss, is overwhelming. Trauma results when such overwhelming stress exceeds one’s ability to cope. There are three distinct types of trauma: acute, chronic, and complex. Acute trauma describes what people are living through now, meaning the trauma is the result of a single event- the corona virus. Trauma can become chronic depending on the duration of an event; in this case how long people are required to shelter-in-place with all the problems attendant to that (loss of income, lack of childcare, family violence, etc.). Chronic bullying is traumatizing for children and it leads to changes in the brains’ ability to think clearly. At the very least, bullied children worry and their worries influence their actions. They try to hide and they learn to avoid their bullies. They often become worried, anxious adults. For those who endured bullying victimization as children, the trauma is complex. Those adults deal with childhood trauma and its effects in an ongoing way. Now they are dealing with the very personal nature of the fear of the virus as well.

    Children can do very little when they are helpless. They don’t have the tools, the wisdom, the resources, or the maturity needed to ameliorate adverse childhood conditions. Adults by virtue of greater years, greater resources, and greater mental capacity are able, much of the time, to deal with difficult circumstances. But COVID-19 extracts its toll despite wisdom, years, or great resources. The virus is an equalizer in this respect. It exerts power over its victims. It is relentless in pursuing a host to control. It searches for any weakness to exploit. COVID-19 acts exactly like a bully. For those who have already been a victim in childhood, this new terror is another bully forcing people to stay inside hiding from its power. In this way, victims of childhood bullying, even with their adult resources, are revisited by an age-old sense of helplessness unique to them.

    For adults intimidated and threatened throughout childhood, helplessness is not new. It has come back again in the shape of something even more powerful and intimidating.

    Photo by Natalia Y on Unsplash 

    The post How childhood trauma resurfaces during COVID-19 appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on April 30, 2020 12:30 PM.

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    The Digital Migration: Lessons About Open Science Arising from the COVID19 Crisis

    This blog post was written Dylan Roskams-Edris, Open Science Alliance Officer, Tanenbaum Open Science Institute, The Neuro. This piece resulted from an ongoing discussion with members of the Canadian open science community, in particular Estrid Jakobsen, Elizabeth DuPre, Zoha Deldar, Nikola Stikov, Stephanie Dyke, Rachel Harding, Jean-Baptiste Poline, and Christine Tardif.

    Open Science Easing the Transition from Lab to e-Lab

    In the wake of COVID19, the world is scrambling to figure out how to continue the functions of normal life while confined to a much smaller world of couches and home offices. Work, family and friend relationships, exercise, entertainment, and all the other elements of normalcy have been upended. The effort to maintain productivity (and, to be frank, sanity) has initiated a mass digital migration; a movement from life to e-life.

    If you are a researcher you are likely dealing with your own unique micro-version of the predicament: how to continue working when you and your lab are self-isolated? In other words, how to replicate as many of the normal functions of a lab as possible in a digital environment; a movement from lab to e-lab.

    Lab meetings have migrated to video-conferencing with relatively little friction; conferences have gone virtual astoundingly quickly; manuscripts are being drafted and figures created – perhaps a tad earlier than originally planned; grants and proposals are being written. These are, however, only a small portion of what researchers do, and leave a huge swath of scientific work untouched and in stasis.

    Those most able to continue useful work are those who, for whatever reason, have access to as much of their work as possible from home. Pictures of researchers lugging multiple work computers home in order to continue data analysis were common in the early days of the crisis.

    There is a subgroup of researchers, however, who can continue work without having to cram several computer towers into the trunk of a car: those who created an up-to-date digital, online representation of their research activities right up to the moment they had to be abandoned. These lucky few, who put in the time and effort to create a comprehensive e-lab prior to the crisis, are for the most part those who already commited to open science. This is, of course, no accident.

    Open Science and e-Labs

    Open science is, at its most practical base, the effort to (1) create an accurate and well organized digital representation of research activities and (2) share that representation with as few barriers as possible so others can effectively check, replicate, rework, reuse, and remix findings. Even the concentration within open science on sharing physical materials – like cell lines, biospecimens, and model organisms – is to enable replication and follow-on research when sharing the information about those materials does not to allow others to generate them themselves due to the unique nature of the material or an inability to make materials locally.

    Researchers who have incorporated open, online sharing of research resources throughout their work – sharing experimental designs and protocols, lab notebooks, data, software, etc – have, in effect, created a digital representation of a significant portion of their activities that can be accessed from anywhere with an internet connection.

    Not to oversell things, open sharing of research resources does not mean that researchers and labs can continue functioning without a hitch in their experimental stride. Much of the actual physical work has necessarily halted. It does mean, however, that many of the inputs to and outputs of their research are available in a digital form; accessible from a couch, desk, or apartment window-sill. While the emphasis from open science advocates in the past has been on ensuring that these digital representations exist so they can be shared, an added advantage has now jumped to the fore: the ability to share your e-lab with your quarantined-self.

    Sharing Your e-Lab with Yourself

    Labs that have, for example, stored experimental data immediately upon collection on open science platforms such as the Open Science Framework, Zenodo, Figshare, Synapse, OpenNeuro, and Dryad now have seamless access to the last bit collected before retreating into quarantine. Analyzing this data may be impossible if the requisite software only exists on a work computer, or you don’t have a license to use it at home; if, however, research software has been openly shared via a platform like Github then it can be accessed from a park bench (assuming a decent wifi signal).

    If the collected data needs to be put into the context of how it was collected, perhaps to elicit input from other lab members about the best way to analyze it, there is no easier way than accessing the relevant protocols through protocols.io or an Open Lab Notebook. Need to know exactly what reagents or model organisms were used in an experiment? If one cannot go check the freezer, cage, or delivery invoice, then checking the relevant Research Resource Identifier (RRID) listed in your shared protocol or notebook is the next best (if not better) thing.

    The list of unanticipated advantages continues. Perhaps you need to get input from a normally-down-the-hall colleague about how to improve your protocol for the future, or eliminate an artifact from some data, or iron out a persnickety bug in analysis software. In the lab you could invite them to pull up a chair as you took them through the issue. Now that is, obviously, impossible. If the protocol, data, or software were shared, however, you could email them the link (or, better yet, persistent identifier), open a videochat window, and collaborate from a distance.

    Sharing Your e-Lab with Your Research Community

    One of the most heartening things I have seen while scrolling through my twitter-feed-turned-emotional-roller-coaster is that self-isolated researchers are engaging with openly shared research resources.

    This is of course the case with COVID19 research, where openly shared software, data, manuscripts, and protocols relevant to the virus are being shared, collected, curated and adapted with blinding speed; but it goes farther than that. Every day I see someone in the neuroscience research community tweet something along the lines of “thank goodness for X piece of openly shared software/data that I can learn about and use from home!”

    When people are cut off from their physical labs and don’t have an e-lab of their own, it is wonderful to see them being able to pick up the tools and resources shared by others. The lessons we are being forced to learn about the fluidity, dynamism, and capacity for collective creativity enabled by sharing research resources will serve us well in the future.

    My sincere hope is that those working with these new found tools and resources take the open ethos to heart and openly reshare any modifications, derived data, and new insights with the research community. Doing so closes the loop, creating a community-based feedback mechanism that encourages further sharing in the future and, more importantly, uses the expertise of the world-wide research community to create ever better science.

    Benefiting the Public and Less Well-off Researchers with an Open e-Lab

    Some of the people involved in shaping (see: arguing about) what open science is quail at the idea that open science has anything to do with equity and equality. They say that it is merely about replicability and transparency and that is it, harumph. What I hope this situation brings to light – as you swear at your institutional VPN for once again dropping you, or find yourself unable to download important papers because of paywalls your institutional account would normally breeze through – is that you are receiving a taste of what it is like outside the gilded ivory tower.

    Such restrictions on access and use are what interested members of the public, or those at research institutes that cannot afford staggering subscription prices, or those in labs not well funded enough to pay for the licenses to fancy analysis software, face every day. The act of openly sharing a paper, a piece of software, a dataset, an equipment design, or whatever else is not just about replicability. Doing so is an act that expands the borders of science, allowing the participation of the previously excluded. It is an act of inclusion not in some abstract post-modern sense, but in the very real sense of choosing where and why to put the fences.

    Sharing Your Open e-Lab with the World

    Beyond the fact that open sharing is useful to the isolated-sharer and their research community, shared research resources have taken on an unprecedented importance in the COVID19 crisis. Stories abound of how sharing genetic sequences and protein structures have led to the discovery of novel treatment targets, diagnostic testing protocols, and the initiation of clinical trials on a timescale that, in the pre-COVID19 era, would be unbelievable. Moreover, the rapid release of results via preprints has allowed the creation of competitions to apply machine learning to generate yet more insights. Though similar mass sharing has occurred during previous outbreaks (e.g. Zika and Ebola), the fact that COVID19’s impact has been global (and, not to put too fine a point on it, has impacted the global north) holds the hope that this time it will stick.

    There is no reason that the same strategies cannot be applied to the ongoing crises in neurological disorders, antibiotic development, and the treatment of rare diseases, to name only a few. Indeed, the kind of massive online collaboration to solve issues around testing, creating ventilators and personal protective equipment, solving protein structures, and identifying novel treatment targets in the context of COVID19 is exactly what open science advocates have been dreaming of for years.

    Barriers to e-Labs and Global Collaboration

    Open science has laid the groundwork for the creation of e-labs and for them to be linked up to enable global collaboration. The COVID19 crisis has, on so many levels, highlighted the importance and promise sharable, digital representations of research activity hold for the future of research. More people than ever are glimpsing the potential that e-labs interlinked into a global digital research ecosystem represents.

    This bright future does not, however, come free of complications. Just as open science reveals the potential of sharing, it also reveals difficulties of coordination and consensus. If research is going to be conducted collaboratively on a global scale we need to make sure that shared resources are findable, accessible, interoperable, and reusable (e.g. FAIR). Doing so can be made easier through technology and sharing platforms, but what it requires most are education, communities collaboratively setting norms around standards and sharing practices, and a commitment to embed open science practices throughout the research lifecycle. The necessary changes in behaviour will require social and cultural innovation on the part of research communities at least as important as any technical advance.

    Another big coordination problem has to do with eliminating research redundancies. Individual researchers within the global community need to coordinate so as to pursue different but complementary efforts. Doing so requires researchers to move past the stage of sharing resources in the hopes that those in their community will find it to engagement with that community. In the old, closed model such coordination was handled (albeit inefficiently) through journals and conferences where community members would be apprised of the work being done by others. The same task now must be undertaken in the digital world. Those of us interested in advancing open science are busily documenting how this is being done for COVID19 research in the hope that we can, after this is over, present an iron-clad case for how research communities can be rebuilt with digitally-mediated coordination planted deep in their hearts.

    Making an Open Future to Benefit Everyone

    I would ask you to deeply consider how you can begin adopting open, collaborative, community based approaches in the future of your research, once the world is rightside-up again. Doing so isn’t just about some abstract idea of openness; it has real benefits for you, your lab, your research community, and the world. COVID is, it is true, producing never before seen destruction of research efforts from which many projects may never recover. Within this destruction, however, lay clues to how research can be remade better, more collaborative, more coordinated and, of course, more open.


    The post The Digital Migration: Lessons About Open Science Arising from the COVID19 Crisis appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on April 30, 2020 12:00 AM.

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    PLOS and Iowa State University Library announce APC-free Open Access publishing agreement

    The following press release was issued on Wednesday, April 29, at 9am Pacific

    SAN FRANCISCO — Iowa State University Library and the Public Library of Science (PLOS) today announced a three-year Open Access agreement that allows researchers to publish in PLOS’ suite of journals without incurring Article Processing Charges (APCs). This partnership brings together two organizations that believe researchers should be able to access content freely and make their work available publicly, regardless of their access to grant funds.

    “We are thrilled to continue our support for Open Access publishing with PLOS under this new agreement,” said Curtis Brundy, Associate University Librarian for Scholarly Communications and Collections at Iowa State University. “Preserving and growing the diversity of scholarly publishers has never been more important, and this agreement reaffirms our commitment to seeing that pure Open Access publishers like PLOS thrive.”

    Under the agreement, which will be implemented in July, Iowa State University Library will be charged an annual fixed flat rate over the three-year term, which will be based on prior years’ publication levels. Iowa State researchers will have unlimited opportunity to publish in PLOS journals over these three years and will not be charged any APCs. This agreement will further PLOS’ mission of making Open Access publishing available to all while ensuring that its journals include research from authors representing a diverse array of disciplines, career stages, and geographies.

    “The agreement with Iowa State University Library is yet another step in our goal of empowering authors who want to participate in Open Access publishing, and it continues the momentum following our recent agreement with the University of California,” said Sara Rouhi, Director of Strategic Partnerships for PLOS. “Both agreements demonstrate our effort to build a truly ‘open to read, open to publish’ environment for authors as well as our commitment to experimentation with our library partners.”

    The post PLOS and Iowa State University Library announce APC-free Open Access publishing agreement appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on April 29, 2020 12:00 AM.

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    The Noble Prize for a Life Well-Lived

    In honor of a beautiful and affectionate cat.

    RIP, beloved Max
    April 19, 2003 April 24, 2020

    So much acrimony and confusion and death...

    In the true meaning of the word, Max lived a noble life.

    “But he was just a cat,” you say. Yes, that's true. But he was loving and kind and selfless until the very end. He was a wonderful companion, and a great source of comfort to me (especially after my partner died in October 2018).

    Max and Sandra
    Feb. 2, 2017

    He was cherished by previous caretakers and human friends, who showered him with gifts.

    Christmas Eve, 2017

    Christmas Day, 2018

    But now he's gone and life continues, filled with acrimony and confusion and death.

    The Very Real Threat of Trump’s Deepfake by David Frum

    While reading this article in The Atlantic, I was immediately struck by how a cat could hold human values and respect human life to a greater extent than the President of the United States. Sounds absurd, doesn't it? But not really. Not any more. Here's David Frum:
    April 26, 2020, was an especially manic day in the presidency of Donald Trump.  ...  something was gnawing at him. Perhaps his business troubles were weighing on him.  ...  Or perhaps Trump was still seething at the widespread ridicule of his press conference of April 23, when he suggested using disinfectant “by injection.” Or perhaps something else had shifted his mood from its usual setting of seething aggrievement to frothing fury.

    Whatever the cause, between early afternoon and near 9 o’clock eastern time, Trump fired off a sequence of crazy-even-for-him tweets and retweets. He demanded that reporters be stripped of the “Noble prizes” they had supposedly been awarded for their reporting on Trump scandals, apparently conflating them with the Pulitzers—and then pretended that his misspelling of Nobel had been intentional.  ...  He retweeted an increasingly wild and weird range of supporters’ Twitter accounts.

    Trump shows no compassion for the suffering around him, no sympathy for the families devastated by the loss of their loved ones, and only hollow praise for the health care workers, the bus drivers, the home delivery drivers, the grocery store clerks, and the sanitation workers who put their lives on the line every day.

    Eternal optimists say “we're all in this together” while sitting at home on Zoom meetings, placing endless orders on Amazon, and fretting about their sourdough starter. I'm only marginally better, but I realize I'm privileged. {I've tried to help financially contributing to homeless organizations, a fund for unemployed hourly workers, bookstores, museums, etc.}

    And obviously I'm way more pessimistic.

    How does this rant honor my cat??

    Case History

    Max was diagnosed with intestinal lymphoma in August 2019 at the age of 16. He also had a murky ailment that made it difficult for him to eat (“his tongue is inflamed” or later, “he has a mass at the base of his tongue”), but the true cause was never confirmed. He was prescribed oral chemotherapy pills three times a week and an oral steroid (prednisolone syrup) twice daily. I declined the chemo pills, opting for quality of life for both of us. Max's oral steroid became unworkable after four doses.

    This was not fair, especially after my wife suffered through Stage 4 cancer for a year.

    Another vet started bimonthly / monthly injections of Depo-Medrol (methyl prednisolone) to reduce the inflammation in his mouth, and as a partial treatment for his lymphoma. It worked wonders (for a while). He ran up and down stairs, played with his toys, and jumped over the red chair!

    He started getting worse in January. His weight was down to 9.5 lbs (4.3 kg), a 2 lb loss in two months. He was prescribed buprenorphine as needed for pain and transdermal mirtazapine as an appetite stimulant. My quest for palatable foods became more and more challenging. I spent hours walking the aisles of pet superstores.

    ADDENDUM (April 28, 2020): How could I forget his stint on an all-chicken diet (KFC no skin of course or grocery store roasted chicken), which he enjoyed for a few weeks until he could no longer eat chicken...

    His last regular appointment was March 9. And then the shelter-in-place orders were issued.

    Pet Care During the COVID-19 Pandemic

    Max's condition was getting worse. Depo-Medrol was less and less effective, and he needed injections every two weeks. The veterinary practice enacted stringent measures to protect its essential workers. In-person appointments were reserved for animals showing signs of extreme pain and suffering. Virtual Vet was used for consults and for recommending treatment plans. We had an appointment on March 27. Max was prescribed his usual meds. I picked them up curbside (calling upon arrival) and paid via contactless transaction. I watched a helpful YouTube video and then administered his subcutaneous injection of Depo-Medrol.

    By April 16, I had grown desperate. The poor fellow was having a severe bout of diarrhea that lasted for days. I tried scheduling a Virtual Vet appointment and called for a refill of buprenorphine. Finally I got through and picked up more meds the next day. These included oral metronidazole, a hideously bitter and distressing medication that made his mouth foam.

    He improved slightly. I was up for hours in the middle of the night, trying to coax him to eat. Some "meaty morsels" and "flaked' varieties were palatable for their gravy. I got out the food processor and whirled them into a very soft format, which he mostly rejected. “But you were just licking the gravy off these meaty morsels!” I told him. Finally I came up with a winning concoction. But this was only a palliative interlude before the inevitable.

    Then I realized I'd established a Palliative Care Unit for my cat.

    On April 23, I could no longer care for him myself. I brought him to the ER for severe dehydration. He had blood work and an "incidental" ultrasound, neither of which he'd had since his initial diagnosis. The results were devastating. Anemia due to suspected blood loss from his GI tract. Elevated white blood cell count (no surprise). Emerging diabetes mellitus (e.g., glucose in his urine), a known side-effect of steroid treatment. He weighed only 3.8 kg (8.4 lbs).

    Most concerning was “free fluid in the abdomen and what looks like masses, possibly lymph nodes and fluid distended bowel loops.”  /  “If he does not improve in the next few days to a week, humane euthanasia should be considered given what we know.”

    I picked him up and brought him home. He hated car rides much more than actual visits to the vet or treatments of any sort. Veterinary staff all loved him. The report from his ER doc even said, “Max is a very good cat.”

    He was withdrawn for several hours. Then he got over it and sat on my lap in the red chair, purring. Here he is, as beautiful as ever.

    The change in Max from that day to the next was astounding. He couldn't hold his head up any more. He tried to drink some water but couldn't manage to do it. I don't think any additional intervention would have improved his condition. I didn't want to wait any longer and had to act quickly.

    I was fortunate to find a caring and compassionate vet who made house calls, and wasn't ridiculously overboard on COVID-19 restrictions. Some said they wouldn't enter the main living area — it had to take place outside or in the garage or in their mobile van. But Max was in a comfortable and familiar environment, at least. And then he didn't have to suffer any longer.

    Max was such a sweet, loving, affectionate cat. He sought me out until the end, until his very last day when he was too weak to do so.

    This is another story of love, and of loss. How we care for the most helpless among us is an enduring sign of our humanity.

    MORE CAT PHOTOS below.

    Max loved to bask in the sun.

    He was very well-read.

    And excellent at camouflage.

    On rare occasions, he pretended to be fierce.

    And in his youth, he was a proud hunter.

    But mostly, he was a non-dominant scaredy cat...

    ...who loved to play with catnip toys...

    ...and snuggle up in the laps of his companions.

    Max and Sandra
    June 27, 2015

    Tragically, I'm forced to go on without them, during an unprecedented time of anxiety and social isolation.

    I love you and miss you both.
    💔 😭 🐈

    in The Neurocritic on April 28, 2020 06:30 PM.

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    Fedora 32 Computational Neuroscience ready-to-install ISO image is now available!

    Download the Fedora 32 Computational Neuroscience image from labs.fedoraproject.org

    Fedora 32 was released today after a full six months of development. There are a lot of improvements and new changes included in this release. You can read the announcement here and the complete release notes here.

    This release is particularly exciting for the NeuroFedora team. It also marks the first release of our first deliverable: the CompNeuro Lab ISO image! The aim of developing such ready to install ISO images that are packed with the necessary tools is to enable users to quickly set up their computers and get down to work, instead of wasting precious time and effort on installing tools individually by hand. While we hope that this will enable researchers by providing them easy access to Free/Open Source research tools, we also hope that the platform will serve as a teaching aid in Computational Neuroscience courses.

    Applications featured in the CompNeuro ISO image.

    This CompNeuro release includes a number of modelling related tools that we were able to package over the release:

    All of these tools have been built with the current best practices in Software Development in mind---this is mandated by the Fedora community's software packaging guidelines. In addition to modelling tools, the ISO image also includes multiple tools used in analysis of data:

    This is not all, though! There's even more Neuroscience software that can be installed from the repositories. Also, since this edition is derived from Fedora, users have access to the complete set of packages that are included in Fedora: all the desktop environments, productivity tools, development tools, and libraries that you can choose from.

    The CompNeuro ISO image is based on the Fedora Workstation product that uses the modern GNOME desktop environment. It provides a clean interface integrated with a plethora of daily use productivity and development tools:

    Screenshot of the GNOME desktop environment.

    Screenshot of the GNOME desktop environment with applications.

    If GNOME isn't to your liking, though, there are other options. You can install any Fedora "spin" and install the software you need there also. Whatever you choose, you'll be ready to work in no time:

    • download a Fedora image,
    • install the tools you need,
    • get to work!

    Feedback is welcome

    This is the team's first deliverable. There is a lot of Free/Open Source software out there that still needs to be included in NeuroFedora. If you use a tool that's not on our list, please let us know. If you experience any issues or have ideas for improvement, please do let us know. You can contact the team using any of our communication channels.

    Developing NeuroFedora is also a great learning experience, especially for students. As a volunteer based community project, we learn skills and tools together and share knowledge freely with each other. No skills or experience are necessary to join the community. You can find what you want to do, and gather the required knowledge as you go at your own pace. We strongly encourage students to join the team, contribute their bit, and learn more about the tools use in Neuroscience while they do it.

    We'd love to hear from you. Please get in touch.

    in NeuroFedora blog on April 28, 2020 02:05 PM.

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    Six tips for teachers who see emotional abuse

    The scars of emotional abuse are invisible, deep, and diverse; and unfortunately, emotional abuse likely impacts more students than we think.

    Emotionally abusive behavior broadly consists of criticism, degradation, rejection, or threat. Emotional abuse (also known as psychological maltreatment or verbal assault) can happen anywhere, both within and outside of families, and can refer to a single severe incident or a chronic, ongoing pattern. Educators, caregivers, coaches, school mental health professionals, administrators, and peers are all capable of acting emotionally abusive toward school-age youth. That is part of its insidious invisibility; despite emotional abuse being highly involved in childhood abuse cases, it is often forgotten and overlooked. This type of interpersonal trauma is typically chronic and cuts deeply, as it is associated with mental and physical health issues (e.g., anxiety, depression, stress, sleep problems, self-harm) during the school years and beyond.

    Even with this existing knowledge, emotional abuse remains misunderstood, minimized, unseen, and unreported by many, including school professionals. We outline three things teachers need to know about emotional abuse and three things they can do to meet the needs of students experiencing emotional abuse.

    What to know

    The impact on the student determines the occurrence of emotional abuse more than the behavior that caused it. 

    There is no legal or clinical universal definition of emotional abuse. For example, two students with a parent teasing them about their appearances may react differently, in part based on context and relationship with the parent. Emotional abuse would be determined by the impact on the student, rather than the teasing alone.

    Emotional abuse is detrimental to both a student’s way of thinking and feeling. 

    Children create their sense of self from stories that others construct about them. Students may believe the destructive narratives that are told to them. That is, these harmful words may impact students at their core—shifting how they think about themselves and the world, and how they feel about themselves and others.

    There are numerous ways that emotional abuse may manifest. 

    Emotional abuse is not simply hearing harmful words. The context around the experience of emotional abuse are varied and diverse. A student may internalize or externalize their behaviors, or something in between. If a school-aged youth is repeatedly told that she is worthless, then the student may be meek in class. If a student is threatened repeatedly, then she may act aggressively toward others.

    What to do

    Take care of your emotional needs and your emotional health.

    Educators cannot support students if they cannot support themselves. As some students may constantly hear emotionally destructive words in their home environments, teachers certainly do not want to bring any semblance of that into their schools. Nevertheless, working with students can be tiring and frustrating. If their emotional energy is low, teachers may react rather than respond to difficult situations that unexpectedly arise. Rather than taking a breath, teachers might begin to punitively scold or admonish a student. Teachers need to take care of their emotional needs so that they do not parallel any unhealthy at-home behaviors in the classroom.

    Foster sharing through strong relationships. 

    Try to examine the life contexts behind a student’s behaviors. Rather than focusing on what is wrong with students, be curious about the circumstances in students’ lives that may influence how they act in school. To have a firmer understanding, teachers need to create brave spaces in our schools and classrooms so that students may feel comfortable sharing with adults. Students often regard educators as more effective guardians in violence protection than police or security, which speaks to the importance of continuing to cultivate this trust. When students share feelings, provide positive reinforcement by expressing your gratitude or by giving a thoughtful, affirming response.

    Know the laws around mandated reporting, and communicate with transparency.

    Check state regulations and learn to whom to report and how to report within your district or county. If and when suspicion or reports of abuse arise, reach out to your school mental health professionals. Encourage your administrators to grow emotional abuse awareness, prevention, and intervention initiatives so that others feel willing to report even in instances of suspected abuse. Openly discuss what happens after a report is made, as this transparency allows for students to feel more comfortable with the idea of reporting.

    Words are powerful, and as such, can be weaponized and wounding. Words can also be healing, spoken with gentleness and justice. Teachers should listen wholly to their students and their unstated needs; let teachers use their minds and words wisely and act knowingly.

    Featured Image Credit: Image by Okan AKGÜL on Pixabay

    The post Six tips for teachers who see emotional abuse appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on April 25, 2020 09:30 AM.

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    Don't Inject Malaria Into Your Brain

    The strange story of one of the most shocking medical 'treatments' ever invented — cerebral impaludation, or the injection of malaria-infected blood into the brain.

    in Discovery magazine - Neuroskeptic on April 24, 2020 11:00 PM.

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    Jacques Wadiche PhD

    Jacques Wadiche (UAB School of Medicine) talks to us about multivesicular neurotransmitter release (MVR) in the CNS. He takes us through recent work from his lab that gets at PKA-dependent molecular regulation of MVR whereby synaptic release depends on the number of docked vesicles available for release upstream of release probability. Duration: 51 minutes Discussants:(in alphabetical order) Matt Higgs (Res Asst Prof, UTSA) Salma Quraishi (Res Asst Prof, UTSA) Charles Wilson (Ewing Halsell Chair, UTSA) acknowledgement: JM Tepper for original music.

    in Neuroscientists talk shop on April 24, 2020 04:56 PM.

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    The control of plastic inhibition over excitatory synaptic plasticity leads to the joint emergence of sensory coding and contrast invariance

    This week on Journal Club session Damien Drix will talk about the paper "The control of plastic inhibition over excitatory synaptic plasticity leads to the joint emergence of sensory coding and contrast invariance".

    Visual stimuli are represented by a highly efficient code in the primary visual cortex, but the development of this code is still unclear. Two distinct factors control coding efficiency: Representational efficiency, which is determined by neuronal tuning diversity, and metabolic efficiency, which is influenced by neuronal gain. How these determinants of coding efficiency are shaped during development, supported by excitatory and inhibitory plasticity, is only partially understood. We investigate a fully plastic spiking network of the primary visual cortex, building on phenomenological plasticity rules. Our results show that inhibitory plasticity is key to the emergence of tuning diversity and accurate input encoding. Additionally, inhibitory feedback increases the metabolic efficiency by implementing a gain control mechanism. Interestingly, this led to the spontaneous emergence of contrast-invariant tuning curves. Our findings highlight the role of interneuron plasticity during the development of receptive fields and in shaping sensory representations.


    Date: 24/04/2020
    Time: 16:00
    Location: online

    in UH Biocomputation group on April 24, 2020 01:02 PM.

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    An online summer school for computational neuroscience

    Megan Peters, Konrad Kording and the people behind neuromatch are building an online summer school for computational neuroscience (July 13 – 31st). If you’re reading this blog – chances are you should be a student in this class or a TA. It’s going to be awesome! 3 straight weeks of computational neuro education. Designed for PhD student or postdoc experimentalists in mind, what sets it apart is matching, the same technology behind neuromatch. Become part of small tight-knit group of trainees with similar interests – bond, share, learn. But wait, there’s more:

    • Low TA to student ratio (6-10)
    • Lectures with world-class computational neuroscientists
    • Tutorials in Python, cloud-based in Google Colab: take your theoretical knowledge and apply to your own data
    • Inclusive: 100$ tuition (waivable)

    I loved summer school (CSHL computational neuroscience: vision). I made some life-long friends and have memories to last a lifetime. We want it to be better than a real-life summer school. Better by being more inclusive, matching you with more diverse people, offering multiple levels of support, and being accessible to people at different stages in their career.

    Syllabus is here. Student form is here. TA form is here. YOU HAVE UNTIL APRIL 27 TO SIGN UP, DO IT NOW.

    Teaching at scale

    Most real-life elite education is expensive and exclusive. In online education, it’s possible to scale to huge audiences for a fraction of the cost, and let everybody in – including people of disadvantaged backgrounds. MOOCs can have excellent learning materials – better production values, materials that resist the test of time, scannable lectures. Training educators in the latest methods can be done at scale.

    The biggest disadvantage of MOOCs is high attrition – up to 95% of people that sign up for MOOCs drop out. New models are appearing that have the accessibility of online learning and the critical social component of real-life learning. At Stanford, Chris Piech and Mehran Sahami started Code in Place, an effort to bring CS education to people at home during covid19 times. It’s a massive effort – 8,000 students from all over the world accompanied by 800 section leaders (including me!). Several factors have kept dropout to a minimum (< 20% after 2 weeks):

    • A low TA-to-student ratio
    • matching TAs to students based on learner characteristic (age, location)
    • engaging materials
    • a very high standard for TAs (Top affiliations are Stanford, Google and MIT)
    • a tough preparatory assignment to make sure the students entering class were motivated

    I was very excited when Konrad announced that they were working on a summer school, fresh off my Code in Place experience, so I contacted him and have joined the team to help (in a small way) organize this thing. There are a handful of experiments in teaching computational neuroscience at scale, the most successful in my opinion being the Neuronal Dynamics online book, tutorials, and lectures. Imagine that, plus TAs, your own wolf pack, live Q&A – community. That’s what we’re aiming for.

    in xcorr.net on April 21, 2020 02:15 PM.

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    Civil Disobedience in Science Publishing?

    Fighting the system of scientific authorship, one author list at a time?

    in Discovery magazine - Neuroskeptic on April 18, 2020 11:00 PM.

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    Service Announcement: Planned maintenance on Friday, April 17, 2020

    On Friday, April 17, 2020, arXiv staff will be performing planned maintenance to improve the overall quality of the service. On Friday from 2:15 PM to 4:15 PM EDT arXiv.org will still be available. However, users may experience significant service disruptions, including to the submission service. At the end of the planned maintenance, full functionality will be restored. Thank you for your understanding as we work to ensure a high-quality experience for all our users.

    We are also planning similar maintenance for the following two dates:

    • Friday, April 24, 2:15 PM to 4:15 PM EDT
    • Friday, May 1, 2:15 PM to 4:15 PM EDT

    in arXiv.org blog on April 16, 2020 01:00 PM.

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    The Neuroscientist, A Field Guide

    How to spot a neuroscientist in the wild

    Neuroethologist in the wild. Image credit: Pixabay

    We here report the discovery of a new species of the genus Homo, for which we propose the binomial Homo Neuroscientus. Despite dating their last common ancestor with Homo sapiens to within a mere hundred years ago, the evolutionary pressure of being forced to reckon with the most complex organ in known existence has driven rapid divergence in Neuroscientus. This has given rise to an absurdly overextended obsession with the brain, while atrophying other, normal features of the genus Homo. Indeed, in our field studies we found the sense of social etiquette to be vestigial at best.

    Over two decades of close observation we have identified a number of sub-species. While we believe these sub-species to be technically capable of interbreeding, they are rarely seen interacting in the wild, and so must be considered distinct. Here we present a field guide to identifying these sub-species from their characteristics


    There are a number of species that attempt to mimic Homo Neuroscientus, but are easily distinguished upon close observation. Two in particular are noteworthy:


    Sapiens that append the prefix “neuro-” to any random noun to make it sound smart and brain-y. Particularly egregious examples include neuro-marketing, neuro-law, and neuro-criticism. Frequently confuse neuroscience with psychology.


    A sub-species of Sapiens easily identified by their mantra “I’ve got a theory for how the whole brain works”. Scourge of inboxes. Somehow oblivious that the collective efforts of the highly intelligent few hundred thousand members of the below Homo Neuroscientus sub-species have been ultimately aimed at that very same thing, across all scales at which brains work, for about a hundred years — yet have not constructed a working theory.


    The Electrophysiologist

    The recorder of single neurons, lowerer of electrodes. Notable tribes include the patch-clampers, whose cruel initiation rites require attaching a micrometer-scale piece of glass to the body of a neuron ten times smaller than the thickness of a human hair. Some among this tribe, possibly insane, attempt the same in awake, moving animals. They are easily distinguished from other Neuroscientus by the rhythmic beating of their heads against the lab bench when losing yet another neuron after just three trials of behaviour are complete.

    The Systems Neuroscientist

    Distinguishable from the electrophysiologist by trying to record from many neurons at the same time, and relate them to something in the outside world. Comes in many tribes, from the sensory obsessives, the memorists and decisionists, to the motor wagglers, through others that identify themselves by blobs of the brain — the corticians, cerebellites, the basal gang, the hippocampites, the amygdalarians — to yet others that identify with the type of brain — the worm-wranglers, the fly-fanciers, the sea-sluggers. To the naive observer these tribes would all seem to be working towards the same goal, but vicious internecine wars frequently erupt within and between tribes.

    Insufferably smug since members of their subspecies were awarded a Nobel Prize in 2014 (“we’re a real science now”), they are nonetheless handicapped by the crudeness of their tools, which has led to the Humphries Uncertainty Principle: they can either record precisely when neurons send spikes but not know exactly where they are, or know precisely where they are but not know exactly when they send spikes (they call these “multi-electrode recording” and “calcium imaging”, respectively).

    The Cognitive Neuroscientist

    This subspecies is more intensely interested in us Sapiens than any other. We find it useful to distinguish a number of breeds, albeit with some overlap:

    Neuroimager — often referred to by other subspecies as “a psychologist with a magnet”, they adore rainbow colours. A deeply superstitious people, yet highly intelligent. In their writings frequent references are made to “Bonferroni”, possibly a deity, and they will cross themselves and mutter curses to the heavens upon hearing the phrase “dead salmon”. But the complex incantations necessary to turn the magnetic alignment of oxygen-depleted haemoglobin into a measurable signal of brain activity is testament to their ingenuity.

    Scalp tickler — a “psychologist with a hairnet”, readily identified by their distinctive calls. Anthropologists have transcribed some of these calls (lit. “P100”, “N2”), but have yet to discern their meaning. Some authorities subdivide a further breed, the Magnetiser, a psychologist with a quantum thingy.

    The Paddlers — believe that waving a magic wand near the scalp of a Sapiens will variously cause involuntary movement, enhance their mathematical ability, or let them experience the presence of god(s).

    The Neuroanatomist
    Was thought to be going extinct, until the Connectomics Explosion approximately 15YA rapidly diversified the gene pool, with many new, previously unrecorded phenotypes appearing.

    Neural Engineer
    Consider the brain to be a feedback loop. Fiddles with amplifier settings until the squealing stops.

    Behavioural Neuroscientist
    Attempts to infer the workings of the brain from watching a rodent press a lever. Talks almost entirely in capital letters (example transcript: “the US will become the CS, but leave the UR intact”).

    Attempts to infer the workings of the brain from watching an animal go about its daily routine. Barely on speaking terms with Behavioural Neuroscientists.

    Slightly hormonal. Obsessed with how everything sloshing around the brain that isn’t a neurotransmitter affects brain cells. Believes a “raster plot” is a graph drawn by a Bob Marley fan.

    Molecular neuroscientist
    Applies the tools of close cousins the molecular biologist to the brain. Loves the stuff floating inside cells, especially proteins and complex chains of chemicals signalling to each other. Unable to distinguish the brain from the liver without assistance.

    Obsessed with the expression of bits of DNA and RNA in brain cells. Unable to distinguish the brain from yeast without assistance.

    Clinical Neuroscientist
    Haughty and proud, these interact the most with Homo sapiens, bringing their skills to treat the damaged and sick among that closely-related species. Males of this sub-species are thought to be born wearing a suit and tie.

    Computational Neuroscientist

    Often gaunt, frequently shunning daylight, these shy creatures have also a number of distinctive breeds. Recent gene sequencing work on this sub-species has revealed evidence of lateral gene transfer from known species of Physicists, Mathematicians, and Computer Scientists. The consequent melange of languages spoken among members of this sub-species often collapses interactions into mutual bafflement.

    Circuit modeller — Literal-minded to a fault, these build exact scale models of bits of brain. Often try to show them to their fellow Systems Neuroscientists working on the same bit of brain, but suffer frequent barbs and social rejection (“Suited for a more specialist journal”).

    The Algorithmics — Seek the Holy Grail of the step-by-step instructions by which the brain works. Once discovered that deep-lying neurons, which may or may not contain dopamine, send a signal that looked like the difference: [actual value of what happened] — [predicted value of what happened]. Have been banging on about it for the past 25 years.

    Compartmentalist — Uses a thousand equations to describe a single neuron, none of whose parameters are experimentally determined. Often found weeping silently into a drink at conference bars. Worship at the Church of Rall.

    The Bayesians — Have discovered a hammer, and are determined to use it on absolutely bloody anything that’s not already nailed down.

    Karl Friston

    Want more? Follow us at The Spike

    Twitter: @markdhumphries

    The Neuroscientist, A Field Guide was originally published in The Spike on Medium, where people are continuing the conversation by highlighting and responding to this story.

    in The Spike on April 13, 2020 03:11 PM.

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    Please click on image to visit https://annadumitriu.co.uk/

    Please click on image to visit https://annadumitriu.co.uk/

    in Anna Dumitriu: Bioart and Bacteria on April 13, 2020 01:11 PM.

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    New mobile-friendly survey results

    We are so proud and honored to serve the arXiv community who, despite the global turmoil caused by the COVID-19 crisis, are more committed than ever to advancing scientific research. At arXiv our commitment to improving the platform with changes large and small continues as well.

    We recently held a survey to assess new incremental updates to the mobile-friendly display of the abstract page. First of all, we want to extend a huge thank you to all of the survey participants. Participation levels were high and we really value your time and your insights.

    In our survey we asked participants to review the proposed abstract page on their mobile device and then rate its usability against the current live page:

    Survey comparison of the old and new layouts

    Some of the main changes include reducing the height of the header, adding mobile-friendly navigation and search links, and moving the download button. We also made the citations section (not shown in the screenshots above) more user friendly on touch screens.

    Users overwhelmingly found the proposed abstract page style improved their experience on mobile devices:

    • Yes, I prefer the new style: 94.81%
    • No, I prefer the old style: 5.19%

    Users also provided valuable feedback on other aspects of the UI which we are cataloging to inform future updates. We will push these mobile-friendly edits to the live site this week, so if you access arXiv on your phone you’ll notice some changes on the abstract page.

    Thank you for helping us improve arXiv.

    -The arXiv NG team

    Want to join our next user testing survey? From time to time arXiv sends out surveys, previews to new changes, and other testing opportunities to interested users. To join our user testing group sign up here. User testing is integral to arXiv’s development process and we welcome your feedback.

    in arXiv.org blog on April 13, 2020 01:10 PM.

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    The importance of character during war

    Nearly 20 years of war following the events of September 11 has resulted in advances in military psychology that stand to improve the well-being of all people, military and civilian alike. The symbiotic relationship between psychology and the military traces back to World War I. With the advent of US involvement in the war, the army and navy had to select and train hundreds of thousands of new soldiers and sailors for increasingly technical jobs. Compared to nineteenth-century wars, World War I required military personnel to operate far more advanced and complicated equipment including aircraft, tanks, and communications systems. To match military personnel to jobs in which they would excel, the military turned to psychologists to develop new aptitude tests rapidly. The tests developed for the military vastly improved the reliability and validity of aptitude testing. Such testing became common in civilian institutions after the war.

    Similarly, World War II stimulated psychologists to conduct further research on how to diagnose and treat combat stress and psychological injuries of war. With millions of Americans having served in the war, this knowledge provided a significant boost to clinical psychology. World War II also created a new area of psychology, human factors engineering. Engineers needed psychologists to help them understand the limits of human perceptual and cognitive capabilities in order to design ever more complex weapons and communications systems. The Vietnam War saw the emergence of the understanding of posttraumatic stress disorder, first studied among soldiers and veterans, but soon recognized to be a risk for anyone exposed to severe trauma. Our current understanding of PTSD, its causes, and how to treat it are due in no small measure to the efforts of military psychologists.

    In the same manner, the war on terrorism has resulted in a renewed effort by military psychologists to better understand factors that enable military personnel to perform at their best, as well as to better understand suboptimal adjustment or pathology. This emerging research promises benefits to civilians as well. A great example is the military’s research on character and its links to individual and team performance.

    Positive character traits like integrity, determination, and courage have long been identified as essential attributes of military personnel. The emergence of positive psychology in the late 1990s provided a new science-focused perspective on character among military personnel. The results of almost 20 years of research are now providing a clearer picture of the role of positive character in leading others in dangerous contexts. For example, trust — an essential element in leadership in any domain — is heavily dependent on the character traits of integrity, caring for others, and moral courage. Both research and practical leadership experience demonstrate the critical role of character in trust and leadership.

    Cadets at the nation’s service academies live under an honor code that dictates they will not lie, cheat, or steal, nor tolerate those who do. Military affiliation trumps nationality when it comes to the ranking of top character strengths. In comparing US military academy cadets with Royal Norwegian Naval Academy cadets and US civilian college students, military psychologists discovered that US cadets were more similar to their Norwegian cadet counterparts than they were to US civilian college students. The strongest character attributes among the military cadets regardless of nationality were honesty, hope, bravery, persistence, and teamwork. For the US civilian college students, the highest strengths were kindness, sense of humor, honesty, and judgment.

    Army researchers have discovered strong links between individual character and personal adjustment and have developed a program to enhance positive character among its soldiers. Military psychologists have found that positive character traits such as hope and optimism, persistence, self-regulation, social intelligence, and leadership contribute to the emotional and social sense of well-being, and to a sense of meaning and purpose in life. Soldiers high in these and related character strengths are less vulnerable to combat stress, perform better at their jobs, and are more likely to remain in the military compared to those low in these strengths.

    Research on character provides just one of many intriguing examples of how military psychology continues to contribute to our knowledge of general psychology. After all, the challenges and stresses that military personnel face are far too easily found in other walks of life. Military research on both positive individual and organizational character have significant implications for how to optimize individual and team performance in law enforcement agencies, sports teams, schools, and in corporations. Thus, the efforts of military psychologists continue to provide insights into human behavior that stand to help us all to perform at our best and to live our lives to the fullest.

    Featured photo by Vladislav Nikonov on Unsplash.

    The post The importance of character during war appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on April 13, 2020 09:30 AM.

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    Why we like a good robot story

    Jim and Kerry Kelly live in a small town in the rural Midwest. Their sons, Ben, six, and Ryan, twelve, attend the local public school. Their school district is always short staffed. The closest town is 40 miles away and the pay for teachers is abysmal.

    This year, the district’s staffing has hit a critical low: Class size will have to be huge, and there’s limited money for aides who might help with the teaching load, which will further discourage teacher applications. The school board considers accepting underqualified teachers. Parents are up in arms. Teachers and principals are stressed. The situation comes to a head at a school board meeting that drags on past midnight with shouting, frustration, threats, and anger. But, it’s too important to back off. Children’s futures are at stake.

    In the next week, the superintendent finds a possible solution. The state has money available to help school boards implement technology in qualified districts. The Kellys’ town qualifies. They can receive funds to buy robots to serve in the classrooms. The robots can assume some of the teaching load, improve teaching quality, and relieve the overcrowding.

    Ten years ago, this would have been unthinkable. Soulless machines educating our children? But, solutions are few, and the superintendent has found reports of success from other schools. He sells his plan well, and against all expectations, the school board agrees. The following fall, the Kelly kids, like all the kids in the district, have a robot in the classroom.

    At the half-year mark, the school board reviews their decision. In six-year-old Ben’s class, the results are outstanding. Kids learn fast—pretty much as fast from the robot as from the human teacher. And, the kids like the interactions with the machines. The teacher can accomplish more and is less stressed in the process. Everyone is pleased.

    But Ryan’s class, at age eleven, has a far different experience. The robot used in their class is identical to the one in Ben’s class—very human-like. By January, the kids hate it. They call it names; they hit it; they learn little from it. By midyear, it sits in a corner, scorned by students and teacher alike.

    This scenario is fiction, but it reflects the real world. Many school districts are hurting for staff, and robots are entering the classroom. In Japan, Robovie speaks and teaches English with elementary school children, like Robosem does in Korea. In the United States, RUBI teaches children Finnish. Child-like robots are helping autistic children practice social interactions through imitation-teaching games.

    Using robots as teachers makes some sense. Children learn much of their knowledge from others: parents, teachers, peers. Children trust that 8 × 8 = 64, that Earth is round, and that dinosaurs are extinct, not because they have uncovered these facts themselves but because reliable sources have told them so. Research shows that children are adapted to learn general knowledge from human communication. The phenomenon is known as “trust in testimony.”

    But, do children trust the testimony of robots? Does it matter if the robot behaves, responds, or even looks like a human? If children learn from a robot, do they learn in the same way they learn from a human teacher? Excellent questions.

    Research shows that when children as young as preschool age learn from other people, they monitor their informants’ knowledge, expertise, and confidence. They remember whether a person has given them accurate information in the past. They also monitor an informant’s access to information: Did she see the thing she is telling me about? They attend to the person’s qualifications: Is he a knowledgeable adult or a naïve child?

    Surprisingly little is known about how and if children learn from robots. Because robots are machines, children could see them as infallible, like calculators or electronic dictionaries. If so, they might accept any information from a robot without considering if it is accurate. Or, children might see robots as a more fallible machine: a toaster that burns the toast, a virtual assistant that can give wrong or even outlandish answers or an alarm clock that goes off in the middle of the night. If so, they might resist a robot’s teachings.

    Young children clearly can and do learn from robots, and they are appropriately choosy about the sort of robot teachers they accept. Research also shows that young children are more likely to learn from and accept robot teachers that are older children—just like in Ben Kelly’s first grade classroom—and older children are less likely, even unlikely, to do so—like in Ryan Kelly’s sixth grade classroom.

    Isaac Asimov’s book, I, Robot, is primarily about morality and robotics: how robots interact with humans for good or evil. Most of the stories revolve around the efforts of Dr. Susan Calvin, chief roboticist for the fictional U.S. Robotics and Mechanical Men, Incorporated (USRMM), the primary producer of advanced humanoid robots in the world. She worries about aberrant behavior of advanced robots, and she develops a new field, robopsychology, to help figure out what is going on in their electrical (“positronic”) brains.

    All robots produced by USRMM are meant to be programmed with the “Three Laws of Robotics:”

    • A robot may not injure a human being or, through inaction, allow a human being to come to harm.
    • A robot must obey the orders given it by human beings except where such orders would conflict with the First Law.
    • A robot must protect its own existence as long as such protection does not conflict with the First or Second Laws.

    But in Asimov’s stories, flaws are found in the robots and their prototypes. These lead to robots imploding, harming people, and in one key case, killing a man.

    I, Robot stories have spawned numerous spin-offs, continuations, and commentaries. A 2004 episode of The Simpsons (titled “I, D’oh Bot”) featured a robot boxer named Smashius Clay. Smashius, self-defeatingly, follows all of Asimov’s three laws and loses to every human he fights.

    The Twentieth Century Fox 2004 film, I, Robot, starred Will Smith as detective Dell Spooner of the 2035 Chicago police department. Dell investigates a murder of the roboticist Dr. Alfred Lanning, which may have been at the hand of a USRMM robot.

    Currently, robots like Robovie (or NAO or RUBI or other robots designed to interact with adults or with children) don’t have moral codes programmed in. But then, they also don’t have anything like full positronic machine intelligence. Conversely, we don’t have laws or codes about how to treat robots. For example, should a really human-like robot have rights? In November 2017, the Kingdom of Saudi Arabia granted a very human-looking robot, Sophia, citizenship. This set off an uproar about rights among women in Saudi Arabia. For example, Saudi women must veil their faces when they are in public; Sophia appeared in public and on TV without a veil.

    Researchers, robot designers, parents, and teachers have become increasingly concerned that interactions with robots will promote antisocial behaviors. A hitchhiking robot who traveled a bit around Europe, taking pictures and carrying on conversations with other travelers, was vandalized and destroyed after several extended weeks in the United States. And, it’s easy to imagine a world where robots displace humans from jobs and so are attacked and sabotaged by those they’ve displaced.

    Research suggests that antisocial behaviors toward robots can be reduced by modifying the robots. Preschool children in a classroom comforted a robot with a hug and protected it from aggression when it started to cry after being damaged or played with too roughly. At least one study has shown that younger children say a robot should be treated fairly and should not be psychologically harmed after having conversed and played with the robot for fifteen minutes.

    Every year, robots become a larger part of our lives. You can find robots in malls, hotels, assembly lines, hospitals and, of course, research labs. The National Robotics Initiative foresees a future in which “robots are as commonplace as today’s automobiles, computers, and cell phones. Robots will be found in homes, offices, hospitals, factories, farms, and mines; and in the air, on land, under water, and in space.”

    And robots are becoming more and more present in the lives of children. They are already teaching children in classrooms and helping them in hospitals. Robovie is just one of many robots that have been manufactured in the last few years designed to be used with children–created to play games, answer questions, read stories, and even watch children unsupervised.

    This unbridled production of hopefully child-friendly robots certainly needs more research. But, it’s clear that in some ways and at some ages children can successfully learn from robot teachers who actively interact with them.

    Featured Image by Andy Kelly from Unsplash

    The post Why we like a good robot story appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on April 09, 2020 12:30 PM.

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    arXiv recognizes the work of the scientific community

    As the world continues to grapple with the COVID-19 pandemic, arXiv staff and leadership would like to extend a heartfelt thanks to our community of volunteers, as well as the authors submitting their work to arXiv.org.

    More than 180 moderators, representing 22 countries across the globe, have continued to sift through thousands of submissions, ensure quality, and post research on arxiv.org despite significant disruptions to their personal and professional lives.

    Since the World Health Organization declared the outbreak a “public health emergency of international concern” on January 30, 2020, more than 26,000 scholarly works have been announced on the site, including many related to the coronavirus. March 2020 was the second busiest month in arXiv history, with 14,415 new papers posted. This is a testament to the astounding effectiveness of arXiv’s moderators. It also reflects the incredible vibrancy of the global research community and the fact that the pursuit of knowledge continues despite the pandemic. We’re proud that arXiv is used extensively to share knowledge across disciplines and across the world.

    Members of the Scientific and Member Advisory Boards also continue to honor their commitment to arXiv, meeting with the new executive director, corresponding via email, and contributing their perspectives on operations and aspirations for 2020 and beyond.

    Here at arXiv, our staff has been working remotely for several weeks now, like so many of our colleagues. And so it is from our home offices that, again, we thank our volunteers and share our gratitude for the strong arXiv community that remains connected during this difficult time. Thank you.

    in arXiv.org blog on April 06, 2020 07:24 PM.

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    The surprising scientific value of national bias

    Emotions seem by their very nature to defy scientific analysis. Private and evanescent, and yet powerful and determining, feelings resist systematic observation and measurement. We are lucky to catch a glimpse in a facial expression or inflection of speech. The emotions of animals are all the more difficult. Without words to communicate what might be in their minds or on their nerves, animals–ranging from the complex to the simple–remain nearly a closed emotional book for even the cleverest experiment. A century ago Robert Yerkes, then at Harvard, registered these frustrations. Little is “of more obvious importance scientifically than affection,” he wrote in his Introduction to Psychology, in 1911, but its study lags behind investigation of “cognitive consciousness.” Convenient as it might be to assume animals are machinelike anyway, our behavior in the laboratory, he observed earlier in his Journal of Comparative Neurology and Psychology in 1906, betrays our logic. “Even those who claim that animals are automata do not treat them as such.”

    Shrewd as Yerkes was about his specialty of animal behavior, he would have been puzzled by the idea that national loyalty influenced his science. His research ethos was empiricism: Infer conclusions from carefully collected facts. As he succinctly advised in 1904 in the same journal, “experiment much and speculate little.” Other Americans agreed. John B. Watson’s “Psychology as the Behaviorist Views It” of 1913 proposed to make the field “purely objective” by jettisoning the “yoke of consciousness.” That a conscious mind exists at all, in Watson’s view, was mere supposition. It makes sense that it was the German-born émigré ornithologist, Ernst Mayr, who recognized the American devotion to practicality as a national bias. When his Dutch friend, Niko Tinbergen, planned lectures for a US tour in 1946, Mayr wrote to him that “American scientists do not care for too much speculation but like thorough analysis of observed phenomena.” Indeed, deficient experimentation and excessive theorizing became a polemical weapon in international debate. Intellectual precision was–and is–the mark of good science, but American investigators of animal sensibility once claimed it as their special national possession.

    Although the danger of scientific myopia nurtured by pride is obvious, these Americans’ faith in their superior practice ironically became a path forward toward internationalism. Their zeal for conducting animal behavior experiments produced real insights into affective experience. They had something to contribute abroad. In the process, they traveled the world for fieldwork, made far-flung professional acquaintances, and opened the door to refugee scientists displaced by the twentieth century’s political turmoil. Scientific passion stoked nationalism, but also gradually undermined it.

    Researcher L.W. Cole works with a raccoon, 1905. Used with permission from Yale Library.

    Animal experiments became one area of American expertise. Nonhuman subjects, by their very lack of language and inability to deceive in self-reports, were a perfect fit for a method based on external observation. The variety of species studied included the proverbial white rat, but many others as well. Although Yerkes spent three decades after World War I focused on primates, he had earlier measured learning in newts, frogs, mice, crows, and pigs. His colleague Edward Thorndike watched chicks, cats, and dogs escape from puzzle boxes, and Yerkes’s student L. W. Cole did the same with raccoons. So much scrutiny of animals expanded the researchers’ appreciation of their personalities. Intelligence, understood as skill acquisition, was the original question. Mood and temperament were annoyances. A tired rat knew where to find the bit of bread, but stopped running for it. It is not surprising that the emotions themselves eventually caught scientific interest. Donald Griffin rattled his field in The Question of Animal Awareness of 1976 when he declared, against reigning local wisdom, that animals are conscious. They have “not only images and intentions, but also feelings, desires, hopes, fears.” His revolutionary claim was the endpoint, however, of a typical American career. Three decades before, Griffin discovered how bats maneuver in the dark by echolocation, a kind of intelligence. His wonder at the animal mind deepened over the years.

    To be sure, American scientists never had a monopoly on insight into animal behavior. The counterexample of Darwin is enough to deflate any sense of supremacy. Their enthusiasm for controlled animal experiments produced so many competent studies, however, that they may have had an outsized influence. One British book of 1915, Investigation of Mind in Animals by E. M. Smith, borrowed nearly all of its illustrations from American publications. Although the Americans favored laboratory work for its rigor, they increasingly went into the field to witness the vast number of species in native habitats. Yerkes traveled to Senegal in 1929 in pursuit of great apes, and Griffin to Venezuela in 1952 to observe the nocturnal navigation of oilbirds. Often welcomed as respected authorities, they were also exposed to the world’s problems. Walter Cannon of Harvard celebrated “free intellectual intercourse without respect to national boundaries” in his plenary speech at the International Physiological Congress in Leningrad in 1935, published by the state press as Chemical Transmission of Nerve Impulses. His trip by train from Vladivostok to reach the meeting, however, was a sobering political lesson. Seeing prisoners laboring at gunpoint along the tracks in Siberia made for “a queer kind of horror that seizes you now and then,” his wife Cornelia wrote of the trip. Cannon may well not have had immediate doubts about the virtues of his own country, but he surely registered the pressures of nationalism at the borders of science.

    Scientist C. R. Carpenter setting up equipment in Thailand in 1937 to record gibbon calls. Used with permission from Penn State Library.

    World War II fully exposed the catastrophic cost of national arrogance. International science advanced in its wake. Supported by American colleagues, Mayr achieved US citizenship in 1950 after a decade of government surveillance as a suspect alien. Although the new politics of internationalism was influential, just as crucial was the internal dynamic of science to push its practitioners beyond parochialism. The same high standard that impelled these Americans to apprehend animals in all their complexity–including animal emotions–underwrote growing internationalism. Precisely because the American science of animal behavior was embedded in political life, it had the power to change minds.

    Featured image from Pixabay.

    The post The surprising scientific value of national bias appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on April 03, 2020 12:30 PM.

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    Scraping webpages with developer tools and Selenium

    There’s a lot of interesting statistics you can do by scraping websites, whether it’s reading tables from Wikipedia, grabbing and aggregating climate change tables from government websites, or quantifying the exponential growth of covid-19 articles on Medium. Many of these pages will have easy-to-use methods to download the data in a develop-friendly format, for example CSV or JSON. For others, you’ll have to rely on scraping web pages, an ancient, dark art. In this article, I’ll introduce you to some of the tools of the trade to do so in Python.

    Identifying targets with developer tools

    Both Chrome and Firefox have developer tools (Shortcut: Ctrl+Shift+I). These tools allow you:

    • Visualize the HTML, JavaScript, and CSS behind a webpage
    • See the traffic between your browser and the internet, include late http requests triggered by JavaScript
    • Execute custom JavaScript that can read and modify the DOM of a webpage
    • Identify where a particular UI element is created in the page’s HTML

    These can help you identify which part of a page you need to scrape. Let’s say, for instance, that we want to find out how the top article of a major news website changes as a function of time during a time of crisis (as of now, covid-19). Perhaps we’ll want to retroactively run an analysis of the sentiment behind the headline, the focus (health, business, etc.), the frequency of updates, or of how these headers co-vary with numbers released by different governments.

    Here I’ll use the New York Times as the example webpage. What we’d like is to grab, every half-hour, the title of the biggest headline. With developer tools, I can easily use the Picker tool (Ctrl+Shift+C) to highlight the biggest headline on the page.

    Here I find that the biggest headline is a span with a class name of balancedHeadline. Let’s look at how we can grab this information with Selenium.

    Selenium: remote control browsers

    The method I’ll showcase here uses Selenium: we use a headless browser (that is, an instance of Firefox or Chrome that’s running “invisibly”) that navigates to the website we care about. Once on the webpage, we can inject javascript, simulate clicks or manipulate the DOM to get to the information we need. This is a rather heavyweight solution compared to, say, using urllib to grab the data and parsing it with BeautifulSoup. However, the big advantage we get is that the headless browser actually runs the javascript on the page and loads all the extra assets – it’s literally like a person navigating to the website. Sometimes, it can be the only solution, especially if the information we need:

    • is dynamically loaded
    • is hidden behind authentication layers
    • requires emulating clicks and interacting with JavaScript

    In Python, we can easily install Selenium with:`

    pip install selenium

    Then we’ll need to install a WebDriver – this will allow your favorite web browser to be manipulated via Python. Here I installed the Firefox webdriver on the Ubuntu platform. I followed the instructions here on the Selenium website, downloading the gecko webdriver and extracting the binary to /usr/bin. You can check that you’ve done the installation by running a tiny bit of Python:

    from selenium import webdriver
    driver = webdriver.Firefox()

    Running this code opens up Firefox and navigates to the website. Notice the unusual appearance of the browser: the url bar is a different color than usual, and there’s a robot icon next to the address.

    A remote-controlled version of Firefox

    We can grab the information in at least a couple of ways:

    • We could inject some Javascript into the page and use document.querySelectorAll("span.balancedHeadline") to grab the headline
    • We could read the DOM to find the right span

    Let’s use the second method:

    from selenium import webdriver
    from selenium.webdriver.common.by import By
    from selenium.webdriver.support.ui import WebDriverWait
    from selenium.webdriver.support import expected_conditions as EC
    driver = webdriver.Firefox()
    element = WebDriverWait(driver, 10).until(
        EC.presence_of_element_located((By.CLASS_NAME, "balancedHeadline"))

    Running headless and automating

    Although the explicit window is useful for debugging, if you want to run this script every half-hour, you’ll want to run this in a headless browser. A headless browser doesn’t display a window, so it won’t pop up over your other windowsand capture your inputs. In addition, we’ll want to save the data to disk, which we can easily accomplish like so:

    from selenium import webdriver
    from selenium.webdriver.common.by import By
    from selenium.webdriver.support.ui import WebDriverWait
    from selenium.webdriver.support import expected_conditions as EC
    from selenium.webdriver.firefox.options import Options
    options = Options()
    options.headless = True
    driver = webdriver.Firefox(options=options)
    element = WebDriverWait(driver, 10).until(
        EC.presence_of_element_located((By.CLASS_NAME, "balancedHeadline"))
    with open('/home/pmin/Documents/headless-browser/top_news.txt', 'a') as f:
        f.write('"' + str(datetime.datetime.now()) + '","' + element.text + '"\n')

    Cron job

    All that’s left now is to set up a cron job to run this script every 15 minutes. First, we’ll need a shell file. We could run python directly, but I installed selenium inside of a special conda environment called headless-browser, so my shell file activates this environment before, like so:

    source /home/pmin/miniconda3/etc/profile.d/conda.sh && \
    conda activate headless-browser && \
    python /home/pmin/Documents/headless-browser/grab_headline.py

    I saved this file as /home/pmin/Documents/headless-browser/grab_headline.sh. Running crontab -e, I added an entry that looks like this:

    # m h  dom mon dow   command
    */15 * * * * /home/pmin/Documents/headless-browser/grab_headline.sh 2>&1 /var/log/grab-headline.log

    You can use this website to figure out what incantations to give to cron for different schedules. I also captured any output or error into an error log. If you don’t want to have to leave your computer on all the time to do this, you can run cron jobs inside of a cloud service instead.


    A final tweak we’ll need to deal with is authenticating. Sometimes the website we’re trying to scrape requires us to be logged in. It’s possible for the headless browser to use the same cookies and credentials as the regular browser you use. To do so, you need to locate the name of the default profile in Firefox. Locate a directory that finished with .default with:

    ls ~/.mozilla/firefox/

    In my case, I found a directory called lasd74g9.default. Putting everything together, here’s my final script:

    import datetime
    from selenium import webdriver
    from selenium.webdriver.common.by import By
    from selenium.webdriver.support.ui import WebDriverWait
    from selenium.webdriver.support import expected_conditions as EC
    from selenium.webdriver.firefox.options import Options
    options = Options()
    options.headless = True
    profile = profile = webdriver.FirefoxProfile(profile_directory='/home/pmin/.mozilla/firefox/lasd74g9.default')
    driver = webdriver.Firefox(firefox_profile=profile, options=options)
    element = WebDriverWait(driver, 10).until(
        EC.presence_of_element_located((By.CLASS_NAME, "balancedHeadline"))
    with open('/home/pmin/Documents/headless-browser/grim_news.txt', 'a') as f:
        f.write('"' + str(datetime.datetime.now()) + '","' + element.text + '"\n')

    in xcorr.net on April 02, 2020 04:41 PM.

  • Wallabag.it! - Save to Instapaper - Save to Pocket -

    Cyberspecies Proximiy

    This week on Journal Club session Anna Dumituru will talk about her project named "Cyberspecies Proximity" on which she is working together with Alex May.

    Cyberspecies Proximity explores what it will mean to share our sidewalks, elevators and transport systems in close proximity with mobile intelligent robots. The work challenges audiences to confront the technological, ethical, and societal questions raised by the advent of urban socially-aware robots.

    The robotic artwork combines the way-finding technologies of delivery and maintenance robots with an ability to communicate non-verbally, and to manipulate our emotions through body-language. The robot is able to move around an exhibition space using a predefined map created using SLAM technology. It reacts and responds to the body language of audience members through a multi-layered face, skeleton and movement tracking algorithm.

    The small and fragile humanoid form is dressed in the clothes of a worker, its frail and insignificant body reminds us of the social groups that will be most affected by future automation. The robot’s head and hands are made from 3D printed grey PLA and it intentionally avoids categorisations of race and gender. The project forces us to consider issues of ownership of public spaces as well as the broader ethical implications of how we design robots and behave towards them.

    Cyberspecies Proximity is a project by Anna Dumitriu and Alex May, created in collaboration with the Human Robot Co-Mobility Project of the New Technologies Team at Schindler. The project was supported by a Vertigo STARTS Residency, and the artwork was programmed in C++ and FUGIO, the Open Source Visual Programming System created by Alex May.


    Due to current unusual circumstances, this Journal Club will be held online as a conference on 8COM0108-0000-2019 module. In order to attend, you must be a member of that module. The conference room will be created on Friday and all of the module members will be notified about that with an email. Once the conference is created and started, module members will be able to join it by visiting the module website on Canvas, and then selecting "Conferences" section. Any queries should be directed to Emil Dmitruk via email (e.dmitruk@herts.ac.uk).

    Date: 03/04/2020
    Time: 16:00
    Location: Online conference on 8COM0108-0000-2019 module- more details will be announced on Biocomputation Slack group.

    in UH Biocomputation group on April 01, 2020 09:36 PM.