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    Contact tracing through friendship groups identifies additional syphilis and gonorrhea cases

    Contact tracing for disease control

    Syphilis and gonorrhea incidence have increased enormously in recent decades, necessitating innovative approaches. The rising prevalence of syphilis and gonorrhea, together with the increase in prevalence of resistant gonorrhea, makes contact tracing an important tool for disease control. In connection with the opioid epidemic, syphilis is now common in rural areas. However, people infected with stigmatized diseases such as syphilis and gonorrhea may be reluctant to reveal all of their sexual contacts. Reasons for not revealing all contacts may include internalized stigma, cognitive dissonance, or beliefs that certain types of sexual contacts do not “count.”

    Asking for friends might identify more sexually transmitted infection (STI) cases because friends may participate within the same sexual network, or some friends might be non-romantic sexual partners. One survey even found 77% of Grindr users report looking for friendship, more than the percentage seeking dating (67%), one-on-one sex (62%), or group sex (17%).[i]

    Our study

    Patients who were diagnosed with syphilis and gonorrhea in Baltimore City STI clinics were asked to name the most important people in their lives, with questions such as whom they eat meals with, who would take them to medical appointments, who would go to the store for them, or lend them $25. After patients named their friends and social contacts, they were asked to name their sexual contacts. Both social and sexual contacts were invited to the STI clinic for testing, and to name their own social and sexual contacts.

    Using this information for patients whose contacts visited the STI clinic, we created a network showing the friendship and sexual contacts and the STI test results.  We identified new cases of both syphilis and gonorrhea within each network.

    Figure 1
    New cases of syphilis

    In Figure 1, the network shows new cases of syphilis identified by asking for social contacts in the large red squares.The small squares are males, and circles are females. Shapes colored red are the participants who tested positive for syphilis. The green arrows are social network connections and the black are sexual network connections. Biological strain analysis for the organism that causes syphilis (T. pallidum) found that the disease strains matched across connected individuals, suggesting that individuals were connected within the same sexual network, although not necessarily directly: the friends may have had sex together or have a sex partner in common that does not appear in the graph. It’s remarkable here that for many pairs where both were infected with syphilis (syphilis-concordant dyads, for short), no sexual partners appear in the graph, and in a few cases both are male.

    Figure 2
    New cases of gonorrhea

    We did the same for gonorrhea.  As before, new cases of gonorrhea identified by asking for social contacts are the large red squares. The small squares are males, and circles are females. Shapes colored red are the participants who tested positive for gonorrhea. The green arrows are social network connections and the black are sexual network connections.

    The additional cases of syphilis and gonorrhea identified by asking friendship ties suggest that they under-reported their sexual contacts. These friendship ties may actually be sexual ties that were not reported as sexual; many of these ties were same-sex, and same-sex ties were stigmatized in this community, especially at the time that the data were collected (2001-05). Alternatively, these friendship ties may represent participation in the same sexual networks, such as engaging in a sexual relationship with the same person or people, who were not observed in the data.

    Learning from COVID-19

    Given existing strains on public health resources, public health policy must be creative. Traditionally, contact tracing is done by Disease Intervention Specialists. However, the 2008 recession resulted in large cuts to public health agencies that were never reversed. The Disease Intervention Specialists currently do not have enough resources even to contact all sexual contacts of index cases of syphilis and gonorrhea, so they prioritize vulnerable populations, such as pregnant women. Public health agencies simply do not have resources to contact the friends of index cases, and index cases may not cooperate anyhow.

    However, large technology companies have created privacy-preserving innovations in SARS-coronavirus-2 contact tracing protocols that have been deployed in state health department contact tracing apps. These contact tracing protocols identify nearby phones using Bluetooth and approximate the distance and duration. Public health authorities create COVID-19 contact tracing apps using these protocols that can specify distance and time duration for potential coronavirus contacts. These protocols or health department apps could be extended to contact tracing for other diseases. Changing the parameters for distance and duration on public health contact tracing apps could identify potential sexual contacts, allowing these apps to be used for STI contact tracing. The transition to these COVID-19 contact tracing apps has been bumpy, with technological limitations, low uptake, and lack of public trust, especially in government. The Bluetooth distance detection doesn’t do well near shiny surfaces or in public transit buses or trains, and while that’s a large problem for COVID-19 contact tracing, it’s not a problem for STIs. As with many US problems, low public trust in government is the limiting factor for contact tracing, whether traditional or by app.

    [i] Landovitz R, Tseng C, Weissman M, Haymer M, Mendenhall B, Rogers K, Shoptaw S. Epidemiology, sexual risk behavior, and HIV prevention practices of men who have sex with men using GRINDR in Los Angeles, California. J Urban Health. 2013; 90(4):729–739.

    The post Contact tracing through friendship groups identifies additional syphilis and gonorrhea cases appeared first on BMC Series blog.

    in BMC Series blog on October 21, 2020 05:22 AM.

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    Naked mole-rats invade neighboring colonies and steal babies

    Naked mole-rats — with their subterranean societies made up of a single breeding pair and an army of workers — seem like mammals trying their hardest to live like insects. Nearly 300 of the bald, bucktoothed, nearly blind rodents can scoot along a colony’s labyrinth of tunnels.

    New research suggests there’s brute power in those numbers: Like ants or termites, the mole-rats go to battle with rival colonies to conquer their lands. 

    Wild naked mole-rats (Heterocephalus glaber) will invade nearby colonies to expand their territory, sometimes abducting pups to incorporate them into their own ranks, researchers report September 28 in the Journal of Zoology. This behavior may put smaller, less cohesive colonies at a disadvantage, potentially supporting the evolution of bigger colonies. 

    Researchers stumbled across this phenomenon by accident while monitoring naked mole-rat colonies in Kenya’s Meru National Park. The team was studying the social structure of this extreme form of group living among mammals (SN: 6/20/06).

    Over more than a decade, the team trapped and marked thousands of mole-rats from dozens of colonies by either implanting small radio-frequency transponder chips under their skin, or clipping their toes. One day in 1994, while marking mole-rats in a new colony, researchers were surprised to find in its tunnels mole-rats from a neighboring colony that had already been marked. The queen in the new colony had wounds on her face from the ravages of battle. It looked like a war was playing out down in the soil.

    “Naked mole-rats are better known for their cooperation within colonies than competition between colonies,” notes Stan Braude, a biologist at Washington University in St. Louis. But over the course of the long-term study, Braude and his colleagues found that 26 colonies expanded their tunnels by digging into burrow systems occupied by neighboring colonies. In half of these cases, the invaded colony fled to a different arm of their tunnel system as the invaders expanded their territory. In the other half of cases, the invaded colony was entirely displaced, and the original mole-rats were never encountered there again. In four incursions, researchers caught invading mole-rats in the act, and in three of those, the bigger colony was doing the invading. 

    Genetic analysis, which was not available during the original research, later confirmed that during the 1994 invasion, the aggressors didn’t just evict the vanquished. They also pup-napped at least two youngsters. The pups grew up to become workers within their captors’ society.

    This lust for conquest had been seen before in the species, but only in captive colonies. Confirmation that these conflicts happen naturally in the wild means that they may have some influence on the evolution of the mole-rats’ crowded social lives, Braude says. The total eviction of smaller colonies by larger ones presents a previously unconsidered factor that makes it “important for this species to live in as large a group as possible.”

    Nothing about these “crazy beasts” surprises evolutionary biologist Chris Faulkes anymore. “The burrow is a massively valuable resource because it is so costly — in terms of energy — to excavate and build,” says Faulkes, of Queen Mary University of London. It makes sense that mole-rats would not only defend it, but try to pilfer this resource from others. 

    Since group size is so important to naked mole-rats, Faulkes says it’s interesting that workers from the different colonies don’t join together after an invasion. Only pups are added to the invading colony. 

    “The numbers of these kidnapped pups is really rather small, and these incidences of kidnapping may not be that frequent,” he says. “Given that, I’m not sure how much that really contributes to building large colony numbers.”

    The researchers argue that since there’s such a narrow window of time after birth when a mole-rat can be stolen, the fact that these pup-nappings were documented at all may mean the behavior is fairly common.

    Other forces may also be at play in facilitating the rise of large, tight-knit mole-rat colonies, like the spotty distribution of food resources in their harsh, dry habitat. 

    “Staying safe and finding food are absolutely important,” agrees Braude. Invasions might even abet that, contributing to the success of a mole-rat society. For instance, inhabiting a larger tunnel system may mean more access to the nutritious tubers the mole-rats find and feed upon underground.

    Warfare isn’t the only strategy naked mole-rats have to boost their colony’s geographic and genetic influence. Some naked mole-rats are specially equipped with abundant fat reserves that allow them to journey long distances aboveground. These “dispersal morph” individuals interbreed with other colonies’ members and can potentially establish brand new colonies. 

    in Science News on October 20, 2020 04:00 PM.

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    PLOS and Transparency (including Plan S Price & Service Transparency Framework)


    As a non-profit, mission-driven organization PLOS abides by our commitment to transparency. We openly share information and context about our finances, including target revenue amounts in some of our emerging business models. The Plan S Price & Service Transparency Framework provided us — and other publishers — a clear, uniform structure to share information about the services we perform and a percentage breakdown of how these are covered by the prices we charge. Many of our mission-driven publishing activities go well beyond peer review and production services. We provide commentary on some of these services, including how the varied editorial setups of our journals contribute to different percentage price breakdowns per title. We encourage other publishers to be transparent and openly share their data via such frameworks. And, we remain confident in showcasing how our prices cover our reasonable costs for a high level of service, with some margin for reinvestment.

    Full Post

    Since our founding in 2001, PLOS has maintained a firm commitment to transparency. Transparency informs our work within communities. It drives our approach to open science practices & policies. And it underpins our willingness to share financial data. Here are three examples of our commitment in action:

    1. Every year we provide financial transparency via the publication and contextualization of our IRS filings (2018 financial overview available here; our 2019 overview will be available in November)
    2. We participate in broader efforts within the publishing community to encourage greater understanding around pricing and the costs of Open Access publishing (see immediately below for the Plan S example)
    3. Our new collective action business model for PLOS Medicine and PLOS Biology — Community Action Publishing — openly shares how much revenue is required for PLOS to run these specific journals. We will redistribute revenues beyond the target back to community members

    This year, we are especially grateful to cOAlition S for spurring the scholarly publishing community, broadly, to engage with transparency via its Plan S Price & Service Transparency Framework.

    PLOS Response to Plan S

    In early 2020, PLOS (together with nine other publishers1) piloted one of the two approved pricing transparency frameworks for cOAlition S. We are now sharing the figures PLOS provided as part of this initiative to provide context to our own pricing and to further promote this kind of transparency broadly within the community. We encourage other publishers to be transparent and openly share their data as well. (Please see the post on price transparency by our friends at F1000 Research here.)

    Before diving into discussion of figures, we want to restate two underlying principles.  

    • PLOS does not charge for any activity for the sole purpose of profit. We do not seek or need revenue surplus for return to shareholders, but rather to support and reinvest in our mission.
    • Our organizational activities are developed to meet the needs of researchers, our prices cover our reasonable costs for our high level of service plus some margin for reinvestment, and our drives for efficiency are to enable as good an author experience as possible.

    The Plan S Price & Service Transparency framework invited publishers to divide Article Processing Charge, per journal, into seven categories of activity2:

    • Journal and community development efforts, including commissioning content, researching editorial board members, and scope development
    • Submission to desk reject or acceptance
    • Peer review management by staff/remunerated people, including management of submissions that are ultimately rejected
    • Acceptance to publication, including typesetting, conversation, and production tasks
    • Services after publication, including ethics checks and queries, usage statistics, long-term preservation and access monitoring
    • Sales & marketing to customers or of articles, including marketing campaigns
    • Author and customer support, including queries about licensing, citations, and author system troubleshooting

    PLOS’ pricing breakdown (which is only one element of the data captured in the spreadsheet) for 2019 is presented in the table below.

    PLOS Computational BiologyPLOS GeneticsPLOS PathogensPLOS Neglected Tropical DiseasesPLOS BiologyPLOS MedicinePLOS ONE
    APC price$2,350$2,350$2,350$2,350$3,000$3,000$1,595
    % of price for journal and community development14%14%14%14%20%18%13%
    % of price from submission to desk reject or accept15%16%16%15%25%27%21%
    % of price for peer review management12%12%14%13%21%23%13%
    % of price for services from acceptance to publication22%21%21%21%12%12%20%
    % of price for services after publication11%11%10%11%6%6%12%
    % of price for sales & marketing to customers or of articles16%16%14%15%11%8%13%
    % of price for author and customer support10%10%11%11%5%6%8%

    The above is a relatively good way of illustrating the breadth of activities that occur at PLOS, and which our income supports. However, like any framework or metric, it strips away some of the detail and nuance so we wanted to provide some overarching commentary and highlight a few observations.  

    Varied Editorial structures drive varied price allocation

    Currently, PLOS has two types of editorial setup across our seven journals. 

    • PLOS Biology, PLOS Medicine, and PLOS ONE are supported by senior in-house editorial teams (including Editors-in-Chief, an Executive Editor, Senior Editors, and Associate Editors) working in conjunction with external editorial boards. 
    • PLOS Computational Biology, PLOS Genetics, PLOS Neglected Tropical Diseases, and PLOS Pathogens each have external Editors-in-Chief and Associate Editors (who are full time members of the research, medical, health, and/or academic communities).

    The in-house editorial teams (a.k.a. Staff Editors) comprise salaried PLOS employees and are editorially independent. We see this combined expertise of dedicated Staff Editors and leading scientists in the field as an important aspect of the publication process for these titles. Our Staff Editors work to guide researchers through submission and peer review. They also partner with our external Academic Editors, experts in the field, to provide guidance. This unique editorial model ensures expertise, fairness and efficiency for each manuscript. This internal and external resourcing structure is reflected in the greater price share for activities related to “initial triage” and “peer review management” for these particular titles. 

    Beyond editorial and production

    Between 43% – 61% of our journals’ price covers the editorial/production work of receiving submissions, coordinating their peer review, and production and online publication of accepted articles. The remainder of the price covers the broader and deeper work of services before and after the publication process, including marketing, author support, and ethics checks, among other things — each of which is critically important. As examples:

    • PLOS has a highly regarded publishing ethics team that handles all  ethical and scientific concerns involving submissions and published articles. It also works to raise awareness of publication ethics standards, develops policies and processes to address integrity issues (at scale) prior to publication, and participates in broader discussions about publication ethics policies and practices.
    • PLOS engages closely with research communities (e.g. by attending/organizing conferences/events/workshops, these days mostly online) to ensure the journals and their policies truly reflect the research interests and values of these fields and communities. We operate in both global and local contexts, therefore it is ever more important to ensure we reflect the values of the diverse communities of researchers whom we publish.
    • PLOS has a dedicated, proactive media team that collaborates with authors, institutions, science media centers and journalists to communicate research to both scientists and society. Consequently, articles published in our journals receive great attention in the media. The team also develops policies and participates in industry conversations about best practices (e.g. preprints and the media). 
    • PLOS’ Outreach team promotes articles, invites submissions, promotes initiatives like calls for papers, and has also created widely used and well-regarded resources such as the Peer Review Center and the Writing Center
    • PLOS pilots, develops, and leads the way in Open Science practices, from creating new software to be able to publish peer review histories at scale, to patiently cultivating trust in science via a rigorous approach to preprints and preprint commenting
    • PLOS is constantly working to make Open Access easier, more efficient, and fair for researchers from all demographics, geographies, and disciplines. This is both via new business model development, and policy engagement

    We hope the full data and above commentary can give you some new insights. At PLOS we are proud of what we do. It is our privilege to devote our time and energy towards such crucial matters as increasing trust in science. We will always do this in partnership with the research community. And, perhaps, there has never been a more important time to be doing this.

    If you have any questions, please email community@plos.org

    If conversation about this data extends to social media, please follow along @PLOS.

    Thank you for reading!



    1. Annual Reviews, Brill, The Company of Biologists, EMBO Press, European Respiratory Society, F1000 Research, Hindawi, IOP Publishing, Springer Nature
    2. Information Power’s spreadsheet outlines these categories in more detail 

    The post PLOS and Transparency (including Plan S Price & Service Transparency Framework) appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on October 20, 2020 03:09 PM.

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    After Cheating On A Test, People Claim To Have Known The Answers Anyway

    By Emily Reynolds

    Cheating is common, ranging from benign instances like looking up an answer on your phone during a pub quiz, to the fairly major, such as using a series of coughs to fraudulently bag yourself a million pounds on a popular TV game show. But wherever we fall on that scale, research suggests, we’re still likely to think of ourselves as honest and trustworthy.

    There’s something of a tension here — we’re seemingly both prone to cheating and convinced of our own integrity. Matthew L. Stanley and colleagues from Duke University have one explanation for this apparent contradiction in their latest paper in Psychonomic Bulletin & Review: when we cheat, we claim we knew the answers all along.

    Before the start of the study proper, the team conducted a pilot test with 95 participants, who were shown 24 general knowledge questions; half were easy (“how many legs does a spider have?”) while the other half were more difficult (“Which nation was the first to ratify the United Nations charter in 1945?”). No participants correctly answered any of the 12 difficult questions.

    In the first study, 147 participants saw these 24 questions and had to type in the answers. Before answering, they were told the correct answer would be visible to them, upside down in a small font on the bottom right of their screens. Looking at the answer, they were told, as well as looking things up online, was considered cheating.

    After a short unrelated task, participants were shown the same questions, this time with the answers included. They then indicated whether or not they had known the answer to the question before the beginning of the study.

    These participants fared better than those in the pilot: they correctly answered 14% of the difficult questions. Given that nobody in the pilot group correctly answered these questions, this suggests that participants were cheating. And when they answered these difficult questions correctly, participants were also more likely to report that they knew the answer all along. That is, even though they likely cheated, they claimed to have known the answer anyway.

    In a second study, participants were assigned to one of two conditions. The first — the cheating condition — replicated the initial study: participants were shown the correct answers on the bottom right hand of their screen. In the control condition, participants had no opportunity to cheat, but were shown the correct solution immediately after answering each question.

    Unsurprisingly, those in the cheating condition answered more of the difficult questions than those in the control condition — and were more likely to later report that they knew the answers all along too.

    In the final study, all 412 participants were able to see the answer on their screen — only this time, those in the control condition were told they could look at the answer if they didn’t know it themselves. As in the previous two studies, those in the cheating condition were subsequently more likely to indicate that they knew the answer all along, suggesting yet again a link between perceived (or claimed) knowledge and cheating.

    The findings fit into a wider body of research that suggests we’re liable to lie to ourselves about who we are or how we behave. We distance ourselves from past mistakes or forget them altogether, and see ourselves as increasingly moral over time. What the study doesn’t explain is how people are experiencing these mistakes themselves. Are they just lying about having known the answer, fully aware that they’re not telling the truth? Or is there a level of self-deception: do people truly believing that they had the solution all along?

    The study also poses interesting questions about how to prevent cheating. If we’re able to believe we’re honest and trustworthy literally immediately after engaging in duplicitous behaviour, making appeals to morality might not work: people might simply think “I would never do something like that!” Techniques that completely foreclose the possibility of cheating may have more mileage.

    Cheaters claim they knew the answers all along

    Emily Reynolds is a staff writer at BPS Research Digest

    in The British Psychological Society - Research Digest on October 20, 2020 01:31 PM.

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    Macchiarini victim to Swedish prosecutor: “Claudia is alive and must be called to testify”

    Macchiarini's victim Paloma Cabeza speaks out again, fearing she doesn't have much time left. She appeals to the Swedish prosecutor for justice in the deadly trachea transplant scandal.

    in For Better Science on October 20, 2020 12:22 PM.

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    Even the deepest, coldest parts of the ocean are getting warmer

    Things are heating up at the seafloor.

    Thermometers moored at the bottom of the Atlantic Ocean recorded an average temperature increase of about 0.02 degrees Celsius over the last decade, researchers report in the Sept. 28 Geophysical Research Letters. That warming may be a consequence of human-driven climate change, which has boosted ocean temperatures near the surface (SN: 9/25/19), but it’s unclear since so little is known about the deepest, darkest parts of the ocean.

    “The deep ocean, below about 2,000 meters, is not very well observed,” says Chris Meinen, an oceanographer at the U.S. National Oceanic and Atmospheric Administration in Miami. The deep sea is so hard to reach that the temperature at any given research site is typically taken only once per decade. But Meinen’s team measured temperatures hourly from 2009 to 2019 using seafloor sensors at four spots in the Argentine Basin, off the coast of Uruguay.

    Temperature records for the two deepest spots revealed a clear trend of warming over that decade. Waters 4,540 meters below the surface warmed from an average 0.209° C to 0.234° C, while waters 4,757 meters down went from about 0.232°C to 0.248°C. This warming is much weaker than in the upper ocean, Meinen says, but he also notes that since warm water rises, it would take a lot of heat to generate even this little bit of warming so deep.

    It’s too soon to judge whether human activity or natural variation is the cause, Meinen says. Continuing to monitor these sites and comparing the records with data from devices in other ocean basins may help to clarify matters.

    in Science News on October 20, 2020 12:00 PM.

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    Fire ants build little syphons out of sand to feed without drowning

    The threat of death is no obstacle for some hungry fire ants. To escape drowning while feeding on sugary water, black imported fire ants built syphons out of sand that moved the water to a safer spot.

    A range of animals, including birds, dolphins, primates and even ants, use objects as tools (SN: 12/30/19; SN: 6/25/20; SN: 6/24/19). Ants often employ debris or sand grains to carry food. But this is the first time that the insects have been observed adjusting their tool use to build relatively complex structures in response to a problem, researchers report October 7 in Functional Ecology.

    In the wild, black imported fire ants (Solenopsis richteri) typically eat honeydew produced by aphids. In the lab, entomologist Jian Chen of the U.S. Department of Agriculture’s Agricultural Research Service in Stoneville, Miss., and colleagues provided the ants with containers of sugary water. The insects have a hard, water-repellent outer covering called a cuticle, and can typically float on a liquid — and sure enough, the insects floated and fed without a problem.

    The researchers then reduced the water’s surface tension with a surfactant to make it more difficult for the ants to float. While some ants drowned, most stopped entering the containers and instead used grains of sand placed nearby to build structures leading from the inside of a container to outside of it. Those structures acted like syphons. Within five minutes of building one, nearly half of the water was drawn out through the sand pathway, allowing the ants to feed safely.

    “The fact that ants are building little syphons is new and interesting,” says Valerie Banschbach of Gustavus Adolphus College in Saint Peter, Minn., who was not involved in the study. The insects’ “flexibility to act in a creative way responding to a situation suggests that they have higher cognitive abilities than what is traditionally believed.” 

    In this time-lapse video, watch how most black imported fire ants avoid drowning by using grains of sand to build relatively sophisticated structures around containers of sugar water. In experiments, it took the ants more than 90 minutes to shift the sand to the containers and do the construction work. Those structures act as syphons to draw the water out of the containers and to a safer place for the ants to feed. 

    How the insects were able to sense the change in the water’s surface tension is unknown. Some ants that drown initially could be releasing chemical messengers, Chen says, or maybe the ants taste a difference in the water, or a combination of both.

    Black imported fire ants are native to South America but have made their way to parts of North America where they are regarded as invasive. The insects can damage crops such as corn, soybeans and okra, and can also sting humans.

    A major goal of the project, Chen says, is to develop new pest control measures by better understanding how the ants may behave in their natural habitat. Different types of surfactants are often added to pesticides to help them spread better, the researchers say, so ants could potentially be exposed to similar conditions in the wild as they were in the lab.

    For now, Chen is content to marvel at the industrious insects. “Ants are so amazing,” he says. “We have just scratched the surface of the ant world.”

    in Science News on October 20, 2020 10:00 AM.

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    Hands up! Carpal tunnel expert loses 12th paper for misconduct

    You can no longer count on two hands the number of retractions tallied by  Young Hak Roh, an orthopedic surgeon at Ewha Womans University in Korea found guilty of “intentional, repetitive, and serious misconduct.” The hand specialist has notched his 12th retraction in the wake of the institutional investigation, which, as we reported in July, … Continue reading Hands up! Carpal tunnel expert loses 12th paper for misconduct

    in Retraction watch on October 20, 2020 10:00 AM.

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    Open Access Week 2020: Building Equity and Inclusivity in Science

    It’s the start of Open Access Week 2020 and this year’s theme focuses on “Open with Purpose” with equity and inclusivity as the focal point for the third consecutive year.

    Why are we still talking about this?

    At this time, the need for international collaboration and access without restrictions is acutely apparent with COVID-19 pausing regular activities, such as conferences, libraries and other in person events. Building equity and inclusivity will create a stronger environment for scientists to ask questions or see problems from a different perspective. It’s also integral for organizations to reflect on what they can do to help researchers from every background get their research to the communities that need it.

    Looking to an inclusive future
    OA helps break down many of the barriers researchers face by sharing their findings to a vast readership. Yet, a number of hurdles still stand between them and the final article. At PLOS, we support researchers at every stage of their career, research and discipline. Open Science further increases transparency and visibility of their work so that all researchers can more easily be recognized for their contributions. With a host of journals and a variety of article types and early sharing methods such as preprints and preregistered reports — researchers will have the opportunity to showcase the full breadth of their findings. 

    We recognize that as an organization we can do much more to assist those in the scientific community that experience challenges due to their gender, race, culture and more. In a blog post by Editorial Director Joerg Heber, he outlines our support for a diverse and inclusive community and the areas we’ll continue to improve on to recognize and minimize bias, further diversify our leadership and contributors.

    Be counted for your work

    OA provides the community with the accessibility to your research to see, cite, and share it. Your research and contributions in the community are vital to scientific advancements. Be proud, in whatever stage of your career, of what you’ve achieved and get the recognition for your contributions, be that through your ORCID iD or citations. The OA community is increasingly adapting to the needs of ECRs. Transparency and early sharing practices for every stage of the research process are becoming increasingly common to support researchers in demonstrating their contributions, beyond just publications. Be the first to report your findings with preprints and preregistration, just two ways in which you can highlight your progress early when you’re applying for funding and new positions. 

    PLOS is always searching for new ways we can make publishing and acknowledging your work easier. Whether that means building a more inclusive framework to ensure credit is shared equitably among contributors, or supporting researchers in making their work more visible.  In a new policy announced last week, we’re providing better support to transgender authors with live articles published under names that do not reflect their identity. Our staff will be happy to help update your records and help you keep your previous credits. 

    Publishing an academic study is an achievement for researchers to be proud of, and it is important that the name on the paper reflects who the authors are. 

    Implementing name changes for published transgender authors

    Open Access is more important than ever

    In a time where COVID-19 proves to be a challenging obstacle with restrictions to labs and libraries, it is integral that we’re inclusive of the many groups in the scientific community — researchers around the world need access to content anywhere, anytime. OA is the key to providing fast, public access to research with no restrictions or embargoes. The global benefit of open research is powerful and will help maintain the continuation of scientific advancements.

    At the heart of inclusivity, cost plays a major role in separating researchers from the Open Access journals they would like to publish in. Over this year we’ve made great strides in partnering with institutions and consortia to bridge the gap between cost for prospective PLOS authors. And we’re continuing to experiment with new models that get closer to a truly open to read, open to publish ideal, equitably distributing the costs of publishing so that the burden of payment doesn’t fall on authors. 

    Next steps for a fair and diverse future

    We will continue to improve our processes and endeavour to be advocates for equity and inclusivity in OA and the broader academic community. Beyond 2020, scholarly communication will need to continue the work around creating inclusive environments for researchers by examining the struggles of systemic inequities, acknowledge bias by working with editors and reviewers, and ultimately take action to create a more accessible future for all. More updates to come! 

    The post Open Access Week 2020: Building Equity and Inclusivity in Science appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on October 19, 2020 04:34 PM.

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    A rope bridge restored a highway through the trees for endangered gibbons

    With acrobatic leaps, Hainan gibbons can cross a great gully carved by a 2014 landslide in the forest on China’s Hainan Island. But when a palm frond caught by the vaulting apes to steady their landing started to sag, researchers rushed to provide a safer route across.

    Though slow to adopt it, the gibbons increasingly traveled a bridge made of two ropes that was installed across the 15-meter gap, researchers report October 15 in Scientific Reports. The finding suggests that such tethers could also help connect once-intact forests that have been fragmented by human activities and aid conservation efforts of these and other canopy dwellers.

    “Fragmentation is becoming an increasing problem,” says Tremaine Gregory, a conservation biologist at the Smithsonian’s National Zoo and Conservation Biology Institute in Washington, D.C., who wasn’t involved in the study. “It’s probably going to be, along with climate change, one of the biggest challenges for biodiversity in decades.”

    The landslide damaged an arboreal highway, a preferred route through the trees that the apes use to traverse the rainforest. Hainan gibbons (Nomascus hainanus) are almost strictly arboreal, and forest fragmentation can divide the already critically endangered primates (SN: 8/6/15) into smaller breeding populations, says Bosco Chan, a conservation biologist at the Kadoorie Farm and Botanic Garden in Hong Kong. That can lead to inbreeding or local groups dying out.

    Only about 30 individuals remain of this species, all living in a nature reserve on Hainan Island. For the group of nine gibbons studied, the researchers didn’t want the animals to get hurt crossing the gap.

    Enter the rope bridge. It took months for the gibbons to catch on, but about 176 days after the bridge’s installation, camera traps captured the gibbons taking to the ropes. “I was very excited when [the gibbons] first started using it,” Chan says.

    Hainan gibbons use a rope bridgeTo cross a gully created by a landslide, some Hainan gibbons dangle and swing from a rope bridge installed by researchers, while others walk across, sometimes using the upper rope as a handrail.Kadoorie Farm and Botanic Garden

    Eventually, the scientists observed the gibbons crossing the bridge about as frequently as the animals had traveled that stretch of forest before the landslide. Females and juveniles preferentially used the bridge, while an adult male never used it, and nearly grown juveniles rarely did.

    Though the scientists expected the animals would swing along under the bridge using their arms, Chan says, many preferred to walk as though on a tightrope, using one rope as a handrail, or to climb along the ropes using all their limbs. Occasionally, gibbons scampered across without holding on with their upper limbs. For now, the bridge provides a temporary solution while transplants of native trees grow and other trees regenerate.

    Such artificial bridges provide a sensible and innovative approach to help gibbons get around safely, says Susan Cheyne, a primatologist based in Oxford, England, and vice chair of the International Union for Conservation of Nature’s Section on Small Apes, who advised the Hainan project. “We want them to stay up in the canopy.” On the ground, gibbons may get hit by cars, get into fights with dogs or be exposed to parasites that the animals wouldn’t typically encounter.

    What’s more, the Hainan gibbons’ adoption of the bridge suggests that it’s a “tool that other primate conservation groups could potentially use,” Cheyne says, as these gibbons are a “relatively fickle species. They are not overly keen on using new things,” she says.

    Beyond primates, other animals may use such crossings too. The team also saw two squirrels and another rodent use the bridge. Depending on where canopy bridges are located, marsupials or rodents could benefit, though observing such creatures to know for sure could be a challenge if they are nocturnal.

    in Science News on October 19, 2020 04:00 PM.

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    Rethinking Research Assessment:Addressing Institutional Biases in Review, Promotion, and Tenure Decision-Making (part IV)

    Authors: Ruth Schmidt is an Associate Professor at IIT’s Institute of Design and Anna Hatch is the program director for DORA. PLOS supports DORA financially via organizational membership, and PLOS is represented on the steering committee of DORA.

    In part one of our series we showed how objective comparisons are not equitable . In our second part of this series we showed how individual data points can accidentally distract from the whole. In part 3 we explored how we gauge value by association. In our final installment we get into how incumbent processes and perceptions have the advantage.

    The deep legacy traditions held by many academic institutions can be powerful, contributing a sense of continuity and identity and reducing the need to continually reinvent the wheel. But when these organizational habits and norms become too normalized, and old processes and structures persist because “that’s how we’ve always done this,” they can create an unhealthy sense of insularity that excludes new ideas and people.

    One contributing factor to this is Confirmation bias, which describes peoples’ tendencies to dismiss evidence that doesn’t fit their initial judgments or preconceptions, even if these presumptions are grounded in subjective experiences and limited data. Failing to gather and consider counter-evidence makes us more likely to fall into old ways of thinking, such as cherry-picking information from a CV to confirm the view we already have, or dismissing potential warning signs because a candidate has already been accepted as a good fit.

    Status quo bias, sometimes known as “effort aversion,” reflects our tendency to take the path of least resistance unless there are strong reasons not to. This can lead to situations where people stick with recognizably flawed processes because the effort to fix them or adopt new ones is perceived as too much effort. For example, the continued use of citations to indicate research quality is driven in part by the fact that it’s perceived as familiar and easier, not necessarily better, than using alternate indicators of real-world impact. For academic institutions — never known as stealthy and agile entities even in the best of times — this can cause significant paralysis, keeping demonstrably subpar structures in place long past their usefulness.

    What can institutions do?

    Make it easy. Sometimes the biggest barriers to adopting new behaviors are actually smaller than one might expect, such as not knowing where to start or a lack of clarity about the value of doing things differently. Making the benefits of new behaviors concrete, salient, and simple to grasp makes both starting and follow-through easier.

    Question what you “know.” Sticking with old assumptions tends to reward those with more traditional backgrounds, which comes at the expense of attracting new or more diverse talent. Productively pushing back on assumptions — even assigning the role of playing devil’s advocate during deliberations — can force all involved to be crisper and more defined about what qualities matter, and why.

    Broaden notions of success. New processes can only go so far if definitions for success (and who’s invited to the table) aren’t also revisited. Setting, publicizing, and adhering to goals that look beyond traditional norms or value alternate experiences can broaden the diversity of individuals under consideration.

    Incumbent systems, processes, and structures are inherently advantaged, partly due to familiarity and partly because our tendency toward effort aversion tells us it’s almost always easier to stick with the old, however flawed, than introduce something new. This is especially true when those in positions of seniority have benefited from these legacy systems as their careers have progressed, and when in many cases entire academic careers spent at an individual institution may mean limited insight into even how to do things differently. But the need to introduce more equitable decision-making into RPT decisions to increase the presence of minoritized candidates, researchers, and faculty is very real, and will not happen without a combination of serious intent and structural support. Without active intervention, one model of current post-doc to faculty transitions has indicated that faculty diversity will not otherwise significantly increase until 2080. This is too little, too late.

    To encourage the adoption of more equitable hiring, and RPT processes, the authors are collaborating on a series of tools for DORA to assist institutions in experimenting with new processes, indicators, and principles. Available here.


    We thank Stephen Curry for very helpful comments. We also thank Stephen, Olivia Rissland and Stuart King for and the accompanying briefing document on the DORA webpage. 

    The post Rethinking Research Assessment:Addressing Institutional Biases in Review, Promotion, and Tenure Decision-Making (part IV) appeared first on The Official PLOS Blog.

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

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    Giving Week: Why arXiv?

    Four million monthly users. 1.7 million articles. More than one billion downloads.

    The numbers are clear: arXiv is a critical resource.

    But what these numbers don’t reveal? The impact arXiv has had on individual people across the globe.

    The excitement of a grad student posting their first article. The junior faculty member who just earned tenure, thanks to research originally shared on arXiv. The productive researcher whose library cannot afford to subscribe to all the right journals. The weekly research group meeting to discuss the most recent arXiv papers. The interdisciplinary collaboration sparked by an arXiv submission. The machine learning enthusiast who tinkers with the arXiv dataset, future discoveries yet unknown.

    “arXiv is like air.”

    These are the words of an arXiv-er. In other words, arXiv is free, totally necessary, and easy to take for granted.

    But arXiv is not free to produce, which is why we’re asking you to join arXiv’s community of supporters with a donation during International Open Access Week, from October 19th through the 23rd. We urge you to consider recurring payments in any amount.

    More than 80% of arXiv’s operating budget comes from voluntary contributions from the Simons Foundation, member institutions, and individuals like you. Your contribution will help ensure that arXiv remains a non-commercial, community resource.

    Donate Button

    in arXiv.org blog on October 19, 2020 01:30 PM.

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    “Awe Walks” Can Boost Positive Emotions Among Older Adults

    By Emma Young

    After the age of about 75, people tend to feel more anxiety, sadness and loneliness, and less in the way of positive emotion. Strategies to prevent or at least counteract these deteriorations are badly needed, and new research by a team in the US, published in the journal Emotion, has now identified one apparently promising strategy: so-called “awe walks”.

    As Virginia Strum at the University of California and her colleagues note, awe is a positive emotion felt by people “when they are in the presence of something vast that they cannot immediately understand”. A walk through a desert, a beautiful piece of art, a wedding — all of these things, and more, can lead to feelings of awe.

    Earlier work shows that when we feel awe, our focus shifts from our self to the wider world, leading us to perceive ourselves as being less significant, or “smaller”, and also making us feel more socially connected to our community. This could lead to a rise in positive, prosocial emotions, the team reasoned — and might help to combat typical age-related increases in negative emotions and loneliness.

    To investigate the potential of their awe walk idea, the team recruited 52 healthy adults aged 60 to 90, half of whom formed a control group. Both groups were told to take a 15 minute outdoor walk, ideally alone, every week for eight weeks, and to take three photographs of themselves each time — one before, one during and one after the walk.

    Only the awe group was told that “with the right outlook, awe can be found almost anywhere, but it is most likely to occur in places that involve two key features: physical vastness and novelty”. This group were asked to tap into their “sense of wonder” and to try to go somewhere new each week.

    The participants completed a battery of surveys before, during and after their walk programmes. And the team found some key differences between the two groups. Firstly, as the researchers had predicted, the awe group reported feeling more awe while walking. Over time, they also felt more socially connected, and reported bigger increases in positive emotions — including prosocial emotions such as gratitude and compassion, and also joy — while they were walking. The boost in prosocial emotions, specifically, carried through into everyday life. Daily distress also decreased more over time in the awe group.

    The team also analysed the participants’ photographs. They concluded that, with more walks under their belt, the smiles of those in the awe group became more intense. Whether you consider smiles to be expressions of happiness, as the team does, or social signals of a willingness to affiliate, this could potentially lead to more positive social interactions. Unlike the control group, over time, members of the awe group also came to occupy less physical space, relative to the background, in their selfies. The researchers interpret this as reflecting that the awe group were feeling “smaller” over time.

    As the team cautions, most of the participants were White and highly educated, so the results may not generalise to other groups. However, the fact that they were mostly highly educated could be significant in itself. The participants did not complete personality tests. But educational achievement is associated with greater openness to experience, a personality trait that entails enjoying new things. If the awe group were particularly open to experience then presumably they enjoyed the novelty of walking somewhere new each time, and this may have led to an increase in positive emotions.

    What about the finding that, over time, the awe group took up less space in their selfies? Again, they were told to try to walk somewhere new each time — and that vast spaces are more likely to trigger awe. It certainly seems possible that, with growing confidence, they chose to travel to renowned beauty spots, rather than a local park, say, and selfies at those beauty spots may be more likely to contain large background features such as a mountain (which features in the paper as an example of a “big background” constituent of one awe group selfie).

    Whatever the reasons behind the findings, the work does suggest that — for highly educated, healthy older people, at least — “awe walks” are beneficial. And, despite the potential risks associated with encouraging older people to walk alone in vast, unfamiliar natural settings, there could clearly be physical health benefits, too.

    Big smile, small self: Awe walks promote prosocial positive emotions in older adults

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

    in The British Psychological Society - Research Digest on October 19, 2020 12:03 PM.

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    We still don’t know what COVID-19 immunity means or how long it lasts

    Even as U.S. President Donald Trump claims his bout with COVID-19 has granted him immunity, reports of people getting the disease a second time are emerging. While reinfection still appears to be rare, it remains unclear to what extent immunity can truly protect a person. 

    Immunity is also in the news because a debate is simmering among scientists over herd immunity, the point at which enough people are immune to a pathogen to slow its spread (SN: 3/24/20). While herd immunity might put the end of the pandemic in sight, experts estimate that around 40 to 60 percent of a population would need to be infected to reach it.

    One group of researchers is pushing for governments to reach herd immunity without a vaccine, by allowing COVID-19 to spread among those at low risk while protecting vulnerable populations. This approach, however, puts the entire population at risk of significant illness and death, another group argues in a letter published October 14 in the Lancet.

    Because SARS-CoV-2 is a new virus, scientists can’t say how long a person will be protected after they’ve recovered from an infection. If immunity wanes quickly, that sets the stage for recurrent outbreaks unless there’s a vaccine, the authors say.

    Here’s what we know so far about our long-term defenses against the coronavirus: 

    What does “immunity” really mean?

    To scientists, immunity means a resistance to a disease gained through the immune system’s exposure to it, either by infection or through vaccination. But immunity doesn’t always mean complete protection from the virus. 

    How does the body build immunity?

    The immune system has two ways to provide lasting protection: T cells that remember the pathogen and trigger a rapid response, and B cells that produce antibodies — proteins the body makes to fight off a specific pathogen.

    Ideally, long after a person has recovered from an infection, these antibodies stick around in their blood. Then if the person is exposed to the same pathogen again in the future, those antibodies recognize the threat and work to prevent another infection from taking hold.

    So-called “memory T cells” also stick around. Ideally, they live up to their name and recognize a previously encountered pathogen and either help coordinate the immune system or kill infected cells.  

    With one type of immunity, called sterilizing immunity, the virus never gets a chance to begin replicating and never infects a cell. Sterilizing immunity, however, is hard to achieve. More often, people achieve partial immunity, which provides a rapid response that may make the second bout of the disease less severe, or less easily transmitted to others.

    It’s unclear what type of immunity people who have recovered from COVID-19 have, and only time will tell. A vaccine could possibly trigger a stronger immune response than a natural infection, although it’s yet to be seen if that will be the case for the coronavirus vaccines in trials (SN: 7/10/20). 

    If a person has antibodies, are they immune?

    For some illnesses, like measles, antibodies may last a lifetime. But for SARS-CoV-2, the jury is still out. It’s unknown how long antibodies last in the blood, or — importantly — whether their presence is a sign of immunity. Just because a person has antibodies, it doesn’t mean they are effective at fighting the virus.

    Neutralizing antibodies are ones that halt the virus in its tracks, stopping it from infecting a host cell and replicating. Such antibodies typically recognize the virus’ spike protein, which helps it break into host cells. So far, those kinds of antibodies have been a focus of studies seeking to understand whether a person may be immune.

    “For the majority of people, it does appear that they are generating neutralizing antibodies,” says Aubree Gordon, an epidemiologist at the University of Michigan in Ann Arbor. “So that’s promising.”

    Yet it’s still unknown what amount of neutralizing antibody is sufficient for protection. And even if they are protective, it’s unclear how long these immune proteins stick around. Studies of recovered COVID-19 patients have shown that antibodies for the coronavirus can wane after a SARS-CoV-2 infection, but overall, their levels remain relatively stable over a span of three to six months.

    Because the coronavirus only began its sweep around the world at the beginning of the year, “there’s just been a limited time for people to study this,” Gordon says.

    Some data suggest the immune system might not have a great memory for coronavirus infections. One study found that during a COVID-19 infection, the organ that produces memory B cells — long-lived cells that will rapidly produce antibodies if a person is re-exposed to a pathogen — doesn’t properly activate the cell types capable of becoming memory B cells. Without that immunological memory, antibodies for SARS-CoV-2 may not last very long, researchers report August 19 in Cell.

    “Maybe that means that those memory responses are going to be on the short side,” says Brianne Barker, an immunologist at Drew University in Madison, N.J.

    What do we know about T cells?

    Studies have shown that COVID-19 patients typically develop an immune response involving T cells. Even recovered patients without a detectable antibody response have T cells in their blood, researchers report October 15 in Emerging Infectious Diseases.

    But the role of T cells in infection and immune memory remains unclear. Studies have shown that memory T cells can persist in patients who were infected with the coronavirus responsible for the 2003–2004 SARS outbreak for up to 11 years after recovery. Since that virus no longer circulates, however, it’s impossible to say whether those T cells might be protective.

    Some people may already have T cells that can recognize pieces of the new coronavirus (SN: 5/15/20). Those immune cells may be left over from previous exposures to coronaviruses that cause the common cold, researchers report August 4 in Science. These cross-reactive T cells might help reduce the length or severity of COVID-19 illness. On the flip side, such T cells could make the disease worse, perhaps by overstimulating the immune system and causing a condition called cytokine storm, which is behind some severe COVID-19 cases.

    Can you get the coronavirus twice?

    Researchers have now documented a small number of cases where people have been infected with the coronavirus twice. The first such case was reported in Hong Kong, with additional reports the United States, the Netherlands and elsewhere (SN: 8/24/20).

    But it’s still unclear how common reinfections are. And with only a handful of cases so far, “we can’t really say that reinfections are telling us a whole lot at this point,” Barker says, either about immunity or whether vaccines will provide long-term protection or will need to become part of our yearly routine, like flu shots.

    Some reinfections are expected; some people’s immune memory may not be potent enough to prevent the infection entirely, though it may prevent them from getting sick.

    It’s hard to prove that someone has been reinfected, because researchers need to conclusively show that two different viruses caused each infection, Barker says. That requires genetic testing. What’s more, experts are not necessarily on the lookout for such cases, especially in people who are not displaying symptoms.

    What does all of this mean for herd immunity?

    Without knowing how long immunity lasts after an infection, and how much that varies from person to person, it’s impossible to know whether ending the pandemic through herd immunity is even possible. What is clear, experts say, is that attempting to reach herd immunity without a vaccine will lead to more illness and death.

    “Promoting the concept of ‘herd immunity’ … as an answer to the COVID-19 pandemic is inappropriate, irresponsible and ill-informed,” Thomas File Jr., president of the Infectious Diseases Society of America, and Judith Feinberg, chair of the HIV Medicine Association, said in a statement October 14.

    And to date, herd immunity is still far off. “Throughout the United States, we are nowhere near herd immunity,” Gordon says. “Taking the approach of herd immunity through natural infection will lead to hundreds of thousands of unnecessary deaths.” 

    in Science News on October 19, 2020 12:00 PM.

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    Heating deltamethrin may help it kill pesticide-resistant mosquitoes

    A few minutes in the microwave made a common insecticide about 10 times more lethal to mosquitoes in lab experiments.

    The toxin deltamethrin is used around the world in home sprays and bed nets to curb the spread of mosquito-borne diseases like malaria — which kills over 400,000 people each year, according to the World Health Organization. But “mosquitoes the world over are showing resistance to deltamethrin and [similar] compounds,” says Bart Kahr, a crystallographer at New York University who has helped develop a more potent form of deltamethrin by heating it.

    This form of deltamethrin may stand a better chance of killing insecticide-resistant pests, Kahr and colleagues report online October 12 in the Proceedings of the National Academy of Sciences. Malaria has been essentially eradicated in the United States, but more effective pesticides could be a boon for regions like sub-Saharan Africa, where the disease is a major public health problem.

    Kahr’s team increased the potency of commercial deltamethrin dust spray simply by melting a vial of it — either by heating it to 150° Celsius in an oil bath for five minutes or by popping it in a 700-watt microwave for the same amount of time. While the microscopic deltamethrin crystals in the original spray have a haphazard structure, which looks like a jumble of misaligned flakes, the melted deltamethrin crystals solidified into starburst shapes when they cooled to room temperature.

    deltamethrin crystals in typical insecticide spray (left) and a new version (right)The deltamethrin crystals in typical insecticide spray (left microscope image) contain “lots of individual leaflets that are kind of oriented in a helter-skelter manner,” says crystallographer Bart Kahr of New York University. In a new version of the spray, deltamethrin crystals are shaped more like starbursts, with fibers growing out from a single point (right).Jingxiang Yang

    Chemical bonds between deltamethrin molecules in the starburst-shaped crystals are not as strong as those in the original microcrystal structure. “The molecules are intrinsically less happy, or settled, in the arrangement,” Kahr says. So, when a mosquito lands on a dusting of starburst-shaped crystals, it should be easier for deltamethrin molecules to be absorbed into the insect’s body via its feet.

    The researchers tested the more potent version of deltamethrin on lab-bred mosquitoes from two species: Anopheles quadrimaculatus, which can spread malaria, and Aedes aegypti, which can transmit other life-threatening diseases, such as Zika and dengue (SN: 1/8/19). Forty mosquitoes of each species were released into petri dishes coated in the original deltamethrin dust spray, and another 40 into a dish covered in the new form of the insecticide.

    That altered version of deltamethrin knocked out about half of exposed A. quadrimaculatus mosquitoes within 24 minutes. In contrast, it took nearly five hours for the original spray to knock out half of exposed Anopheles — about 12 times as long. Likewise, it took only 21 minutes for the new spray to knock out half of exposed A. aegypti, while it took the original spray over three hours.

    Although A. quadrimaculatus can carry the parasite that causes malaria, this mosquito species is native to North America, where the disease is not a major public health crisis. To ensure the new type of deltamethrin would be effective in the world’s malarial hot spots, “we need to do these experiments with species called gambiae and funestus, which are the African Anopheles mosquito species,” Kahr says, as well as the six major malaria-spreading Anopheles species in South Asia.

    Heat treatment for deltamethrin sprays “might increase their toxicity, but there are several obvious experiments that we would need to do before we would even think about adding this to the production system,” says Janet Hemingway of the Liverpool School of Tropical Medicine in England, who studies mosquito insecticide resistance.

    First, researchers need to test the new version of the insecticide against pesticide-resistant mosquitoes. Mosquito resistance to deltamethrin, along with other chemicals in the class of synthetic pesticides known as pyrethroids, is a growing problem (SN: 6/29/12). “My prediction … is that [the insects] would be highly resistant to both forms,” Hemingway says.

    Researchers also need to ensure that the more toxic form of deltamethrin is safe for people to be around, says Hemingway, who was not involved in the study. “Bottom line — interesting observation, but one that is a good distance from something that could be implemented.”

    in Science News on October 19, 2020 10:00 AM.

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    “I do wish that journal editors would not take six years to perform an investigation and to retract.”

    In July 2014, Elisabeth Bik notified PLOS ONE that she’d found three papers in the journal by a group of researchers who had clearly manipulated figures in the articles.  More than six years later, the journal has finally retracted the publications.  The authors were affiliated with the Fourth Military Medical University in Shaanxi, China. The … Continue reading “I do wish that journal editors would not take six years to perform an investigation and to retract.”

    in Retraction watch on October 19, 2020 10:00 AM.

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    Using machine learning to accelerate materials science

    Award-winning researcher develops high-throughput software to automate the calculation of materials properties

    in Elsevier Connect on October 19, 2020 08:41 AM.

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    Weekend reads: How retracted work continues to spread; claims of PhD thesis plagiarism in the wine industry; Brexit and research integrity

    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. The week at Retraction Watch featured: Researchers face disciplinary action as dozens of their studies fall … Continue reading Weekend reads: How retracted work continues to spread; claims of PhD thesis plagiarism in the wine industry; Brexit and research integrity

    in Retraction watch on October 17, 2020 01:58 PM.

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    Remdesivir doesn’t reduce COVID-19 deaths, a large WHO trial finds

    Remdesivir, an antiviral drug that was the first found to combat COVID-19, doesn’t reduce deaths from the disease, a large international study found.

    The World Health Organization’s Solidarity trial, which combined data from 405 hospitals in 30 countries, randomly assigned more than 11,000 people hospitalized with COVID-19 to receive one of four drugs or standard care, which could include other drugs such as steroids. The tested drugs include remdesivir, the antimalaria drug hydroxychloroquine, an anti-HIV drug called lopinavir and interferon-beta1a. Interferon is an immune system chemical that triggers the body’s antiviral defenses.

    None of the drugs showed any benefit in reducing deaths, the need for ventilation or the length of hospital stays, researchers report October 15 in a preliminary study posted at medRxiv.org. The work has not been vetted by other scientists yet, and some analyses may change during the peer-review process, experts say.

    Other studies had already shown that neither lopinavir — given in combination with ritonavir, a drug that boosts lopinavir’s levels in the body — nor hydroxychloroquine were effective against the novel coronavirus (SN: 3/19/20; SN: 8/2/20). These studies, in addition to the new data, deliver a clear message that those drugs are not helpful for treating COVID-19, says David Brett-Major, a medical epidemiologist at the University of Nebraska Medical Center in Omaha.

    But remdesivir has been shown to shave four days off of hospital stays in a trial conducted by the U.S. National Institute of Allergy and Infectious Diseases (SN: 4/29/20). In that study, the drug “showed a trend toward reducing deaths,” but the result wasn’t statistically meaningful. Preliminary results from small studies conducted by remdesivir’s maker, Gilead Sciences of Foster City, Calif., also suggested that drug might cut the chance of dying from the disease (SN: 7/13/20).

    The drug currently has emergency authorization from the U.S. Food and Drug Administration for use in all hospitalized patients.

    In the WHO study, 301 of 2,743 people hospitalized with COVID-19 taking remdesivir died, compared with 303 of 2,708 people in the group getting standard care. That result indicates that remdesivir doesn’t have a mortality benefit, says Helen Boucher, chief of infectious diseases at Tufts Medical Center in Boston.

    But that doesn’t mean remdesivir isn’t helpful, she says. Shortening hospital stays is the reason remdesivir has been embraced, at least in the United States, Boucher says. The new WHO study aside, “the data we have now suggests it’s a four-day benefit, 11 days versus 15 days” with a placebo, she says. “That’s significant for people who are sick in the hospital.”

    “I’m very comfortable as a physician recommending this medicine based on the data showing a shorter time to be better,” Boucher says.

    Although the new WHO study found that remdesivir doesn’t reduce length of hospital stays, the trial was designed to show only whether the drugs could reduce the risk of dying. So its conclusions about whether remdesivir shortens hospital stays or cuts the risk of going on a ventilator need a closer look, Brett-Major says.

    That’s also in part because the WHO study combined data from hundreds of hospitals in 30 countries. A closer analysis of data from individual study sites may show a clearer picture of how remdesivir performed in different settings. Hospitalization time and whether someone is put on a ventilator may also depend on other factors, such as how many hospital beds or ventilators are available. Remdesivir may still improve outcomes for individual patients in the right circumstances, Brett-Major says.

    In the short term, the new study probably won’t change how remdesivir is used, says Joanne Turner, an immunologist and vice president for research at the Texas Biomedical Research Institute in San Antonio. But as more studies are done, “we’ll get clarity on when it should be used,” she says.

    Many hospitalized patients, for example, are suffering more from overexuberant immune systems trying to fight off the virus. By that time, it may be too late for a drug that prevents viral replication like remdesivir to make a difference. In the WHO study, “if the drug did stop viral replication [for patients], it clearly wasn’t changing outcomes for them,” Turner says. “This will make doctors think about whether this drug is really useful in very sick people.”

    But giving remdesivir to sick people earlier might help, experts say. Boucher and colleagues are part of a study testing the drug in people who are newly diagnosed with COVID-19 to see if can prevent hospitalization and severe disease.

    in Science News on October 16, 2020 09:59 PM.

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    Can supplements really help fight COVID-19? Here’s what we know and don’t know

    Consumers have long turned to vitamins and herbs to try to protect themselves from disease. This pandemic is no different — especially with headlines that scream “This supplement could save you from coronavirus.”

    It also helps to have celebrity enthusiasts. When President Donald Trump was diagnosed with COVID-19, his pill arsenal included Vitamin D and zinc. And in an Instagram chat with actress Jennifer Garner in September, infectious diseases expert Anthony Fauci touted vitamins C and D as ways that might generally boost the immune system. “If you’re deficient in vitamin D,” he noted, “that does have an impact on your susceptibility to infection. I would not mind recommending, and I do it myself, taking vitamin D supplements.”

    But whether over-the-counter supplements can actually prevent, or even treat, COVID-19, is not clear. Since the disease is so new, researchers haven’t had much time for the kind of large experiments that provide the best answers. Instead, scientists have mostly relied on fresh takes on old data. Some studies have looked at outcomes of patients who routinely take certain supplements — and found some promising hints. But so far there’s little data from the kinds of scientifically rigorous experiments that give doctors confidence when recommending supplements.

    Here’s what we know today about three supplements getting plenty of attention around COVID-19.

    Vitamin D

    What it is: Called “the sunshine vitamin” because the body makes it naturally in the presence of ultraviolet light, Vitamin D is one of the most heavily studied supplements (SN: 1/27/19). Certain foods, including fish and fortified milk products, are also high in the vitamin. 

    Why it might help: Vitamin D is a hormone building block that helps strengthen the immune system.

    How it works for other infections: In 2017, the British Medical Journal published a meta-analysis that suggested a daily vitamin D supplement might help prevent respiratory infections, particularly in people who are deficient in the vitamin.

    But one key word here is deficient. That risk is highest during dark winters at high latitudes and among people with more color in their skin (melanin, a pigment that’s higher in darker skin, inhibits the production of vitamin D).

    “If you have enough vitamin D in your body, the evidence doesn’t stack up to say that giving you more will make a real difference,” says Susan Lanham-New, head of the Nutritional Sciences Department at the University of Surrey in England.

    And taking too much can create new health problems, stressing certain internal organs and leading to a dangerously high calcium buildup in the blood. The recommended daily allowance for adults is 600 to 800 International Units per day, and the upper limit is considered to be 4,000 IUs per day.

    What we know about Vitamin D and COVID-19: Few studies have looked directly at whether vitamin D makes a difference in COVID.

    In May, in the BMJ Nutrition, Prevention & Health, Lanham-New and her colleagues published a summary of existing evidence and concluded that there’s only enough to recommend vitamin D to help with COVID-19 prevention for people who are deficient. That paper made inferences from how vitamin D works against other respiratory tract infections and immune health.

    More than a dozen studies are now testing vitamin D directly for prevention and treatment, including a large one led by JoAnn Manson, a leading expert on vitamin D. An epidemiologist and preventive medicine physician at Harvard Medical School and Brigham & Women’s Hospital in Boston. That study will analyze if vitamin D can affect the course of a COVID-19 infection. The trial aims to recruit 2,700 people across the United States with newly diagnosed infections, along with their close household contacts.

    The goal is to determine whether newly diagnosed people given high doses of vitamin D — 3,200 IU per day — are less likely than people who get a placebo to experience severe symptoms and need hospitalization. “The biological plausibility for a benefit in COVID is compelling,” she says, given the nutrient’s theoretical ability to impede the severe inflammatory reaction that can follow coronavirus infection. “However the evidence is not conclusive at this time.”


    What it is: Zinc, a mineral found in cells all over the body, is found naturally in certain meats, beans and oysters.

    Why it might help: It plays several supportive roles in the immune system, which is why zinc lozenges are always hot sellers in cold and flu season. Zinc also helps with cell division and growth.

    How it works for other infections:  Studies of using zinc for colds — which are frequently caused by coronaviruses — suggest that using a supplement right after symptoms start might make them go away quicker. That said, a clinical trial from researchers in Finland and the United Kingdom, published in January in BMJ Open did not find any value for zinc lozenges for the treatment of colds. Some researchers have theorized that inconsistences in data for colds may be explained by varying amounts of zinc released in different lozenges.

    What we know about zinc and COVID-19: The mineral is promising enough that it was added to some early studies of hydroxychloroquine, a drug tested early in the pandemic. (Studies have since shown that hydroxychloroquine can’t prevent or treat COVID-19 (SN: 8/2/20).)

    In July, researchers from Aachen University in Germany wrote in Frontiers of Immunology that current evidence “strongly suggests great benefits of zinc supplementation” based on looking at similar infections including SARS, another disease caused by a coronavirus. For example, studies suggest that giving zinc reduces the risk for death from a pneumonia infection. The researchers cite evidence that zinc might help prevent the virus from entering the body, and help slow the virus’s replication when it does.

    Another review — also based on indirect evidence — published August 1 in Advances in Integrative Medicine also concluded that zinc might be helpful in people who are deficient.

    In September, researchers from Hospital Del Marin Barcelona reported that among 249 patients studied, those who survived COVID had higher zinc levels in their plasma (an average of 63.1 mcg/dl) than those who died (43mcg/dl).

    Overall, though, the jury is still out, says Suma Thomas, a cardiologist at the Cleveland Clinic Foundation, who in June led a team that reviewed the evidence for popular supplements in the Cleveland Clinic Journal of Medicine. Given what’s already known, zinc could possibly decrease the duration of infection but not the severity of symptoms, she said, particularly among people who are deficient. About a dozen studies are now looking at zinc for COVID treatment, often with other drugs or supplements.

    Thomas and her colleagues are comparing symptom severity and future hospitalization in COVID-19 patients who take zinc with and without high doses of vitamin C with those who receive ordinary care without the supplement. Results are expected soon, she says.

    Vitamin C

    What it is: Also called L-ascorbic acid, vitamin C has a long list of roles in the body. It’s found naturally in fruits and vegetables, especially citrus, peppers and tomatoes.

    Why it might help: It’s a potent antioxidant that’s important for a healthy immune system and preventing inflammation.

    How it works for other infections: Thomas cautions that the data on vitamin C are often contradictory. One review from Chinese researchers, published in February in the Journal of Medical Virology, looked at what is already known about vitamin C and other supplements that might have a role in COVID-19 treatment. Among other encouraging signs, human studies find a lower incidence of pneumonia among people taking vitamin C, “suggesting that vitamin C might prevent the susceptibility to lower respiratory tract infections under certain conditions.”

    But for preventing colds, a 2013 Cochrane review of 29 studies didn’t support the idea that vitamin C supplements could help in the general population. However, the authors wrote, given that vitamin C is cheap and safe, “it may be worthwhile for common cold patients to test on an individual basis whether therapeutic vitamin C is beneficial.”

    What we know about Vitamin C and COVID-19: About a dozen studies are under way or planned to examine whether vitamin C added to coronavirus treatment helps with symptoms or survival, including Thomas’ study at the Cleveland Clinic.

    In a review published online in July in Nutrition, researchers from KU Leuven in Belgium concluded that the vitamin may help prevent infection and tamp down the dangerous inflammatory reaction that can cause severe symptoms, based on what is known about how the nutrient works in the body.

    Melissa Badowski, a pharmacist who specializes in viral infections at the University of Illinois at Chicago College of Pharmacy and colleague Sarah Michienzi published an extensive look at all supplements that might be useful in the coronavirus epidemic. There’s still not enough evidence to know whether they are helpful, the pair concluded in July in Drugs in Context. “It’s not really clear if it’s going to benefit patients,” Badowski says.

    And while supplements are generally safe, she adds that nothing is risk free. The best way to avoid infection, she says, is still to follow the advice of epidemiologists and public health experts: “Wash your hands, wear a mask, stay six feet apart.”

    in Science News on October 16, 2020 06:09 PM.

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    Thirsty Mice And Virtual Reality: The Week’s Best Psychology Links

    Our weekly round-up of the best psychology coverage from elsewhere on the web

    For the first time, researchers have looked at what happens in the brain when people take the psychedelic drug salvinorin A, from the plant salvia divinorum. The team found that the drug disrupts the default mode network, a set of areas that are normally synchronised when we’re not engaged in any particular task, similar to the effects found for the “classical” psychedelic drugs like psilocybin. But the subjective effects of salvinorin A are quite different to the effects of those other drugs, leaving some researchers questioning how important the default mode network really is to the psychedelic experience. Daniel Oberhaus, who participated in the trial, has the story at Wired.

    A study in the 1980s claimed that married couples begin to look more alike over time — but now a larger replication has failed to find any evidence that that is true. Instead the new study suggests that people tend to partner up with those who already look similar to them, reports Ian Sample at The Guardian.

    It’s been more than a decade since the replication crisis became a well-known issue in psychology, and in science more generally. So has anything changed? Not a lot, writes Kelsey Piper at Vox, although there have been some small victories along the way.

    How people behave in virtual reality scenarios can provide insight into their personality, writes researcher Stephen Fairclough at The Conversation. His team created a VR environment in which participants had to navigate across ice blocks suspended high above the ground. People who took a more risk-averse approach to the task tended to be higher in neuroticism. The study highlights privacy issues around VR, Fairclough writes, as it suggests companies could profile users’ personality.

    Many New Yorkers fail to show up to court for low-level offenses so researchers have helped the city redesign its court summons to “nudge” people into attending. The tweaks to the form included displaying the key information such as date and court location more prominently, as well as highlighting the consequences of not showing up, and resulted in 13% fewer missed court dates, reports Catherine Matacic at Science.

    Scientists have identified how different types of thirst are encoded in the brain (in mice, at least). Different combinations of neurons in a region called the circumventricular organ were active when mice needed pure water, compared to when they needed water and salt (as you might after a sweaty workout). And depending on which set of neurons the researchers later stimulated, mice chose to drink either just water or a mouse “sports drink”, reports Jon Hamilton at NPR.

    Finally, there’s more this week on how researchers are analysing the words used on social media to make inferences about the emotional state of the population. According to some psychologists, these methods show that our collective mood is pretty low, writes Casey Schwartz at the New York Times. But others say that the language used on Twitter is far from representative of how the general population is feeling.

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

    in The British Psychological Society - Research Digest on October 16, 2020 02:27 PM.

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    Turning space images into music makes astronomy more accessible

    Put into music, telescope observations of the center of the Milky Way create a tranquil tune, glittering with xylophone and piano notes. The iconic Pillars of Creation in the Eagle Nebula, meanwhile, sound like an eerie sci-fi score. And the supernova remnant Cassiopeia A is a sweeping symphony.

    These musical renditions, or sonifications, were released on September 22 by NASA’s Chandra X-ray Center. “Listening to the data gives [people] another dimension to experience the universe,” says Matt Russo, an astrophysicist and musician at the astronomy outreach project SYSTEM Sounds in Toronto.

    Sonification can make cosmic wonders more accessible to people with blindness or visual impairments, and complement images for sighted learners. SYSTEM Sounds teamed up with Kimberly Arcand, a visualization scientist at the Harvard-Smithsonian Center for Astrophysics in Cambridge, Mass., to create the new pieces.

    Christine Malec, a musician and astronomy enthusiast who is blind, vividly recalls the first sonification she ever heard — a rendering of the TRAPPIST-1 planetary system that Russo played during a planetarium show in Toronto (SN: 2/22/17). “I had goosebumps, because I felt like I was getting a faint impression of what it’s like to perceive the night sky, or a cosmological phenomenon,” she says. Music affords data “a spatial quality that astronomical phenomena have, but that words can’t quite convey.”

    The new renditions combine data from multiple telescopes tuned to different types of light. The sonification of an image of the Milky Way’s center, for instance, includes observations from the Chandra X-ray Observatory, optical images from the Hubble Space Telescope and infrared observations from the Spitzer Space Telescope. Users can listen to data from each telescope alone or the trio in harmony.

    New data “sonifications” translate telescope images into songs. Listen to observations of celestial objects around the Milky Way, from the galactic center to the star-forming Pillars of Creation in the Eagle Nebula.

    As a cursor pans from left to right across the image of the galactic center, showing a 400-light-year expanse, Chandra X-ray observations, played on the xylophone, trace filaments of superhot gas. Hubble observations on the violin highlight pockets of star formation, and Spitzer’s piano notes illuminate infrared clouds of gas and dust. Light sources near the top of the image play at higher pitches, and brighter objects play louder. The song crescendos around a luminous region in the lower-right corner of the image, where glowing gas and dust shroud the galaxy’s supermassive black hole.

    Layering the instruments on top of each other gives the observations an element of texture, Malec says. “It appealed to my musical sense, because it was done in a harmonious way — it was not discordant.”

    That was on purpose. “We wanted to create an output that was not just scientifically accurate, but also hopefully nice to listen to,” Arcand says. “It was a matter of making sure that the instruments played together in symphony.”

    But discordant sounds can also can be educational, Malec says. She points to the new sonification of supernova remnant Cassiopeia A: The sonification traces chemical elements throughout this great plume of celestial debris using notes played on stringed instruments (SN: 2/19/14). Those notes make a pretty harmony, but they can be difficult to tell apart, Malec says. “I would have picked very different instruments” to make it easier for the ear to follow — perhaps a violin paired with a trumpet or an organ.

    While sonification is a valuable tool to get the public interested in astronomy, it also has untapped potential to help professional astronomers analyze data, says Wanda Díaz-Merced, an astronomer who is also at the Harvard-Smithsonian Center for Astrophysics but was not involved in the project (SN: 10/22/14).

    Astronomers including Díaz-Merced, who is blind, have used sonifications to study stars, solar wind and cosmic rays. And in experiments, Díaz-Merced has demonstrated that sighted astronomers can better pick out signals in datasets by analyzing audio and visual information together rather than relying on vision alone.

    Still, efforts to sonify astronomy datasets for research have been rare. Making data sonification a mainstream research method would not only break down barriers to pursuing astronomy research, but may also lead to many new discoveries, she says.

    in Science News on October 16, 2020 10:00 AM.

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    Study finding patients of female surgeons fare better is temporarily removed

    An Elsevier journal has, for the moment, removed a paper which found that the patients of female surgeons fare better than those treated by men. Although the journal didn’t provide an explanation for the move — unfortunately not unusual for Elsevier — a spokesman for the publisher told us that reader complaints about the methodology … Continue reading Study finding patients of female surgeons fare better is temporarily removed

    in Retraction watch on October 16, 2020 10:00 AM.

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    Research manager shares tips to succeed in a post-COVID world

    Dr. Charlotte Wray coordinates a birth cohort study on the relationships between childhood development and adult outcomes

    in Elsevier Connect on October 16, 2020 09:57 AM.

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    Research 2030 podcast: Can the reward system learn to love open science? Part 2 with Véronique de Herde

    A former Secretariat Coordinator and Open Science Ambassador for Eurodoc and early-career researcher shares her views on open science and evolving the reward system

    in Elsevier Connect on October 16, 2020 09:29 AM.

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    Transition to open access creates a challenge for Global South

    Report looks at how to achieve an equitable transition to open access for researchers in developing countries

    in Elsevier Connect on October 16, 2020 09:15 AM.

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    The FDA has approved the first treatment for Ebola

    There is now an approved treatment for Ebola, one of the world’s deadliest diseases. 

    The U.S. Food and Drug Administration announced October 14 that Inmazeb, a cocktail of lab-made antibodies developed by the pharmaceutical company Regeneron, can be used to treat adult and pediatric patients with Ebola. The announcement comes less than a year after the FDA greenlit the first Ebola vaccine (SN: 12/20/19).

    “This is a big development,” says Erica Ollmann Saphire, an immunologist at the La Jolla Institute for Immunology in San Diego, Calif. Ebola virus causes severe illness, including fever, vomiting, diarrhea and bleeding. Outbreaks of the disease, discovered in the 1970s, can kill 25 to 90 percent of those infected (SN: 2/11/19). Previously, people could only be helped by supportive therapies, like replacing lost fluids, Saphire says. “But this approval means Ebola is now a treatable disease.” 

    Inmazeb was evaluated along with three other experimental Ebola treatments in a clinical trial conducted in the Congo in 2018 and 2019 amid the second largest outbreak of the disease (SN: 8/12/19). During the trial, 33.8 percent of people treated with Inmazeb died after 28 days, compared with 51 percent of people who received a different treatment. 

    The drug consists of three different monoclonal antibodies, human-made antibodies designed to mimic those produced naturally during an immune response. One gums up structures on the Ebola virus that allow it to infiltrate human cells, while the other two recruit immune cells to clear out the virus and infected cells.

    Saphire, who heads a research consortium focused on studying antibody treatments for Ebola, says that given the drug’s two-pronged approach to fighting the virus, “the Regeneron cocktail is exactly the sort of complementary approach our research predicted would be most efficacious.” (Regeneron Pharmaceuticals is a major financial supporter of the Society for Science & the Public, which publishes Science News.)

    Inmazeb, which is delivered intravenously, has been used to treat patients in the ongoing Ebola outbreak in the Congo under compassionate use protocols. The new FDA approval will remove regulatory hurdles, Saphire says, allowing local doctors and medical aid groups like Doctors Without Borders to more easily obtain the drug from national stockpiles in the United States and deploy them in affected areas.

    In July, Regeneron and the U.S. Biomedical Advanced Research and Development Authority announced an agreement whereby the company would produce Inmazeb for a national stockpile over the next six years.

    in Science News on October 15, 2020 04:48 PM.

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    A spherical star cluster has surprisingly few heavy elements

    A strange, newly measured clump of stars orbiting the nearby Andromeda galaxy has the lowest level of heavy chemical elements ever seen in one of these mysterious star clusters. Named RBC EXT8, this globular cluster is also surprisingly massive, challenging theories for how such clusters and some galaxies form, astronomers report online October 15 in Science.

    “It’s a very unusual object,” says astrophysicist Oleg Gnedin of the University of Michigan in Ann Arbor, who was not involved in the new discovery.

    Globular clusters are crowded, spherical collections of stars that orbit a galaxy’s center, though most, including RBC EXT8, live in the galactic outskirts. The clusters are typically billions of years old, so their stars tend to be chemically pristine, meaning they formed before the universe had time to create much of any of the elements heavier than hydrogen or helium, which astronomers lump together as “metals.”

    Previous observations of these clusters in the Milky Way and other galaxies had suggested that there’s a limit to how low a globular cluster’s metal content can be. The most metal-poor clusters were about 300 times less rich in heavy elements like iron than the sun, but no less.

    But spectra of RBC EXT8, some 2.5 million light-years away, show that the cluster’s metal content is about 800 times less than the sun’s. The globular cluster that held the previous record for lowest “metallicity” has three times that amount.

    “It was completely unexpected that we would find a globular cluster that is so metal poor,” says astronomer Søren Larsen of Radboud University in Nijmegen, the Netherlands.

    RBC EXT8The bigger, fuzzy blob in the inset image at left is RBC EXT8, a globular cluster that orbits about 88,000 light-years from the center of the galaxy Andromeda (shown at right). The cluster has surprisingly few heavy elements for its size, a new study finds.© 2020 ESASky, CFHT

    What’s more, given its metal-poor status, this cluster is surprisingly massive, weighing about 1.14 million times the mass of the sun. (A mid-weight globular cluster is about 100,000 solar masses, but some clusters reach 3 million solar masses. RBC EXT8 is heavy, but not the heaviest.)

    That mass makes the cluster even harder to explain because across the cosmos, the more massive a galaxy or cluster is, the more heavy elements it normally has.

    There are several potential explanations for that trend, but one is simply that more massive galaxies or globular clusters have more stars. A star fuses heavy elements in its core and sprinkles them around its host cluster or galaxy as it ages. Sufficiently massive stars can explode in a supernova, spreading those metals to become part of the next generation of stars (SN: 8/9/19). So more stars means more opportunity for metals to accumulate locally.

    More massive objects also have the advantage of gravity, which lets them better hold on to the metals that they do have and remain a cohesive group for billions of years. Less massive globular clusters dissolve into their host galaxies over time.

    Those trends together could have explained the apparent “metallicity floor” for globular clusters — all of the less massive, more metal-poor clusters have broken apart over the eons.

    RBC EXT8 turns that conventional wisdom on its head. “It’s too big to have as low metallicity as it has,” Gnedin says. “That’s the conundrum.”

    Astronomers aren’t sure how globular clusters form in general, but they probably grow within galaxies, rather than forming outside of them and being pulled in later. And so the clusters reflect the characteristics of their galaxies: small, metal-poor galaxies end up with small metal-poor globular clusters, and vice versa. But based on RBC EXT8’s metal content, it’s galactic birthplace would be less than a million solar masses, so smaller than the globular cluster itself – which is a paradox.

    As a result, the cluster challenges some simplified models of galaxy formation. But it doesn’t completely break them, Gnedin says. “It’s one object, it’s not going to overturn things,” he says. “It just makes us people working on these issues have to work harder” and be more open-minded about other ways that galaxies could form.

    Open-mindedness and willingness to explore is perhaps responsible for the new finding about RBC EXT8’s metals. Larsen and colleagues spotted the globular cluster at the beginning of a night of observing with the Keck telescope in Hawaii in October 2019. “It was really a serendipitous discovery,” he says. He had a spare hour before the globular clusters in galaxy M33 that his team was planning to look at rose above the horizon, so the observers picked another cluster “more or less at random” to fill the time.

    “At first, I couldn’t really believe that what was coming out [in the observations] was right,” Larsen says. “But I kept working on it, and it turned out to hold up.”

    in Science News on October 15, 2020 02:58 PM.

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    2-Minute Neuroscience: Cerebral Cortex

    The cerebral cortex is the outermost layer of the brain, and is involved in a long list of brain functions---including most of the higher functions often associated with human cognition. In this video, I discuss the appearance, cellular architecture, and functional subdivisions of the cerebral cortex.

    in Neuroscientifically Challenged on October 15, 2020 02:19 PM.

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    CORE Recommender now supports article discovery on arXiv

    CORE logo

    arXiv readers now have a faster way to find articles relevant to their interests. From an article abstract page, readers can simply activate the CORE Recommender to find additional open access research on similar topics.

    The Recommender, part of the arXivLabs toolset, was developed by CORE, a global aggregator of open access scientific content, which provides access to millions of full texts. CORE’s mission is to aggregate all open access research outputs from repositories and journals worldwide and make them available to the public. In this way, CORE facilitates free unrestricted access to research for all.

    To generate a list of recommended works, the tool utilizes an algorithm based on the article’s full text and metadata, including title, authors, and abstract. The suggestions come both from arXiv and other resources in the CORE collection, and as many as five articles with freely accessible full texts might be recommended. A detailed explanation and discussion of the algorithm, by CORE founder Petr Knoth and his coauthors, is available on arXiv.

    These recommendations benefit readers, who will access relevant information more quickly, and authors, whose open access content will become more visible to interested readers.

    “I am very excited about this partnership as arXiv and CORE are both fully embracing the same vision of openness to research for all,” said Petr Knoth, founder and head of CORE. “This partnership will further improve open access infrastructure. It will help arXiv users to discover open access research papers relevant to their work from across the whole network of open access repositories.”

    “We are happy to welcome CORE to the arXivLabs family,” said arXiv executive director Eleonora Presani, “and we believe the Recommender will help arXiv users discover the content most relevant to their research.”

    arXiv values openness, community, and the privacy of user data and only works with partners that abide by the same principles. Like all third party collaborators, CORE will only have access to minimal and anonymized data about arXiv users, and only for the purpose of ensuring the correct functioning of the arXivLabs features. Any other use not included in a written consent from arXiv is strictly prohibited. Upon user request this data, and another other data connected to the user can be permanently deleted.


    arXiv abstract page with CORE recommender

    in arXiv.org blog on October 15, 2020 02:00 PM.

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    A New Take On The Marshmallow Test: Children Wait Longer For A Treat When Their Reputation Is At Stake

     By guest blogger Sofia Deleniv

    Most people — even the non-psychologists among us — have at some point heard of the legendary marshmallow test, which measures the ability of preschool children to wait for a sweet treat. Researchers have found that the amount of time children are willing to wait for their marshmallow is surprisingly predictive of various life outcomes, such as educational attainment during adolescence, as well as social competence and resilience to stress throughout development. A recent fMRI brain scan study even found that people’s performance as kids is related to their ability to suppress their impulses, and is reflected in neurological signatures of cognitive control, 40 years later.

    The test is clearly tapping into something crucial that shapes children’s futures to a considerable degree. But what exactly is it? Does the test  capture an ability that is akin to intelligence or intrinsic cognitive control, or might performance be a marker of some other underlying factor — such as the privilege of living in a supportive home where children can develop the trust capacity that enables them to wait for a reward?

    The list of potential explanations is long — and now it has received a surprising new addition from a study recently published in Psychological Science. Fengling Ma from Zhejiang Sci-Tech University and colleagues have discovered that children can radically improve their performance on the marshmallow test if they believe their social reputation might be at stake — an effect that begins to emerge as early as three years of age.

    In the original experiments, conducted at Stanford University in the 1970s, preschool-age children were left in a room with a highly desired treat (e.g. a cookie or marshmallow), and a less appealing one — oftentimes a pretzel. They received the following offer: if they could wait for fifteen minutes on their own, they could eat their favourite treat. If the wait became unbearably long, they could always bring back the experimenter. But then they could only have the less exciting snack.

    Waiting the full fifteen minutes is a challenge, especially if the treats are tauntingly on full display. Children participating in the original experiment waited an average of just over three minutes under these conditions. And the recent study found that waiting was just as difficult for more than 270 three- and four-year-olds from preschools in one Chinese city. In these experiments, children were asked to choose between a single instantaneous reward (a colourful sticker or a cookie), and double the reward if they waited quarter of an hour. Under baseline conditions, fewer than 25% of children had the patience to make it to the end.

    But this figure dramatically changed in two other conditions, where children were made aware of the possibility that their performance might affect their reputation. Here, the experimenter told each child that either their teacher or friend would find out how long they ended up waiting for their reward. This had a radical impact on behaviour: 40% of children waited till the end when they thought their performance would be communicated to a peer, while almost 70% did so when they believed their teacher would find out about their wait.

    These results are interesting given that the experimenter did not explicitly mention to the children that waiting longer was a desirable behaviour. Instead, kids seemed to understand that patience is a socially valued attribute, and adjusted their behaviour in the hopes of being perceived favourably by other people. The fact that children waited longer when their teacher, as opposed to peer, was their theoretical spectator is intriguing. It implies that children as young as three can make sophisticated judgements about the value of their audience and strategically alter their behaviour to impress them.

    The fact that a desire for social recognition radically improved children’s performance offers us much food for thought. For years, many researchers have assumed that the key to the marshmallow test’s ability to predict children’s future success lay in its ability to measure their cognitive control. There is, after all, clear value in being able to suppress impulses in favour of more deliberative behaviours. Alternatively, some researchers have argued, the test taps into some other cognitive skill that might have been shaped by a child’s environment. In this debate, largely centred on cognitive abilities, “soft” social skills have perhaps taken a backseat. And yet the new study points at a new, and previously unsuspected, ingredient of good marshmallow test performance: a child’s awareness of the behaviours people value, such as patience, might be just as important. Perhaps it is the marshmallow test’s ability to tap into social perceptiveness that holds the key to this simple test’s ability to predict future success, time and time again.

    Delay of Gratification as Reputation Management

    Post written by Sofia Deleniv for the BPS Research DigestSofia holds a degree in Experimental Psychology and has just completed her PhD in Neuroscience at the University of Oxford, where she investigated sensory processing using a mix of electrophysiology and computer modelling. In 2015, she decided to try her hand at science writing by starting her blog ‘The Neurosphere‘. Since then, her work has appeared in magazines such as the New Scientist and Discover. You can visit her Twitter feed for updates on her written work and other exciting bits of science.

    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 October 15, 2020 11:33 AM.

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    The Adventures of a Mouse Malignancy Group Portraitist

    Smut Clyde was busy with yet another Chinese paper mill. A plastic ruler was deployed.

    in For Better Science on October 15, 2020 10:15 AM.

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    A documentary and a Bollywood film highlight two disparate paths in mathematics

    There’s no one way to be a mathematical genius.

    Shakuntala Devi had little formal education. Maryam Mirzakhani attended graduate school at Harvard University. Two films chronicle how each woman became famous for her own variety of mathematical prowess.

    The two women’s skills took vastly different forms: Devi was known for her blazingly fast mental arithmetic, while Mirzakhani made strides in the mathematics of surfaces, becoming the first woman to win one of the highest honors bestowed on mathematicians, the Fields Medal.

    The contrast between the two women is echoed in the divergent styles of the two films: One is a Bollywood biopic heavy on emotional drama, and the other is a documentary replete with mathematical lingo.

    Born in India in 1929, Devi grew up in an impoverished family. As recounted in the Hindi-language film Shakuntala Devi, available with subtitles on Amazon Prime, she could make complex mental calculations at a rapid-fire pace, even as a small child. Devi became a performer, touring internationally and stunning observers with her feats, which outpaced computers in the 1970s and ’80s.

    While fun, the movie features bouts of cheesy dialog that may be off-putting to some viewers. But others will enjoy the scenes that re-create some of Devi’s most famous achievements, such as taking the 23rd root of a 201-digit number in under a minute, and multiplying two 13-digit numbers in less than 30 seconds. Careful viewers might be able to glean a few number facts from the film, but the movie focuses on Devi’s fraught relationships — particularly with her daughter — rather than on the details of mental math algorithms.

    Watch the trailer for Shakuntala Devi.

    Secrets of the Surface, available on the online video platform Vimeo, recounts Mirzakhani’s life via interviews with her friends, teachers and colleagues. Although Mirzakhani preferred reading to mathematics at first, her mathematical talent soon became apparent. As a high school student in Iran in the 1990s, she twice won gold medals in the International Mathematical Olympiad. But aside from the youthful mathematical interests Devi and Mirzakhani shared, the two women’s backgrounds couldn’t be more different. Mirzakhani attended a high school for gifted girls and studied mathematics at Sharif University of Technology in Tehran before heading to Harvard and eventually a professorship at Stanford University.

    Mirzakhani’s work focused on the geometry of surfaces, such as doughnuts with multiple holes. Her work has connections to other fields such as string theory, the mathematics-intensive branch of physics that attempts to describe the universe as composed of tiny, vibrating strings.

    The film includes beautifully clear descriptions and visualizations — for example, lines winding around a doughnut shape illustrate Mirzakhani’s study of the number of closed loops that can form on various curved surfaces. These visual aids elucidate the complicated mathematical concepts underlying Mirzakhani’s work, for which she won the Fields Medal in 2014. Three years after receiving that honor, Mirzakhani died of cancer at just 40 years old. In the film, interviews with students at her former high school reveal what an inspirational figure she still is. “I think she’s raised the bar for girls, but beside that, she has opened up a new way,” says student Dorsa Majdi.

    Watch the trailer for Secrets of the Surface.

    Devi likewise inspired schoolchildren, promoting math as fun and unintimidating and authoring books about numbers. Watching the two films, I couldn’t help but wonder how Devi’s life might have been different had she been privileged with the type of schooling Mirzakhani received. In the biopic’s depiction, Devi seems to yearn for such an opportunity. She is portrayed staring longingly at children attending a school at which she is paid to perform, but which she can’t afford to attend.

    in Science News on October 15, 2020 10:00 AM.

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    Editors say they won’t retract intelligent design paper despite subject being “not in any way a suitable topic” for their journal

    The editors of a journal that published a highly controversial paper on intelligent design say retraction is off the table, at least for the moment.  The drama involves an article in the September issue of the Journal of Theoretical Biology, an Elsevier title, titled “Using statistical methods to model the fine-tuning of molecular machines and … Continue reading Editors say they won’t retract intelligent design paper despite subject being “not in any way a suitable topic” for their journal

    in Retraction watch on October 15, 2020 09:42 AM.

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    How planting 70 million eelgrass seeds led to an ecosystem’s rapid recovery

    In the world’s largest seagrass restoration project, scientists have observed an ecosystem from birth to full flowering.

    As part of a 20-plus-years project, researchers and volunteers spread more than 70 million eelgrass seeds over plots covering more than 200 hectares, just beyond the wide expanses of salt marsh off the southern end of Virginia’s Eastern Shore. Long-term monitoring of the restored seagrass beds reveals a remarkably hardy ecosystem that is trapping carbon and nitrogen that would otherwise contribute to global warming and pollution, the team reports October 7 in Science Advances. That success provides a glimmer of hope for the climate and for ecosystems, the researchers say.

    The project, led by the Virginia Institute of Marine Science and The Nature Conservancy, has now grown to cover 3,612 hectares — and counting — in new seagrass beds. By comparison, the largest such project in Australia aims to restore 10 hectares of seagrass.

    The results are “a game changer,” says Carlos Duarte. “It’s an exemplar of how nature-based solutions can help mitigate climate change,” he says. The marine ecologist at King Abdullah University of Science and Technology in Thuwal, Saudi Arabia is a leader in recognizing the carbon-storing capacity of mangroves, tidal marshes and seagrasses.

    The team in Virginia started with a blank slate, says Robert Orth, a marine biologist at the Virginia Institute of Marine Science in Gloucester Point. The seagrass in these inshore lagoons had been wiped out by disease and a hurricane in the early 1930s, but the water was still clear enough to transmit the sunlight plants require.

    researcher collecting seagrass seedsA researcher collects seeds from a restored seagrass meadow in a coastal Virginia bay.Jay Fleming

    Within the first 10 years of restoration, Orth and colleagues witnessed an ecosystem rebounding rapidly across almost every indicator of ecosystem health — seagrass coverage, water quality, carbon and nitrogen storage, and invertebrate and fish biomass (SN: 2/16/17).

    For instance, the team monitored how much carbon and nitrogen the meadows were capturing from the environment and storing in the sediment as seagrass coverage expanded. It found that meadows in place for nine or more years stored, on average, 1.3 times more carbon and 2.2 times more nitrogen than younger plots, suggesting that storage capacity increases as meadows mature. Within 20 years, the restored plots were accumulating carbon and nitrogen at rates similar to what natural, undisturbed seagrass beds in the same location would have stored. The restored seagrass beds are now sequestering on average about 3,000 metric tons of carbon per year and more than 600 metric tons of nitrogen, the researchers report.

    Seagrasses can take a hit. When a sudden marine heat wave killed off a portion of the seagrass, it took just three years for the meadow to fully recover its plant density. “It surprised us how resilient these seagrass meadows were,” says Karen McGlathery, a coastal ecologist at the University of Virginia in Charlottesville.

    She believes the team’s work is more than just a great case study in restoration. It “offers a blueprint for restoring and maintaining healthy seagrass ecosystems” that others can adapt elsewhere in the world, she says.

    Reestablished eelgrass bed near VirginiaReestablished eelgrass beds off Virginia not only store carbon efficiently, they also support rich biodiversity, such as the seahorse seen here.VIMS

    Seagrasses are among the world’s most valuable and most threatened ecosystems, and are important globally as reservoirs of what’s known as blue carbon, the carbon stored in ocean and coastal ecosystems. Seagrass meadows are among the most efficient storers of carbon on Earth, preventing carbon from escaping to the atmosphere as heat-trapping carbon dioxide. These underwater prairies also support near-shore and offshore fisheries, and protect coastlines as well as other marine habitats. Despite their importance, seagrasses have declined globally by some 30 percent since 1879, according to an Aug. 14 study in Frontiers in Marine Science.

    “The study helps fill some large gaps in our understanding of how blue carbon can contribute to climate restoration,” says McGlathery. “It’s the first to put a number on how much carbon restored meadows take out of the atmosphere and store,” for decades and potentially for centuries.

    The restoration is far from finished. But already, it may point the way for struggling ecosystems such as Florida’s Biscayne Bay, once rich in seagrass but now suffering from water quality degradation and widespread fish kills.  Once the water is cleaned up, says Orth, “our work suggests that seagrasses can recover rapidly” (SN: 3/5/18).

    McGlathery also believes the scale of the team’s success should be uplifting for coastal communities. “In my first years here, there was no seagrass and there hadn’t been for decades. Today, as far as I can swim, I see lush meadows, rays, the occasional seahorse. It’s beautiful.”

    in Science News on October 14, 2020 04:00 PM.

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    The first room-temperature superconductor has finally been found

    It’s here: Scientists have reported the discovery of the first room-temperature superconductor, after more than a century of waiting.

    The discovery evokes daydreams of futuristic technologies that could reshape electronics and transportation. Superconductors transmit electricity without resistance, allowing current to flow without any energy loss. But all superconductors previously discovered must be cooled, many of them to very low temperatures, making them impractical for most uses.

    Now, scientists have found the first superconductor that operates at room temperature — at least given a fairly chilly room. The material is superconducting below temperatures of about 15° Celsius (59° Fahrenheit), physicist Ranga Dias of the University of Rochester in New York and colleagues report October 14 in Nature.

    The team’s results “are nothing short of beautiful,” says materials chemist Russell Hemley of the University of Illinois at Chicago, who was not involved with the research.

    However, the new material’s superconducting superpowers appear only at extremely high pressures, limiting its practical usefulness.

    Dias and colleagues formed the superconductor by squeezing carbon, hydrogen and sulfur between the tips of two diamonds and hitting the material with laser light to induce chemical reactions. At a pressure about 2.6 million times that of Earth’s atmosphere, and temperatures below about 15° C, the electrical resistance vanished.

    That alone wasn’t enough to convince Dias. “I didn’t believe it the first time,” he says. So the team studied additional samples of the material and investigated its magnetic properties.

    Superconductors and magnetic fields are known to clash — strong magnetic fields inhibit superconductivity. Sure enough, when the material was placed in a magnetic field, lower temperatures were needed to make it superconducting. The team also applied an oscillating magnetic field to the material, and showed that, when the material became a superconductor, it expelled that magnetic field from its interior, another sign of superconductivity.

    The scientists were not able to determine the exact composition of the material or how its atoms are arranged, making it difficult to explain how it can be superconducting at such relatively high temperatures. Future work will focus on describing the material more completely, Dias says.

    When superconductivity was discovered in 1911, it was found only at temperatures close to absolute zero (−273.15° C). But since then, researchers have steadily uncovered materials that superconduct at higher temperatures. In recent years, scientists have accelerated that progress by focusing on hydrogen-rich materials at high pressure.

    In 2015, physicist Mikhail Eremets of the Max Planck Institute for Chemistry in Mainz, Germany, and colleagues squeezed hydrogen and sulfur to create a superconductor at temperatures up to −70° C (SN: 12/15/15). A few years later, two groups, one led by Eremets and another involving Hemley and physicist Maddury Somayazulu, studied a high-pressure compound of lanthanum and hydrogen. The two teams found evidence of superconductivity at even higher temperatures of −23° C and −13° C, respectively, and in some samples possibly as high as 7° C (SN: 9/10/18).

    The discovery of a room-temperature superconductor isn’t a surprise. “We’ve been obviously heading toward this,” says theoretical chemist Eva Zurek of the University at Buffalo in New York, who was not involved with the research. But breaking the symbolic room-temperature barrier is “a really big deal.”

    If a room-temperature superconductor could be used at atmospheric pressure, it could save vast amounts of energy lost to resistance in the electrical grid. And it could improve current technologies, from MRI machines to quantum computers to magnetically levitated trains. Dias envisions that humanity could become a “superconducting society.”

    But so far scientists have created only tiny specks of the material at high pressure, so practical applications are still a long way off.

    Still, “the temperature is not a limit anymore,” says Somayazulu, of Argonne National Laboratory in Lemont, Ill., who was not involved with the new research. Instead, physicists now have a new aim: to create a room-temperature superconductor that works without putting on the squeeze, Somayazulu says. “That’s the next big step we have to do.”

    in Science News on October 14, 2020 03:00 PM.

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    Visible Reminders Of Inequality Can Raise Support For Taxing The Wealthy

    By Emily Reynolds

    Most of us are aware of the vast inequality that exists in the world — and even if we’re not, exposure to that information can change how we behave. Research has found that we’re more likely to take risks when exposed to inequality and that it can make high-income individuals less likely to be generous.

    It can also change the way people feel about public policy, as Melissa L. Sands and Daniel de Kadt from the University of California, Merced find in a new study in Nature. They explored real-world inequality in low-income neighbourhoods in South Africa — and found that visible reminders of unequal socioeconomic status can  raise support for taxation of the wealthy.

    South Africa, like many other countries, has high levels of inequality, largely related to apartheid and colonialism: World Bank figures suggest that the top 1% of earners in South Africa own 71% of assets while the bottom 60% own just 7%. The study itself took place in Soweto, an area which has particularly low socioeconomic status both within the country and within its province, Gauteng. The average annual household income in the seven neighbourhoods in which the study took place is 32,000 rand — half the average annual income for Black South Africans.

    The methods were simple. Participants were approached by a petitioner, who either asked for support for a policy that would redistribute wealth through higher taxation of the wealthy or for a policy related to renewable energy. On some occasions, a BMW 3 Series was placed at the location; on others, the car was absent.

    Overall, participants were 9% less likely to stop to sign either petition when the car was nearby. But after controlling for this baseline “suppressive effect”, the team found that  participants were actually 11% more likely to sign the wealth tax petition than the renewable energy one in the presence of the BMW. That is, the car, a reminder of inequality, seemed to increase support specifically for the issue of taxation.

    The findings strengthen the case of a 2015 survey, also analysed by the team, which also indicated that Soweto residents exposed to more inequality where they lived (e.g. those more likely to see signs of wealth within a kilometre of their home) were more likely to support higher taxation of the wealthy. This wasn’t the case when conspicuous signs of inequality were further away, visible within five or ten kilometres. This all suggests that visible markers of inequality make people more likely to want to do something about it.

    The study didn’t explore the willingness of participants to engage in other acts of resistance, or the longevity of such actions. As Colin Tredoux and John Dixon point out in this op-ed about the study, signing a petition is an example of normative resistance — a pretty acceptable way of registering dissent. Whether displays of inequality would spur people onto more active protest would be interesting to explore, as would tracking how such feelings endure over time. And what of those with a higher income themselves? It’s unclear whether the presence of a fancy car would have the same effect on that group — so what might prompt them into supporting social policies that help the many?

    Further work could also look at the meaning local people ascribe to such displays of inequality. The team notes that Soweto is a site of serious racial stratification — and it’s difficult to untangle issues of race and colonialism from issues of income inequality. Does the car represent racial or class stratification, both or even neither? A follow-up survey may help delve deeper into these issues.

    Local exposure to inequality raises support of people of low wealth for taxing the wealthy

    Emily Reynolds is a staff writer at BPS Research Digest

    in The British Psychological Society - Research Digest on October 14, 2020 01:25 PM.

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    Is the COVID-19 Pandemic a Traumatic Stressor?

    Have worries and experiences around COVID-19 caused a rise in PTSD?

    in Discovery magazine - Neuroskeptic on October 14, 2020 12:30 PM.

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    How Venus flytraps store short-term ‘memories’ of prey

    A Venus flytrap’s short-term “memory” can last about 30 seconds. If an insect taps the plant’s sensitive hairs only once, the trap remains still. But if the insect taps again within about half a minute, the carnivorous plant’s leaves snap shut, ensnaring its prey.

    How Venus flytraps (Dionaea muscipula) remember that initial touch has been a mystery. A new study reveals that the plants do so using calcium, researchers report online October 5 in Nature Plants.

    Scientists know that some plants have a type of long-term memory, says study coauthor Mitsuyasu Hasebe, a biologist at the National Institute for Basic Biology in Okazaki, Japan. One example is vernalization, whereby plants remember long periods of winter cold as a signal to flower in the spring. But short-term memory is more enigmatic, and “this is the first direct evidence of the involvement of calcium,” Hasebe says.

    Even though the carnivorous plant, famous for its jawlike leaves, has no brain or nervous system, it can apparently count to five and distinguish between live prey and things like rain, which could inadvertently trigger its leaves to snap shut, wasting energy (SN: 1/24/16). Previous research suggested that calcium plays a role in this process, but with the help of genetic engineering, Hasebe and colleagues were able to actually see calcium in action.

    After a hair inside a Venus flytrap is tapped once, calcium floods the leaves’ cells, which researchers could observe after genetically engineering plants to glow when calcium was present. A second tap, a few seconds after the first, brings more calcium into the cells, brightening the glow and causing the trap to snap shut.

    The researchers added genes to the Venus flytraps that produce a protein, which glows green when exposed to calcium. When the team tapped one of the trap’s sensory hairs, the base of that hair began glowing, and then the glow spread through the leaf before beginning to fade. When the researchers touched the hair a second time — or touched a different hair on the leaf — within about 30 seconds, the trap’s leaves lit up even brighter than before, and the plant quickly snapped shut.

    The results show that the flytrap’s short-term memory is a waxing and waning of calcium within leaves’ cells, the researchers say. Each time a sensory hair is triggered, it signals the release of calcium. When the calcium concentration reaches a certain level, achieved by that second, faster surge of calcium, the trap closes.

    Still, the research doesn’t reveal all of the plant’s secrets. To sense prey, “the flytrap operates a fast electrical network” that can convert a fly or other insect’s movement into small voltage changes that ripple across the plant’s cells, says coauthor Rainer Hedrich, a biophysicist at the University of Würzburg in Germany. Scientists are still unsure how the calcium memory system works in tandem with that electrical network to activate the plant’s snap.

    “The close association of calcium and electrical signal is known in ordinary plants, so it was also expected in the Venus flytrap,” says Andrej Pavlovič, a plant physiologist at Palacký University in Olomouc, Czech Republic who wasn’t involved in the study. But the most interesting part of the research was getting the trap to glow, he says. Such genetic transformations are common in frequently studied plants, but more difficult to do in less well-studied predatory plants, so successfully engineering the flytrap’s genes to make the plant glow “is a great leap forward in studies on carnivorous plants.”

    in Science News on October 14, 2020 10:00 AM.

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    The bizarre anti-vaccine paper a Florida professor has been trying to have retracted to no avail

    Fly, meet elephant’s back. Robert Speth has spent the last 19 months trying to get two of the world’s largest medical publishers to retract an article he considers to be a “travesty” of pseudoscientific claims and overtly anti-vaccination bias. In the process, he has uncovered slipshod management of a journal’s editorial board that angered, among … Continue reading The bizarre anti-vaccine paper a Florida professor has been trying to have retracted to no avail

    in Retraction watch on October 14, 2020 10:00 AM.

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    4 experts on how to advance sustainable development

    What do we really need to do to achieve the UN SDGs by 2030?

    in Elsevier Connect on October 14, 2020 09:56 AM.

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    New APC-free Open Access agreements test alternative funding models

    The following press release was issued on Wednesday, October 14th at 12:01 Pacific.

    SAN FRANCISCO — Jisc, the digital solutions provider for education and research in the UK, and the Public Library of Science (PLOS) today announced two 3-year Open Access (OA) agreements that allow researchers to publish in PLOS journals without incurring article processing charges (APC). This is the first time that a large university consortium has provided collective agreements as an alternative to APCs at this scale. Jisc and PLOS will also collaborate on future data, metrics, and tools for institutions to evaluate OA publishing agreements.

    “Jisc has always been a priority partner, given its high profile, its large existing institutional account base with PLOS, and leadership role in the library community,” said Sara Rouhi, director of strategic partnerships for PLOS. “It’s always exciting to partner with a forward-leaning organization whose values and priorities around Open Access and Open Science align with our own. We also look forward to sharing the fruits of this partnership with the broader community.”

    Caren Milloy, Jisc’s director of licensing, adds: “We are pleased to have reached these pioneering agreements with PLOS, which will make it easier for researchers to publish OA and offer affordability and sustainability to institutions. These collective action agreements have the potential to help shape the future of OA funding.”

    Under the flat fee agreement, which begins on January 1, 2021, annual fixed prices will cover uncapped publishing in five PLOS journals[1] for corresponding authors affiliated with participating Jisc institutions as well as custom reporting and collaboration on future reporting standards initiatives. The PLOS Community Action Publishing agreement, facilitates uncapped publishing in PLOS’ two highly selective journals[2] through a collective action model. Both corresponding and contributing authors affiliated with participating Jisc institutions are eligible. The model itself is predicated on cost recovery, capped margins, and redistributing revenues above target back to community members.

    These agreements empower authors who want to participate in Open Access publishing, and support a diverse scholarly communication ecosystem for researchers and readers. 

    [1] PLOS journals include PLOS Genetics, PLOS Computational Biology, PLOS Pathogens, PLOS Neglected Tropical Diseases and PLOS ONE

    [2] PLOS Medicine and PLOS Biology

    The post New APC-free Open Access agreements test alternative funding models appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on October 14, 2020 07:16 AM.

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    Glowing blue helps shield this tardigrade from harmful ultraviolet light

    When blasted with ultraviolet radiation, a newly discovered species of tardigrade protects itself by glowing blue.

    Tardigrades, microscopic animals also known as water bears or moss piglets, are nature’s ultimate survivor. They’re game for temperatures below –270° Celsius and up to 150° C and can withstand the vacuum of space, and some are especially resistant to harmful UV radiation (SN: 7/14/17). One species shields itself from that UV radiation with glowing pigments, a new study suggests. It’s the first experimental evidence of fluorescent molecules protecting animals from radiation, researchers report October 14 in Biology Letters.

    “Tardigrades’ tolerance for stress is extraordinary,” says Sandeep Eswarappa, a biochemist at the Indian Institute of Science in Bangalore, India, “but the mechanisms behind their resistance is not known in most [species].”

    He and his colleagues investigated these mechanisms in a new tardigrade species from the genus Paramacrobiotus that the scientists identified and then grew in the lab after plucking specimens from a mossy wall on campus. Eswarappa found that like many other tardigrades, these Paramacrobiotus are resistant to ultraviolet radiation. After sitting under a germicidal UV lamp for 15 minutes — ample time to kill most microbes and give humans a skin lesion — all Paramacrobiotus specimens survived, seemingly unfazed by the ordeal.

    The secret of how these water bears persisted eluded Eswarappa and his team until one day when the researchers happened to view a tube of the ground-up tardigrades in a UV transilluminator, used to visualize fluorescence in the lab. To the team’s surprise, the tube glowed blue. “It was our mini-eureka moment,” Eswarappa says.

    Molecules fluoresce when they absorb higher energy light and release lower energy light. Some biologists have suggested that fluorescent pigments could shield certain animals, such as comb jellies or corals, from UV radiation, though such powers hadn’t been shown in the lab (SN: 11/17/17).

    tardigrade under normal lightResearchers suspect that the reddish-brown spots in this microscopic Paramacrobiotus tardigrade, seen here under normal light, absorb damaging ultraviolet rays and, in turn, emit harmless blue light.H.R. Suma

    Individual Paramacrobiotus vary in how much they fluoresce, the team found, and more fluorescent tardigrades are more resistant to UV light. After one hour of UV exposure, 60 percent of strongly fluorescent individuals survived more than 30 days, while all less-fluorescent specimens died within 20 days.

    To further link fluorescence with protection, the researchers soaked roundworms and individuals from a tardigrade species that isn’t resistant to UV light in a bath of glowing Paramacrobiotus extract. Thus endowed, both animals were more UV tolerant compared with individuals immersed in only water.

    The experiments clearly show that the pigments are “a mechanism for UV tolerance in these animals, and that’s a nice step forward,” says Paul Bartels, an invertebrate zoologist and tardigrade expert at Warren Wilson College in Asheville, N.C., who wasn’t involved in the study. “It’s a really cool study.”

    Eswarappa was surprised to find that the tardigrades’ glow played a role in UV protection, since “the finding of fluorescence was serendipitous.” He suggests that the fluorescent pigments absorb UV rays, emitting harmless blue light, though the study can’t say precisely how the pigments confer protection. The glow itself, for example, may simply be an ancillary effect of the pigments, and not involved in UV shielding. Eswarappa speculates that the glowing pigments may help these water bears survive in southern India, where summertime UV levels can be extreme.

    in Science News on October 13, 2020 11:01 PM.

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    A glowing zebrafish wins the 2020 Nikon Small World photography contest

    While seeking answers to scientific questions, it’s worth sometimes taking a step back to appreciate the world’s exquisiteness.

    For developmental biologists Daniel Castranova, Bakary Samasa and Brant Weinstein, some of that delicate beauty is inside a zebrafish. While working in Weinstein’s lab at the National Institutes of Health in Bethesda, Md., Castranova and Samasa snapped a stunning photograph of a young zebrafish, illuminating never-before-seen parts of its lymphatic system.

    The photo comes from research that sought to determine whether zebrafish have lymphatic vessels inside their skulls. The lymphatic system helps clear toxins and waste from the body, and previously researchers thought only mammals had such structures close to the brain.

    But zebrafish have those vessels too, Castranova and colleagues report in preliminary research posted in May at bioRxiv.org. The team used fish that had been genetically modified to have lymphatic vessels that fluoresce orange under certain conditions, with skeletons and scales that glow blue. Because fish are easier than mammals to raise and image in the lab, Castranova says, the finding could help scientists more easily study the role of the brain’s lymphatic system in neurological diseases like brain cancer or Alzheimer’s.

    After taking the photo — a composite of 350 images taken with a confocal microscope — on a busy work day, “I never even looked at the picture for a couple of weeks,” Castranova says. “And then when I looked at it at some point post-data processing, I was like ‘Wow.’”

    Even if it took Castranova a bit to appreciate what he had in hand, judges for the 2020 Nikon Small World photomicroscopy competition realized that it was a winner. The photo snagged first place in the 46th annual contest. The results were announced October 13.

    Here are some our favorite photographs from this year’s competition.

    Inside a clownfish egg

    clownfishA developing clownfish (Amphiprion percula) embryo won second place in the contest. The series of photos documents the embryo’s growth (from left to right) on day one, morning and evening of day three, day five and day nine.Daniel Knop/Natur und Tier-Verlag NTV

    Over nine days, German photographer Daniel Knop watched an embryo grow from a striking golden yolk sac into a baby clownfish (Amphiprion percula) to produce this second place–winning photo.

    The composite image, created by stacking together multiple photos that had been taken while the embryo was in motion, documents stages of the embryo’s development from left to right. The first egg shows the newly growing fish hours after fertilization, with a white cluster of extra sperm cells still on the outside of the egg. The subsequent embryos depict the fish twice on the third day of development (morning and evening), as well as the fifth and ninth days, hours before the fish hatched.

    Tongue of a snail

    snail tongueThis colorful depiction of part of a snail’s tongue, at 40 times magnification, shows its structure in three dimensions. Sections colored blue are farthest from the viewer and those colored hot pink are closest. The image placed third in the competition.Igor Siwanowicz/HHMI

    When neurobiologist Igor Siwanowicz’s lab mate’s aquarium was taken over by freshwater snails, Siwanowicz decided to snap a photo of part of one snail’s tongue, earning him third place in the competition.

    The appendage, magnified 40 times, was photographed in layers with a laser to reconstruct the tongue in three dimensions. The pieces closest to the viewer are colored hot pink; the farthest bits are blue. The tongue’s comblike projections scrape algae off of surfaces for food.

    “I chose this image to show that in nature, beauty can be found in the most unexpected places, like a snail’s mouth,” says Siwanowicz, of the Howard Hughes Medical Institute’s Janelia Research Campus in Ashburn, Va., and second-place winner in the 2019 contest (SN: 10/21/19).

    Lab-grown hairs

    skin organoidShown at 20 times magnification, this skin organoid (colored blue) sports human hair follicles (stubby projections) and nerves (red). The image earned an honorable mention.Karl Koehler and Jiyoon Lee/Boston Children’s Hospital & Harvard Medical School

    Neuroscientist Karl Koehler and biochemist Jiyoon Lee, both of Boston Children’s Hospital and Harvard Medical School, captured this image of human hair follicles budding off of a cluster of lab-grown skin cells, broadly called an organoid, in a lab dish. Other types of organoids exist for various parts of the body, such as the gut and brain.  

    It takes about four to five months for a skin organoid to grow in the lab. The structures develop nerves that connect specialized cells in hair follicles, much like the neural circuit system that allows us to feel touch, and could one day help develop better skin grafts. This lab-grown skin develops inside-out, Koehler says. So the surface that grows hair is inside the clump of cells, and viewers see the base of hair follicles. The team published their findings June 3 in Nature.

    Majestic moss

    skin organoidMoss capsules, like the one pictured here at 10 times magnification and shown in false-color, release hundreds of thousands of spores that are carried by the wind to new parts of the forest to grow. The photo is an Image of Distinction in this year’s Nikon Small World photo contest.Miroslav Žít

    Miroslav Žít, an amateur photographer from Prachatice in the Czech Republic, snapped this photo of a stunning moss capsule packed with spores almost ready to take flight. Capsules perch on top of stems that extend from blankets of moss.

    The spores ride the wind once released, sometimes traveling long distances and staying dormant until conditions are right for growth.

    Viral infection

    mouse paw infected with Chikungunya virusThis mouse paw has been infected with the Chikungunya virus (colored pink at the bottom part of the paw), a pathogen that causes painful inflammation of the joints. The rodent’s immune response to the virus, in the form of immune cells called microphages, is shown in blue and general tissue is colored orange. The image won an honorable mention.Jonard Corpuz Valdoz, Pam Van Ry and Richard Robison/Brigham Young Univ.

    Researchers at Brigham Young University in Provo, Utah combined more than 2,200 photos taken with a confocal microscope to create this vivid shot of a 1-centimeter-long mouse paw infected with the Chikungunya virus.

    Chikungunya is a disease that can result in debilitating joint pain. Biochemists Jonard Corpuz Valdoz and Pam Van Ry teamed up with microbiologist Richard Robison to take a peek at how a mouse responds to the infection, in the hopes of shedding light on how the virus spreads in animals, including humans. The image shows that immune cells called macrophages have rushed to the paw to fight the virus.

    Baby bat

    fruit bat embryoThis image of a Seba’s short-tailed fruit bat embryo (Carollia perspicillata) is colored to show its skeleton in green and cartilage in orange; it placed 20th in the photo competition.Dorit Hockman/ Univ. of Cape Town, Vanessa Chong-Morrison/UCL

    While participating in an embryology course at the Marine Biological Laboratory in Woods Hole, Mass., Vanessa Chong-Morrison, a developmental biologist then at the University of Oxford, prepared this image of a Seba’s short-tailed fruit bat (Carollia perspicillata) embryo for picture day.

    Chong-Morrison, now at University College London, and Dorit Hockman of the University of Cape Town in South Africa took snapshots of the developing bat’s skeleton, capturing small areas at a time. Hockman is also a developmental biologist who studies how bat hands grow into “impressive wings.” The pair then stitched together the images to produce the final photo, which was edited to show the bat’s bones in green and cartilage in orange.   

    A work of amino acid art

    L-glutamine and beta-alanine crystalsWhen in a warm solution of ethanol and water, amino acids L-glutamine and beta-alanine form crystals, photographed here in a 13th place–winning photo at four times magnification.Justin Zoll/Justin Zoll Photography

    No, this photo isn’t an abstract painting. It’s a portrait of the crystals that form after two amino acids — L-glutamine and beta-alanine — are heated in a solution made of ethanol and water. One of the compounds, L-glutamine, is a building block for proteins and ensures that the immune system can function. The other, beta-alanine, helps with muscle endurance.

    Justin Zoll, a photographer based in Ithaca, N.Y., merged multiple images of crystals taken at four times their normal size into a panorama to show the crystals’ intricate details in a wider field of view. When the crystals interact with a multiple beams of polarized light, the arrangement of their molecules reflects stunning colors, he says.

    in Science News on October 13, 2020 03:08 PM.

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    PLOS accesses Dimensions on Google Cloud’s BigQuery

    Digital Science and PLOS are pleased to announce an agreement which will provide PLOS, the leading Open Access (OA) publisher with access to Dimensions on BigQuery. Dimensions is a comprehensive database that covers the full research and innovation lifecycle. BigQuery, Google Cloud’s serverless and secure multi-cloud data warehouse, enables PLOS to analyse the full metadata of Dimensions and use it to inform strategy and decision-making across the organization.

    This follows the recent Digital Science partnership with Google Cloud, which was designed to remove barriers to data access, analysis and visualization for organizations across the research and innovation ecosystem. In today’s environment, stakeholders in the research and innovation ecosystem are seeking to make better, evidence-based decisions. To do this, they need greater access to contextual information, while at the same time protecting the security of their own data.

    Dimensions is a research information platform which has been developed to provide a comprehensive view on the research process and activities  – going beyond publications and citations. While covering 112 million publications with 1.2 billion citations, Dimensions also interlinks data from $1.8 trillion of funded grants, 583,000 clinical trials, 40 million patents, 453k policy documents and 1.5 million datasets. 

    PLOS has been using Dimensions Analytics and the Dimensions API since early 2020, and is also an existing Google BigQuery user. This latest agreement therefore fits seamlessly with PLOS’s own data strategy, providing their staff Dimensions data on Google BigQuery to help shape their business development strategy, monitor trends in the OA landscape — such as providing evidence to support Open Access Transformative Agreements, and create custom dashboards and reports that can be securely accessed and shared across their organization. PLOS will now be able to combine their own internal data with Dimensions external data sources, helping create a 360° view of the research landscape.   

    Kristen Monahan, Data & Insights Senior Manager, said:“PLOS already relies on Dimensions for baseline data about institutions and funding to assist in our agreement discussions and uses a combination of Dimensions and internal data for business analytics. Also having access to Dimensions data via Google BigQuery gives us tremendous freedom to analyse and integrate Dimensions data across our organization.” 

    Christian Herzog, CEO Dimensions, said: “We’re very pleased that, through this agreement, PLOS staff will get unprecedented access to the Dimensions database. This brings them full flexibility to perform advanced analytics at industry-leading speeds and create personalized dashboards and reports. More importantly, however, it brings them greater access to the contextual information in Dimensions that supports their thoughtful approach to informed, evidence-based decision-making.”

    Users can now start exploring the free COVID datasets here – https://console.cloud.google.com/marketplace/product/digitalscience-public/covid-19-dataset-dimensions

    The post PLOS accesses Dimensions on Google Cloud’s BigQuery appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on October 13, 2020 02:53 PM.

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    Community Comments Continued: An update on the preprint commenting pilot at PLOS

    Around 11 months ago we announced our year-long  preprint commenting pilot to connect bioRxiv comments on preprints that are under consideration at select PLOS journals to the editors handling those articles. (The journals in the pilot are PLOS Computational Biology, PLOS Genetics, PLOS Neglected Tropical Diseases, and PLOS Pathogens.)

    We have one month left on this pilot, and in the interest of making the most of this, we also want to hear from YOU, the open science community. Have you ever received public feedback on a preprint? Do you comment on preprints? Privately or publicly? Do you read preprints but feel that you can’t give feedback?

    If you answered yes to any of the above, we want to hear from you.  Tell us your preprint story here.

    As we anticipated, during this pilot the majority of eligible preprints haven’t received any public comments on the bioRxiv platform. Staff facilitating this pilot have observed that, while some preprints receive high quality feedback in the comments, most do not. Also, the timing of preprint commenting has not always lined up with the peer review process, so that preprints have received detailed feedback after an editorial decision had already been made. 

    Pilot programs provide an opportunity to take the ongoing temperature of the community regarding innovations in scholarly communication and researcher behaviors. A 2019 survey reported that 53% of preprint posters do so in order to receive feedback. So how should we interpret this slow uptake of commenting on the bioRxiv platform?

    We could easily assume that there just isn’t a lot of interest in preprint commenting. Yet a recent flash survey of reviewers across all the PLOS journals (not just the ones in this pilot) revealed that at least 11% of those surveyed had provided public feedback on a preprint. While a few reported giving private feedback, the majority of respondents told us that they read preprints but don’t comment on them. 

    Furthermore, ASAPbio recently found that more than 50% of researchers indicate that the opportunity for early feedback on preprints was very beneficial, suggesting that authors could benefit from preprint commenting. 

    In the early stages of this pilot we already knew (from the same 2019 survey above) that researchers have reported a preference for private feedback, and that most researchers who have received feedback have received it privately via email or conversation, or, if publicly, via Twitter. Our pilot, which only covered comments left on the bioRxiv platform, had no way of noting whether any comments were actually coming to the authors via other channels.

    When we launched this pilot we also talked about why we engage with preprints. We see preprints as an important step towards opening up peer review to more voices beyond those expressly invited by the editors. Far from being a side-step around peer review, as some detractors see them, we see preprints as a way of getting even more eyes, and therefore reviews, on an article undergoing peer review. As our Chief Scientific Officer, Veronique Kiermer, wrote in a post during Peer Review Week, preprints maximize and diversify peer review in a way that the traditional process cannot, in a way that complements that traditional process and makes it even stronger. This is all “a celebration of peer review in different forms”!

    Therefore, we remain committed to providing greater opportunities for research communities to participate in reviews of preprints, while promoting transparency in peer review, but we will now consider how we could refine processes around facilitating engagement with preprints during the peer review process. We believe that maximizing and diversifying the voices involved in peer review is simply a behavior we must patiently cultivate, and we will use the lessons learned from the pilot to help us.

    Remember, please complete the survey! We have one month of the pilot left to go, and we would like to complement our final report with the findings from this survey.

    And, please watch this space for more posts about preprints, peer review, and all the ways in which we’re working with the research community to improve trust in science.

    Note: This blog was written by Harry Porter, a program assistant at PLOS.

    The post Community Comments Continued: An update on the preprint commenting pilot at PLOS appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on October 13, 2020 02:40 PM.

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    Brian Deer’s book on Andrew Wakefield: “The Doctor Who Fooled the World”

    My review of the new book by Brian Deer about what became the biggest medical scandal in recent history: Andrew Wakefield's fraudulent research on MMR vaccines and his antivax campaigning which continues even today.

    in For Better Science on October 13, 2020 10:07 AM.

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    Pufferfish may be carving mysterious ‘crop circles’ near Australia

    Japan’s white-spotted pufferfish are renowned for producing complex, ringed patterns in the sand. Now, 5,500 kilometers away in Australia, scientists have discovered what appear to be dozens more of these creations.

    While conducting a marine life survey out on Australia’s North West Shelf near subsea gas infrastructure with an autonomous underwater vehicle, marine ecologist Todd Bond spotted a striking pattern on the seafloor, more than 100 meters deep.  “Immediately, I knew what it was,” recounts Bond, of the University of Western Australia in Perth. Bond and his colleagues continued the survey, ultimately finding nearly two dozen more.

    Until now, these undersea “crop circles” were found only off the coast of Japan. First spotted in the 1990s, it took two decades to solve the mystery of what created them. In 2011, scientists found the sculptors — the diminutive males of what was then a new species of Torquigener pufferfish. The patterns are nests, meticulously plowed over the course of days and decorated with shells to entice females to lay their eggs in the center. 

    A hovering autonomous underwater vehicle (HAUV) deployed along subsea natural gas infrastructure off Australia’s coast in September 2018 captured footage of something surprising: a rippled ring carved into the sand. Researchers eventually discovered nearly two dozen of these circles, similar to the elaborate nests crafted by white-spotted pufferfish males near Japan, making it the first such find outside Japan. While it’s not known what species created the Australian rings, an unidentified pufferfish was seen fleeing the site of one of them.

    While there’s no video confirmation that pufferfish are building the nests in Australia, the structures are nearly identical to those in Japan, even sharing a similar number of ridges, Bond and his colleagues report in the November 2020 Journal of Fish Biology. And when a colleague deployed an underwater video system in the area, the contraption luckily landed almost directly atop a circle and captured footage of a small pufferfish fleeing the formation. 

    The Australian circles lie in much deeper waters than Japan’s — 130 meters or more deep compared with about 30 meters deep in Japan. Australian pufferfish known in the area typically inhabit more shallow waters, raising questions about the identity of the species responsible.

    Bond says the images captured of the likely piscean culprit are too poor to make a definitive identification. The circles could have been made by the same species that builds Japan’s nests, the white-spotted pufferfish (Torquigener albomaculosus), or the culprit could be a different, local species — possibly one totally new to science. 

    “It is surprising to find the circles … at a depth where there is not much light,” says Elisabet Forsgren, a behavioral ecologist at the Norwegian Institute for Nature Research in Trondheim. If the nests are meant to be a visual signal to attract females, they may be hard to see in such a dim spot.

    Bond says that the discovery raises more questions that may ultimately help us understand the evolution of pufferfishes, a group already awash in eccentricities. Not only are they among the most toxic vertebrates on Earth, but they’ve completely lost their ribs and pelvic bones to make room when they “puff” with water (SN: 8/1/19). Among the questions: If the Australian circles are made by a different species from Japan’s, did the two fishes’ artistic skills evolve separately?

    “It’s kind of humbling to know that there’s so much out there that we don’t know,” says Bond. “It’s also a little bit scary as well. This is a reflection of, obviously, a key part to the reproduction of maybe a new species, but we just know nothing about it. We didn’t even know these existed.”

    in Science News on October 13, 2020 10:00 AM.

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    In which a researcher named Das plagiarizes from another researcher named Das, one with 20 retractions

    Sometimes things get pretty meta around here.  Exhibit A: The journal Current Medical Chemistry has retracted a 2012 paper for plagiarizing from a 2011 article — and the senior authors of each article share the same last name.  Ho hum, you say. But that name is one that might be familiar to RW readers. Here’s … Continue reading In which a researcher named Das plagiarizes from another researcher named Das, one with 20 retractions

    in Retraction watch on October 13, 2020 10:00 AM.

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    How Well Do You Know Yourself? Research On Self-Insight, Digested

    By Emma Young

    “There are three things extremely hard: steel, a diamond, and to know one’s self.” – Benjamin Franklin, Poor Richard’s Almanac, 1750.

    Franklin was writing over 250 years ago. Surely we humans have learned strategies since then to aid self-insight — and avoid well-known pitfalls. Most of us are familiar, for example, with the better-than-average effect, the finding that most of us rank ourselves above average at everything from driving ability to desirable personality traits (even though of course we can’t all be right). So armed with this kind of knowledge, are we better placed now to view ourselves accurately? And if not, how can we get better at this — and what benefits can we expect?  The following studies provide some illuminating answers…

    I feel like I’m smarter than other people

    The better-than-average effect may be old news, but results from a recent systematic survey of Americans’ beliefs about their own intelligence (the first to be conducted in 50 years) found that about 70% of men and 60% of women agreed with the statement: “I am more intelligent than the average person.” The team was forced to conclude that Americans’ “self-flattering beliefs about intelligence are alive and well several decades after their discovery was first reported.” Other work has found that our over-estimates of our intelligence can be staggeringly huge — around 30 IQ points, on average, according to a study by Gilles Gignac and Marcin Zajenkowski published last year (which also found that we tend to over-estimate our romantic partner’s intelligence even more than our own). The sobering lesson is that you’re probably a lot less smart than you think are.

    OK, but I at least know the limits of my knowledge

    The “Dunning-Kruger effect” relates specifically to the tendency of people who are poor at a task to over-estimate their ability at it. As David Dunning has written: “The scope of people’s ignorance is often invisible to them.” (Although see Gignac and Zajenkowski again, with a paper from this year arguing that the effect is (mostly) a statistical artefact).

    This over-confidence can be dangerous both to the individual, and to others. For example, a US study of student pilots found that those who’d scored lower on a pilot knowledge test “grossly overestimated their ability” while higher-scoring students tended in fact to under-estimate theirs. The same effect has been noted among other groups such as chemistry students. In this case, students who’d scored less than 50% on one exam had predicted that they’d get an average of 69%, while their actual average mark was just under 37%. That’s a massive discrepancy. If you don’t know that you’re under-prepared for a test, this is clearly a problem.

    Fine. But you can’t deny that I know who I am!

    How well do you know your own personality as it fluctuates from moment to moment? This was explored in a recent study, which found that participants had self-insight into their momentary levels of extraversion and conscientiousness, but weren’t great at rating how agreeable they were being at any given time. As the researchers write: “This apparent self-ignorance may be partly responsible for interpersonal problems”.

    However, when it comes to personality in general — your fairly stable, trait levels of extraversion, agreeableness, and so on — there’s some rare good news when it comes to self-insight. According to a large-scale review of data on self-reports of personality vs personality ratings from others, published in Psychological Science in 2018, we’re actually pretty good at judging ourselves in this way. In fact, the work revealed that if anything, we’re harsher judges of our personality than other people are. This was a surprise to the researchers, who’d assumed, based on other work in this field, to find a positive self-bias.

    But I know what I like, right?

    If you love salt and vinegar crisps, say, but hate cheese and onion, then fair enough. No one’s going to argue that you’re mistaken. But if you tell me you love coffee, I might be less accepting. It turns out that it’s not always that easy for us to tell the difference between liking something and wanting it.  A study published this year found that “heavy” coffee drinkers (people who drank three or more cups a day) actually want coffee a lot more than they like it. The implication is that they drink it mostly or entirely to feed their addiction, rather than for pleasure.

    How can I get better at knowing myself?

    Well, the people around you could be more honest: in general, other people don’t help us to correct our biases. Too often, feedback from employers, family, and friends is vague, and overly positive, according to research led by Zlatan Krizan at Iowa State University. “As a society, we make the wrong trade-off by thinking that boosting self-esteem is going to boost performance, and that rarely happens,” Krizan says. “That empty praise of telling someone they’re great, or pretending there are not skill differences when there are, can really become a problem.”

    As well as seeking honest feedback, and bearing in mind the better-than-average effect, it could also be worth practising humility. Research published in the journal Self and Identity suggests that people who are more modest about their degree of self-knowledge actually know themselves better.

    But is it important to have accurate self-knowledge?

    No one likes a narcissist. But there could be some benefits to thinking you’re better than you are. They relate to the optimism bias — the fact that we tend to over-estimate the likelihood of positive events in our lives, like getting a top promotion, and under-estimate our chances of suffering everything from a divorce to a car crash. Optimism is important for mental and physical health. So perhaps having inflated self-views is important for our wellbeing, too. In fact, according to the results of a study published last year in Nature Human Behaviour, this may well be the case. The participants completed various tests of cognitive and emotional abilities and then reported how well they thought they’d done on all these tests. They then spent a week completing daily diaries, in which they reflected on their levels of satisfaction with their career, relationships and life in general.

    The researchers found that having accurate self-insight was not related to higher levels of satisfaction in any of these areas. The data even suggested that people who most over-estimated their abilities had the highest levels of life satisfaction. Still, it’s worth noting that feeling great about your life and performing to your highest level are two different things. People with accurate self-knowledge may be more driven to improve, and achieve more.

    A word of caution

     Our understanding of the potential pluses or minuses of accurate self-insight is, according to a recent review, “clouded” by all kinds of issues, including differences between studies in the way self-insight is measured, and also fundamental differences in types of self-deception. (Self-deception may sometimes stem from an individual’s desire to defend their self-esteem, but other times exist simply because a person hasn’t really engaged in close self-assessment.) Jennifer Beer and Michelle Harris write that the currently available research “does not allow us to confidently conclude that self-insight has advantages over some types of self-insight failure (or vice versa).” They conclude by calling for “more systematic investigation of why, when, where and for whom self-insight is costly or beneficial.”

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

    in The British Psychological Society - Research Digest on October 13, 2020 08:57 AM.

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    Open Access Week at Cornell begins with arXiv’s live virtual event on October 19

    Cornell's OA Week Logo of an open lockOn October 19 at 4pm EDT, arXiv will kick off Cornell’s participation in Open Access Week with a free panel discussion, Rapid Response: How arXiv and other open access resources are adapting to research community needs during the pandemic. This virtual event will feature arXiv’s executive director, Eleonora Presani, as well as John Inglis, co-founder of bioRxiv and medRxiv, and Sebastian Kohlmeier, CORD-19 Project Manager and Senior Manager, Semantic Scholar, Allen Institute for Artificial Intelligence.

    This event is open to all. We invite you to join us on October 19, 2020 at 4pm EDT / 8pm UTC.

    Launch the Rapid Response Webinar
    Webinar ID: 962 9874 9236
    Passcode: 954076


    Giving Week

    arXiv’s live panel discussion also launches arXiv’s Giving Week, October 19-23, our biannual fundraising drive. Voluntary contributions from foundations, members, organizations, and individuals comprise more than 85% of arXiv’s budget, and we are grateful for each and every donation we receive. Please consider getting a head start on giving week and showing your support for open access, open science, and the arXiv community by contributing today.


    More Open Access Week Events

    A second Open Access Week event hosted by Cornell is Building Equity in Education with Open Education Resources, with panelists Stacy Katz, Open Resources Librarian-STEM Liaison at CUNY Lehman, Regina Gong, OER and Student Success Librarian at Michigan State University, and Amanda Larson, Affordable Learning Instructional Consultant at The Ohio State University. Join this important webinar discussion on October 22 at 11am.

    International Open Access Week is a global, community-driven week of action to open up access to research. The event is celebrated by individuals, institutions, and organizations across the world. Check out #OAWeek on Twitter for more events and information.


    in arXiv.org blog on October 12, 2020 09:11 PM.

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    Implementing name changes for published transgender authors

    At PLOS we are committed to addressing the needs of all research communities to improve diversity, equity and inclusion. One of the concerns for some of our transgender and non-binary authors is around changes to their names and how these are reflected in the academic record. In particular, the names assigned to transgender or non-binary persons at birth can represent a stigma, and these names are sometimes referred to as deadnames. 

    Although authors can change their name on their ORCiD profiles themselves, changes to their published academic record have been difficult to implement since, traditionally, changes are limited to correcting author or publisher errors. We believe there is no reason for this to be a barrier. Publishing an academic study is an achievement for researchers to be proud of, and it is important that the name on the paper reflects who the authors are. Therefore, across all PLOS journals we will now honor requests from transgender and non-binary authors of published papers to update their names. 

    The relevant papers will be “republished”, meaning that they will be fully replaced online, and that their indexing metadata (which affects how the author list appears in PubMed, Web of Science, Google Scholar, etc.) should subsequently be updated accordingly. This replaces the author name fully, yet ensures that citation information such as the DOI for the paper remains the same. All previous citations to the paper remain valid. To maintain the author’s privacy, no notice of the name change will be attached to the replaced paper. 

    We strive to support our authors and address issues around equality and inclusion, and welcome any enquiries from transgender authors interested in updating names on their past publications. There is no requirement for authors to do so, this is entirely at their discretion. To initiate this process, simply email us at the relevant journal office. What matters to us is the person who authored the paper, and we want to ensure that the published academic record reflects their correct identity.

    The post Implementing name changes for published transgender authors appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on October 12, 2020 02:41 PM.

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    Rethinking Research Assessment: Addressing Institutional Biases in Review, Promotion, and Tenure Decision-Making (part III)

    Authors: Ruth Schmidt is an Associate Professor at IIT’s Institute of Design and Anna Hatch is the program director for DORA. PLOS supports DORA financially via organizational membership, and PLOS is represented on the steering committee of DORA.

    In part one of our series we showed how objective comparisons are not equitable. In our second part of this series we showed how individual data points can accidentally distract from the whole. Now in part 3 we explore how we gauge value by association.

    While we often give individual data points too much weight, we also face a related, but distinct, tendency to see patterns where they may not exist, or to apply less-than-sound mental models to define the relationships between items. This means that our interpretations of future likelihoods, personal abilities, and relative importance are often skewed, which in turn can impact how we judge risk or prioritize options.

    Not surprisingly, the Halo effect also contributes to this tendency, as seen in cases where highly rated or prominent institutions and journals (and individuals associated with them) receive the benefit of the doubt based on reputation. While this associative property can feel like a useful shortcut, it can cause decision-makers to overlook or override important data that should give us pause. For example, noting that an applicant shares one’s alma mater or trained under one’s former mentor might unfairly bolster their reputation based on factors that have little to do with the quality of their own work.

    Another classic behavioraleconomics concept known as Availability is equally relevant. This describes our tendency to fall back on or place a higher weight on anecdotal, top-of-mind, or easily recalled data when making choices. In doing so, availability reduces our power to be fair-minded and equitable, because we end up dismissing other important evidence and missing the bigger picture. Availability can occur when individual or memorable anecdotes are prioritized in academic assessment, like overweighting a single experience or leaning too heavily on someone’s anecdotal recollection to inform a hiring decision. It can also lead to over-valuing recent data, like getting a well-known grant, instead of pursuing a fuller picture of scholarly productivity that would yield a more well-rounded decision.

    What can institutions do?

    Structured information gathering. These tendencies are more likely to occur when there’s no formal mechanism to gather data, increasing the likelihood individual memories or perceptions will dominate judgment and decision-making. The use of structured formats, like interview protocols and narrative format CVs, can keep decision-makers focused on agreed-upon qualities rather than on the vagaries of individual interactions and reflections and also ensure greater consistency of information across candidates.

    Force long-term thinking. Short-term thinking tends to come more naturally than planning for the future, which means that the attributes we consider important are often more oriented toward immediacy over the longer term. Explicitly articulating and considering longitudinal values and goals, in addition to short-term needs, can help decision-makers concretize the potential outcomes, both pro and con, of decisions. 

    Contextualizing narratives. Traditional CVs are not known for their ability to demonstrate the big picture. Asking applicants to provide supplemental narratives that highlight and articulate their most meaningful contributions can convert commonly used shortcut characteristics for quality and productivity into more human form. This can re-center the conversation around research impact that extends beyond citations and academic circles to include demonstrable real-world change and improved outcomes, and provide concrete definition to otherwise vague terms like “world-class” and “significant contribution.”

    In our final installment next week, we’ll call out how incumbent processes and perceptions have the advantage.

    To encourage the adoption of more equitable hiring, and RPT processes, the authors are collaborating on a series of tools for DORA to assist institutions in experimenting with new processes, indicators, and principles. Available here.


    We thank Stephen Curry for very helpful comments. We also thank Stephen, Olivia Rissland and Stuart King for and the accompanying briefing document on the DORA webpage. 

    The post Rethinking Research Assessment: Addressing Institutional Biases in Review, Promotion, and Tenure Decision-Making (part III) appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on October 12, 2020 02:37 PM.

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    Journal retracts paper claiming that group of Indigenous Americans were Black Africans

    A journal has retracted a paper on the origins of a group of Indigenous Americans after readers said the basis of the paper was long discredited. The paper, “Early pioneers of the americas: the role of the Olmecs in urban education and social studies curriculum,” was written by scholars at the University of North Carolina … Continue reading Journal retracts paper claiming that group of Indigenous Americans were Black Africans

    in Retraction watch on October 12, 2020 02:27 PM.

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    ‘Great Adaptations’ unravels mysteries of amazing animal abilities

    Great Adaptations
    Kenneth Catania
    Princeton Univ., $27.95

    Neurobiologist Kenneth Catania’s passion for scrutinizing odd animal adaptations all started with a creature with a 22-point star on its face.

    Catania first saw a star-nosed mole (Condylura cristata) in a children’s book. Later as a 10-year-old, he found a dead one near a stream close to his home in Columbia, Md. From then on, he kept his eyes peeled for more. He had to wait until he was in college, when he landed a research position that required him to trap star-nosed moles in Pennsylvania’s wetlands. At the time, no one knew what that unique nose was good for, and he wanted to figure it out.

    In Great Adaptations, Catania describes his pursuit of the mystery behind the mole’s wiggly star-shaped appendage (it helps the subterranean animal sense prey without using sight) as well as a slew of other animal tricks. The account of his adventures as a biological sleuth provides a detailed look at curiosities such as how “hangry” water shrews execute the fastest documented predatory attack by a mammal and how cockroaches resist becoming zombies during parasitoid wasp attacks (SN: 10/31/18).

    “It’s part of human nature to be intrigued by mysteries, but the mystery only gets us to the door,” he writes. “You never know what you might find on the other side.”

    In search of answers, Catania has set up some odd, but amusing, experiments. To film wasps attacking cockroaches, he built a set fit for a horror flick, by filling a tiny kitchen with warning signs and a plastic human skull for the wasp to store its zombified victim in. Keeping with the horror theme, he also stripped the paint off decorative severed zombie arms and offered the plastic limbs to electric eels (Electrophorus electricus) to show that the animals leap out of the water as an attack strategy (SN: 6/9/16).

    Each chapter follows a logical flow as Catania describes his discoveries, from what first piqued his interest in an animal to his ultimate findings. Science, however, is rarely as straightforward as he makes it seem. Catania’s scientific detective work didn’t always go off without a hitch, but, he notes, including all the failures would have meant a much longer book. Even so, the book alludes to some ideas that didn’t pan out. “The animals are always able to do something unexpected and more interesting than I’d imagined,” he writes.

    For instance, the notion that a tentacled snake (Erpeton tentaculatum) might use the short appendages close to itsmouth to lure in nearby fish, just like snapping turtles dowith their tongues, turned out to be wrong. Instead, the tentacleshelp a snake sense a fish’s position in the water andknow when to attack. What’s more, the snakes have hackedtheir prey’s natural escape reflexes. In a fatal mistake, fishflee in the wrong direction — straight toward a snake’smouth — when duped by a twitch of the snake’s neck rightbefore the predator strikes.

    Catania’s lighthearted yet informative narrative presents science in a way that’s easy for anyone with a basic knowledge of biology to understand. But even the most seasoned expert will likely learn new details, the type that never make it into a scientific paper. For a particularly daring experiment, in which Catania offered his own arm for an electric eel’s shock to measure the shock’s electricity, Catania admits that he certainly couldn’t subject another animal or a student volunteer to the unpleasant jolt (SN: 9/14/17). His own arm was the “obvious solution.”

    In page after page, Catania’s enthusiasm and awe for the animals shine through. When he discovered tentacled snakes are born knowing how to strike at prey rather than learning through failure, Catania recalls that he couldn’t “find enough superlatives to sum up these results.” He also describes a fight between a parasitoid wasp and a cockroach as an “insect rodeo.” The wasp attacks a cockroach’s head in an attempt to lay an egg, but in defense the roach “bucks, jumps, and flails with all its might.”

    Some of that enthusiasm will likely rub off on readers and spark a sense of wonder. Great Adaptations packs in plenty of astounding details about some remarkable creatures. As Catania puts it: “I’ve stopped assuming I know the limits of animal abilities.”

    Buy Great Adaptations from Amazon.com. Science News is a participant in the Amazon Services LLC Associates Program. Please see our FAQ for more details.

    in Science News on October 12, 2020 10:00 AM.

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    Researchers face disciplinary action as dozens of their studies fall under scrutiny

    A group of obstetrics researchers in the Middle East is facing disciplinary action after questions were raised about the validity of the data in dozens of their published studies.  The tale — involving contaminated clinical trials, potentially fabricated PhDs, findings of misconduct that went ignored, accusations of terrorist sympathies and unresponsive journals — requires some … Continue reading Researchers face disciplinary action as dozens of their studies fall under scrutiny

    in Retraction watch on October 12, 2020 10:00 AM.

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    Leaders Can Feel Licensed To Behave Badly When They Have Morally Upstanding Followers

    By Emma Young

    Countless studies have investigated how a leader’s behaviour influences their followers. There’s been very little work, though, on the reverse: how followers might influence their leaders. Now a new paper, published in the Journal of Applied Psychology, helps to plug that gap with an alarming finding: good, morally upstanding followers can create less ethical leaders.

    M. Ghufran Ahmad at the Lahore University of Management Sciences and colleagues ran a series of studies on participants in an executive training programme at a business school in Pakistan. All were senior or mid-level managers, from a variety of organisations. These, then, were the “leaders”. The people that they managed were the “followers”.

    In an initial study, the team found that the more a participant felt that their followers engaged in “organizational citizenship behaviour” (OCB) — such as going out of their way to be “good” to other employees — the more “moral credit” that leader felt they had personally accrued. The concept of moral credit relates to the theory that we each balance good and bad behaviours, to maintain a kind of moral equilibrium. A good deed ups our moral credit, while a bad one depletes that credit. While this phenomenon has been found for individuals, it’s thought to apply to groups, too: if one member behaves morally, others can feel licensed to behave less well.

    The team then ran follow-up online studies on fresh batches of participants. These revealed that when a leader was encouraged either to feel more narcissistic (in this case, more responsible for their group’s success) or to identify with their followers (by reflecting on characteristics that they shared with their group, for example), they were especially likely to feel that their own moral credit had risen as a result of good behaviour by their followers.

    These studies all involved experimental manipulations and vignettes, however. And they didn’t tackle the critical question: can vicarious moral credit free leaders to actually behave more badly?

    To get closer to a real-world scenario, the team ran a field study involving 250 managers, all again from the same course. These participants completed four online surveys over two days. They reported on follower OCBs, the extent to which they identified with their followers, their perceived levels of moral credit, levels of narcissism and also any unethical behaviour that they themselves engaged in — such as doing personal business on company time or passing blame for errors to an innocent coworker.

    The team found that these leaders were indeed more likely to behave badly when they felt themselves to be in moral credit as a result of good behaviour by their subordinates. Tallying with the earlier findings, this effect was especially strong when leaders were narcissistic and/or closely identified with their followers.

    “Across multiple studies, our findings indicate that follower OCB can provide leaders with moral credit to engage in subsequent unethical behaviour,” the team writes.

    If good teams can foster unethical behaviour among leaders, this insight is relevant to all kinds of organisations, not just businesses. It’s important, too, that leaders who felt closer to the people that they managed were even more susceptible to the effect. As the researchers write: “Our findings provide further support for the notion that close relationships between leaders and followers are not always a good thing”.

    There are a few caveats. One, the studies were all conducted in Pakistan, which, the team notes, is more collectivistic than the UK or US, for example. Similar studies in other countries will be needed to explore whether these findings hold in more individualistic cultures.

    Clearly much more work is needed to explore the extent to which leaders actually use moral credit to engage in bad deeds in the workplace, or at home, or elsewhere — and over what kind of timescales. Also, what might temper the effect? Are leaders who see themselves as “good people” less susceptible to it, perhaps? And how does each individual’s good or bad behaviour influence the others in the group? If we each have a moral equilibrium, an individual who performs a good deed will surely then feel licensed to behave less well themselves — but does the behaviour of their manager have any impact? There are all sorts of outstanding questions that new studies in this area will hopefully answer.

    Can good followers create unethical leaders? How follower citizenship leads to leader moral licensing and unethical behavior.

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

    in The British Psychological Society - Research Digest on October 12, 2020 08:48 AM.

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    Why open access is at the core of our publishing mission

    An Elsevier leader talks about how we’re expanding our support for open access and open science

    in Elsevier Connect on October 12, 2020 08:37 AM.

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    Sperm teleportation between Massimo Fioranelli and Alireza Sepehri

    "Even if we be under force and have to return to Galileo times, theories are going theirselves. [...] Describing some subjects for them is similar to speaking of flying with airplane for people around 1000 years ago. I don’t wonder if they kill us for these theories as in Galileo times." - Massimo Fioranelli, a looney

    in For Better Science on October 12, 2020 06:00 AM.

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    Weekend reads: A prominent journal goes wrong; medical journals and politics; a journal with an editorial board full of dead people

    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. The week at Retraction Watch featured: A retraction — and a lawsuit — for the “Prince … Continue reading Weekend reads: A prominent journal goes wrong; medical journals and politics; a journal with an editorial board full of dead people

    in Retraction watch on October 10, 2020 01:28 PM.

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    Fundamental constants place a new speed limit on sound

    Sound has a speed limit. Under normal circumstances, its waves can travel no faster than about 36 kilometers per second, physicists propose October 9 in Science Advances.

    Sound zips along at different rates in different materials — moving faster in water than in air for example. But under conditions found naturally on Earth, no material can host sound waves that outpace this ultimate limit, which is about 100 times the typical speed of sound traveling in air.

    The team’s reasoning rests on well-known equations of physics and mathematical relationships.  “Given the simplicity of the argument, it suggests that [the researchers] are putting their finger on something very deep,” says condensed matter physicist Kamran Behnia of École Supérieure de Physique et de Chimie Industrielles in Paris.

    The equation for the speed limit rests on fundamental constants, special numbers that rule the cosmos. One such number, the speed of light, sets the universe’s ultimate speed limit — nothing can go faster. Another, known as the fine-structure constant, determines the strength with which electrically charged particles push and pull one another. When combined in the right arrangement with another constant — the ratio of the masses of the proton and electron — these numbers yield sound’s speed limit.

    Sound waves, which consist of the vibrations of atoms or molecules, travel through a material as one particle jostles another. The wave’s speed depends on various factors, including the types of chemical bonds holding the material together and how massive its atoms are.

    None of the sound speeds previously measured in a variety of liquids and solids surpass the proposed limit, condensed matter physicist Kostya Trachenko and colleagues found. The fastest speed measured, in diamond, was only about half the theoretical maximum.  

    The limit applies only to solids and liquids at pressures typically found on Earth. At pressures millions of times that of Earth’s atmosphere, sound waves move faster and could surpass the limit.

    One material expected to boast a high sound speed exists only at such high pressures: hydrogen squeezed hard enough to turn into a solid metal (SN: 6/28/19). That metal has never been convincingly created, so the researchers calculated the expected speed instead of using a measurement. Above about 6 million times Earth’s atmospheric pressure, the sound speed limit would be broken, the calculations suggest.

    The role of the fundamental constants in sound’s maximum speed results from how the waves move through materials. Sound travels thanks to the electromagnetic interactions of neighboring atoms’ electrons, which is where the fine-structure constant comes into play. And the proton-electron mass ratio is important because, although the electrons are interacting, the nuclei of the atoms move as a result.

    The fine-structure constant and the proton-electron mass ratio are dimensionless constants, meaning there are no units attached to them (so their value does not depend on any particular system of units). Such dimensionless constants fascinate physicists, because the values are crucial to the existence of the universe as we know it (SN: 11/2/16). For example, if the fine-structure constant were significantly altered, stars, planets and life couldn’t have formed. But no one can explain why these all-important numbers have the values they do.

    “When I have sleepless nights, I sometimes think about this,” says Trachenko, of Queen Mary University of London. So he and colleagues are extending this puzzle from the cosmic realm to more commonplace concepts like the speed of sound. Trachenko and coauthor Vadim Veniaminovich Brazhkin of the Institute for High Pressure Physics, in Troitsk, Russia, also reported a minimum possible viscosity for liquids in the April 24 Science Advances.

    That viscosity limit depends on the Planck constant, a number at the heart of quantum mechanics, the math that governs physics on very small scales. If the Planck constant were 100 times larger, Trachenko says, “water would be like honey, and that probably would be the end of life because the processes in cells would not flow as efficiently.”

    in Science News on October 09, 2020 06:00 PM.

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    Heard about the study claiming men who carry guitar cases are more attractive? It’s been retracted.

    A controversial psychologist has lost a bizarre paper which claimed that men who carry guitar cases do better with the ladies. The article, which had appeared in the journal The Psychology of Music in 2014, was one of many papers by Nicholas Guéguen that have raised eyebrows among his peers and some data sleuths — … Continue reading Heard about the study claiming men who carry guitar cases are more attractive? It’s been retracted.

    in Retraction watch on October 09, 2020 05:17 PM.

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    Lawyer for researcher deposed in $112.5 million Duke case asks us to remove a post

    We receive occasional demand letters from attorneys here at Retraction Watch. Perhaps the most memorable was one in 2013 from an attorney claiming to represent Bharat Aggarwal. That prompted Popehat’s Ken White to enlarge our vocabulary by using the word “bumptious” in a post about the letter. To that library of letters we can now … Continue reading Lawyer for researcher deposed in $112.5 million Duke case asks us to remove a post

    in Retraction watch on October 09, 2020 10:00 AM.

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    Body Language And Spooky Science: The Week’s Best Psychology Links

    Our weekly round-up of the best psychology coverage from elsewhere on the web

    If you want to get on a cat’s good side, it’s worth mastering the art of the “slow blink”. Cats “smile” by blinking slowly, and now researchers have found that they respond positively to humans who do the same. Participants who performed a slow blink were more likely to receive one from their cat, reports Sara Rigby at BBC Science Focus. Cats were also more likely to approach an experimenter who had just slow-blinked. 

    The idea that people in big cities are less likely to help strangers seems to be a myth. Researchers conducted experiments across 24 UK towns and cities in which they planted “lost” letters and items, or attempted to cross the road. There was no link between population density and people’s willingness to help out by returning items or stopping to let the experimenter cross, reports Natalie Grover at The Guardian.

    Scared of ghosts? Maybe science can help put you at ease. At Popular Science, Jake Bittle looks at the various psychological and physiological mechanisms that can explain why people report seeing apparitions, from basic human suggestibility to the effects of psychedelic mould.

    If it feels like you are living in a political bubble, you’re not alone: a recent survey found that 40% of Americans don’t have a close friend who is voting for a presidential candidate other than the one they prefer. At The Conversation, Melanie Green argues that social media is partly to blame for this polarisation, as is the increasing tendency to tie our individual identity to our political views.

    It’s probably unsurprising to learn that many of us have reported feeling deprived of touch during lockdown. At BBC Future, Claudia Hammond takes a look at the studies that have explored the importance of human touch to our wellbeing, both before and during the pandemic. And don’t forget to check out our recent podcast on staying connected in the “new normal”.

    How much can we really learn about someone’s internal states based on their body language? There’s a small industry of analysts who claim to be able to understand how a person is thinking or feeling based on specific gestures. But psychologists are sceptical, writes Ramin Skibba at Undark.

    Apes engage in “playful teasing” just like human toddlers, responding to requests in bizarre ways or playing silly games. At Science, Lucy Hicks talks to anthropologist Erica Cartmill about the implications of this behaviour for understanding the evolutionary history of humour

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

    in The British Psychological Society - Research Digest on October 09, 2020 09:50 AM.

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    Kumsal Bayazit at EU Gender in Science Symposium: “ We must make progress across all dimensions of diversity.”

    Elsevier CEO stresses inclusion, diversity and intersectionality in keynote at EU Gender in Science Symposium

    in Elsevier Connect on October 09, 2020 09:14 AM.

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    30 years later, physics journal retracts paper that blamed feminism for many of society’s ills

    For those of you who think that critiques of feminism have no place in journals about physics, the Canadian Journal of Physics agrees. But it took them 30 years to get there.  The journal has retracted a 1990 article by a notorious male chauvinist who claimed, among other things, that feminism was responsible for an … Continue reading 30 years later, physics journal retracts paper that blamed feminism for many of society’s ills

    in Retraction watch on October 08, 2020 08:06 PM.

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    Science retracts paper as authors blame pandemic for image issues

    Science has retracted a paper it published in July by a group of authors in China over concerns about two images in the article — problems the researchers have attributed to chaos in their group due to the COVID-19 pandemic. The paper, “Proton transport enabled by a field-induced metallic state in a semiconductor heterostructure,” was … Continue reading Science retracts paper as authors blame pandemic for image issues

    in Retraction watch on October 08, 2020 05:52 PM.

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    Getting real about kidney transplant timelines

    Getty images

    One of the biggest aspects in taking care of patients with advanced chronic kidney disease is planning for future renal replacement needs, either dialysis or transplant options. The benefits of transplantation over dialysis are widely accepted and if someone is a medically cleared, they should be encouraged to pursue transplantation. Dialysis counseling and education is individualized for patients depending on their other medical conditions, support systems, and transplant candidacy.   For those patients that are cleared medically and have potential live donors, discussions about home dialysis training and permanent dialysis access are curtailed. The assumption that the time on dialysis will be short and therefore effort towards arteriovenous access creation or home dialysis training seems wasted. But is the wait time really that short?

    This week in BMC Nephrology, Dr. Slyvestre et al. report on 9300 incident dialysis patients listed and cleared for transplantation, and highlight the potential complications of catheter procedures or infections and associated increased risk of death during the wait time. Most striking was the median time to transplantation for both deceased donor recipients of 15 months and 9 months for those with live donors.

    The potential year on dialysis therapy, even with potential donors, raises a few questions for nephrologists. Are we adequately preparing patients for that time on dialysis while they are waiting for workup and the potential delays? Should we be looking at the home dialysis options more? Are we putting patients at risk of a tunneled dialysis catheter infection that could have more significant complications such as disseminated infection requiring prolonged antibiotics or delay their surgery. The wait times also suggest perhaps a closer look at the process of workup for donors to see if there are ways to streamline.

    Are we putting patients at risk of a tunneled dialysis catheter infection that could have more significant complications

    Having a discussion with the patient’s transplant team to get a realistic time frame for the live donor surgery is going to be an important part of the decision making process. It will be a very different approach if a patient has a surgical date in 2 months versus a patient who has a potential donor but it is very early in the process. On the flip side, it would be important to share the information with patients so they are not getting discouraged with the wait times. Additionally, the decisions that they will make about dialysis options would be more informed.

    This need is further amplified against the backdrop of the COVID-19 pandemic and it’s impact on transplantation. While healthcare systems around the world were overwhelmed by the influx of cases, there was a need to pause on “elective” procedures. Kidney transplantation rates fell as providers scrambled to balance the risk of immunosuppression and the risk of infection from COVID-19. The transplant evaluation process is further slowed by the inability to do in person visits for a multi-disclipinary team evaluation and delays in necessary testing for medical clearance as routine testing for things like mammograms and colonoscopy were on hold. Transplant centers are actively surveilling local rates of infections and mortality rates from COVID-19 and modifying evaluation and listing processes based on the resources available.

    While there is desire to move forward with transplantation, it needs to be done in a way to maintain the safety of donors and recipients. Nephrologists need to recognize the fluid nature of the transplantation process and help guide their patients through this process.

    The post Getting real about kidney transplant timelines appeared first on BMC Series blog.

    in BMC Series blog on October 08, 2020 04:10 PM.

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    New arXivLabs feature provides instant access to code

    Today, arXivLabs launched a new Code tab, a shortcut linking Machine Learning articles with their associated code. arXivLabs provides a conduit for collaboration that invites community participation while allowing arXiv developers to focus on core services. This Code feature was developed by Papers with Code, a free resource for researchers and practitioners to find and follow the latest Machine Learning papers and code.

    When a reader activates the Code tool on the arXiv abstract record page, the author’s implementation of the code will be displayed in the tab, if available, as well as links to any community implementations. This instant access allows researchers to use and build upon the work quickly and easily, increasing code accessibility and accelerating the speed of research.

    Screenshot of abstract page with code tab highlightedUnder the abstract on an arXiv record page, you can now find code.


    Authors can also directly link code to their arXiv papers directly from their arXiv user page by clicking on the PwC icon next to the paper title. From there they will be directed to Papers with Code where they can add their code. Once an official implementation is added, the official code section will show up on the arXiv abstract page. From the Papers with Code site, researchers can also explore similar methods to determine which might suit their purposes best.

    screenshot of arXiv user page, with links to Papers with Code next to each paperarXiv user page, with links to Papers with Code next to each paper


    arXiv values openness, community, and the privacy of user data and will only work with partners that abide by the same principles. All data on Papers with Code is freely available and is licensed under CC-BY-SA. Like all third party collaborators, Papers with Code will only have access to minimal and anonymized data about arXiv users, and only for the purpose of ensuring the correct functioning of the arXivLabs features. Any other use not included in a written consent from arXiv is strictly prohibited. Upon user request this data, and another other data connected to the user can be permanently deleted. PwC also developed arXiv’s new classifier tool.

    arXiv thrives on collaboration and encourages everyone to submit ideas for enhancing arXiv at nextgen@arxiv.org.


    in arXiv.org blog on October 08, 2020 02:42 PM.

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    Phone Calls Help Create Closer Bonds Than Texting

    By Emily Reynolds

    For its many flaws, it’s hard to deny that technology has improved our ability to communicate with one another. We now have a huge range of options when it comes to speaking to our friends and family, whether we’re texting, IMing, or sending them emails.

    With such a smorgasbord of choices available to us, it can be easy to forget the humble phone call. And according to new work published in the Journal of Experimental Psychology: General, a reticence to pick up the phone might also be robbing us of stronger connections with those we love.

    In their first study, Amit Kumar from the University of Texas at Austin and Nicholas Epley from the University of Chicago looked at the experience of reconnecting with an old friend. Participants were first asked to think of someone they had fallen out of touch with, stating how long it had been since they interacted and rating the current closeness of their relationship.

    Participants then imagined reconnecting with their old friend, and were asked whether they would prefer to contact them by phone or email and how they felt the interaction would go. They were then randomly assigned to actually connect with the friend either via email or by phone over the next week.

    Even though the majority of participants believed they would form a stronger bond over the phone than via email, 67% stated they would prefer to get in touch by email (a number that rose to 72% among participants who successfully completed the full experiment). This may be because of perceived awkwardness: the majority also felt that a phone call would be more awkward. Of the participants who managed to get in touch with an old friend, those assigned to the phone condition reported feeling a significantly stronger bond than those assigned to the email condition — and in the end felt no more awkward.

    The next study looked at new friends. Participants were put into pairs and assigned to one of three groups — text chat, audio chat, or video chat. To get close to their new friend, participants interacted via a “sharing game”, in which both parties ask and answer intimate questions (e.g. “can you describe a time you cried in front of another person?”). Before completing the tasks, participants predicted how well they would get to know their partner, how much they would enjoy the conversation, how strong a bond it would foster, and how awkward it would be to chat.

    Although participants did not expect different outcomes across the different forms of communication, they again felt more connected with their partner via voice-based media than when simply using text. Participants anticipated awkwardness across all three categories (which may be more to do with the very intimate and unusual task than with specific communication methods themselves), though those expectations were unfounded.

    In a final study, participants were again asked to imagine reconnecting with an old friend, rating how connected or awkward they expected to feel over email or phone and indicating their preferred method on a seven-point scale. The results suggested that expectations are a key driver of our choices — the more participants expected to feel connected via phone or email, the more they preferred to communicate in that form, and the more awkward they anticipated feeling the more likely they were to avoid that method.

    The study suggests that worries about negative interactions could make people avoid potentially meaningful phone chats. But it doesn’t explain why calls are apparently so powerful. What is it about voice-based chats that make them so fulfilling? And do new forms of communication such as voice notes — voice recordings almost like voicemail — have the same effect? It would be worth exploring whether this kind of asynchronous communication has similar benefits to real-time audio and video calls.

    There are plenty of jokes and memes about younger generations hating voice calls, and consumer research has suggested that many of us do indeed use our devices for everything other than speaking on the phone. The idea that people (sometimes incorrectly) anticipate awkwardness is not too much of a reach and is backed up by findings from this paper.

    But there are likely to be some individual differences here which haven’t been fully explored. A voice note might allow someone who’s shy and really does hate phone calls to communicate within their boundaries. For others, instant messaging might make them feel more present in their loved ones’ daily lives. And a long email back-and-forth might take the pressure off needing to reply instantly and give time to engage more deeply, potentially fostering a more philosophical bent to a conversation. Personality and context surely has a role to play here — and might make interesting grounds for future research into the nuances of digital communication.

    It’s Surprisingly Nice to Hear You: Misunderstanding the Impact of Communication Media Can Lead to Suboptimal Choices of How to Connect With Others

    Emily Reynolds is a staff writer at BPS Research Digest

    in The British Psychological Society - Research Digest on October 08, 2020 01:32 PM.

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    Honoring the 2020 Nobel Laureates with free access to their research

    Read the Nobel Prize winners’ most relevant papers published by Elsevier, as we celebrate their achievements in science

    in Elsevier Connect on October 08, 2020 01:17 PM.

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    Journal retracts plant paper because authors plagiarized from a garden site — and several papers

    A Springer Nature journal has retracted a paper it published in July after learning that the authors manipulated and plagiarized images galore.  The paper, “Novel green synthesis and antioxidant, cytotoxicity, antimicrobial, antidiabetic, anticholinergics, and wound healing properties of cobalt nanoparticles containing Ziziphora clinopodioides Lam leaves extract,” appeared in Scientific Reports. Its authors were affiliated with … Continue reading Journal retracts plant paper because authors plagiarized from a garden site — and several papers

    in Retraction watch on October 08, 2020 10:54 AM.

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    Gruesome Descriptions Can Make Crimes Seem Worse — But Judges And Lawyers Are Immune To This Bias

    By Matthew Warren

    We often like to think of ourselves as impartial decision-makers — but of course, nothing could be further from the truth. Our day-to-day thoughts and behaviours are biased in all kinds of ways. But is the same true for people in the legal profession, which prides itself on its supposed objectivity and fairness?

    According to a new study in Humanities and Social Sciences Communications, judges and lawyers may be immune to at least some of the biases that affect the rest of us. In particular, their judgements seem less prone to the biasing effects of emotive language.

    Sandra Baez from Universidad de los Andes in Colombia and colleagues recruited 45 judges, 60 attorneys, and 64 control participants with no experience in law. All participants read a series of 24 scenarios in which someone inflicts harm on a victim, causing damage to property, injury, or death. In half of the scenarios the harm was accidental (e.g. the protagonist kills someone with his car after his brakes fail) and in half it was intentional (e.g. the protagonist speeds up to kill someone after seeing them on the road).

    Half of the participants were given descriptions in plain language, in which the basic facts were laid out. In the car scenario, for example, they were told that the victim lies on the ground and eventually dies. But the other half were given gruesome descriptions, with graphic details about what exactly happened to the victim as they died.

    After reading each scenario, the participants rated the morality of the protagonist’s actions, the severity of harm caused to the victim, and the amount of punishment they felt that the protagonist deserved.

    Overall, participants rated intentional harms as morally worse than accidental ones. But the language used was also important. Control participants who read scenarios framed in gruesome language rated them as more morally wrong that those who read plain language. For judges and attorneys, however, the kind of language used didn’t make a difference. This suggests that emotional language can bias people towards making more severe judgments, at least when it comes to judging morality. But legal professionals seem to be immune to this bias.

    In a subset of participants, the authors also found that changes in heart rate variability — a physiological measure of emotional arousal — were related to people’s moral judgement ratings when reading gruesome descriptions. But, again, this was only true for control participants. So it seems that gruesome language might provoke emotional physiological reactions which lay people use to guide their moral judgements, but which legal professionals have learned to ignore.

    All three groups of participants also rated intentional harms as more severe, and assigned harsher punishments for them, than those caused by accident. But judges and attorneys rated accidental harms as less severe and assigned a less harsh punishment for them than did controls. These results imply that those in the legal profession may also be better able to focus on a perpetrator’s intentions when harms are caused accidentally, and so take this into account when making decisions about punishment.

    It’s not all good news: lawyers and judges still rated harms as more severe when caused on purpose than by accident, even though the “objective” amount of harm — e.g. damage to property — was exactly the same in both conditions. The authors say that this is an example of the “harm magnification effect”, in which people overestimate harms that are caused intentionally. This could lead to inflated legal sentences in some cases, they add.

    And of course, we already know judges are prone to other biases: they may impose stricter punishments on BAME defendants, for instance, and can be swayed by neuroscientific explanations of a defendant’s behaviour. Still, it seems that legal professionals’ training and expertise mitigates at least some human biases in decision-making.

    The impact of legal expertise on moral decision-making biases

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

    in The British Psychological Society - Research Digest on October 07, 2020 11:22 AM.

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    4 ways we can support racial equality as publishers

    Elsevier colleagues talk about steps they have taken to become more ethnically inclusive – in webinar with Copyright Clearance Center

    in Elsevier Connect on October 07, 2020 11:03 AM.

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    Using agile technology to accelerate Covid research publication

    Elsevier colleagues in technology, data science and operations worked together to speed up the submissions process for COVID-19 papers

    in Elsevier Connect on October 07, 2020 10:36 AM.

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    Elsevier journal disavows, but does not retract, paper on intelligent design

    An Elsevier journal has disavowed, but not yet retracted, a paper creationists are calling a “a big deal for the mainstreaming” of intelligent design.  The article, “Using statistical methods to model the fine-tuning of molecular machines and systems,” appeared in the September issue of the Journal of Theoretical Biology, but has been online since June. … Continue reading Elsevier journal disavows, but does not retract, paper on intelligent design

    in Retraction watch on October 07, 2020 10:00 AM.

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    Gregg Semenza: real Nobel Prize and unreal research data

    "Even after people have been telling you for, you know, 20 years or more that it’s going to happen, no one expects it." -Gregg Semenza, Nobel Prize winner 2019

    in For Better Science on October 07, 2020 09:47 AM.

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    Seeing Red Or Feeling Blue? People Around The World Make Similar Associations Between Colours And Emotions

    By Emma Young

    As an English-speaker, I might “see red” with anger, go “green” with envy or, on a bad day, “feel blue”. To me, it seems natural to associate certain colours with particular emotions — but is the same true for people around the world? And if so, do we all make the same emotion/colour matchings? These questions have been investigated in a new study, published in Psychological Science, which has produced some fascinating results.

    An international team of 36 researchers, led by Domicele Jonauskaite at the University of Lausanne, analysed data gathered through the ongoing online International Colour-Emotion Association survey. A total of 4,598 adults from 30 different nations on six continents used an emotion “wheel” to report their perceptions of associations between 12 different colour terms and the 20 discrete emotions marked in “spokes” on that wheel. They could match each colour term to as many emotions as they liked, or to none, and also indicate the intensity of each emotion that they associated with a colour.

    The team found that all of the nationalities in the study did indeed match colours to emotions. “The cross-modal association of colour with emotion is a universal phenomenon,” they conclude. What’s more, there were clear global similarities across the matches. Participants tended to link black with sadness, fear and/or hate; red with love and/or anger; pink with love, joy and/or pleasure; grey with sadness and/or disappointment; yellow with joy; orange with amusement; and white with relief. Across all countries, black and red were the colours most likely to be associated with emotions of any kind, while brown was the least likely. When a colour was matched to a particular emotion, the emotional intensity ratings from the various nationalities were similar.

    However, some intriguing differences between nations also emerged. For example, Nigerians associated red with fear as well as love and anger; Chinese people associated white with sadness as well as relief; unlike other nationalities, Egyptians did not associate joy and other positive emotions with yellow; and Greeks associated purple with sadness, whereas other nationalities tended to associate purple with positive emotions.

    So what explains the commonalities in responses, and also the differences?

    Some apparently universal emotion-colour links might stem from common physiological responses to different prompts. For example, a threat that we are determined to counter is associated with both a rush of blood to the face and with feelings of anger. This could, then, explain the global tendency to match red and anger.

    In some cases, the reasons for discrepancies are pretty clear, too. While English people, for example, traditionally wear black to funerals, white is usually worn in China, and, the researchers note, Greek people occasionally wear darker shades of purple while in mourning.

    The team also found that the closer one nation was to another, either geographically or in terms of linguistic similarity, the more similar their colour-emotion matches were likely to be. Cultural and/or linguistic differences in how colour terms are understood or used across nations could then account for the variations in matches seen between countries, the team writes.

    However, differences in physical environments could have an influence too. For example, the team’s own recent work on people from 55 nations revealed that exposure to sunshine affects the degree to which yellow is matched with joy — specifically, yellow was perceived as being more joyful in colder and rainier countries.

    A few other interesting findings came out of the team’s new analyses. Of the nationalities included in the study, people from Finland, Lithuania and New Zealand made the most colour-emotion term matches, while people from Azerbaijan and Egypt made the fewest. (Why? The team don’t know). Also, men and women made the same associations.

    There are a few limitations with the study, however. One obvious one is that the participants were all computer-literate. Perhaps they had been exposed via the internet to colour-emotion matches common in other countries and languages, and this could have helped to drive global similarities between the responses.

    Still, as the team concludes: “Given our current knowledge, we suggest that colour-emotion associations represent a human psychological universal that likely contributes to shared communication and comprehension. Thus, the next time you feel blue or see red, know that the world is with you.”

    Universal Patterns in Color-Emotion Associations Are Further Shaped by Linguistic and Geographic Proximity

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

    in The British Psychological Society - Research Digest on October 06, 2020 02:16 PM.

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    Elsevier scientist builds model to predict COVID-19 severity in veterans

    For US government challenge, teams used AI to build models that predict the severity of COVID-19

    in Elsevier Connect on October 06, 2020 12:25 PM.

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    Swiss € 57 million Elsevier deal: A first critical evaluation after 8 months (14 August)

    Particularly disturbing is the fact that a 4-year contract was signed right away. Why not start with a 1-2 year contract in order to gain experience and to be able to correct any undesirable developments, like those which now come apparent? Now, swissuniversities has given up all its trump cards for four years and may soon have to advertise hybrid OA Elsevier if the publication volume does not develop as anticipated. It would actually be desirable if fewer Swiss authors were to publish in hybrid journals from Elsevier, but in genuine Open Access journals. The signal that this agreement sends out to genuine Gold Open Access publishers is also fatal. Without a public call for tenders, Elsevier has been awarded a mega-contract, while those publishers who have actually been striving for OA for years and can deliver it more cheaply will be left out in the cold. With a PAR fee of over 4500 EUR, the price level is already extremely high, which once again shows that OA in Switzerland does not fail because of the lack of money. The money has now been used to buy 30% OA from Elsevier. But for the 100% that swissuniversities wants to achieve by 2024, a lot still has to happen.

    in Open Access Tracking Project: news on October 06, 2020 11:14 AM.

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    ‘Prince of panspermia’ has a paper retracted, and sues Springer Nature

    A neuroscientist once dubbed the “prince of panspermia” has lost a 2019 paper claiming that Venus may hold life seeded from Earth.  The paper, titled “Life on Venus and the interplanetary transfer of biota from Earth,” was written by Rhawn Gabriel Joseph, whose affiliations have included outfits called Astrobiology Associates of Northern California San Francisco … Continue reading ‘Prince of panspermia’ has a paper retracted, and sues Springer Nature

    in Retraction watch on October 06, 2020 10:00 AM.

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    The secret COVID-19 cure of Pasteur Lille

    There is a miracle drug for COVID-19, but it is secret. Enterprising researchers at Institute Pasteur in Lille ask for €5 million.

    in For Better Science on October 06, 2020 08:57 AM.

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    Rethinking Research Assessment: Addressing Institutional Biases in Review, Promotion, and Tenure Decision-Making (part II)

    Authors: Ruth Schmidt is an Associate Professor at IIT’s Institute of Design and Anna Hatch is the program director for DORA. PLOS supports DORA financially via organizational membership, and PLOS is represented on the steering committee of DORA.

    In part one of our series on institutional biases in review, promotion, and tenure decision making we showed how objective comparisons are not equitable. In our second part of this series we’ll show how individual data points can accidentally distract from the whole.

    Some pieces of data, such as the reputation of an applicant’s mentor or institution, or publishing in highly respected journals, are “shinier” than others. This can give initial or exceptional data points and personal reference points more perceived importance than they warrant, and privilege them over other available information.

    The notion of anchoring, described in our first post, can keep us from more even-handed or equitable judgments about data points due to the fact that we are typically heavily swayed by initial pieces of data. In a personal context, for example, when the first item on a menu is $15, other offerings that cost $12-13 seem like a pretty good deal. If, by contrast, the first item is $7, that $13 item is likely to feel comparatively overpriced. An academic version of this can occur when the first person to interview for a position sets the bar — for better or worse — for others who interview after them. Just as we can’t ever truly “unhear” something once we’ve heard it, initial anchors for value persist longer than we might expect, and tend to impact our perception of the information that follows.

    An additional factor that can compromise our ability to accurately gauge data points is the Halo effect, in which positive impressions of individual attributes influence our overall opinions of people or products; for example, a candidate from a prestigious institution may be assumed to have more potential than one from a lesser known university. But giving preferential treatment to people based on attributes they inherited, or which signify a small component of their overall value, may also reinforce inequitable norms by using current hierarchies as a stand-in for more thoughtful deliberation. This keeps us from considering otherwise worthy candidates or considering individuals against equal criteria.

    What can institutions do?

    Create intentional diversity: The halo effect and anchoring can be amplified when the definition of what is valuable in academic assessment is implicit and goes unquestioned. Assembling diverse teams — across gender, seniority, cultures, and under-represented minoritized populations — brings a range of perspectives and experiences into decisions, which forces us to interrogate our own assumptions about value and quality.

    Question institutional norms: Becoming more institutionally open-minded can be challenging when everyone is steeped in the same environment and set of processes. Looking outside your individual institution or discipline can provide a reality check on processes, and also broaden a sense of what’s “normal,” or even possible.

    First things last: Academics are traditionally used to seeing classic “halo” data — schools, affiliations, and publications — early and prominently in review, promotion, and tenure materials or dossiers. Placing reputation-based indicators at the end of applicant materials can reduce preconceived notions or premature perceptions of quality.
    To encourage the adoption of more equitable hiring, and RPT processes, the authors are collaborating on a series of tools for DORA to assist institutions in experimenting with new processes, indicators, and principles. Available here.

    We thank Stephen Curry for very helpful comments. We also thank Stephen, Olivia Rissland and Stuart King for and the accompanying briefing document on the DORA webpage.

    The post Rethinking Research Assessment: Addressing Institutional Biases in Review, Promotion, and Tenure Decision-Making (part II) appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on October 05, 2020 02:54 PM.

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    Almond, no joy: Plant geneticist in Iran up to at least six retractions

    A plant geneticist in Iran is up to at least six retractions for misuse of figures and other material from previously published papers.  The newest retraction involves a 2017 paper in Scientific Reports, a Springer Nature publication, titled “Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of … Continue reading Almond, no joy: Plant geneticist in Iran up to at least six retractions

    in Retraction watch on October 05, 2020 11:42 AM.

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    People Who Want To Be More Empathic May Also Develop “Liberal” Moral Values

    By Emily Reynolds

    No matter how happy you are in yourself, there’s probably something about your personality you’d like to change. Maybe you feel you’re too uptight or want to be more outgoing, or perhaps you’d like to be less moody or more tolerant of other people’s shortcomings.

    It’s likely that such a change in personality will have some kind of social consequence, whether that’s in your relationship with your spouse or your ability to get on with your colleagues. But it might also affect which moral values you hold important.

    That’s what Ivar R. Hannikainen and colleagues suggest in a new paper in the Journal of Research in Personality. They found that growth in one area, empathy, was associated with a shift in moral foundations to a more classically “liberal” style of morality.

    The study took place over fifteen weeks, with 414 participants answering weekly “waves” of questions. First, they filled in measures exploring two facets of empathy: empathic concern and perspective-taking. Empathic concern reflects someone’s reaction to suffering (e.g. “I often have tender feelings for people less fortunate than me”), while perspective-taking looks at their tendency to take other points of view (e.g. “I try to understand my friends better by imagining how things look from their perspective”).

    Participants also filled in a questionnaire looking at five “moral foundations”, or fairly broad moral values which people may prioritise in different ways. These consisted of care, fairness, loyalty to one’s ingroup, respect for authority, and observance of “purity” (for instance, keeping sexual impulses in check).

    Both of these sets of questions were repeated throughout the fifteen weeks of the study. During the first wave only, participants were also asked about their desire to change empathic concern and perspective-taking — “I want to have tender feelings towards people less fortunate than me”, for example. Demographic data, including political orientation, was also measured.

    As in previous work, moral foundations were linked to political orientation: liberals were more concerned with the values of fairness and care than conservatives, who identified more closely with statements related to purity, authority and loyalty.

    But what of empathy change? The results suggested that people can increase their levels of both empathic concern and perspective-taking: participants who had more of a desire to grow in both areas indeed saw increasing scores over the fifteen weeks. These goals also had an impact on moral foundations: those who expressed a desire to become more empathic also increased in the areas more closely linked to liberalism (fairness and care) and decreased on those areas related to conservatism (purity, authority and loyalty). Those who reported an actual increase in either facet of empathy also increased in fairness and care (though they didn’t decline in purity, authority and loyalty).

    The fact that participants saw an increase in their levels of empathy seems like positive news. But whether they were actually more empathetic and able to take others’ perspectives is hard to say considering the study relied on self-reporting. Combining self-reports with observer data may improve the validity of the findings. And although the increase in empathy was associated with a more “liberal” pattern of moral values, it’s unclear whether people’s political views actually changed (indeed, conservatives would likely argue that fairness and care are not purely liberal qualities).

    Why might an increase in empathy see your moral foundations change? Co-author William Chopik argues that it may be to do with opening yourself up to other arguments. “Being a better perspective-taker exposes you to all sorts of new ideas, so it makes sense that it would change someone,” he said. “When you become more empathic, it opens up a lot of doors to change humans in other ways, including how they think about morality and ideology – which may or may not have been intended.”

    Moral migration: Desires to become more empathic predict changes in moral foundations

    Emily Reynolds is a staff writer at BPS Research Digest

    in The British Psychological Society - Research Digest on October 05, 2020 10:55 AM.

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    Dirty diseased Neanderthals

    Who brought us COVID-19? The Neanderthals. The susceptibility to the SARS-CoV2 coronavirus, but also to diabetes, obesity, allergies, skin diseases, smoking and autism all happened because your great-[...]-great-grandfather could not keep his todger in his trousers many thousands of years ago.

    in For Better Science on October 05, 2020 06:05 AM.

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    New classifier adds transparency to arXiv submission process

    arXiv’s classification tool is now based on an algorithm developed by Papers with Code. Like the previous classifier, this one helps place research articles in proper categories. This process is vitally important because proper categorization helps readers find the information they seek — and assures authors that their work will be found by the right audience.

    The arXiv author experience will remain the same during the article submission process. The classifier automatically uses the title and abstract of a submitted article as input. Then, a machine learning model matches the research article to existing arXiv categories. If the model finds a match with a category different from the author selected category, a new recommendation will be proposed. Authors can either accept the new category recommendation or ignore it.

    The new arXiv classifier code is publicly available on github, and this transparency is one key difference between the new classifier and its predecessor. arXiv values openness, and providing the machine learning methodology that underlies the classifier ensures that anyone can use and build upon it. arXiv only collaborates with partners that share arXiv’s values of openness, community, excellence, and user data privacy.

    The developers, who are avid arXiv readers and authors, offered their expertise to help arXiv improve the user experience. They experimented with several approaches and ended up using two open source models, ULMFiT and fastText, trained on over 1.6 million abstracts and 120 thousand full text articles, respectively. Combined with a standard method that stratifies the data to address large category imbalance, this approach ensures that the new classifier proposes appropriate categories.

    arXiv continues to explore new and innovative ways to categorize articles and input from the community is welcome.


    in arXiv.org blog on October 05, 2020 05:00 AM.

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    Weekend reads: ‘Unicorn poo’ and other fraudulent COVID-19 treatments; disgraced researchers and drug company payouts; a fictional account of real fraud

    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. The week at Retraction Watch featured: Two retractions of an Oxford lab’s papers from a major … Continue reading Weekend reads: ‘Unicorn poo’ and other fraudulent COVID-19 treatments; disgraced researchers and drug company payouts; a fictional account of real fraud

    in Retraction watch on October 03, 2020 01:54 PM.

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    Conspiracy Theories And Winter Wellbeing: The Week’s Best Psychology Links

    Our weekly round-up of the best psychology coverage from elsewhere on the web

    Displaying empathy towards others seems like an obvious virtue — but it can have a dark side, writes Richard Fisher at BBC Future. Empathising with a single, identifiable individual can divert time and money away from causes that could benefit many more people, for instance. And bad actors can harness our tendency to empathise with those who are similar to us in order to get us to act aggressively towards the out-group.

    We often think of punishment as a tool to exact revenge on those who have wronged us. But this can’t be the whole story, because we also punish those who haven’t directly caused harm, but who have not distributed resources fairly, write researchers Paul Deutchman and Katherine McAuliffe at The Conversation. The pair suggests that punishment was used by our ancestors not only to deter bad behaviour, but also to level the playing field .

    When there is stigma surrounding a disease, it can make it harder to bring it under control — and Covid-19 is no different. At Science, Vaishnavi Chandrashekhar examines the history of health-related stigma and its relationship with racism and prejudice, and looks at how stigma has hampered public health efforts during the current pandemic.

    A recent Pew survey of 20 countries around the world has found that, in general, people are pretty trusting of scientists. But the survey also revealed some interesting trends: in English-speaking countries, for instance, conservatives were far less trusting of scientists than liberals. John Timmer has the details at Ars Technica.

    What kind of person is prone to believing conspiracy theories? Benedict Carey takes a look at The New York Times.

    And while we’re on the subject, Neuroskeptic covers a particularly strange conspiracy theory at Discover Magazine. It involves the pineal gland, a region of the brain which has somehow become the subject of all kinds of bizarre beliefs over recent decades.  

    Finally, as it gets colder and the days draw in, we could perhaps learn something from a study of Norwegians living in the Arctic Circle. Residents of Tromsø who viewed winter as a season to enjoy had better wellbeing than those who saw it as a boring or limiting time of the year. This suggests that developing a positive “winter mindset” could help you get through the coming dark months, writes David Robson at The Guardian.

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

    in The British Psychological Society - Research Digest on October 02, 2020 02:57 PM.

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    Duo that used legal threats to force scientists to pay for a tool face off in court

    Steven Trubow and Donald Morisky made a small fortune through a controversial company that licensed, often at what researchers thought were exorbitant rates, a tool to scientists, wielding the cudgel of costly legal action if they balked at payment.  Now, in what critics of the pair will doubtless find a delicious irony, the pair is … Continue reading Duo that used legal threats to force scientists to pay for a tool face off in court

    in Retraction watch on October 02, 2020 10:00 AM.

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    The power and weakness of data and modeling in COVID-19

    3 key takeaways from a webinar on using data science to fight COVID-19 and mitigate future health crises

    in Elsevier Connect on October 02, 2020 08:56 AM.

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    Here’s How The Experience Of Regret Develops Through Childhood

    By Emma Young

    Edith Piaf famously regretted nothing. But regret is an important emotion, because it can lead us to avoid repeating mistakes, or to heal damaged relationships. It’s also an emotion that many of us feel on a regular basis. “Regret is ubiquitous and powerful,” write Teresa McCormack at Queen’s University Belfast and colleagues in a new paper published in Current Directions in Psychological Science. “It is one of the most frequently mentioned emotions in conversation and affects a huge variety of everyday choices.”

    Though there’s been plenty of work on regret in adults, much less is known about how it develops in children. In this new review, McCormack and her colleagues consider what we do know about its development, and outline the major gaps still left to fill. There are implications not just for the basic understanding of regret but also for informing educators in nurseries and schools. After all, even young children are expected to feel bad about harming others — but, depending on their age, there are limits to just what they can feel in such a scenario.

    Research suggests that by the time they are six years old, most children are able to feel at least some sense of regret. In their own work, the team has found that children are more “sad” when they take a risk and it doesn’t pay off. (In this case, 6- and 7-year-olds had to choose between a “safe” box, which gave them an equal chance of winning either 7 or 10 tokens to put towards a prize, or a “risky” box, which gave them an equal chance of winning 16 tokens or only one.) The team also found that children who experienced most regret were most likely to go for a safer option the following day — so regret did affect their decision-making. 

    Follow-up work on the same age group revealed that a sense of regret can also encourage children to wait longer for a bigger reward. This is significant because, as the authors write: “‘Hot’ emotional responses are sometimes portrayed as being something that ‘cold’ cognition needs to overcome for delaying gratification”. But the results show that regret, which is of course an emotion, can itself drive a child’s decision to delay gratification.  This suggests, then, that it’s sensible to let children make their own mistakes (at least, when the outcome is not significantly harmful). Warning words from a sensible adult may not be as effective at directing wise decision-making as “hot” regret.

    For adults, regret can stem not just from a sense of having made the “wrong” decision but a feeling of having missed an opportunity. It seems that this type of regret doesn’t emerge until about the age of 8 — and even then it matures slowly. Even adolescents aren’t as responsive to this type as regret as adults. It’s possible that they can’t anticipate regret as well as adults can, either. Research on younger children finds that though most 6-year-olds can feel regret, they can’t reliably predict that they will feel regret in one particular future scenario, compared with another.

    Exactly when this ability emerges is still unclear — but, as the researchers point out, if an adolescent has a still only partially developed ability to anticipate regret, they may make risky decisions, such as not using contraception.

    Adults can of course feel regret not just in relation to ourselves, but also in relation to our behaviour towards other people. We might regret not being more gracious about an unwanted birthday gift, for example, or regret not calling a friend who we later discover was going through a difficult time.

    Last year, McCormack and her colleagues explored this kind of “interpersonal” regret in groups of 5- to 6-year-olds and 7- to 9-year-olds. In this study, children collected stickers to win a prize, and could also give their stickers to other children. When the younger children discovered that they had kept a sticker that they didn’t ultimately need but which, if they had given it to another child, would have allowed that child to win a prize, they didn’t seem to experience any regret. However, the 7- to 9-year-olds did. The team also found that the children who experienced this type of regret were more likely to act pro-socially on a subsequent task. As the team writes, “This latter finding suggested that interpersonal regret can result in children acting more kindly.”

    A lot more work is still needed to investigate how this type of regret drives moral development. And there are other major unanswered questions. Little has been done to explore how regret affects children’s and adolescents’ decisions out of the lab, in the real world, for example.

    Overall, though, the team concludes that the work to date paints a picture of regret as a “sophisticated emotion that develops relatively late in childhood” — as well as one that we clearly need to understand better.

    Regret and Decision-Making: A Developmental Perspective

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

    in The British Psychological Society - Research Digest on October 01, 2020 12:58 PM.

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    23 years across 4 sites and 3 continents: my Elsevier journey

    3 reasons my work at Elsevier is not “just a job”

    in Elsevier Connect on October 01, 2020 07:43 AM.

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    Neuralink in a Dozen Pigs

    In a far-ranging chat with Kara Swisher, Elon Musk talked about sustainable energy, brain implants, the stupidity of the press, and more. He gave a casual update on the “Three Little Pigs” demo of Neuralink's 1024-channel chip, finally admitting that his lofty goals are in a “very, very primitive stage”:

    Elon Musk: You can make people walk again. You could solve extreme depression or anxiety or schizophrenia or seizures. You could give a mother back her memory so she could remember who her kids are, you know. Basically, if you live long enough, you’re going to get dementia of some kind. And you’ll want to have something to help you. [NOTE: here, he didn't acknowledge the potential for advancements in biological treatments for dementia.]

    Kara Swisher:  Could it program in empathy? Or other things? Do you imagine that being part of this? [LAUGHTER] Or hey you could—

    EM: You could technically program anything. So empathy is probably a good one.

    KS: So where are we in doing this?

    EM: So where we are right now is we’re still in a very, very primitive stage. Where thus far we’ve had a lot of successful implants in pigs. And we now have a pig that has had an implant that’s working well and it’s been there for over three months. And we now have implanted about a dozen pigs. And the sensors are working well. A large part of a pig brain is about its snout. So you can literally rub the pig on its snout and we can detect exactly where you touch the snout. [NOTE: “Yeah, that's called somatotopic mapping,” said John Hughlings Jackson in 1886.]

    Listen to the podcast: Elon Musk: ‘A.I. Doesn’t Need to Hate Us to Destroy Us’ 

    In a conversation with Kara Swisher, the billionaire entrepreneur talks space-faring civilization, battery-powered everything and computer chips in your skull.

    Bonus!! Musk on Trump:

    Kara Swisher: Do you like him? Are you voting for him?

    Elon Musk: [SIGHING] I mean, I’m — to be totally frank I’m not — I mean, I think — let’s just see how the debates go. You know?

    KS: That’s going to be your thing, the debates?

    EM: Well, I think that is probably the thing that will decide things for America.

    KS: Why is that?

    EM: I think people just want to see if Biden’s got it together.

    KS: Mm-hmm. And if he does?

    EM: If he does, he probably wins.


    He hasn't yet tweeted about the disgraceful dumpster fire... 


    in The Neurocritic on October 01, 2020 07:05 AM.

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    To broaden the impact of your research, ‘let other people talk’

    University of Oxford-based winner of Scopus Young Researcher Award embraces interdisciplinary research

    in Elsevier Connect on October 01, 2020 06:51 AM.

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    The Myths of the Pineal Gland

    A COVID-19 conspiracy theory is the latest in a long line of myths about the pineal gland.

    in Discovery magazine - Neuroskeptic on September 30, 2020 10:00 PM.

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    Paolo Macchiarini indicted for aggravated assault in Sweden

    Swedish prosecutor opened a criminal indictment against Paolo Macchiarini. The scandal surgeon will have to stand court trial for all 3 deadly plastic trachea transplants he performed at Karolinska.

    in For Better Science on September 30, 2020 01:26 PM.

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    Astronauts Need A Decent Night’s Sleep Too

    By Matthew Warren

    As I write this post, I’m struggling a little to put words onto the page. I didn’t sleep well last night, and my tiredness has taken its toll on my ability to concentrate. But at least I’m sat at my desk at home and not, say, in control of a massive hunk of metal filled with fuel and electronics, hurtling through space at thousands of kilometres an hour. Because a new study in Scientific Reports has found that astronauts need to get enough sleep too — and when they don’t, their performance suffers.

    Erin Flynn-Evans from NASA Ames Research Center and colleagues studied people taking part in a spaceflight simulation on Earth. They weren’t actually astronauts, but “astronaut-like” participants, who all met NASA’s physical standards for space flight, as well as other criteria (such as having Master’s degree in a STEM subject). The participants lived in the Human Analog Research Exploration (HERA) habitat, a self-contained unit designed to mimic living and working conditions during space exploration. This paper included data from five separate “missions”, each of which involved four participants living together in the HERA habitat for 45 days (though one of the missions had to be cut short due to a hurricane).

    Throughout each mission, the participants had a variety of tasks to complete, such as “extravehicular activities” and scientific work. Once every three days, at five points throughout the day, they also completed the psychomotor vigilance task, which simply involves watching a screen and pressing a button whenever a light randomly appears.

    Importantly, each weekday participants were only allowed five hours of sleep; at the weekend they were allowed eight hours. They weren’t permitted to nap, and could only drink caffeine before 2pm. The researchers could therefore look at how performance on the psychomotor vigilance task changed across the course of the mission, as well as specifically on days when the “astronauts” got more or less sleep.

    The team found that participants’ performance worsened as the mission went on, with reaction times on the task becoming slower. Interestingly, participants’ self-reported fatigue didn’t decline across the course of the mission, suggesting that tests like this may provide a better measure of performance than simply asking astronauts how they’re feeling. Participants were also slower and missed more of the lights in the task on days when they got only five hours of sleep, compared to days when they got eight hours.

    Overall, the authors conclude, the findings “suggest that simply meeting the criteria required to be an astronaut is not in itself a determinant of resilience to chronic sleep restriction”. This isn’t entirely surprising — after all, astronauts are only human, and people in other professions with rigorous training requirements, such as pilots, are also adversely affected by lack of sleep.

    Of course, there are some obvious limitations to the study: although it simulated a space mission, it was still conducted on Earth; similarly, the psychomotor vigilance task isn’t necessarily a good representation of the complex jobs astronauts need to perform. It’s also worth noting that the changes in reaction times on the task were pretty small, in the region of tens of milliseconds difference between the beginning and end of the missions, and there was lots of variation between participants. It would be interesting to explore these in more detail: are there particular characteristics that make astronauts’ performance more or less likely to suffer after a lack of sleep?

    Still, the research does suggest that many days or weeks of poor sleep may build up to impair astronauts’ day-to-day functioning: an important insight given that this is the sort of time frame for future missions to the moon or beyond. And while NASA does allow crewmembers to sleep for eight hours per night on missions, astronauts themselves report actually sleeping for just six hours. So, the researchers say, it will be important to consider ways to promote better sleep while in space.

    Changes in performance and bio‑mathematical model performance predictions during 45 days of sleep restriction in a simulated space mission

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

    in The British Psychological Society - Research Digest on September 30, 2020 11:17 AM.

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    Rethinking Research Assessment: Addressing Institutional Biases in Review, Promotion, and Tenure Decision-Making

    Authors: Ruth Schmidt is an Associate Professor at IIT’s Institute of Design and Anna Hatch is the program director for DORA. PLOS supports DORA financially via organizational membership, and PLOS is represented on the steering committee of DORA. This blog is part one in a 4-part series.

    The field of behavioral economics emerged in the 1970s from the confluence of psychology with human judgment and decision-making, grounded in the realization that humans don’t always act “rationally” or in their best interests. Real-word applications of behavioral economics are often focused on consumers and citizens, such as increasing the percentage of adults who receive influenza vaccinations or helping people save for retirement. However, the same decision-making biases that we wrestle with in our personal lives also show up in professional settings. In fact, our misguided assumptions of rationality and expertise in academia may actually make us more prone to cognitive biases than we think. So when making decisions on behalf of others in hiring, review, promotion, and tenure, it is even more important to protect against shortcuts and habits in our thinking.

    Although recognizing personal biases is important, bias training that teaches individuals how to become more aware of decision-making tendencies has been shown to have a limited impact on actual behaviors. Instead, creating new structural and institutional conditions — in the parlance of behavioral economists, creating new “choice architectures” to scaffold decision-making processes — is often more effective when attempting to reduce bias in the interest of promoting and supporting more equitable practices.

    While not a comprehensive set, we’ve identified four major barriers to equitable decision-making in hiring, review, promotion, and tenure processes that commonly result from biased thinking. In the next 4 weeks we will provide examples of what these barriers are, the specific cognitive biases that feed them, and recommendations for overcoming these barriers at an institutional level. Part one delves into Objective comparisons.

    1. “Objective” comparisons are not necessarily equitable.

    Qualitative judgments are often notoriously difficult to make, in part because their “apples and oranges” nature makes it challenging to say a single option is truly better.This can lead to well-meaning efforts to reduce complexity, such as using proxies to simplify comparisons. While qualities that can be more easily measured or ranked are appealing because they feel less subjective, the temptation to rely on quantifiable indicators to signal quality has some significant implications on decision-making.

    In addition to oversimplifying options in an effort to make them more comparable, the urge to measure things can imbue measurability itself with outsized importance. But as Campbell’s Law has long made clear, once indicators are accepted as a way to gauge value, they start to lose meaning as objective measures. Instead, they increase the temptation to focus on a narrow set of activities and reduce investment in reviewing other meaningful, but less rewarded, achievements. Publishing research in venues with high Journal Impact Factors (JIFs) is a classic example: Due to the perceived importance of citations and “high-quality” publications in promotion and tenure dossiers, decisions about what research to conduct, submit, and publish can lead evaluators to prioritize research with a higher likelihood of getting published in the “right” journals over other forms of impact.

    A second form of objectivity bias is the Matthew effect, which describes the tendency forresources to flow to those who already have them. This can occur when a lack of time or motivation to vet results means that decision-makers default to preconceived ideas about what seems good, such as when researchers with long track records of grants receive a disproportionate amount of new funding. Another example of the Matthew effect is when highly cited references become more cited in part becauseresearchers see that they’re highly cited, rather than because they are more relevant or higher quality. This tendency is more likely to increase as our reliance on automation as a means to customize or deliver content grows, such as in social media where popular items are more heavily promoted in newsfeeds or where items recommended by Amazon attract more hits.

    Finally, the notion of anchoring — a cornerstone of early behavioral economics research, in which the first piece of data we see or hear defines the reference point against which subsequent data is compared — can create a false sense of objectivity and inadvertently emphasize relative comparisons between options rather than their actual values. For example, receiving a $2 million dollar grant one year may anchor one’s expectations for the value of future grants, causing a $1.2 million grant to feel comparatively disappointing. But anchoring can also manifest in a more general, qualitative context, such as when using one’s own personal life as an “anchor’ to judge others’ experiences.

    What can institutions do?

    Contextualize data. Relying wholly on quantifiable measures can contribute to a false sense of objectivity. Structured interview and review protocols can reduce inequities in review, promotion, and tenure (RPT) decision-making. Balancing the use of quantitative metrics with qualitative inputs, like narrative CV formats that capture more intangible qualities, can help create a counterweight by contextualizing data points.

    Diversify standards. The temptation to anchor on old assumptions of what good researcher performance looks like often arises out of habit. To counter the urge to use a narrow or an anecdotal set of data that emphasize legacy notions of importance, institutions and decision-makers can elicit and select standards gathered from a wider set of sources and based on a more holistic set of values.

    Balance quantitative and qualitative measures. The human tendency to bend our behaviors to meet quantifiable targets is stronger than we think. Institutions should actively identify and recognize where setting specific, quantifiable goals may reinforce some behaviors at the expense of others. Institutions should make sure that what is being measured adheres to organizational or disciplinary goals and values, like achieving real-world impact, rather than what is easiest to measure, such as university rankings.

    Next Monday we’ll tackle how individual data points can accidentally distract from the whole.

    The post Rethinking Research Assessment: Addressing Institutional Biases in Review, Promotion, and Tenure Decision-Making appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on September 29, 2020 03:13 PM.

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    Even Imaginary Barriers Can Prevent Kids From Cheating On Tests

    By Emma Young

    How can you discourage kids from copying each other on tests? You could always use a simple frame to separate them, or even a ruler to draw an imaginary line between their desks. When these behavioural “nudge” techniques were used in new research published in Current Directions in Psychological Science, they significantly reduced cheating among 5 to 6-year-olds. This shows “that even seemingly unremarkable features of children’s environments can nudge them to act honestly,” write the researchers, led by Li Zhao at Hangzhou Normal University in China.

    The team set out to explore the extent to which a physical, spatial barrier might also act as a barrier against moral transgressions. In each of a series of four studies, a child was seated a small table and given a set of counting problems, which were impossible to complete in the allotted time. A short distance away was another identical table, on which the experimenter put the answer sheet before leaving the room. Though all the children were instructed not to cheat, from a purely practical perspective, it was easy to do so. In fact, in the control conditions, when there was no barrier (real or imaginary) between the child’s table and the answers, hidden cameras showed that about half did indeed look at the answers.

    However, the team found that a barrier of some sort did make a difference. In the first study, a metal frame either fitted with transparent plastic cheating or simply left empty was placed between the tables. In both scenarios, the child could easily see the answers if they wanted to — but the frame with the sheeting cut the cheating rate to about 15%, while the empty frame reduced cheating to just under 30%.

    In the second and third studies, the team moved the barrier into a variety of positions around the tables. They found that to reduce cheating, the barrier had to be in the child’s eye line when they looked towards the other table.

    In the fourth study, there was no physical barrier at all. Instead, before leaving the room, the experimenter used a toy magic wand to outline what she said was an “invisible frame” between the tables. This imaginary barrier was about as effective as the empty frame was in the first study at reducing cheating.

    Why did a simple frame, and even an imaginary frame, reduce cheating? One possibility, the researchers say, is that from a very young age, children learn to use environmental cues to guide their movements. So, for example, they might learn that while it’s okay to play football in an open park, it’s not okay to pass through a gate in a neighbour’s fence, to play football in their garden. It’s possible that children generalised this type of learning, viewing the barriers as dividers between a permissible space and a prohibited space.

    In English, of course, we even talk about “crossing the line” between acceptable and unacceptable behaviour. (I seem to tell my children that they’ve crossed the line on an almost daily basis.) These were Chinese children. I don’t know if Mandarin has the equivalent metaphor, but if it does, this might have influenced their children’s behaviour — or, if the study were to be replicated in an English-speaking country, perhaps cheating might be reduced still further.

    As the team notes, though the frame was always in place when the child sat down, and the experimenter didn’t even refer to it (except for when it was imaginary), the children may well have made the implicit assumption that someone had put it there for a reason — presumably to stop them from cheating. So kids’ ability to tap into this sort of social cue could be part of the reason why they were less inclined to cheat.

    This study was on young children. Would a physical barrier have the same impact on cheating in older kids? In this study, older children had a higher rate of cheating than younger children (no matter what the experimental condition) — but the frames were just as effective at reducing cheating, no matter what the child’s age. So it’s possible that older children would be susceptible to the frame effect, too.  

    More work is clearly needed to examine the specific mechanisms that underlie the new findings, and to explore just how barriers might be used in real classrooms and exam halls.

    The moral barrier effect: Real and imagined barriers can reduce cheating

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

    in The British Psychological Society - Research Digest on September 29, 2020 01:46 PM.

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    Know Your Brain: Putamen

    Where is the putamen?

    In this coronal brain section, the putamen is the region colored light purple. The globus pallidus and caudate are also shown in the image.

    In this coronal brain section, the putamen is the region colored light purple. The globus pallidus and caudate are also shown in the image.

    The putamen is a subcortical structure that is part of a group of structures known as the basal ganglia. It is also a component of the dorsal striatum, which includes the putamen and the caudate nucleus. The putamen is adjacent to the globus pallidus, and the putamen and globus pallidus together are sometimes referred to as the lentiform or lenticular nucleus.

    What is the putamen and what does it do?

    As a component of the basal ganglia, the putamen is best known for its role in facilitating movement. To understand the putamen’s role in movement, it’s helpful to think about how the basal ganglia as a whole may contribute to movement. While this has not been determined definitively, one popular hypothesis suggests that the basal ganglia are important for facilitating desired movements while at the same time inhibiting unwanted and/or competing movements. To read more about the basal ganglia and this purported function, see this article.

    Watch this 2-Minute Neuroscience video to learn more about the basal ganglia.

    The putamen (and striatum as a whole) is thought to act as a critical input area for the basal ganglia. In other words, to accomplish their movement-related functions, the basal ganglia need to receive information from the cerebral cortex about movements that you want to make. Much of this information travels first to the putamen or the caudate via a pathway called the corticostriatal pathway.

    Most of the neurons in the putamen contain the neurotransmitter GABA and extend out of the putamen to other regions of the basal ganglia— specifically the globus pallidus and the substantia nigra. These neurons that leave the putamen create pathways that are thought to be involved in either the facilitation or inhibition of movements (depending on the pathway). Research suggests that neurons in the putamen are activated before and during movement—especially movement of the limbs and torso. It is thought that the firing of these putamen neurons contributes not only to the initiation of a movement, but also to the decision to make a movement and the selection of a movement to make.

    For years, the putamen was considered to be primarily devoted to movement. But more recent research has begun to point to an expanded role for the putamen. For example, it is now thought that that the putamen is also involved with learning and memory, language, and emotion.

    Dysfunction in the putamen could be a factor in a number of disorders, but is strongly linked to problems with motor function. Huntington’s disease (HD), for example—which is characterized by rapid and spasmodic involuntary movements—is associated with the degeneration and death of neurons in the caudate and putamen. These neurons may be involved with the inhibition of unwanted movements, and their degeneration in HD may cause involuntary movement to be more difficult to suppress.

    Neurodegeneration in the basal ganglia is also the hallmark pathological sign of Parkinson’s disease (PD), a condition that causes slow, labored movement along with tremors (among other symptoms). With PD, the neurodegeneration occurs primarily in the substantia nigra, but other areas of the basal ganglia—like the putamen—are also affected. Additionally, abnormalities in dopamine function in the putamen are thought to contribute to the movement problems PD patients experience.

    References (in addition to linked text above):

    Mink JW. The basal ganglia: focused selection and inhibition of competing motor programs. Prog Neurobiol. 1996 Nov;50(4):381-425.

    Purves D, Augustine GJ, Fitzpatrick D, Hall WC, Lamantia AS, Mooney RD, Platt ML, White LE, eds. Neuroscience. 6th ed. New York. Sinauer Associates; 2018.

    in Neuroscientifically Challenged on September 29, 2020 09:14 AM.

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    arXivLabs: a space for community innovation

    Image of arXiv smiley bones flaskarXiv has launched a new, formalized framework enabling innovative collaborations with individuals and organizations.

    “Members of our community want to contribute tools that enhance the arXiv experience, and we value that kind of community engagement,” said Eleonora Presani, arXiv Executive Director.

    arXivLabs, a concept developed years ago, acts as a conduit for collaboration. Now, it appears as a physical space on the article record page, and, importantly, sets guidelines for collaborations between arXiv and third parties, ensuring that partners share arXiv’s values of openness, community, excellence, and user data privacy.

    “The arXivLabs framework complements other collaborative projects such as arXiv’s Kaggle dataset,” said Presani, “and demonstrates how great results are achieved when the community works together.”

    arXiv readers will now find a new feature, below existing content on the article record page, that reflects the new framework. The arXivLabs tabs highlight different experimental tools developed by collaborators, and will be updated as new tools become available. These add value and functionality for both readers and authors.

    For example, the Bibliographic Explorer displays information about works that cite and are cited by arXiv papers and their published versions. This enables discovery of relevant research by providing user-friendly navigation of an article’s citation tree. The Explorer, developed by Matt Bierbaum, was already available on the site, and will now be featured in the “Bibliographic Tools” tab.

    Another tool, the CORE Recommender, facilitates the exploration of relevant open access papers from a global network of research repositories and is now accessible on the “Recommenders” tab.

    arXiv’s third party collaborators will only have access to minimal and anonymized data about arXiv users, and only for the purpose of ensuring the correct functioning of the arXivLabs features. Any other use not included in a written consent from arXiv is strictly prohibited. Upon user request, this data, and another other data connected to the user can be permanently deleted.

    Screenshot of arXiv record page with arXivLabs tabs

    in arXiv.org blog on September 28, 2020 07:05 PM.

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    Scientists are flawed, stressed, inspired, kind… we are human

    This post was written by Alexia A., Hannah Dee, Karel Green, Alison Young and Yolanda Ohene from Scientists are Humans and Rebecca Kirk from PLOS 

    Kindness matters, in life generally, but also in the research environment. This simple concept was behind the launch two years ago of the website Scientists Are Humans, with the aim to support scientists to move the research culture to be more kind; with the aim to change the game. We want to amplify even more voices on the site, including yours, so please get in touch to share your story (we are flexible about format and posts can be anonymous).

    The website was one outcome of the Gamechangers for diversity in STEM (Science, Technology, Engineering and Maths) event in London run at the Turing Institute. This two-day workshop initiated and fostered projects to support more diversity in STEM. The concept of Scientists Are Humans is that the challenges faced by minorities in STEM could be ameliorated with more understanding and more kindness. One of the ways we can build understanding is by telling our stories, and listening kindly when others tell their stories. 

    So why is kindness so important? A look at the content of the website quickly makes it clear how it can make a huge difference. In the past two years the website published articles reporting from picket lines, about the BLM movement, on leaving academia, on struggling and completing PhDs, on being an ally, on mental health and on being brave – amongst many others. The variety of voices, and the clarity with which they speak has been inspiring, thought provoking and has humanized the science and scientists.

    The importance of our manifesto for being more kind could not be more important as we all find our own ways to manage the particular challenges that we are facing at the moment. We all need to be more kind, and we will all benefit from a profession with kindness at its core.

    The post Scientists are flawed, stressed, inspired, kind… we are human appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on September 28, 2020 01:51 PM.

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    Selfish And Combative People Don’t Actually Get Ahead At Work

    By Emily Reynolds

    In popular culture, there’s an idea that lots of successful people are… well, not that nice. From Glengarry Glen Ross to The Apprentice, there’s a litany of bad bosses and aggressive success stories in film and television. The message seems to be that to get ahead you need to ditch the niceties and think about number one.

    This stereotype might not reflect what’s really going on, however. In a new longitudinal study published in PNAS, a team from the University of California, Berkeley and Colby College tracked individuals over a fourteen year period, looking to see what became of those who were more disagreeable (not a cohort many of us would particularly long to be in).

    They found that selfish, combative, and manipulative people have no real advantage at work — not because there are no benefits to such behaviour, but because its positive and negative impacts cancel each other out.

    In the first study, Cameron Anderson and colleagues measured the Big Five personality traits of 457 participants during their university years. Then fourteen years later, when those participants were in the workforce, the team assessed participants’ power in the organisation, their view of their influence in the workplace, and organisational culture — how aggressive, criticising, political or selfish a participant felt it was.

    Those who were most disagreeable at the first measurement did not have more power at the second, regardless of their age, gender or ethnicity — suggesting that selfishness and aggression do not result in higher levels of power or attainment.

    In the second study, the team looked more closely at workplace behaviours in another group which had been followed in a similar way. Behaviours were grouped into four categories: dominant behaviour (e.g. “I am willing to bully others to achieve important goals”), political behaviour (e.g. “I build alliances with important people”), communal behaviour (e.g. “I care about others’ wellbeing”) and competent behaviour (e.g. “I make important contributions to my team’s success”). Importantly, coworkers also rated participants on these same workplace behaviours, as well power and organisational rank.

    Coworker ratings largely agreed not only with one another but also with participants’ own ratings of themselves, suggesting that self-insight was fairly accurate. And the results showed that those who engaged in more dominant, political, communal and competent behaviour had higher levels of power. Personality-wise, people who were more extraverted 14 years previously engaged more in each of these categories, doing “everything right”, as the team put it, to attain higher power. Those with disagreeable personalities, however, only engaged in more dominant behaviours — and fewer communal ones.

    So whilst dominant behaviour might get you ahead in some ways, it’s clear that other, more prosocial, types of behaviour are also a key part of the process. If you’re a disagreeable person, being selfish might enhance your power to some extent, but failing to be generous and kind can cancel this out.

    This might not be the case, however, in certain environments — if you work in an industry where prosocial behaviour is neither valued nor particularly useful, disagreeable people may be more likely to reach positions of power.

    Future research could take the opposite approach: do people become more selfish and disagreeable once they’re in positions of power, and do those kinds of traits help them keep it? It may be that power really does corrupt — or we might find that it’s mere tropes around aggression that perpetuate the myth that nice guys finish last.

    People with disagreeable personalities (selfish, combative, and manipulative) do not have an advantage in pursuing power at work

    Emily Reynolds is a staff writer at BPS Research Digest

    in The British Psychological Society - Research Digest on September 28, 2020 08:52 AM.

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    We arrived at Vitamin D as COVID-19 cure

    It was only logical that COVID-19 will be cured with vitamin supplements. Peer-reviewed science is now catching up with the bustling Vitamin D market.

    in For Better Science on September 28, 2020 06:00 AM.

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    The "Synergistic Core" of the Human Brain?

    Are synergistic interactions the fundamental drivers of complex cognition?

    in Discovery magazine - Neuroskeptic on September 26, 2020 05:00 PM.

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    Opscidia: Fighting Fake News via Open Access

    n recent years, fake news has become a growing problem in the international information landscape. More and more projects deal with how to expose and avoid them. One of them is the project of Charles Letaillieur and Sylvain Massip. With a tool for the general public, the two want to support checking simple messages for their truthfulness with the help of open access publications and of artificial intelligence.

    in Open Access Tracking Project: news on September 26, 2020 08:43 AM.

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    Backpacks And Bird Brains: The Week’s Best Psychology Links

    Our weekly round-up of the best psychology coverage from elsewhere on the web

    Many birds have impressive cognitive abilities such as good memory, tool-making talents, and problem-solving skills — yet they don’t have the part of the brain called the neocortex which is key to those abilities in mammals. But now researchers have discovered that a region of the pigeon brain called the pallium seems to be organised in a similar way to mammals’ neocortex, reports Virginia Morell at Science, suggesting it is responsible for bird cognition.

    Most of us would go out of our way to avoid hurting others. But why do some people “harm the harmless”? At The Conversation, Simon McCarthy-Jones has written a primer on psychopathy, sadism, and “dark” personality traits

    In a new preprint, researchers report finding changes in the volume of certain brain areas after the COVID-19 lockdown. A total of 50 volunteers were scanned in Israel in 2019 and then again in May-July 2020, after the country’s first lockdown. The team found increases in the volume of the amygdala and nearby regions, which they suggest could relate to emotional stress. At Discover Magazine, Neuroskeptic takes a more detailed look at the study, with — as you’d expect — a healthy dose of scepticism.

    Neuroscientists have created a prototype backpack that can take EEG measurements and provide brain stimulation — and it even includes a virtual reality system too. The device could allow researchers to study brain function while people are moving around, writes Rebekah Tuchscherer at Science, though only patients with neural implants are able to use it.

    People of African ancestry are underrepresented in genetics and neuroscience research. At NPR, Jon Hamilton has the story of an initiative seeking to change that.

    What causes people to stutter? Research has suggested that stuttering could be related to different patterns of connectivity within the brain, or increased levels of dopamine. Some studies have implicated mutations in particular genes as well. At BBC Future, Amber Dance examines the evidence.

    Skin-to-skin contact could reduce newborn babies’ neural response to pain, reports Jason Goodyer at BBC Science Focus. Researchers found a dampened pattern of brain activity in response to a needle prick when mothers held their baby against their skin rather than against their clothing. However it remains to be seen whether this altered response actually relates to reduced perception of pain.  

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

    in The British Psychological Society - Research Digest on September 25, 2020 02:43 PM.

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    Interview with Bruno Pichler

    Bruno Pichler studied medicine, obtained a PhD in neuroscience, worked in the labs of Arthur Konnerth, Tom Mrsic-Flogel and Troy Margrie, and was R&D manager at Scientifica, before founding his own company, INSS, “to provide the international neuroscience community with bespoke hard- and software solutions and other consulting services”. He is not only a highly experienced builder and designer of two-photon microscopes but also a very friendly and open human being. So I was very happy to have the opportunity to ask him a couple of questions.

    The interview took place on September 8th 2020 in a virtual meeting and lasted around 1.5 hours. Afterwards, I transcribed, shortened and edited the recorded interview. For a brief orientation, here’s an ordered but non-exhaustive list of the topics discussed:

    Why neuroscience?
    How to get into optics and programming
    Role models
    Projects in academia
    Why didn’t you become a PI?
    At Scientifica
    Founding one’s own company
    Performance checks for a 2P scope
    How to clean optics
    The detection path
    Teaching people how to solve problems
    Fixed-wavelength lasers
    Multiplexed acquisition
    Advice to young scientists
    Bluegrass music

    If you find any questionable statements, you should consider blaming my editing first.

    And since the entire interview is quite long, take a cup of tea, and take your time to read it


    Peter Rupprecht: You studied medicine before you started your PhD. What was your motivation to do a PhD in neuroscience, and to continue in neuroscience afterwards?

    Bruno Pichler: This was just something that happened: I really loved the first years of medical school, basic science, physics, biology, anatomy, physiology, and all that. But halfway through medical school when the clinical work started, I realized that it wasn’t for me. So I looked for new inspiration, and I stumbled upon the website of Arthur Konnerth’s lab. I called on a whim and half an hour later I was in his office, and he offered me a job. He said, “why don’t you take a year off from medical school and start working towards a PhD here?” So I worked full-time in the lab for a year, and then went back to finish medical school. But at that point I had no interest in a career in clinical medicine, I just wanted to complete the medical degree and then work in the lab and continue my PhD. – So, not much thought behind it, it’s just how things transpired.

    (c) Bruno Pichler

    PR: The medical studies did not really prepare you well for the more technical aspects of what you have been doing afterwards. How did you learn all of this, for example optics, or programming?

    BP: Again, it was just something that happened: there were microscopes that needed troubleshooting, there were things I didn’t understand, and every time I didn’t understand something, I tried to find more information about it. Some of the information sticks with you – and that’s how you learn and how you get into optics and software.
    For example, there was some custom-written image analysis software in the lab and I didn’t really understand what it did to the data, so I sat down with the guy who wrote it and asked about all the calculations it made and then I cautiously started to make some changes to it – and it just naturally emerged from there. I never consciously sat down and said, “oh, I want to learn programming!” I had a problem in front of me that I needed to solve, and so I solved it. And whatever I learned while solving it is now part of my knowledge.

    “People who inspired me were often those in support roles, like the lab technicians who taught me how to pipette, or the engineers in the electronic and mechanical workshops.”

    PR: So would you describe yourself as a problem-solver?

    BP: I think that is probably an accurate description. My main driving force is that whenever I see a technical problem, I want to find an elegant solution for it. I can’t help it.

    PR: Did you have a role model as a scientist, or somebody who inspired you to continue with neuroscience?

    BP: I definitely have a few people who inspired me, but I wouldn’t say I had a ‘role model’. There’s obviously the intellectual giants like Richard Feynman or Horace Barlow. Then there are the scientists that I worked with, Arthur Konnerth, Tom Mrsic-Flogel, Troy Margrie, and of course all the colleagues in those labs. But, on a very practical level, people who inspired me were often those in support roles, like the lab technicians who taught me how to pipette, or the engineers in the electronic and mechanical workshops. For example, Werner Zeitz, the electronics guy in Arthur Konnerth’s lab, who is known for his famous Zeitz puller (https://www.zeitz-puller.com/). We were building a two-photon resonant scanner with Werner back in 2004/2005, and he built a 19” rack-mountable device box – no labels on it, just unlabeled pots and BNC connectors – which transformed the scanning data into a TV image and sent it to a frame grabber card. Nowadays, we do this in software but it was all done in hardware at the time. Same with the mechanical guy, Dietmar Beyer: He was such a skilled manual machinist, and he would just make whatever we needed without any CNC machining. Another guy that really inspired me back as a PhD student was Yury Kovalchuk. He was a senior postdoc at the time. He knew everything about two-photon microscopy, and he was building an AOD scanner back in 2004/2005. It was the way he understood these systems and explained everything to me whenever I had any questions – those kind of people inspired me.

    PR: From your entire academic career, what was your most rewarding project, big or small?

    BP: That’s so difficult to say, because everything is kind of rewarding. What I can certainly say is that I don’t believe in putting off reward for a long time, and the idea that ‘the more you suffer, the bigger the reward’. I like it when you have smaller rewards, but more frequently.

    PR: I can definitely relate to this… but at least scientific publications usually do not come so frequently. If you have to choose, which scientific publication where you took part in would you like to highlight, and what was your contribution?

    BP: There was a paper in 2012 by Kamilla Angelo in Troy Margrie’s lab (paper link). I came very late to the party, all the experiments had already been done, the first version of the manuscript had been completed, and Troy just asked me to read it and give some comments. I noticed something in the analysis where the manuscript didn’t actually show unambiguously one aspect of the claim in the paper. We tried to come up with some way to design new experiments to prove that unambiguously, but at some point it occurred to me that you could just do it with the existing data, just with a different type of analysis. And once the idea had come up of doing this pair-wise scrambling of all the data points and then calculating pair-wise differences, it was very quick and easy to write some code to analyze it. And it supported exactly what we thought it would support, but now unambiguously. That felt really rewarding, to be able to nail something that would have otherwise required more experiments with a bit of clever analysis, that was really cool.

    PR: Sounds like that! Especially your PI was probably really happy about this, because it saved a lot of trouble.

    BP: I guess so. The paper would have been highly publishable without my input, but it was just ever so slightly better with my input; and that’s good enough for me.

    “I was always more of a Malcolm Young than an Angus Young.”

    PR: Why did you not become a PI yourself?

    BP: Well, to start with, I was never really PI material …

    PR: What would you define as PI material?

    BP: Are you okay with an AC/DC reference? Would you understand what I mean when I say “I was always more of a Malcolm Young than an Angus Young”?

    PR: No, not really …

    BP: Malcolm Young was the rhythm guitarist in AC/DC, he was always in the background and played this steady rhythm, whereas Angus Young is the flamboyant lead guitarist in his school uniform who runs up and down the stage and is the focal point of attention for the audience. When I say “I was always more of a Malcolm Young than an Angus Young”, I’m talking about having a rock-solid line of people in the back who make sure that the lead guitarist and the lead singer can shine: I like to be in that role at the back. As a PI, you have to represent the lab, you have to present your work outside, you have to sell the ideas to funding bodies… so you have to have a little bit more of a flamboyant and outgoing nature. I’m too shy for this, so the PI path was never really on the cards for me to begin with. I was quite happy to be a sort of a medium level scientist – except that I felt there was more I could do to help other people. It felt self-indulgent to just play around with cool technology and have brainy conversations with smart people in the lab. I wanted to provide some value for others.

    PR: And then you chose Scientifica. Why Scientifica? How did that happen?

    BP: I did not really choose Scientifica. I wasn’t actually looking for a job when I left academia. My plan was to go back to the Bavarian Alps and work as a skiing instructor –that’s what I had done before I went to medical school. I figured that it would be really nice to do that again for a season, to pass the time until some new opportunity floated past. And then it just so happened that the opportunity to work at Scientifica floated past earlier than I had anticipated. They rang me and said, “we’ve heard you’re leaving academia and we’re looking for a software person to do some custom stuff for Scientifica’s two-photon customers”, and I was like “well, that sounds like a good idea”, and then I joined Scientifica. There was no job interview, there was no searching for a job, the job found me.

    PR: How was the work like at Scientifica?

    BP: Initially it was mostly intended to be customization of software, for example little Matlab add-ons for Scanimage or stuff like that. But then we also needed a resonant scanning system, and there wasn’t really any software available for resonant scanning before Vidriotech started …

    PR: … and then you wrote SciScan.

    BP: And that’s when I wrote SciScan. I had already written a software for resonant scanning in Labview some years before – for the frame-grabber that we discussed earlier, so I already knew what to do. While writing SciScan I also became involved in the hardware development of the resonant scanner, with the mechanical engineer and the electrical engineer. And so the job role gradually moved towards R&D management.

    PR: I’m a bit younger, so I don’t know whether the resonant scanners always came from Cambridge Technology, or was there a different provider? Or did you build the scanners in-house at Scientifica?

    BP: No, the resonant scanners were always the same as back in 2003 when I first started using them. The manufacturer was originally called General Scanning Inc, then it became GSI Lumonics, which later merged with Cambridge Technology, which was then bought by Novanta. There was a number of name changes involved, but no changes to the product.

    PR: Have you tried out resonant scanners from other companies as well?

    BP: I’m only aware of one other resonant scanner that is suitable for what we’re doing and that’s from a company called EOPC. I have not actually worked with their resonant scanners yet, but I will be in probably about two weeks from now. We have bought two of their resonant scanners, because they can be synchronized with each other.

    PR: Sounds like a challenging project. Probably with two pulsed lasers?

    BP: No, it’s about temporal multiplexing with a single laser. We want the scanners to run in synchrony so that we can use a single data acquisition system for the two paths.

    “When I was a scientist, I was building stuff myself because there wasn’t any company that I could go to and ask them to build it for me. And when I started INSS that was still true.”

    PR: Okay, this makes sense. – After Scientifica, you founded your own company, INSS. What was the biggest challenge when you got started? And why did you found your own company?

    BP: The ‘why’ is very easy to explain: When I started with Scientifica, I was very close to the customers, I was building custom software modules, was interacting with scientists very closely when it came to making hardware modifications to any of the existing products or new suggestions for new hardware products. As the company grew bigger, I got more into a management role. I felt I was getting a little bit too far away from the customer and more involved in managing people and conducting things internally. It is a whole different style of working when you want to make something that is not a prototype but a production item where you want to sell 100 pieces of. Then you have to think more about questions like, how can we design it in a way that you can build it routinely and efficiently, and you have to think about all the supply chain, and build assembly instructions, and how you teach people to do that. There’s a lot of work in the background that is relatively far away from the actual experiment that the neuroscientist is going to do with that microscope and I felt like I wanted to get closer to that again. Also, if you want to sell hundreds of microscopes, it’s not really economically viable to do individual customer specials. From a business development perspective it’s perfectly understandable that Scientifica wanted to have a more standard offering and make off-the-shelf turn-key systems. But that was not so much what I was interested in. I like getting involved in changing things, not making the same thing all the time. I also felt that this sort of very customized, individualized service was not something that was available. When I was a scientist, I was building stuff myself because there wasn’t any company that I could go to and ask them to build it for me. And when I started INSS that was still true. If you’re a scientist you either buy a microscope that someone has designed to fit many purposes, but it may not be perfect for your very specific purpose. And I thought, well, surely there’s a need for modifying, customizing, making something perfect for a particular experiment and stripping out everything else that may not be needed. If you custom-build it from off-the-shelf components, you can save a lot of money. And surely from the money that people save they’d be quite happy to give me some of it, if I advise them how to do it.

    PR: Didn’t it feel like shaky ground when you started? I mean, you were responsible for everything, and you didn’t get a salary anymore.

    BP: I think what helped a lot is that I’ve been involved in the music scene, and I knew a lot of musicians that were self-employed. They were getting money from gigs and teaching and playing on other people’s records and they were making a living without being employed – and I felt I could do the same thing. I had been playing gigs, I knew how to ask a pub owner to pay us money for providing music in the pub. And I figured, conceptually it wouldn’t be much different whether I come to your lab and build something for you, or whether I come to your pub and play a gig for you. You just ask beforehand how much you’re going to get paid for the gig, and if it isn’t enough to cover the costs then you can’t play that gig – it’s not exactly rocket science. It was good that I’d done it for a few years in the music business, it gave me a lot more confidence that this would work out in the microscope consulting business, too.

    PR: INSS is based in the UK. Have you been affected by the Brexit so far, or will you be affected by it?

    BP: I haven’t been affected by Brexit yet, everything is still the same until the end of 2020. Nobody knows what sort of forms we will need to fill in next year, and what sort of new hoops we might need to jump through. I’m not going to start worrying about that now because I don’t know what it’s going to be. – Don’t get me wrong: Brexit will be disastrous on so many levels, especially now, piling onto the coronavirus crisis. And of course it’s also a little bit disappointing… I’ve lived in this country for 13 years and I feel like I made a nice contribution, doing science, paying taxes, playing music. And then all these people feel that someone like me shouldn’t be here because we’re a burden on the country and they’d rather pull up the drawbridge; and they think it’s worth taking all these economic consequences of a no-deal Brexit just to keep people like me out of their country. But if that’s what the majority voted for, then I just have to deal with this somehow. I’m reasonably optimistic that I’ll find some way to navigate these new circumstances!

    PR: I get the impression that you are quite optimistic in general. Do you think this is a requirement for being self-employed?

    BP: I think it’s probably a requirement if you don’t want to live a life in misery. You have to be somewhat optimistic or at least relaxed about what the future might hold because the future is kind of uncertain. You’re not going to know what’s going to happen. If you worry about it, it will not change the fact that the future is uncertain. So you might as well say “I’ll jump down that bridge when I get there”.

    PR: If you don’t mind, let’s talk about some technical questions … after you set up a two-photon microscope in somebody’s lab, how do you quickly check its performance? Do you have a specific routine?

    BP: The quickest performance check is to image a pollen grain slide. You check how the spiky pollen grains look like, whether you can section them nicely and how the field of view [FOV] is like. Once you’ve done it a few times, it is everything you need to get a quick qualitative idea of whether everything is working fine. If you want to do it more quantitatively then you obviously want to image beads, you want to check your field flatness, you want to get your precise FOV measurements with some grids, and so on. We have a routine that we’re working with that we constantly improve, but in the majority of cases that’s not even necessary.

    PR: I think there are some companies which sell special calibration slides or samples. When would this be useful, or do you think it is overkill?

    BP: I would love to use those, but they are not really suitable for 2P. You are talking about the Argolight probes?

    PR: Yes…

    BP: So, they specifically mention that you shouldn’t be using them with 2P, or you use them at your own risk. Also, they cost about 8’000 euros. I don’t really want to spend 8’000 euros on something where I can quickly exceed the damage threshold, and that’s why I haven’t used them. I would love to have something like that if it’s available for two photon. In the meantime, I’ll stick with these electron microscopy grids and beads and pollen grains. – What are your thoughts on those, have you tried anything like that?

    PR: Several years ago I also wanted to check the field curvature for a two-photon microscope and borrowed a quite expensive calibration slide from the confocal microscopy facility, but I managed to destroy it, and that’s when I stopped experimenting. Usually, I just use beads and fluorescent plastic slides. Not so much pollen grains, because I have destroyed the slides several times.

    BP: (curious) How do you destroy a pollen grain slide?

    PR: Just by leaving the slide somewhere in the setup, until something makes the glass break; which happened to me twice so far. I also made some simple pollen samples in agar, but that’s not possible in winter or autumn. So I’m usually sticking to beads. But in principle I agree, pollen slides are ideal, you quickly find the samples and you can also check how the fluorescence yield changes across the FOV. Do you make your own pollen grain slides?

    BP: We’re using pollen slides from Carolina Biological Supply Company. They make these ready-made pollen grain slides for schools and educational settings and the slide is like five dollars or something.

    PR: I didn’t know they were so cheap! The first scanning confocal microscope that I used [a Leica SP5] had come with a pollen slide, and I had been instructed to treat the slide very carefully, because it was so expensive… So it’s good to know that it can be really cheap! – Just another question about two-photon microscopes: which preamplifier would you recommend for a standard resonant scanning two-photon microscope?

    BP: We often use the Thorlabs preamps, the TIA60, and we also use the Thorlabs PMTs with the built-in preamps, which is quite convenient. You control them through USB, and you can set the amplifier bandwidth in software.

    PR: I thought the bandwidth was fixed at 60 MHz?

    BP: Yes, for the TIA60 preamps, it’s fixed at 60 MHz. For the PMTs with the built-in preamplifiers, you can choose between, I think, 80 MHz, 2.5 MHz and 200 kHz. When we need higher bandwidth for something, then we would use Femto preamps.

    PR: Which one is your preferred preamp from Femto?

    BP: I use the 400 MHz one.

    “For me, cleaning always starts with these little rubber ball dust blowers.”

    PR: Let’s talk about objectives… If you were postdoc in a lab and could choose any objective for testing, which one would you choose?

    BP: I had a Nikon 25x NA1.1 when I was in Troy’s lab, and that’s a really nice objective. For the typical applications I was working at – population calcium imaging – that’s just a beautiful objective. I wouldn’t really need to try anything else. I’m sure there are other applications that would benefit from some of these newer Olympus long working distance objectives, but it’s so application specific, and there’s good uses for all of them. So, without having a particular experiment in mind, it would be difficult to answer the question.

    PR: For these Olympus objectives, I think the working distance is something like 4 or 8 mm. Does the 8 mm make any sense for neuroscience applications?

    BP: Again, it depends on your application, right? These objectives were primarily designed for cleared brains, where you don’t have much of a choice, you either use a long working distance or you’re not imaging all of it.

    PR: Ok, I didn’t know that it was for designed for cleared brains. Now, this makes much more sense to me. – Speaking about objectives, how do you usually clean optical elements? Do you use tap water or distilled water, or can you recommend any other protocols?

    BP: For me, cleaning always starts with these little rubber ball dust blowers. You just try to blow everything off that might be there. If that doesn’t work with the blower, you get out the compressed air can. From there, we’ll go to distilled water, and then Purosol. If I can’t get it off with that, I would go to isopropyl alcohol, and then to methanol. But we’re usually dealing with new microscopes, so in the vast majority of cases, we don’t have to go past the compressed air can.

    PR: What do you do with dichroics if they’re dirty or if there’s sticky dust on top of them? Is there anything you can do?

    BP: I wouldn’t really want to go far beyond the distilled water on a dichroic. If I can’t get it off with that, I might try the Purosol, but we don’t encounter dirty dichroics very often, because most of the optics we’re working with are brand new.

    PR: Another question about 2P microscopes: I was always wondering about a proper way to test the alignment and performance of collection optics. How do you check whether collection optics are properly aligned?

    BP: I want to capture all the light that’s coming out of the back aperture of the objective. So, if you just put some light source and a diffuser under the objective – that can be the LED on a phone with a bit of lens tissue on top as a diffuser –, you’ll get a large cone of light coming out the back aperture. Then you screw in a little target at the position where your PMT will be sitting. You should see a spot right in the center that has the size of the PMT sensor.

    PR: Just to repeat, it’s important to remove the PMT in this case, right?

    BP: Yes, you need to remove the PMT and put a target in its place. If you want to do it more quantitatively, it gets difficult. You could use a calibrated light source and count how many photons you get through and compare that over many microscopes and so on. But I don’t think anyone is doing that in practice.

    “I don’t want to tell someone how to align a laser, I rather want to be present when they figure it out themselves.”

    PR: Let’s assume a customer writes to you that there’s a problem with their two-photon system, “because the signal becomes weaker”. This is something I also often hear from less experienced colleagues or friends who ask for some help with their setup. What would be your first guess if you don’t know anything else?

    BP: In the first instance I would think of it as a great opportunity to help someone to think systematically about the problem. Because if all they tell me is that “the signal becomes weaker”, then they haven’t really thought about how to communicate a problem in such a way that the other person can do something with it. I would need to know so much more , for example: what’s the signal? what’s the system? what are you measuring? have you done the same experiment over a year, and every day it gets a little bit weaker?, or is that happening within the same animal, or within the same slice? … there’s a thousand different questions. I need to find out what the person means by “signal”, what the person means by “becomes”, what they mean by “weaker”. It’ll be beneficial for that person, and for me, if I can teach them how to clarify their thoughts to themselves, and then communicate them efficiently. Maybe next time they know immediately why it’s becoming weaker simply because they’ve changed the way they think.
    I have to say that I enjoy it very much to help someone to clarify to themselves what the problem is. It’s very rewarding for the person to figure out the problem by themselves, and it’s rewarding for me to teach someone a problem-solving skill that they might not have had before.

    PR: I think you have also participated in some summer schools?

    BP: That’s right, I’ve been at the Cold Spring Harbor imaging course five times – which is great fun, a great location and great teachers. I’m also participating every year at TENSS in Romania, the Transylvanian Experimental Neuroscience Summer School, again a great team of people that are running it with great lecturers and great spirit among students and all the TAs and lecturers. I really enjoy teaching people and helping them to figure things out. I don’t want to tell someone how to align a laser, I rather want to be present when they figure it out themselves. I might nudge them in the right direction, but if I simply told them what to do, I feel I’d be depriving them of a joyful moment of revelation.

    PR: It can also be a bit dangerous to align laser beams, and especially invisible IR beams. To make the laser beam visible, do you use IR viewers?

    BP: I use them occasionally, but only when I have to, so only when I’m working with a fixed-wavelength laser. And even then I try to do as much as I can with viewing cards rather than the viewer itself. Although I tend to go back and forth a little bit between card and viewer.

    PR: For the tunable lasers, do you switch to visible wavelengths or what do you think about the pointing stability of those lasers?

    BP: I usually align everything in the visible range and then, once we switch to IR, I image a uniform slide and check if our alignment is nice and centered. The illumination on the slide tells you whether you’ve gone off a little bit.

    PR: To clarify, I was thinking more about pointing stability when changing the wavelength of the tunable laser for example from 700 nm to 900 nm…

    BP: I don’t think the changes are drastic. But we’re doing the final alignment through the actual scan head based on what we’re seeing on the computer screen from the fluorescent slide, and we’re doing that at 900 or 930 nm anyway. In that sense, the visible beam is only a first approximation.

    PR: But this also means that you have to be quite tall, because otherwise you cannot reach the adjustment screws of the mirrors and at the same time look at the screen to check the fluorescence of the slide…

    BP: Well, you need some access to those screws and a clear visual path to the computer monitor. You can walk around the table and do it from the back, as long as you can see the computer screen, right?

    PR: Yes… probably I was just thinking about some situations in the past where I tried to do this myself and needed to stretch quite far to reach the adjustment screw and at the same time look around the corner to see the screen …

    BP: Have you tried moving the screen?

    PR: Not really … okay, I think you’ve identified the problem, it’s just laziness from my side! – But one more question about objectives: what do you think about two-photon mesoscopes with FOVs of several millimeters? Are they more difficult to build or maintain? Do you think they will become more standard or is it just a trend?

    BP: It completely depends on the application. If there are experiments that you can’t do with a standard FOV microscope, you need a wide FOV microscope. If you want to image two areas simultaneously with cellular resolution that are too far apart for a normal FOV, you don’t really have that much of a choice. A microscope like that is certainly more difficult to build, because you need custom optics for it, which are really expensive, and that is something that will prevent them from becoming really standard in every lab very soon. A lot of experiments don’t require such large FOV microscopes.

    PR: So you don’t think that these objectives or lenses will become much cheaper in the future and allow them to become more standard?

    BP: I don’t think they’ll go down in price very much. And they’re also difficult to maintain, and you need custom pre-chirpers. You basically need a dedicated imaging engineer in the lab who’s maintaining those microscopes, and even if you buy it commercially, for example the 2P RAM mesoscope from Thorlabs, you need someone who’s working with that microscope every day to monitor its performance and fine tune it and so on and so forth. I hope that we’ll see a few more mesoscopes popping up in the future, because there are very interesting questions that you can answer with them, and maybe the prices will come down a little bit. But I don’t think they’ll come down far enough for it to be a standard thing that everyone has.

    “I wouldn’t be surprised if a three-photon microscope is on the cards at some point. We haven’t done it yet, but if someone asks, I’ll be happy to build one.”

    PR: Do you also have any experience with setting up confocal microscopes or light-sheet microscopes and, if yes, how is this different from setting up two-photon microscopes?

    BP: I have not set up a confocal microscope so far, but I have set up a mesoSPIM light sheet microscope that your colleague Fabian [Voigt] in Fritjof [Helmchen]’s lab has designed. It was a very different experience in the sense that this was probably the first time that we’ve built something where we had basically no input in the design, and we were following someone else’s instructions. That was a little bit daunting, simply because I’d never done it before, but Fabian’s documentation is just so excellent that it turned out to be not a problem at all, and in that sense it was not much different to what we usually do when building a two-photon.

    PR: Do you also have any plans of building a three-photon microscope?

    BP: I’m going to build whatever people ask me to build. We’ve done a lot of 2p microscopes, but we’ve also built wide-field microscopes, we’ve built a mesoSPIM, we’re working on a microscope for in-situ sequencing, I’ve helped people with LabView coding. Whatever it is that people ask me, if I have time to do it and it sounds interesting, I’ll do it. And I wouldn’t be surprised if a three-photon microscope is on the cards at some point. We haven’t done it yet, but if someone asks, I’ll be happy to build one.

    PR: So, even if I gave you a lot of money to make you build a 3D AOD-based two-photon scanning microscope, would you give it a try? I’ve heard that it is extremely challenging to make this run stably.

    BP: I would certainly try it – and get the right people involved. I was actually a co-author on an AOD paper some ten years ago with people from Angus Silver’s lab. AOD systems are a little bit finicky, but with the right person, with the right project, with the right collaborators on board, I don’t see why someone who wants an AOD system shouldn’t attempt to build one. I’m sure that some of these teething problems that any new technology always has will be ironed out over the next few years

    PR: So you’re quite optimistic about the future role of AOD scopes for two-photon microscopy?

    BP: For the right applications – yes.

    PR: As we mentioned you also provide your service in order to help your customers save costs. If a lab really wants to save money, would you recommend to buy a fixed-wavelength laser for two-photon microscopy? I’m also not sure whether there are already some 920 nanometer lasers around …

    BP: There are now a few manufacturers that build fixed wavelength 920 nanometer lasers, and if someone says, all I’m going to do with this microscope for the next three or four years is GCaMP imaging and I just want to have a workhorse for that, then that’s certainly a good option. If it’s a young lab that only has a single two-photon microscope in the lab, and they don’t know exactly what sort of projects might come along next year and what sort of dyes they might be using next year, then it’s a bit of a risk to bet all your money on a single wavelength. This is probably more something for labs that have another two-photon with a tunable laser, where they can do experiments in the red or where they can explore other dyes that aren’t excitable at 920 nm.

    PR: Do you have examples for companies which sell fixed wavelength lasers at 920 nm?

    BP: Coherent are selling one now, the Axon 920; Spark Lasers have a few options for 920 nm; there’s Menlo, a company in Munich that sells the Ylmo-930; Toptica have a 920 model, also NKT Photonics – there’s quite a few around now. I haven’t actually tried any of them yet, but it’s certainly going in a direction where we’ll be seeing these more often in the field.

    PR: Another technical question – you mentioned it already: what’s your opinion on multiplexed acquisition? Will it remain a niche product like the mesoscopes, or do you think it will become much more standard?

    BP: Again it depends completely on your application … if you want to image two areas simultaneously without having to jump between them – whether that’s on a mesoscope where you image two different brain areas that are millimeters apart, or whether you want to image a single neuron and you want to image soma and spines both with very zoomed-in resolutions, but without having to jump between them – then multiplexed acquisition can be the right technique. If you don’t have the right question for multiplexed acquisition, then there’s no point getting it. All of these things are only useful in a very particular context that depends on the scientific question that you want to answer.

    PR: I always thought that multiplexed acquisition might be particularly difficult to implement because it’s not only challenging in terms of hardware and optical alignment, but also the software to disentangle the two multiplexed photon streams is not trivial. I was thinking that this combination of both hardware and software challenges might be a bottleneck which prevents many people from doing it?

    BP: Well… you can also de-multiplex the channels in hardware using an analog system. Spencer Smith and Jeffrey Stirman used a nice system in their 2016 Nature Biotechnology paper with a wide FOV (paper link), where they actually had an analog photon-counting system and then just acquired with a standard data acquisition system. They didn’t need to change anything in software because all the photon counting was done in the analog domain. But now, with these gigahertz data acquisition systems, you can acquire the data fast enough, get the laser timing and then assign different acquisition time bins to different channels. Scanimage can do that now, so it’s not really a challenge any more.

    PR: Do you have an opinion about the new vDAQ system of Scanimage? I think it’s not based on National Instruments hardware any more.

    BP: We’ve built a couple of microscopes with those systems, and they seem very nice, very user-friendly. There’s no obvious downside, although I haven’t had a chance to really observe them over the same time periods as I have with National Instruments for over 20 years. But I have very high hopes for these systems, and we’re using them as standard now. The only situation where we’re not using them at the moment is when we have to count photons, because the data acquisition speed is currently 125 MHz max on the vDAQ. But there will be a new vDAQ version coming out later this year, with high-speed acquisition that will then be suitable for photon counting.

    “I had to fly to Okinawa to build a microscope, but I didn’t know whether my toolkit would be there, too.”

    PR: I see. Maybe, to finish up, some fun questions… or maybe not so much fun, let’s see. During your time at INSS, what was your most challenging project?

    BP: One of the first microscopes we built was in Okinawa, Japan. Shipping all the microscope parts to Okinawa was a bit of a challenge. Three of the four boxes arrived without problem, but the box with my toolkit didn’t arrive and was completely lost for about a week or so. UPS didn’t know where it was. They had scanned it in Tokyo, but then lost track of it and had absolutely no idea where it was. I had to fly to Okinawa to build a microscope, but I didn’t know whether my toolkit would be there, too. I had lots of spare parts in the toolkit, and all sorts of specialist tools that were difficult to replace in the shortness of time. That was a challenge to my otherwise unshakable optimism … In the end, the toolkit did arrive and everything was fine; I built the microscope, no problem with that. But then I needed to ship the toolkit back, and UPS kept cancelling the booking and no one on the customer service hotline knew why. We eventually shipped it back with Fedex. It was all very annoying, and I then decided to get a shipping agent who’s now managing all of our shipping for us, and he’s been brilliant.

    PR: Okay, this sounds like a rough start…

    BP: Yes … having these useful conversations with UPS customer service … It makes my blood boil just thinking about it.

    PR: What was the most expensive device you destroyed by accident?

    BP: I don’t really know, I don’t remember.

    PR: You never destroyed an objective?

    BP: I never destroyed an objective, never destroyed a laser; I’ve destroyed scan mirrors, ETLs, stuff like that, probably a few other items in that price range. But I move on from that pretty quickly. I always think of it as a tuition fee that I have to pay, and then I forget about the incident. But the knowledge of what not to do stays with me.

    PR: Which skill do you wish you have learned earlier that would be of use for your current job?

    BP: Hm, all of them! I would love to have university degrees in electronic engineering and optical physics and project management, computer science, business administration, and applied math. Almost every technical thing or business thing that you could learn at a university would be in some way useful to my current job. But I also have to be realistic about how much I can do with the available time. These disciplines have crossed my path sort of superficially, and I’ve picked up what I can. I wish I had a really solid foundation in all of them, but I have to live with my limitations.

    PR: This sounds quite modest, given your expertise in so many domains… if you had to pick one, what would you learn if you had one year for that?

    BP: Probably math. I’d really like to go back to undergraduate level math and learn all the foundations properly.

    PR: From your long experience in research and as a consultant, what kind of advice would you give to students or postdocs who want to learn the skills which are needed to understand a microscope or, more generally, to set up experiments?

    BP: You just have to start, just go and do it. If you want to set up a microscope, go online, google “how to set up a microscope”, and then click your way to the websites where you can find how to set up a microscope. Maybe someone recommends to go to a course, maybe someone recommends a particular Youtube video. You’ll find all the resources that you need. This is such a great time to be alive, because you can find everything that you need online. You can apply for courses like the CSHL course that we discussed about, or TENSS, or numerous other imaging courses. If you don’t get into any of those courses, you can still learn it all online and just start building. A lot of people now offer very simple 3D-printed parts to set up basic optics and teach yourself the skills. You don’t even have to wait until you’re a student or a postdoc, you can do that as a little school project when you’re 12 years old, because all the learning resources are online.

    “I would recommend to stop thinking about a career. I would recommend to think about just getting better and better at whatever it is that floats your boat.”

    PR: So you would encourage self-learning, because that’s the way to learn what you have learned yourself?

    BP: It’s one way that works for me. Other people have different working styles, and your own working style emerges when you start doing something.

    PR: What would be your advice for young scientists like PhD candidates or postdocs who think about a career like yours?

    BP: I would recommend to stop thinking about a career. I would recommend to think about just getting better and better at whatever it is that floats your boat; if you work more like an artist or an artisan and just focus on improving whatever your chosen art or your chosen craft is, then you’re going to get good at it, and then you’ll enjoy doing it. And if you keep an open mind, intriguing opportunities will pop up. And if you pursue these opportunities whenever they present themselves, then you’ll end up with the very tortuous career trajectory that I have, that doesn’t seem to make any obvious sense from outside. But for me, internally, it had a very natural flow. You’re obviously also going to need a massive amount of good luck; but I don’t really have any advice on how to get lucky.

    On a side note, for anyone who’s considering starting their own business or doing something on their own, there’s an old blog post written by a banjo player called Danny Barnes. He writes about how to make a living by playing music (https://dannybarnes.com/blog/how-make-living-playing-music), and while the blog post is ostensibly about music, there’s a lot of advice that applies to any self-employed person, not just musicians; and also not just to self-employed people, it applies to anyone who is in some way in a largely self-directed job – which I guess is the case for most scientists. There are a few paragraphs in there that are more specific to music, but I think it’s just a very good read on how you want to conduct business and life with other people and make a living from it.

    PR: I’m curious, and I’ll check it out! … I think it has become obvious by now that you’re a big music aficionado. On Twitter, you describe yourself, among others, as ‘Bluegrass Dobroist’. Could you explain this to somebody without any clue, like myself?

    BP: A Dobro is an American instrument, it’s like an acoustic guitar that has an aluminium resonator cone built into the body. Originally, it was invented to make a normal guitar louder, a bit like a speaker cone that picks up the vibrations from the strings and projects them outward. The Dobro was invented in the 1920s to make the guitar a little bit louder to be heard over orchestras, and it was kind of popular for a few years, until someone invented an electric guitar that you could just very easily make a lot louder, and then the Dobro fell into obscurity. It’s played in a lap style, and you’re not fretting the strings with your fingers like on a normal guitar, but you use a steel bar that slides up and down the strings.

    (Since I did not fully understand the following explanations, he pulls out a Dobro and simply shows to me via video how it works to play a Dobro.)

    PR: And what is the meaning of ‘bluegrass’?

    BP: Bluegrass originally comes from the American state of Kentucky. Kentucky has a certain type of grass that has a sort of a blue appearance, and that’s why Kentucky is called the bluegrass state. There was a band in the 1940s that came from Kentucky; the band leader was called Bill Monroe and this band was called the Bluegrass Boys. Bill Monroe and the Bluegrass Boys played a very new and unique style of acoustic country music, and then other people started copying that style, and eventually because of the name of the band the style became known as Bluegrass music, and that evolved into a whole genre of music. Now, there’s tons of bluegrass bands, and bluegrass music, bluegrass festivals, and there’s a Grammy for bluegrass music. So, from this one band in the 1940s a very huge branch of music has emerged.

    Bruno Pichler and the Hot Rock Pilgrims.

    PR: Interesting, I didn’t know that.

    BP: I’ll be most happy to talk a lot more about bluegrass music all day long! I love it – I’ve been really involved in this scene for the last 12 years or so, going to festivals almost every weekend – obviously not now with the pandemic, and generally a little less since I started the company and since we had a baby two years ago. I’ve got a lot of other things to do now, but I’m still very much connected to the whole music scene and to the guys in the band and all that. Sometimes during the time when I worked at Scientifica, I was playing five, six, seven gigs a month even though I was living here in East Sussex and drove an hour and a half or two hours into London after work to play gigs and come back during the night to be back at Scientifica in the morning…

    PR: At the end, is there anything else you want to share?

    BP: I want to give a quick shout-out to my team, Angelos, Eleanor, Mark and Simon, who are just a massive pleasure to work with.
    Other than that, if people want any sort of clarification on the things that I’ve mentioned, if people are thinking about transitioning from academia to industry and there are questions popping up, send me an email or hit me up on twitter and I’ll be quite happy to answer questions and give advice!

    PR: Thank you. I think you gave already a lot of good advice here!

    BP: I’m glad to hear that.

    PR: Thank you very much.

    (c) Bruno Pichler

    in Peter Rupprecht on September 25, 2020 08:19 AM.

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    Update: TeX Live 2020 Release October 1, 2020

    The arXiv development team is pleased to announce a major release of the arXiv TeX compilation system, which is 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 update, set to release on October 1, 2020, provides enhanced local add-ons and support for newer font sets. The development team also used this opportunity to address 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.

    Authors should be aware that works submitted between now and September 30, 2020 must adhere to current arXiv TeX guidelines (here and here). Works prepared in accordance with TeX Live 2020 are welcome starting after 8am EDT on October 1, 2020.

    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.

    TeX has many advantages that make it ideal for the archives: it is plain text, compact, and freely available for all platforms, and it also produces high-quality output.

    in arXiv.org blog on September 24, 2020 07:35 PM.

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    Mental health researcher uses AI to achieve what’s important to patients

    A fascinating journey from football data scientist to mental health researcher and team leader

    in Elsevier Connect on September 24, 2020 12:20 PM.

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    Even When You’re A Member Of An Elite Group, It Can Be Demoralising To Rank Lower Than Your Peers

    By Matthew Warren

    Imagine that you are a high-achieving student at a school which, overall, doesn’t perform that well. You know that your grades are better than most of your peers’, so you probably rate your academic ability quite high. You are, in other words, a big fish in a small pond. 

    Now you transfer to a school in which the other students consistently get top marks, perhaps even better than yours. You’re now the small fish in a big pond, and although your own ability has remained the same, you begin to doubt yourself and actually rate yourself lower than you had before.

    This “big-fish-little-pond” effect shows that our academic self-concept can be profoundly shaped by how we compare ourselves to our peers. Now a study in Social Psychological and Personality Science has found that the size of this comparison matters: the effect is even more pronounced when people are extremely high achieving in very low ranked groups, or vice-versa.

    It might seem obvious that when people make more extreme comparisons with their peers, their self-evaluations should receive more of a boost (or take more of a hit, depending on the direction of that comparison). But as Ethan Zell and Tara Lesick from the University of North Carolina note in their new paper, no-one had actually looked into this.

    In the first study, the pair asked 187 people to complete a verbal reasoning test which involved completing sentences. Participants were then told that the same task had been completed by other students from their own university, as well as students from 39 other universities.

    Participants received different information about how they had done relative to their peers at their university, and how well their university scored compared to the other institutions. There were four conditions: big-fish-little-pond (participants did better than 65% of peers; university ranked better than 35% of other institutions); little-fish-big-pond (participants did better than 35% of their peers; university ranked better than 65% of others); huge-fish-tiny-pond (participants did better than 85% of peers; university ranked above just 15% of others); and tiny-fish-huge-pond (participants did better than only 15% of peers; university outranked 85% of others).

    Participants then rated their own verbal ability and performance on the test. As expected, big fish in little ponds — i.e. those who read that they were somewhat above average in a somewhat below average group — gave themselves better self-evaluations than little fish in big ponds. But this effect was accentuated for the other two conditions: huge fish in tiny ponds — i.e. those who read that they were far above average in a far below average group — rated themselves as even better than big fish. Tiny fish in huge ponds rated themselves as even worse than little fish.

    In a subsequent study, the team looked at what happened to this effect when people also received information about their overall level of performance. This is important because in a group that is far above average, someone who scores well below average for that group could still have a pretty good objective performance.

    In this study, some participants in the huge-fish-tiny-pond condition were told they had done better than 35% of all American test-takers, while some in the tiny-fish-huge-pond condition were told they had done better than 65% of Americans.  This meant that participants in the huge-fish-tiny-pond group were 30 percentile points lower than those in the tiny-fish-huge-pond group. And yet, the effect still occurred (albeit at a smaller scale): they rated their abilities as higher than those in the latter group.

    Finally, the researchers found evidence that this effect is driven by people focussing on their own rank within a group, rather than on how their group compares to others. Participants ranked extremely highly in their group rated their abilities as high no matter whether the group was itself of high or low rank. Similarly, those who ranked low in their group rated their ability as low, regardless of their group’s rank.

    Overall the work shows that even if you are a member of an elite group, it can be demoralising to learn that you are a “tiny fish” who is performing worse than your peers, the authors write. Further work is needed to see whether this effect extends to real-world situations, and explore what its repercussions are for people’s career and study choices.

    Taking Social Comparison to the Extremes: The Huge-Fish-Tiny-Pond Effect in Self-Evaluations

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

    in The British Psychological Society - Research Digest on September 24, 2020 12:14 PM.

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    2-Minute Neuroscience: Deep Brain Stimulation

    Deep brain stimulation is a neurosurgical approach that involves the use of brain-implanted electrodes to treat a variety of neurological and psychiatric conditions. In this video, I discuss the uses, general procedure, and hypothesized mechanisms of deep brain stimulation.

    in Neuroscientifically Challenged on September 24, 2020 10:32 AM.

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    Pro-Environmental Beliefs Are Less Likely To Lead To Action Among Those Who Believe In A Controlling God

    By Emma Young

    We all know that it’s vital that we take action to reduce the harm we do to the environment. So understanding the barriers to such action is critical, too. A new paper, published in Personality and Social Psychology Bulletin, identifies a potentially important one: when people believe that it’s important to protect the environment, they’re less likely to act on those beliefs if they’re more religious.

    Kimin Eom at Singapore Management University and colleagues studied Americans — and when they talk about people being “religious”, they’re really talking about being Christian. These caveats are important to highlight up front.

    In the first of three studies, the team analysed pre-existing data on a nationally representative sample of 3,052 US adults. They looked specifically at answers to three categories of questions. Firstly, questions assessed how strongly an individual endorsed the ideas that a) the world is getting hotter; and b) human activity is an important driver of this. Secondly, questions related to “religiosity” — a) their belief in the importance of religion; and b) how often they attend religious services. Finally, the team looked at responses to questions that assessed their level of support for pro-environmental policies.

    The researchers found that climate change beliefs predicted support for pro-environmental policy less strongly among individuals higher in religiosity. In other words, “These results supported the idea that environmental beliefs are less in line with pro-environmental support among those who are more, relative to less, religious.” These results held even when team took into account/controlled for a range of demographic variables, including political orientation, gender, income, education, age and ethnicity.

    In a second study, the team dug deeper into this finding. A total of 424 US students, half from a Christian college and half from a non-religious public university, both in California, completed a series of questionnaires. The first scale explored the extent to which they believed in climate change. The second measured religiosity. The third measured how strongly the participants believed in a “controlling god” — a god who has a plan and controls events in the world. They were then asked to report how often they would perform six environmentally friendly behaviours (such as buying green products instead of regular products and unplugging appliances at night) over the next six months.

    The participants also gave demographic data — and a few potentially important differences between the groups stood out. Namely, the Christian college students were more likely to be Republican and there were fewer women in the Christian group. The team took these group differences into account in their analysis, which revealed that higher religiosity was associated with a stronger belief in a controlling god — and it was the strength of this belief (rather than religiosity per se) that affected their intentions to act in a more environmentally friendly way. (Those with the strongest beliefs in a controlling god were the least likely to indicate that they’d be engaging in such behaviours.)

    Why should this be the case? The authors argue that, if you believe that a god controls what happens in the world, you are less likely to think that any actions that you take will change any given outcome — and so you are less likely to change your behaviour.

    The results from these studies were correlational, however. To explore the idea that belief in a controlling god makes people less likely to act to help the environment, the team ran a third study with 730 Christians. The team measured their environmental beliefs as before. Half then read a passage that described God as the ultimate controller of the world. This was designed to prime them with the idea that God is controlling. The other read an article about why Pluto had been declassified as a planet (a text chosen to have no influence on attitudes to God). Participants also rated the extent to which four adjectives (controlling, commanding, caring, compassionate ) described a god. Next, their intentions to behave in a pro-environmental way were assessed (as in the previous study) and they provided demographic data.

    Climate change beliefs predicted intentions to behave pro-environmentally less strongly when a participant had a stronger concept of God as being controlling. Or to put it another way, believing in a controlling god “weakens the association between environmental beliefs and pro-environmental support”. This study confirms that it’s the belief in a controlling god, rather than a belief in God per se, that weakens that association, the team argues.

    As already noted, though, the religious people in this study were Christians, and they were all American. So the findings may or may not extend to people with other religious beliefs. Also, these studies featured a lot of self-report and assessments of “intention” to act. It would of course be interesting to know whether belief in a controlling god makes any difference to actual, real world behaviour.

    However, as the researchers also point out, when it comes to understanding which sociocultural factors influence environmental attitudes and behaviour, there is still a lot to learn. This work at least starts to plug part of that gap.  

    Religiosity Moderates the Link Between Environmental Beliefs and Pro-Environmental Support: The Role of Belief in a Controlling God

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

    in The British Psychological Society - Research Digest on September 23, 2020 01:15 PM.

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    How to position your journal to serve different needs

    3 strategies for selecting journal content when you’re faced with multiple, or opposing, objectives

    in Elsevier Connect on September 23, 2020 11:36 AM.

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    Our Malady, by Timothy Snyder: book review

    US Historian Timothy Snyder is expert for murderous totalitarian systems. Now, he himself almost died when he succumbed to the inhuman US profiteering industry which America calls healthcare.

    in For Better Science on September 23, 2020 10:45 AM.

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    Report: Mapping research to advance the SDGs

    Elsevier’s analysis reveals gaps and strengths to support the UN’s 2030 Sustainable Development Goals

    in Elsevier Connect on September 22, 2020 09:26 PM.

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    Simultaneous calcium imaging and extracellular recording from the same neuron

    Calcium imaging is a powerful method to record from many neurons simultaneously. But what do the recorded signals really mean?

    This question can only be properly addressed by experiments which record both calcium signals and action potentials from the same neuron (ground truth recordings). These recordings are technically quite challenging. So we assembled several existing ground truth datasets, and in addition recorded ground truth datasets ourselves, totaling >200 neuronal recordings.

    This blog blog posts contains raw movies together with recorded action potentials (black; also turn on your speakers for the spikes!) and the recorded ΔF/F of the calcium recording (blue). These ground truth data are a very direct way for everybody into calcium imaging to get an intuition about what is really going on. (Scroll down if you want to see recordings in zebrafish!)

    Recording from a L2/3 neuron in visual cortex with GCaMP6f, tg(Emx1), from Huang et al., bioRxiv, 2019; a very beautiful recording. Replayed with 2x speed.

    Recording from a L2/3 neuron in visual cortex with GCaMP6f, tg(Emx1), from Huang et al., bioRxiv, 2019. Stronger contamination from surrounding neuropil.

    Recording from a L2/3 neuron in visual cortex with GCaMP6f, tg(Emx1), from Huang et al., bioRxiv, 2019. Note that single action potentials don’t seem to have any impact at all. – The negative transients in the calcium trace stem from center-surround neuropil decontamination (activity of the surround is subtracted).

    Recording from a L2/3 neuron in visual cortex with GCaMP6s, tg(Emx1), from Huang et al., bioRxiv, 2019.

    Recording from a L2/3 neuron in visual cortex with GCaMP6s, tg(Emx1), from Huang et al., bioRxiv, 2019.

    Recording from a L2/3 neuron in visual cortex with GCaMP6f, virally induced, from Chen et al., Nature, 2013. From the left, you can see the shadow of the patch pipette used for recording of extracellular signals.

    Something completely different: recording from a pyramidal neuron in Ca3 with R-CaMP1.07, virally induced, recorded by Stefano Carta, from Rupprecht et al., bioRxiv, 2020. What appears as single events are actually bursts of 5-15 action potentials with inter-spike-intervals of <6 ms.

    A recording that I performed myself in adult zebrafish, in a subpart of the homolog of olfactory cortex (aDp) with GCaMP6f, tg(neuroD), in Rupprecht et al., bioRxiv, 2020. Around second 20, it is visible that even a single action potential can be seen in the calcium signal. However,this was not always the case in other neurons that I recorded from the same brain region.

    Again a recording that I did in adult zebrafish, in the dorsal part of the dorsal telencephalon with GCaMP6f, tg(neuroD), in Rupprecht et al., bioRxiv, 2020.

    What can you do if you want to detect single isolated action potentials with calcium imaging? GCaMP, due to its sigmoid non-linearity, is by often a bad choice and will be strongly biased towards bursts. Synthetic indicators, however, are very linear in the low-calcium regime. – This is a recording that I did myself in adult zebrafish, in a subpart of the homolog of olfactory cortex (pDp) with the injected synthetic indicator OGB-1 in Rupprecht et al., bioRxiv, 2020. Although the temporal resolution of the calcium recording is rather low, the indicator clearly responds to single action potentials. As another asset, the indicator not only fills the cytoplasm of the neuron in a ring-like shape, which makes neuropil-contamination much less of an issue compared to GCaMPs.

    Another recording that I performed in adult zebrafish, in a subpart of the homolog of olfactory cortex (pDp) with the injected synthetic indicator Cal-520 in Rupprecht et al., bioRxiv, 2020. This indicator is much more sensitive compared to OGB-1, but also diffuses less well after bolus injection. – These two minutes of recording only contain 4 spikes (this brain region really is into low firing rates in general), but you can clearly see all of them. If this were a GCaMP recording, you would probably see only a flat line throughout the entire recording.

    For more information, including all 20 datasets with >200 neurons (rather than these excerpts from 11 neurons), check out the following resources:

    in Peter Rupprecht on September 22, 2020 08:51 AM.

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    What do Chinese researchers think about the peer review process?

    The majority of Chinese researchers trust the journal peer review system, while calling for clear instructions, recognition, and a transparent, speedy process

    in Elsevier Connect on September 22, 2020 08:06 AM.

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    The lethal nonsense of Michael Levitt

    “It is not easy when people start listening to all the nonsense you talk. Suddenly, there are many more opportunities and enticements than one can ever manage.”

    – Michael Levitt, Nobel Prize in Chemistry, 2013

    In 1990 Glendon MacGregor, a restaurant waiter in Pretoria, South Africa, set up an elaborate hoax in which he posed as the crown prince of Liechtenstein to organize for himself a state visit to his own country. Amazingly, the ruse lasted for two weeks, and during that time MacGregor was wined and dined by numerous South African dignitaries. He had a blast in his home town, living it up in a posh hotel, and enjoying a trip to see the Blue Bulls in Loftus Versfeld stadium. The story is the subject of  the 1993 Afrikaans film “Die Prins van Pretoria” (The Prince of Pretoria). Now, another Pretorian is at it, except this time not for two weeks but for several months. And, unlike MacGregor’s hoax, this one does not just embarrass a government and leave it with a handful of hotel and restaurant bills. This hoax risks lives.

    Michael Levitt, a Stanford University Professor of structural biology and winner of  the Nobel Prize in Chemistry in 2013, wants you to believe the COVID-19 pandemic is over in the US. He claimed it ended on August 22nd, with a total of 170,000 deaths (there are now over 200,000 with hundreds of deaths per day). He claims those 170,000 deaths weren’t even COVID-19 deaths, and since the virus is not very dangerous, he suggests you infect yourself. How? He proposes you set sail on a COVID-19 cruise.

    Royal Caribbean Wonder of the Sea world's largest cruise ship under  construction - Business Insider

    Levitt’s lunacy began with an attempt to save the world from epidemiologists. Levitt presumably figured this would not be a difficult undertaking, because, he has noted, epidemiologists see their job not as getting things correct“. I guess he figured that he could do better than that. On February 25th of this year, at a time when there had already been 2,663 deaths due to the SARS-CoV-2 virus in China but before the World Health Organization had declared the COVID-19 outbreak a pandemic, he delivered what sounded like good news. He predicted that the virus had almost run its course, and that the final death toll in China would be 3,250. This turned out to be a somewhat optimistic prediction. As of the writing of this post (September 21, 2020), there have been 4,634 reported COVID-19 deaths in China, and there is reason to believe that the actual number of deaths has been far higher (see, e.g. He et al., 2020, Tsang et al., 2020, Wadham and Jacobs, 2020).

    Instead of publishing his methods or waiting to evaluate the veracity of his claims, Levitt signed up for multiple media interviews. Emboldened by “interest in his work” (who doesn’t want to interview a Nobel laureate?), he started making more predictions of the form “COVID-19 is not a threat and the pandemic is over”. On March 20th he said that “he will be surprised if the number of deaths in Israel surpasses 10“. Unfortunately, there have been 1,256 COVID-19 deaths in Israel so far with a massive increase in cases over the past few weeks and no end to the pandemic in sight. On March 28th, when Switzerland had 197 deaths, he predicted the pandemic was almost over and would end with 250. Switzerland are now seen 1,762 deaths and a recent dramatic increase in cases has overwhelmed hospitals in some regions leading to new lockdown measures. Levitt’s predictions have come loose and fast. On June 28th he predicted deaths in Brazil would plateau at 98,000. There have been over 137,000 deaths in Brazil with hundreds of people dying every day now. In Italy he predicted on March 28th that the pandemic was past its midpoint and deaths would end at 17,000 – 20,000. There have now been 35,707 deaths in Italy. The way he described the situation in the country at the time, when crematoria were overwhelmed, was “normal”.

    I became aware of Levitt’s predictions via an email list of the Fellows of the International Society of Computational Biology on March 14th. I’ve been a Fellow for 3 years, and during this time I’ve received hardly any mail, except during Fellow nomination season. It was therefore somewhat of a surprise to start receiving emails from Michael Levitt regarding COVID-19, but it was a time when scientists were scrambling to figure out how they could help with the pandemic and I was excited at the prospect of all of us learning from each other and possibly helping out. Levitt began by sending around a PDF via a Dropbox link and asked for feedback. I wrote back right away suggesting he distribute the code used to make the figures, make clear the exact versions of data he was scraping to get the results (with dates and copies so the work could be replicated), suggested he add references and noted there were several typos (e.g. the formula D_n = C_nP_0 + C_{n-1}P_1 + C_{n-2}P_2 + \ldots + C_{n-29}P_2 clearly had wrong indices). I asked that he post it on the bioRxiv so it could receive community feedback, and suggested he fill in some details so I and others could better evaluate the methods (e.g. I pointed out that I thought the use of a Gaussian for P_n was problematic).

    The initial correspondence rapidly turned into a flurry of email on the ISCB Fellows list. Levitt was full of advice. He suggested everyone wear a mask and I and others pushed back noting, as Dr. Anthony Fauci did at the time, that there was a severe shortage of masks and they should go to doctors first. Several exchanges centered on who to blame for the pandemic (one Fellow suggested immigrants in Italy). Among all of this, there was one constant: Levitt’s COVID-19 advice and predictions kept on coming, and without reflection or response to the well-meaning critiques. After Levitt said he’d be surprised if there were more than 10 deaths in Israel, and after he refused to send code reproducing his analyses, or post a preprint, I urged my fellow Fellows in ISCB to release a statement distancing our organization from his opinions, and emphasizing the need for rigorous, reproducible work. I was admonished by two colleagues and told, in so many words, to shut up. 

    Meanwhile, Levitt did not shut up. In March, after talking to Israeli newspapers about how he would be surprised if there were more than 10 deaths, he spoke directly to Israeli Prime Minister Benjamin Netanyahu to deliver his message that Israel was overreacting to the virus (he tried to speak to US president Donald Trump as well). Israel is now in a very dangerous situation with COVID-19 out of control. It has the highest number of cases per capita in the world. Did Levitt play a role in this by helping to convince Netanyahu to ease restrictions in the country in May? We may never know. There were likely many factors contributing to Israel’s current tragedy but Levitt, by virtue of speaking directly to Netanyahu, should be scrutinized for his actions. What we do know is that at the time, he was making predictions about the nature and expected course of the virus with unpublished methods (i.e. not even preprinted), poorly documented data, and without any possibility for anyone to reproduce any of his work. His disgraceful scholarship has not improved in the subsequent months. He did, eventually post a preprint, but the data tab states “all data to be made available” and there is the following paragraph relating to availability of code: 

    We would like to make the computer codes we use available to all but these are currently written in a variety of languages that few would want to use. While Dr. Scaiewicz uses clean self-documenting Jupyter Python notebook code, Dr. Levitt still develops in a FORTRAN dialect call Mortran (Mortran 1975) that he has used since 1980. The Mortran preprocessor produces Fortran that is then converted to C-code using f2c. This code is at least a hundred-fold faster than Python code. His other favorite language is more modern, but involves the use of the now deprecated language Perl and Unix shell scripts.

    Nevertheless, the methods proposed here are simple; they are easily and quickly implemented by a skilled programmer. Should there be interest, we would be happy to help others develop the code and test them against ours. We also realize that there is ample room for code optimization. Some of the things that we have considered are pre-calculating sums of terms to convert computation of the correlation coefficient from a sum over N terms to the difference of two sums. Another way to speed the code would be to use hierarchical step sizes in a binary search to find the value of lnN that gives the best straight line.

    Our study involving as it did a small group working in different time zones and under extreme time pressure revealed that scientific computation nowadays faces a Babel of computer languages. In some ways this is good as we generally re-coded things rather than struggle with the favorite language of others. Still, we worry about the future of science when so many different tools are used. In this work we used Python for data wrangling and some plotting, Perl and Unix shell tools for data manipulation, Mortran (effectively C++) for the main calculations, xmgrace and gnuplot for other plotting, Excel (and Openoffice) for playing with data. And this diversity is for a group of three!

    tl;dr, there is no code. I’ve asked Michael Levitt repeatedly for the code to reproduce the figures in his paper and have not received it. I can’t reproduce his plots.

    Levitt now lies when confronted about his misguided and wrong prediction about COVID-19 in Israel. He claims it is a “red herring”, and that he was talking about “excess deaths”. I guess he figures he can hide behind Hebrew. There is a recording where anyone can hear him being asked directly if he is saying he will be surprised with more than 10 COVID-19 deaths in Israel, and his answers is very clear: “I will be very surprised”. It is profoundly demoralizing to discover that a person you respected is a liar, a demagogue or worse. Sadly, this has happened to me before.

    Levitt continues to put people’s lives at risk by spewing lethal nonsense. He is suggesting that we should let COVID-19 spread in the population so it will mutate to be less harmful. This is nonsense. He is promoting anti-vax conspiracy theories that are nonsense. He is promoting nonsense conspiracy theories about scientists. And yet, he continues to have a prominent voice. It’s not hard to see why. The article, similar to all the others where he is interviewed, begins with “Nobel Prize winner…”

    In the Talmud, in Mishnah Sanhedrin 4:9, it is written “Whoever destroys a soul, it is considered as if he destroyed an entire world”. I thought of this when listening to an interview with Michael Levitt that took place in May, where he said:

    I am a real baby-boomer, I was born in 1947, and I think we’ve really screwed up. We cause pollution, we allowed the world’s population to increase three-fold, we’ve caused the problems of global warming, we’ve left your generation with a real mess in order to save a really small number of very old people. If I was a young person now, I would say, “now you guys are gonna pay for this.” 

    in Bits of DNA on September 21, 2020 09:44 AM.

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    Jan van Deursen’s senolytics: from bench to failed clinical trial

    Jan van Deursen had to resign from Mayo Clinic over bullying charges. With his company Unity Biotech's phase 2 clinical trial failed, stock devalued and staff laid-off, van Deursen sued me in German court about the reproducibility of his senolytics research.

    in For Better Science on September 21, 2020 06:00 AM.

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    Has the Stress of COVID Affected Our Brains?

    A preprint reports increases in the volume of parts of the brain after lockdown.

    in Discovery magazine - Neuroskeptic on September 19, 2020 12:00 PM.

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    Delighted customers, flexible hours – why working for Elsevier works for me

    From process mining to shorten customer wait time, to our mission to benefit humanity, “I absolutely love it here,” writes Nelly Lukwo.

    in Elsevier Connect on September 18, 2020 08:45 AM.

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    Highlights of the BMC Series: August 2020

    BMC Palliative CareVirtual reality video promotes effectiveness in advance care planning

    Person wearing a VR headset

    Watching a Virtual Reality video was found to be an effective decision-making aid for people making an advance care plan. Advance care planning offers people the opportunity to plan their future care and support, including medical treatment, while they have the capacity to do so. Legislation allowing advance care planning is relatively new in Asia and has been recently introduced in Taiwan. Taiwanese people must complete a consultation before formally documenting their wishes. However, health and legal literacy can be a barrier to people making fully-informed decisions about their future care. Wan-Ting Hsieh showed 120 people a short video in virtual reality that documented typical scenarios in end-of-life care, such as hospice home care and the withdrawal of life support. After viewing the video, participant’s preferences for not accessing the medical treatments shown and the ability to make a decision about their future care increased. The study provides evidence for how VR tools could be further rolled out as decision-making aids and bridge gaps in health and legal literacy for important decisions about their future.


    BMC Public HealthChanges in sedentary behaviour in European Union adults between 2002 and 2017

    Watching TVSedentary behaviors rose between 2002 and 2017 in the European Union, particularly in men. Sedentary behavior is an important risk factor for mortality and continues to be a public health challenge with significant health, social and economic consequences. López-Valenciano et al. analyzed data that surveyed European Union adult citizen’s physical activity and sedentary behaviors. In 2002, half of those surveyed were inactive for more than 4.5 hours each day; by 2017 this had risen to 54.5%. The researchers suggested a number of factors could account for this increase in sedentary behavior, such as longer commutes and labor-saving devices at home and work. The authors also attributed people’s interaction with technology such as smartphones and streaming services with increasing physical inactivity. The study provides supporting data for strengthening public health policies and international efforts to tackle rises in sedentary behavior.


    BMC GenomicsAnalyses of key genes involved in Arctic adaptation in polar bears suggest selection on both standing variation and de novo mutations played an important role

    Polar bearGenomic mechanisms behind the rapid adaption of polar bears to arctic environments have been revealed. Polar bears rapidly evolved several traits from its closest living relative, the brown bear, that has promoted the species’ survival in arctic environments. Castruita et al. studied the genomic mechanisms underpinning how these characteristics were selected in polar bears by analyzing the genomes of more than 100 polar bears and 33 brown bears. The analysis revealed that a combination of standing variation in ancestral gene pools and de novo mutations in polar bear lineages may have promoted the rapid adaption of polar bears to arctic environments. The study provides a comprehensive assessment of the genomic mechanisms behind how polar bears rapidly adapted to the Arctic.


    BMC Infectious DiseasesImproving the impact of non-pharmaceutical interventions during COVID-19: examining the factors that influence engagement and the impact on individuals

    People wearing masks at a bus stopCommunity compliance with non-pharmaceutical interventions in a pandemic may be influenced by the perceived severity of illness in the community. In an effort to flatten peaks of COVID-19 infections, governments have introduced various non-pharmaceutical interventions, such as social distancing, lockdowns, and the use of face-coverings. However, how much of a positive impact these interventions have relies on community understanding, engagement, and compliance. Seale et al. conducted a rapid review of the literature to study the factors that impact community engagement with government interventions. The emerging theme identified by the review was how can an environment be created that supports and promotes the adoption of non-pharmaceutical interventions in the community? The authors suggest integrating community co-design of supporting communications and materials to promote engagement and compliance with interventions.


    BMC Medical Research Methodology Protocol registration issues of systematic review and meta-analysis studies: a survey of global researchers

    Person wearing a yellow jumper typing on a laptopAlmost half of systematic review and meta-analysis authors have never registered the protocol for their study a survey finds. Registering a systematic review protocol promotes transparency, prevents bias, and duplication of work. Cochrane and other bodies recommend prospectively registering systematic review protocols but journals do not mandate it, contrasting with their registration requirements for clinical trials. Tawfik et al. surveyed 270 systematic review and meta-analysis authors to assess researchers’ knowledge and attitudes towards systematic review protocol registration. Survey respondents acknowledged a lack of knowledge surrounding obligation and importance about protocol registration. The study calls for collaborative efforts to raise awareness of the benefits of systematic review protocol registration in the research community.

    The post Highlights of the BMC Series: August 2020 appeared first on BMC Series blog.

    in BMC Series blog on September 18, 2020 07:30 AM.

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    What influences NHS Health Check behaviors?

    Cardiovascular disease (CVD) is the number 1 cause of death globally, with an estimated 17.7 million people having died from CVD conditions in 2015, representing 31% of all global deaths. In England in 2017, more than 124,000 people died from CVD[1]. Changing behaviors related to diet, physical activity, smoking and alcohol intake can reduce CVD risk. The delivery of interventions targeting these behaviors also often requires healthcare professional (HCP) behaviors to change.

    The NHS Health Check

    It is important to understand the extent to which positive behaviors are influenced across the NHS Health Check pathway

    The NHS Health Check (NHSHC), introduced in the English National Health Service (NHS) in 2009, is a national prevention program offered to adults 40-74 years old with the aim of helping them reduce their chance of having a heart attack or stroke through behavior change and, where appropriate, clinical treatment. Since then, national evaluations have highlighted the need to maximize the program’s impact by improving coverage and outputs. To address these challenges, it is important to understand the extent to which positive behaviors are influenced across the NHS Health Check pathway and encourage the promotion or minimization of behavioral facilitators and barriers respectively.

    Our study

    To date research has tended to focus on single populations, e.g. patients or GPs, and specific behaviors, e.g. attending an NHS Health Check. A synthesis of these studies would provide an overarching behavioral picture of those involved in delivery and receipt of NHS Health Checks and so provide the foundations for intervention refinement and development. Our goal was to apply behavioral science frameworks to: i) identify behaviors and actors relevant to uptake, delivery and follow up of NHS Health Checks and influences on these behaviors and ii) signpost to example intervention content.

    The most frequently identified influences were physical opportunity including HCPs having space and time to deliver NHS Health Checks and patients having money to adhere to recommendations to change diet and physical activity.

    We identified 37 studies reporting nine behaviors and influences for eight of these. The most frequently identified influences were physical opportunity including HCPs having space and time to deliver NHS Health Checks and patients having money to adhere to recommendations to change diet and physical activity. Other key influences were motivational, such as beliefs about consequences about the value of NHS Health Checks and behavior change, and social, such as influences of others on behavior change. The following techniques are suggested for websites or smartphone apps: Adding objects to the environment, e.g. provide HCPs with electronic schedules to guide timely delivery of Health Checks to target physical opportunity, Social support (unspecified), e.g. include text suggesting patients to ask a colleague to agree in advance to join them in taking the ‘healthy option’ lunch at work; Information about health consequences, e.g. quotes and/or videos from patients talking about the health benefits of changes they have made.

    Future work

    It should be noted that the recommendations flowing from our findings reflect the types of interventions that we would expect on theoretical grounds to be effective, and this is not a review of effectiveness of interventions. Additional work needs to be done to investigate the extent to which interventions to promote NHS Health Check behaviors target the barriers and facilitators identified in this review. This work would identify any missed opportunities for intervention and inform intervention design and refinement.

    This is the first study, to our knowledge, to apply theoretical models to studies focusing solely on influences on NHS Health Check behaviors and to make specific evidence-informed recommendations

    This is the first study, to our knowledge, to apply theoretical models to studies focusing solely on influences on NHS Health Check behaviors and to make specific evidence-informed recommendations for commissioners and providers, which should be considered as part of the forthcoming NHS Health Check review in order to ensure the program is implemented as effectively as possible for the next 10 years and beyond.[2]



    [1] British Heart Foundation (www.bhf.org.uk/-/media/files/research/heart-statistics/bhf-cvd-statistics—uk-factsheet.pdf)

    [2] Care DoHaS. Advancing our health: prevention in the 2020s – consultation document. In: Care DoHaS, editor. 2019.

    The post What influences NHS Health Check behaviors? appeared first on BMC Series blog.

    in BMC Series blog on September 17, 2020 05:02 AM.

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    Transparency and Trust: Peer Review Week 2020

    This post is written by PLOS’ Chief Scientific Officer Veronique Kiermer

    Peer Review Week is a time to celebrate the outstanding work of reviewers across the scholarly ecosystem. But it also serves as a call to action to examine the systems we have in place and opportunities to improve. 

    This peer review week, the theme couldn’t feel more timely. Trust in science, and peer review more specifically has taken the spotlight as doctors, researchers, and policymakers around the world collaborate to rapidly expand and communicate emerging knowledge about COVID-19. 

    At the same time, the advent of preprints in biomedical sciences has created new challenges to evaluate findings outside the traditional framework of journal peer review, and high profile journal retractions have contributed to raise doubts about the effectiveness of pre-publication peer review. With the flood of information pouring in, public readers and researchers alike face the same question: how do I identify information I can trust? 

    Does Peer Review Work?

    Peer review has long been a staple of the credibility of scientific findings for researchers and for the public.  The process embodies the norm of organized skepticism that helps generate trust in scientific findings—by testing the rigor of thinking and experimentation, and by providing authors with expert feedback to build on. But importantly, peer review is more than the traditional view of pre-publication peer review conducted behind closed doors. Peer review does not stop with publication—in many ways, it only starts there. 

    Recently, in the context of the COVID-19 pandemic, we’ve seen researchers rapidly come together after the publication of high-stake results and point out serious methodological flaws which have led to retractions of articles and withdrawals of preprints. Social media has been an unconventional, yet instrumental tool in coordinated reactions. Some have argued this is a failure of peer review, but we believe it’s actually a celebration of peer review in different forms. 

    A broader view of peer review

    While post-publication peer review remains rare, preprints offer new opportunities to leverage the community in order to address the challenges and limitations of traditional peer review. For example, reviewers and editors commonly acknowledge that it is increasingly difficult to cover all the bases of expertise required to properly analyze articles that have become much more multidisciplinary. Preprint commenting while the article is under review is one possible solution we’ve encouraged to address this gap, by opening up the opportunity for any researcher, anywhere in the world to volunteer their expertise, for consideration by the editor. While commenting on preprints is still rare, it could allow journals to channel within the traditional process the energy that the community already puts in scrutinizing new findings within their specialty before they are formally published in journals. 

    Preprints and preprint commenting can also help with another challenge of journal review: speed. PLOS journals offer authors the option to post preprints on their behalf at submission—after minimal checks for any content with potential to cause harm—so their findings can be disseminated while the journal curation process takes place.  We also participate in initiatives like Review Commons to provide journal-agnostic reviews that can accelerate the peer review process at the author’s destination journal and alleviate the strain of repeated reviews on the peer reviewer community.

    Beyond these practical issues, we must consider systemic challenges and in particular the documented biases in peer review. At PLOS we acknowledge the need to improve the diversity of our reviewer pool to help mitigate such biases and we are committed to this work

    Transparency, transparency, transparency 

    An important prerequisite for all peer review mechanisms to work as effectively as they can is transparency. 

    Transparency facilitates trust. Working to make every step of the research and publication process as Open as possible gives journals, peer reviewers, and the scholarly community more broadly, the means for scrutiny, and a clear understanding of limitations. At the same time, it gives readers deeper insight into the scientific process and the various checkpoints that uphold it. 

    From an author’s perspective, increasing transparency means making all relevant data, code, methodologies, and reagents available so that the scholarly community—starting with reviewers—can validate and reproduce the findings independently. A recent survey by the Center for Open Science indicated that researchers judging preprint credibility were influenced by cues related to open data, code and other openness measures, as well as independent verification of authors claims. 

    Publishing peer review reports as well is important as it makes evident what aspects of the article were (and were not) thoroughly scrutinized pre-publication. All PLOS journals now encourage their authors to publish their peer review history alongside the article, and the uptake is promising.

    Peer review needs better recognition 

    Transparency in peer review is also crucial to recognizing peer review as a first-rate academic output. It is time for this activity, essential to the scientific process, to be considered a scientific output in its own right and to take its due place in the context of research and researchers assessment. With published peer review reports, individual reviewers can choose to take credit by revealing their identity. But recognizing that there are circumstances that call for anonymity, even unnamed reviewers should have this opportunity, and tools like ORCID and Publons allow them to demonstrate their contributions as part of their academic profile. 

    There’s always more we can do to provide the motivation and support for reviewers’ work. Peer review transparency and other visual signs of recognition are a way to start helping researchers leverage their  peer review expertise to advance their careers. 

    Earning trust in peer review

    Despite its challenges, the traditional journal peer review process offers important opportunities to ensure fairness in peer review. And journals have a collective responsibility to make use of these opportunities. First and foremost, we can ensure that every paper reporting a rigorously designed and executed study is peer reviewed—not only the high-stakes findings and the work of well known authors. We can also take proactive measures to limit bias, such as increasing the diversity of reviewer pools, and managing competing interests. We can foster consistent review criteria, and supplement the volunteer peer review reports with additional scrutiny for elements like statistics or ethical research practices. 

    In sum, I believe there are complementary benefits of journal-organized peer review and the process that can take place more organically in the research community post-publication—whether the publication is in a journal or on a preprint server. With more transparency in the system, we can take advantage of all mechanisms of peer review to decide what to trust, and importantly peer review itself can deserve our trust. 

    The post Transparency and Trust: Peer Review Week 2020 appeared first on The Official PLOS Blog.

    in The Official PLOS Blog on September 16, 2020 03:30 PM.

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    Know Your Brain: Subthalamic Nucleus

    Where is the subthalamic nucleus?

    A coronal section of the brain with the subthalamic nucleus highlighted in red.

    A coronal section of the brain with the subthalamic nucleus highlighted in red.

    The subthalamic nucleus is a small collection of neurons situated ventral to the thalamus (i.e., below the thalamus). It is a major component of the subthalamus.

    What is the subthalamic nucleus and what does it do?

    The subthalamic nucleus is considered part of the basal ganglia. The basal ganglia are a group of subcortical nuclei that are involved in a variety of cognitive and emotional functions, but are best known for their role in movement. The precise contributions of the basal ganglia to movement still aren’t fully understood, but one popular hypothesis suggests that the basal ganglia play a critical role in facilitating desired movements, while at the same time inhibiting unwanted and/or competing movements. To read more about the basal ganglia and this purported function, see this article.

    The subthalamic nucleus is considered a critical component of basal ganglia circuits that are devoted to the suppression of unwanted movements. These inhibitory circuits are known as the indirect pathway and the hyperdirect pathway. In both pathways, the inhibition of movement is thought to be traceable back to excitatory glutamate neurons that extend from the subthalamic nucleus to stimulate GABA neurons in the globus pallidus and substantia nigra; these GABA neurons in turn exert an inhibitory influence over neurons in the thalamus that typically prompt movement when they’re excited.

    Watch this video to learn more about the indirect pathway, a circuit in the basal ganglia that includes the subthalamic nucleus and is thought to play an important role in the inhibition of movement.

    The subthalamic nucleus’ role in suppressing unwanted movements may be critical even for the simplest movements. If, for example, you are reaching out to pick up a cup of coffee, your brain must not only activate the muscles necessary for the movement, but inhibit those that would counteract the desired movement. Indeed, even when you are sitting still, unwanted movements (like your hand jerking involuntarily up in the air) must continuously be subdued by your brain. It has been hypothesized that the subthalamic nucleus plays an important role in these types of movement inhibition.

    It’s important to note, however, that the functions of the subthalamic nucleus (and basal ganglia as a whole) are not limited to movement. Recent research suggests the subthalamic nucleus may also contribute to cognitive functions like decision-making, attention, and working memory (among others). And the subthalamic nucleus may be part of circuits that have important influences on emotion as well.

    Some of our understanding of these more extensive roles for the subthalamic nucleus come from studies involving deep brain stimulation, or DBS. DBS is a surgical procedure that involves implanting an electrode in the brain. Once the electrode is in place, it can be prompted to emit electrical impulses that are hypothesized to interfere with neural activity.

    DBS has been found to be especially useful in the treatment of Parkinson’s disease. Parkinson’s disease is characterized by movement problems like slow, effortful movement, and difficulty initiating movements. It is believed that some of these movement-related symptoms stem from overactivity in the subthalamic nucleus. This increased subthalamic nucleus activity may lead to excessive inhibition of movement via the basal ganglia circuits mentioned above.

    Thus, when the electrode in DBS is positioned in or near the subthalamic nucleus, turning the device on can disrupt the inhibitory actions of the subthalamic nucleus and facilitate movement. To learn more about DBS, see this article.

    As mentioned above, the use of DBS has also helped us to appreciate the complexity of the roles of the subthalamic nucleus. Many patients who receive DBS experience not only an improvement of their Parkinsonian symptoms, but also develop side effects that include cognitive and emotional changes like memory disturbances and apathy. It has been proposed that disruption of the function of the subthalamic nucleus might be responsible for these side effects of DBS. It should be said, however, that variability in the side effects of DBS—as well as a poor understanding of exactly how DBS affects brain activity—makes it difficult to say this with certainty.

    Regardless, the evidence collected to date suggests that the subthalamic nucleus is an important area of the brain for motor control and a variety of other actions. Future research will be needed, however, to fully understand the functions of this small—but important—collection of neurons.

    References (in addition to linked text above):

    Bonnevie T, Zaghloul KA. The Subthalamic Nucleus: Unravelling New Roles and Mechanisms in the Control of Action. Neuroscientist. 2019;25(1):48-64. doi:10.1177/1073858418763594

    Heida T, Marani E, Usunoff KG. The subthalamic nucleus part II: modelling and simulation of activity. Adv Anat Embryol Cell Biol. 2008;199:1-vii.

    Temel Y, Blokland A, Steinbusch HW, Visser-Vandewalle V. The functional role of the subthalamic nucleus in cognitive and limbic circuits. Prog Neurobiol. 2005;76(6):393-413. doi:10.1016/j.pneurobio.2005.09.005

    Learn more:

    Know Your Brain: Basal Ganglia

    2-Minute Neuroscience: Indirect Pathway of the Basal Ganglia

    in Neuroscientifically Challenged on September 16, 2020 10:06 AM.

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    For geriatric nurses, the pandemic has brought unique demands and lessons

    A geriatric nursing editor shares “COVID-19 lessons learned from the voices of our geriatric nurses”

    in Elsevier Connect on September 16, 2020 09:57 AM.

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    Academic Dynasties: meet the Nussenzweigs

    Star scientists Michel and Andre Nussenzweig come from a famous family of immunologists. Clare Francis looked at some of their papers.

    in For Better Science on September 15, 2020 11:51 AM.

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    Discrepancies between calcium imaging and extracellular ephys recordings

    To record the activity from a population of neurons, calcium imaging and extracellular recordings with small electrodes are the two most widely used methods that are still able to disentangle the contributions from single units. Here, I would like to briefly mention two papers that try to connect these two approaches by comparing them more or less directly.

    1. Wei et al., A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology, bioRxiv, 2019
      [Update, 2020-09-15: The paper just came out in PLoS Comp Biology just one day after the blog post!]
    2. Siegle, Ledochowitsch et al., Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology, bioRxiv, 2020

    Both papers compare calcium imaging datasets and extracellular ephys datasets, try to connect the results and point out the difficulties in reconciling the approaches.

    Wei et al. use datasets recorded in mouse anterio-lateral motor cortex (ALM). They first focus on approaches to reconstruct spike rates from calcium imaging data (deconvolution) and find several limitations of this approach. On the other hand, they find that a forward model that transforms spiking activity to calcium fluorescence data can reconcile most of these differences.

    The authors also provide a user-friendly website which can be used to explore the transformations between ephys and imaging data (also including datasets with simultaneous ephys-imaging): http://im-phys.org. (Understanding the figures of the paper is however quite useful before exploring the website.)

    From Wei et al., bioRxiv (2019), used under CC BY 4.0 license (excerpt from Fig. 7).

    A large part of the paper focuses on high-level analyses (principal component analysis, decoding of behavior and decision). I would take it as an educational tale of caution which highlights wrong conclusions that could be made based on standard analyses. For example, the slow and variable decay times of calcium imaging data can lead to a dispersion of peak activity that was absent in the ephys data. This dispersion can smear out clearly timed activations of neuronal population into something more similar to a sequence (see Figure 7, of which I have pasted an excerpt above).

    Siegle, Ledochowitsch et al. from the Allen Institute, rather than investigating the effects on higher-level population analyses, focus their attention on the effects seen in single neurons. When comparing a calcium imaging and an ephys dataset recorded in the same brain region (visual cortex V1) in mice that do the same standardized tasks, what differences can be seen in the firing properties of single neurons?

    Due to the high standardization requirements at the Allen Institute, their datasets are probably uniquely qualified to be the basis for such a comparison. Interestingly, they find a couple of clear differences. For example, extracellular ephys data suggest typical firing rates of around 3 Hz (see Figure 2A), which is almost an order of magnitude higher than what has been recorded and estimated from calcium imaging data (see also Figure 7 in our preprint, which estimates spike rates of the same dataset).

    The authors go to great lengths to use forward transformations (similar to Wei et al.) in order to reconcile differences seen for various response metrics (responsiveness, tuning preference, selectivity). However, their conclusion seemed to me quite a bit less optimistic compared to the Wei et al. paper. The authors go into more detail when discussing the potential reasons for the discrepancies, and focus on the recording methods themselves rather than on methods to transform between them. In particular their analysis of inter-spike-interval (ISI) violations in ephys recordings (which indicate that spikes from different neurons contaminate the recording of the neuron of interest) was, in my opinion, particularly interesting and convincing. I also really recommend to anybody the last paragraph of their discussion, from which I only want to cite their note of caution about extracellular ephys recordings:

    From this study, we have learned that extracellular electrophysiology overestimates the fraction of neurons that elevate their activity in response to visual stimuli, in a manner that is consistent with the effects of selection bias and contamination. – Siegle, Ledochowitsch et al.

    One of the reasons why I am writing about these two studies is that I have been working at the interface of calcium imaging and ephys myself, addressing the question, How much information about spike rates can we get out of calcium imaging data? Wei et al. and Siegle, Ledochowitsch et al. take a slightly broader perspective. And, in some way, they show how hard it is to reconcile two (methodological) perspectives on the same phenomenon. (I noticed this in my PhD lab as well, when it came to reconciling results from EM reconstructions of neuronal anatomy and calcium measurements of the same neurons.) Since almost any method in systems neuroscience is technically challenging, we often have in a single lab only a single perspective of a phenomenon, and I think it’s important to always be aware that the conclusions drawn from this perspective might be strongly biased.

    In general, calcium imaging and extracellular ephys are extremely valuable tools to observe the living brain, and we better do anything to understand the properties and limitations of these tools. These studies sometimes might feel a bit like negative results and therefore not very attractive to those who want to advance neuroscience, and I therefore understand why not many are willing to undertake these projects. So I am glad to be able to highlight these two publications here.

    in Peter Rupprecht on September 14, 2020 08:18 PM.

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    Sustainability Science Hub: Using data to drive action on the UN SDGs

    Free access to analytical reports, data sets, tools and other resources for sustainable development

    in Elsevier Connect on September 14, 2020 01:29 PM.

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    Dead horses won’t flog themselves

    "This is electrophoresis porn, readers, a phrase that I never expected to find myself writing." -Smut Clyde

    in For Better Science on September 14, 2020 06:00 AM.

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    Addressing the issue of preventing hearing loss and tinnitus through recreational noise exposure

    Let’s be honest, when most of us attend or take part in noisy recreational activities (e.g., nightclubs, concerts, playing musical instruments, indoor/outdoor sporting activities, motorsports) the last thing we reach for are hearing protection devices (e.g., earplugs and earmuffs). This is despite the fact that these activities can often range in loudness levels over 100 dBA, with the potential to cause hearing symptoms (e.g., dullness in hearing/tinnitus) after 15 minutes of continuous exposure. This is one of the reasons why the World Health Organization estimates that over a billion teenagers and young adults are at risk of hearing symptoms due to recreational noise exposure.

    The use of hearing protection devices is recognized as a method of reducing noise exposure. However, the amount of people using these devices within recreational contexts just ‘some of the time’ can be as low as ~5%, and even fewer people ‘always’ using them. Some people do tend to walk away from loud sources of noise, or go and take a break on a night out (e.g., regeneration break), and this is another method of protecting your hearing.

    In order to improve hearing protection behaviors (e.g., earplugs, earmuffs, regeneration breaks) through interventions it would be beneficial to know how effective previous interventions have been in recreational contexts, and what were the active ingredients (behavior change techniques (BCTs)) of these interventions trying to bring about the change.  Knowing what BCTs have been applied previously, or perhaps not, can help future designers of hearing protection interventions to potentially improve uptake. We conducted a systematic review of any intervention studies that measured a deliberate attempt to increase hearing protection behaviors during noisy recreational activities.

    So what did we find? We found eight studies measuring behavior post-intervention, of which only three were experimental post-test designs (two randomized controlled studies and one quasi). The most common behavior reported was the use of earplugs, seen in all eight studies, with five having a small to medium effect (d ≥ 0·3 ≤ 0·5) at measuring an increase, or difference in earplug use – including all three experimental studies. The overall increase or difference in earplugs being used ‘some of the time’ across all eight studies ranged from 3% -14.6%, but with very few ‘always’ using earplugs people are at risk of acquiring hearing symptoms.

    In terms of BCTs, across all studies we found a total of 17 different techniques had been deployed out of a possible 93 available from within the ‘behavior change technique taxonomy version 1’, with the majority serving an intervention category of ‘education’ (e.g., information about health consequences). With so few BCTs coded it leaves a large scope to test previously unused techniques. However, all three experimental studies restructured the environment by providing free earplugs (e.g., adding objects to the environment), and each measured a small to medium effect for at least one recreational context – perhaps indicating that this should be at least considered for future interventions.

    Overall the results tell us there are very few hearing protection interventions addressing recreational noise exposure, a global hearing health concern, and those that have tackled the issue have had mixed success. Further intervention studies should be conducted that employ randomized controlled designs, with use of systematic approaches to intervention development (e.g. the behavior change wheel), as this will help target specific behavior change techniques in an effort to increase hearing protection behaviors and raise effect sizes.

    Will you be reaching for your earplugs the next time?

    The post Addressing the issue of preventing hearing loss and tinnitus through recreational noise exposure appeared first on BMC Series blog.

    in BMC Series blog on September 14, 2020 05:11 AM.

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    The Secret Lives of Goats

    Goats Galore (May 2019)

    If you live in a drought-ridden, wildfire-prone area on the West Coast, you may see herds of goats chomping on dry grass and overgrown brush. This was initially surprising for many who live in urban areas, but it's become commonplace where I live. Announcements appear on local message boards, and families bring their children.

    Goats Goats Goats (June 2017)

    Goats are glamorous, and super popular on social media now (e.g. Instagram, more Instagram, and Twitter). Over 41 million people have watched Goats Yelling Like Humans - Super Cut Compilation on YouTube. We all know that goats have complex vocalizations, but very few of us know what they mean.

    For the health and well-being of livestock, it's advantageous to understand the emotional states conveyed by vocalizations, postures, and other behaviors. A 2015 study measured the acoustic features of different goat calls, along with their associated behavioral and physiological responses. Twenty-two adult goats were put in four situations:
    (1) control (neutral)
    (2) anticipation of a food reward (positive)
    (3) food-related frustration (negative)
    (4) social isolation (negative)
    Dr. Elodie Briefer and colleagues conducted the study at a goat sanctuary in Kent, UK (Buttercups Sanctuary for Goats). The caprine participants had lived at the sanctuary for at least two years and were fully habituated to humans. Heart rate and respiration were recorded as indicators of arousal, so this dimension of emotion could be considered separately from valence (positive/negative). For conditions #1-3, the goats were tested in pairs (adjacent pens) to avoid the stress of social isolation. They were habituated to the general set-up, to the Frustration and Isolation scenarios, and to the heart rate monitor before the actual experimental sessions, which were run on separate days. Additional details are presented in the first footnote.1

    Audio A1. One call produced during a negative situation (food frustration), followed by a call produced during a positive situation (food reward) by the same goat (Briefer et al., 2015).

    Behavioral responses during the scenarios were timed and scored; these included tail position, locomotion, rapid head movement, ear orientation, and number of calls. The investigators recorded the calls and produced spectograms that illustrated the frequencies of the vocal signals.

    The call on the left (a) was emitted during food frustration (first call in Audio A1). The call on the right (b) was produced during food reward; it has a lower fundamental frequency (F0) and smaller frequency modulations. Modified from Fig. 2 (Briefer et al., 2015).

    Both negative and positive food situations resulted in greater goat arousal (measured by heart rate) than the neutral control condition and the low arousal negative condition (social isolation). Behaviorally speaking, arousal and valence had different indicators:
    During high arousal situations, goats displayed more head movements, moved more, had their ears pointed forwards more often and to the side less often, and produced more calls. ... In positive situations, as opposed to negative ones, goats had their ears oriented backwards less often and spent more time with the tail up.
    Happy goats have their tails up, and do not point their ears backwards. I think I would need a lot more training to identify the range of goat emotions conveyed in my amateur video. At least I know not to stare at them, but next time I should read more about their reactions to human head and body postures.

    Do goats show a left or right hemisphere advantage for vocal perception?

    Now that the researchers have characterized the valence and arousal communicated by goat calls, another study asked whether goats show a left hemisphere or right hemisphere “preference” for the perception of different calls (Baciadonna et al., 2019). How is this measured, you ask?

    Head-Turning in Goats and Babies

    The head-turn preference paradigm is widely used in studies of speech perception in infants.

    Figure from Prosody cues word order in 7-month-old bilingual infants (Gervain & Werker, 2013).

    However, I don't know whether this paradigm is used to assess lateralization of speech perception in babies. In the animal literature, a similar head-orienting response is a standard experimental procedure. For now, we will have to accept the underlying assumption that orienting left or right may be an indicator of a contralateral hemispheric “preference” for that specific vocalization (i.e., orienting to the left side indicates a right hemisphere dominance, and vice versa).
    The experimental procedure usually applied to test functional auditory asymmetries in response to vocalizations of conspecifics and heterospecifics is based on a major assumption (Teufel et al. 2007; Siniscalchi et al. 2008). It is assumed that when a sound is perceived simultaneously in both ears, the head orientation to either the left or right side is an indicator of the side of the hemisphere that is primarily involved in the response to the stimulus presented. There is strong evidence that this is the case in humans ... The assumption is also supported by the neuroanatomic evidence of the contralateral connection of the auditory pathways in the mammalian brain (Rogers and Andrew 2002; Ocklenburg et al. 2011).

    The experimental set-up to test this in goats is shown below.

    A feeding bowl (filled with a tasty mixture of dry pasta and hay) was fixed at the center of the arena opposite to the entrance. The speakers were positioned at a distance of 2 meters from the right and left side of the bowl and were aligned to it. 'X' indicates the position of the Experimenter. Modified from Fig. 2 (Baciadonna et al., 2019).

    Four types of vocalizations were played over the speakers: food anticipation, food frustration, isolation, and dog bark (presumably a negative stimulus). Three examples of each vocalization were played, each from a different and unfamiliar goat (or dog).

    The various theories of brain lateralization of emotion predicted different results. The right hemisphere model predicts right hemisphere dominance (head turn to the left) for high-arousal emotion regardless of valence (food anticipation, food frustration, dog barks). In contrast, the valence model predicts right hemisphere dominance for processing negative emotions (food frustration, isolation, dog barks), and left hemisphere dominance for positive emotions (food anticipation). The conspecific model predicts left hemisphere dominance for all goat calls (“familiar and non-threatening”) and right hemisphere dominance for dog barks. Finally, a general emotion model predicts right hemisphere dominance for all of the vocalizations, because they're all emotion-laden.

    The results sort of supported the conspecific model (according to the authors), if we now accept that dog barks are actually “familiar and non-threatening” [if I understand correctly]. The head-orienting response did not differ significantly between the four vocalizations, and there was a slight bias for head orienting to the right (p=.046 vs. chance level), when collapsed across all stimulus types. 2

    The time to resume feeding after hearing a vocalization (a measure of fear) didn't differ between goat calls and dog barks, so the authors concluded that “goats at our study site may have been habituated to dog barks and that they did not perceive dog barks as a serious threat.” However, if a Siberian Husky breaks free of its owner and runs around a fenced-in rent-a-goat herd, chaos may ensue.


    1 Methodological details:
    “(1) During the control situation, goats were left unmanipulated in a pen with hay (‘Control’). This situation did not elicit any calls, but allowed us to obtain baseline values for physiological and behavioural data. (2) The positive situation was the anticipation of an attractive food reward that the goats had been trained to receive during 3 days of habituation (‘Feeding’). (3) After goats had been tested with the Feeding situation, they were tested with a food frustration situation. This consisted of giving food to only one of the goats in the pair and not to the subject (‘Frustration’). (4) The second negative situation was brief isolation, out of sight from conspecifics behind a hedge. For this situation, goats were tested alone and not in a pair (‘Isolation’).”

    2 The replication police will certainly go after such a marginal significance level, but I would like to see them organize a “Many Goats in Many Goat Sanctuaries” replication project.


    Baciadonna L, Nawroth C, Briefer EF, McElligott AG. (2019). Perceptual lateralization of vocal stimuli in goats. Curr Zool. 65(1):67-74. [PDF]

    Briefer EF, Tettamanti F, McElligott AG. (2015). Emotions in goats: mapping physiological, behavioural and vocal profiles. Animal Behaviour 99:131-43. [PDF]

    in The Neurocritic on September 13, 2020 08:19 PM.

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    In this tech job, “the difference you make gets right to the customer”

    Why e-commerce is such a rewarding area of technology

    in Elsevier Connect on September 11, 2020 01:11 PM.

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    Sexual harassment case number 1,052

    Despite much ado about the #metoo movement in recent years, the crisis of sexual harassment in academia persists without an end in sight. The academic sexual misconduct database now lists 1,051 cases, each of them a tragedy of trauma, unspeakable violations of victims, and dreams destroyed. I’ve written previously about two cases listed in the database (Yuval Peres and Terry Speed). Now, I feel compelled to write about yet another sexual harassment case.

    Adrian Dumitrescu is a professor in the Department of Mathematical Sciences at the University of Wisconsin, Milwaukee. I have known of his work for many years, as we have a shared interest in extremal combinatorics, having both worked on the Erdös-Szekeres “Happy Ending Problem”. Last week a Facebook post was brought to my attention, in which a graduate student describes a horrible case of sexual harassment by Prof. Dumitrescu that occurred during a conference in Boston in 2016.

    This student filed a Title IX complaint with the University of Wisconsin, and I have a copy of the report. The Office of Equity and Diversity (EDS) that investigated the case found that “Based on the totality of the circumstances, the information obtained pursuant to this investigation, and for all the reasons set forth above, EDS concludes that there is sufficient evidence to support a finding, by preponderance of the evidence, of sexual harassment against the Respondent [Prof. Dumitrescu].” Furthermore, the report states that “based on the seriousness of the Respondent’s conduct, EDS believes that disciplinary action is warranted in this matter, and recommends that the Provost refer this case for imposition of discipline”. As I write this post, Prof. Dumitrescu is still listed as a professor at the University of Wisconsin, Milwaukee.

    Notably, after being sexually harassed by the Respondent, and before filing a report with Title IX, the student consulted her Ph.D. advisor. The report describes his response as follows: “[he] told her that the Respondent had a ‘high reputation’ in the field and it was better to ‘avoid trouble’ and not to report her concerns.” And yet she had the courage to report the case, despite the attempt to silence her, and having being threatened by the Respondent, as he coerced her to sleep with him, that if she did not acquiesce to his demands he would not conduct research with her and he might prevent senior scholars at her university from working with her.

    The report details how the sexual harassment impacted the complainant’s research progress and mental well-being. Yet again, a talented young scientist finds herself with debilitating trauma, a career in jeopardy, and powerless in the face of an establishment that excuses harassers.

    The details of this case are of course different than every other sexual harassment case. Each is tragic in its own way. And yet elements of what happened here are to be found in all sexual harassment cases. Power imbalance. Coercion. Threats. Silencing of the victim. Inaction. Banal injustice. This will be case number 1,052 in the academic sexual misconduct database.

    We must do better.

    in Bits of DNA on September 10, 2020 12:29 PM.

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    The Karin Dahlman-Wright Show

    Karin Dahlman-Wright, Karolinska Institute's former president, then vice-president, now rector's counsellor was found guilty of research misconduct, again. This time in 4 papers.

    in For Better Science on September 10, 2020 10:38 AM.

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    The role of masculinity in reforming police departments

    For decades there have been murders of unarmed black people by the police, which in recent years has been exposed and protested by the #BlackLivesMatter movement. This summer, unprecedented numbers of protesters have voiced their outrage in response to the murders of George Floyd and Breonna Taylor, the very recent and utterly senseless shooting of Jacob Black, and countless other acts of violence. Many mayors have announced plans for reform. The protests have rightly focused on the roles of race and racism in police brutality, but more attention needs to be given to the role of gender, particularly as municipalities seek to repair the police force to avoid this unnecessary use of force and violence.

    Using data from the Riverside County Sheriff’s Department in California, a 2008 study found that male officers were three times more likely to commit unwarranted shootings than their female counterparts. Additionally, white male police officers were 57% more likely than Latino male officers to commit such a shooting. These statistics refer to the group that constitutes the majority of police officers in America—white men.

    But even more importantly, the culture of police departments tends to be macho and hyper-masculine—a culture which glorifies violence. This has always been the case but it has intensified as police departments across the county have moved from the community policing approach to militarization, aided by federal grants.

    While among the general public masculinity is seen as synonymous with being male, psychologists view it differently—as a set of social norms, in this case norms for how boys and men should think, act, and feel. Masculinity is problematic in that that most boys are made to feel that they must conform to gender norms—that is, act in ways consistent with their gender. Masculinity is presented as obligatory for most boys, and most boys feel they have no other choice but to conform to masculine norms. This is not true for girls, who are given much more flexibility and latitude when it comes to their performance of gender than are boys. Furthermore, one of the principal functions of masculinity is to establish several hierarchies: of men over women, of white men over men of color, and of straight cisgender men over gay, bisexual, and transgender men.

    To move away from the macho and hyper-masculine culture, police forces must diversify—not only in race but in gender—their ranks and leadership. The presence of many more women, openly LGBTQ people, and non-white officers on the police force, and deploying training designed to heighten awareness of masculinity and its relationship to violence, will be crucial in this regard.

    Although most boys are expected to conform to masculinity norms, most adult men come to accept who they are, even if they do not meet the masculinity ideals. Masculinity is, after all, a tough standard. That is, they come to terms with the messages from their childhoods and recognize that their unique personalities do not fit or need to fit the ideal in all ways, perhaps saying to themselves “I am not the most masculine guy in the world but that’s OK.” A smaller group feels deeply ashamed of themselves for violating the masculine norms. Experimental research using the “precarious manhood” paradigm has shown that such men, when their masculinity is threatened, tend to respond with aggression.

    The research that has been conducted over the past 40+ years shows that one or another scale that measures masculinity is correlated with one or another harmful outcome, many related to violence. Since most adult men do not conform to masculine norms, what accounts for these harmful outcomes? One source is the group of men who respond to threats to their masculinity aggressively. In addition, masculinity’s destructive outcomes also arise from those men who “check all the boxes,” and conform to masculine norms to the greatest extent. These are the men whom we might label as hyper-masculine. Both groups of men tend to populate police departments as currently constituted. Their influence must be diluted by diversifying police forces.

    Featured image by Free-Photos from Pixabay

    The post The role of masculinity in reforming police departments appeared first on OUPblog.

    in OUPblog - Psychology and Neuroscience on September 10, 2020 09:30 AM.

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    Females, younger adults, sexual minorities, and multiracial individuals most vulnerable to adverse childhood experiences

    Adverse childhood experiences related to negative health outcomes

    As researchers, we often try to pinpoint the causes of negative outcomes in adults. What factors contribute to obesity? What about heart disease? Why are some people more prone to depression and anxiety while others are not? Surely it is not random chance why some individuals are more prone to these outcomes while others are not.

    While each outcome may be linked to something specific (i.e., a person’s chance of getting lung cancer increases exponentially if they smoke), there is one factor that has been linked to a variety of negative outcomes like lung cancer, heart disease, anxiety, depression, obesity, unemployment, divorce, and even poor athletic performance.

    What’s the factor that is linked to all of these outcomes?  The term is called “adverse childhood experiences,” or ACEs for short.

    In the 1980s, a researcher named Vincent Felitti ran an obesity clinic in California. Around 50% of the participants dropped out, while the other 50% successfully completed the program. He decided to interview many of the dropouts, and found a common theme: Nearly all of them experienced some form of sexual, physical, or mental abuse as children. Interviews from the group that completed the program revealed only a very small percentage reported the same abuse.

    Felitti eventually collaborated with a colleague, Robert Anda, in a large study of 17,000 individuals. In that study, Felitti and Anda identified eight domains of ACEs: physical abuse, sexual abuse, emotional abuse, parental separation/divorce, interpersonal violence, incarcerated family member, family mental illness, and family substance use.

    Regardless of the event, Felitti and Anda found that the more numerical experiences an individual had, the more likely they were to have negative outcomes as adults.  Essentially, every person has an ACE score, ranging from 0 (no adverse events before the age of 18) to 8 (adverse events in all 8 categories).

    All this said, public health researchers and practitioners in all areas of prevention/intervention (e.g., mental health professionals, substance abuse counselors, etc.), have been trying to develop programs which either 1. Limit the number of ACEs people have, or 2. Help people deal with their ACEs as adults in order to help lessen their effect.

    Our study

    This is where our recent article titled, “The Frequencies and Disparities of Adverse Childhood Experiences in the U.S.” published in BMC Public Health helps advance the field of ACEs.  In the article, we collected the most comprehensive ACEs dataset to date: 211,376 adults across 34 states.

    Over half (58%) of all participants experienced at least one ACE.

    The study helps shed light on precisely who is at-risk for higher ACEs. We report several noteworthy findings.

    1. Over half (58%) of all participants experienced at least one ACE.
    2. Almost one-quarter (22%) experienced three or more ACEs.
    3. Women were more likely to experience ACEs compared to men
    4. Black, Hispanic, and Multi-racial individuals were more likely to have more ACEs compared to White individuals.
    5. People who identify as a sexual minority (lesbian, gay, or bisexual) were more likely to have more ACEs compared to heterosexual individuals.

    Future implications

    So what does this all mean? There are several implications to the study. First, the more we know about ACEs, the greater the chances we have in both preventing ACEs and lessening their effect.  Next, ACEs are not equally distributed amongst the general population.  Some groups have a higher likelihood of experiencing ACEs, making them uniquely more prone to negative outcomes due to ACEs. Having insight into which groups are particularly vulnerable to ACEs is helpful for professionals that work in fields dealing with the repercussions of ACEs (like mental health counselors). Knowledge about which groups have a higher likelihood of ACE exposure will aid in tailoring programmatic responses to these groups.

    For more information regarding ACEs (including the ACEs questionnaire), see the Centers for Disease and Prevention’s (CDC) page on ACEs with additional links and resources.


    The post Females, younger adults, sexual minorities, and multiracial individuals most vulnerable to adverse childhood experiences appeared first on BMC Series blog.

    in BMC Series blog on September 10, 2020 05:06 AM.

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    Time to get moving!

    It is known that chronic kidney disease (CKD) and end-stage kidney disease (ESKD) patients are at an extremely high risk for cardiovascular disease, stroke, and peripheral vascular disease.  In addition, most patients have additional risk factors including diabetes, hypertension, and obesity. Should more be done to help improve their risk and overall health? What if clinicians could prescribe an exercise regimen? Are there additional hemodialysis specific benefits to exercising?

    In a recent BMC Nephrology publication, Bogataj et al. performed a randomised controlled trial to examines the effects of intradialytic cycling and functional training on dialysis adequacy and other biochemical parameters. Participants were divided into a functional training intervention group (with intradialytic cycling) and an intradialytic cycling only control group. For the first eight weeks, participants in the intervention group performed guided functional exercise training three times a week before each dialysis session and additional intradialytic cycling exercise. This included a warm-up, full range of motion exercises with additional weights, and a cool-down with stretching.  For the second eight weeks the same group took the functional training home to do on non-dialysis days. The authors concluded that in both groups the dialysis adequacy improved and was sustained through the entire study; however, additional benefits were found in the intervention group, with promising improvements in the participants’ total cholesterol and low-density lipoprotein (LDL) cholesterol.

    The improvement in dialysis adequacy with exercise during hemodialysis is not new. In 2004, Parsons et al. also conducted an eight week study looking at intradialytic exercise and found that there was enhanced dialysate urea removal. The physiology of how improved dialysis adequacy occurs is thought to be through an increase in muscle blood flow and increase in oxygen extraction, which increases capillary surface area and increases the exchange of substances from the tissue to the vascular compartment. This increased diffusion into the vascular compartment allows for substances like urea to be removed by dialysis.  Therefore, improved dialysis adequacy. Kong et al. demonstrated a 14% increase in dialysis adequacy from 60 minutes of intradialytic exercise.  This increase is equivalent to increasing a dialysis session by 20 minutes. It would be interesting to find out how many of my patients would prefer cycling during dialysis for an hour rather than increasing their dialysis time. Would it be more cost effective to have everyone perform intradialytic exercise rather than increasing dialyzer size or time?

    Would it be more cost effective to have everyone perform intradialytic exercise rather than increasing dialyzer size or time?

    With the Bogataj et al article, there was also improvement in total cholesterol and LDL for the intervention group. There is clear evidence for preventing major cardiovascular events and mortality with lowering LDL for those with normal or slightly abnormal kidney function. For patients with CKD and ESKD, it can still be controversial. Our guidelines do not advocate starting every ESKD patient on a statin but what about lowering cholesterol with exercise? This type of intervention for cholesterol improvement still needs to be studied over a longer period with examining cardiovascular outcomes.

    If budget was not an issue, I might consider purchasing customized cycling equipment for my in-center hemodialysis patients and hiring a kinesiologist or personal trainer to perform rounds in the dialysis unit like our dietician and social worker. With time, I imagine we will have larger, longer duration studies that will further support the idea that a novel exercise prescription strategy has specific health benefits for patients with CKD.

    The post Time to get moving! appeared first on BMC Series blog.

    in BMC Series blog on September 09, 2020 09:14 PM.

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    2-Minute Neuroscience: Meningitis

    Meningitis is a potentially deadly disease characterized by an inflammation of the meninges. In this video, I discuss the meninges and the pathophysiology of meningitis.

    in Neuroscientifically Challenged on September 09, 2020 09:03 AM.

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    Model shows that the speed neurons fire impacts their ability to synchronize

    Researchers delve into networks of virtual brain cells to explore a unique firing behavior.

    in OIST Japan - CNU - Eric De Schutter on September 08, 2020 07:00 AM.

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    Presence and absence of loose synchronization in Purkinje neurons

    8 Sep 2020

    When a group of Purkinje neurons fire rapidly, loose synchronization occurs. This can be seen by the spikes occurring in groups at regular intervals (highlighted in yellow). When Purkinje neurons fire slowly, this synchronization does not occur.

    in OIST Japan - CNU - Eric De Schutter on September 08, 2020 04:16 AM.

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    Membrane voltage in slow and fast firing Purkinje cells

    Image modified from "How neurons communicate: Figure 2," by OpenStax College, Biology (CC BY 4.0).
    8 Sep 2020

    Cell membranes have a voltage across them due to the uneven distribution of charged particles, called ions, between the inside and outside of the cell. Neurons can shuttle ions across their membrane through channels and pumps, which changes the voltage of the membrane. Fast firing Purkinje neurons have a higher membrane voltage than slow firing neurons.

    in OIST Japan - CNU - Eric De Schutter on September 08, 2020 04:12 AM.

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    New JACS EiC Erick Carreira: “correct your work-ethic immediately”

    Erick Carreira's letter to Guido, from 1996. You all saw it probably at some point, and now it's being discussed again.

    in For Better Science on September 06, 2020 01:08 PM.

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    For Mendeley Data winner, sharing FAIR data helps researchers learn from each other

    A research fellow talks about how to create meaningful datasets – and why sharing them benefits all involved

    in Elsevier Connect on September 04, 2020 01:15 PM.

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    How USA embraced research fraud: review of two books

    A review of "The Baltimore Case" by the historian Daniel Kelves and "Science Fictions" by the journalist John Crewdson, which also tell the history of the Office of Research Integrity (ORI).

    in For Better Science on September 04, 2020 08:05 AM.

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    arXiv News: Summer 2020

    We’re always working to improve your experience on arXiv.org. Here’s a summary of recent changes that we hope will make your life as an author easier.

    Improvements for the author experience:

    • We are now allowing more time for TeX to run the compilation, so “time out” errors will occur less frequently.
    • arXiv will detect cases where a second compilation process is needed and run it automatically. This ensures that your bibliography will display correctly.
    • Triggering a second compilation also fixes related footnote formatting issues.

    Smaller bug fixes:

    • Fix on the automatic recognition of arXiv IDs links
    • Fix to hyperref options to support more options for web links

    in arXiv.org blog on September 02, 2020 07:22 PM.

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    Torello Lotti’s Arousal Disorder

    "Low Dose Medicine (LDM) arises from molecular biology, psychoneuroendocrine immunology and quantum physics. As for the use of low doses of the active ingredients of its drugs, it originates from the historical tradition of homeopathy." - Professor Torello Lotti.

    in For Better Science on September 02, 2020 10:13 AM.

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    Challenges university leaders face in an ever-changing world — and strategies to tackle them

    University leaders reveal the opportunities and challenges they face as they forge ahead in an increasingly competitive environment

    in Elsevier Connect on September 02, 2020 06:10 AM.